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ENGINEERED ADENYLATE KINASE VARIANT ENZYMES

20220325257 · 2022-10-13

    Inventors

    Cpc classification

    International classification

    Abstract

    The present invention provides engineered adenylate kinase (AdK) enzymes, polypeptides having AdK activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing AdK enzymes are also provided. The present invention further provides compositions comprising the AdK enzymes and methods of using the engineered AdK enzymes. The present invention finds particular use in the production of pharmaceutical compounds.

    Claims

    1. An engineered adenylate kinase or a functional fragment thereof comprising a polypeptide sequence having at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NOs: 4 and/or 230, wherein the polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set and wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NOs: 4 and/or 230.

    2. The engineered adenylate kinase of claim 1, wherein said polypeptide sequence has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4, and wherein the polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions in said polypeptide sequence selected from 42, 34/35/51, 34/35/51/53/138, 34/35/51/53/172, 34/35/51/76, 34/35/51/76/172/202, 34/35/51/119, 34/35/51/119/172, 34/35/51/172, 34/35/52/53/119/172, 34/35/52/76/119, 34/35/53/76, 34/35/53/202, 34/35/76, 34/35/76/119/172, 34/35/119, 34/35/138, 34/35/138/172, 34/51, 34/51/52/53/76, 34/51/53/76/172, 34/51/53/138, 34/51/53/172, 34/51/76, 34/51/119/138/172, 34/51/131, 34/51/202, 34/76/138/172, 34/119, 34/119/172, 34/138/172, 35/51, 35/51/52/53, 35/51/52/53/76/119/172/202, 35/51/52/53/119, 35/51/53/138/172, 35/51/53/172, 35/51/53/202, 35/51/76, 35/51/76/131, 35/51/76/138, 35/51/76/172, 35/51/119, 35/51/119/138, 35/51/119/138/172, 35/51/119/172, 35/51/172, 35/51/172/202, 35/51/202, 35/52/53/119, 35/52/53/119/138, 35/53/119/131/202, 35/53/119/138, 35/76, 35/76/119, 35/76/119/138, 35/76/119/138/172, 35/76/172, 35/119, 35/119/138, 35/119/172, 35/138/172, 35/172, 35/172/186, 35/172/202, 51, 51/52/53/172/202, 51/53, 51/53/119, 51/53/172, 51/76/119, 51/76/119/172, 51/119/138, 51/119/172/202, 51/138, 51/172, 52/53/76/172/202, 52/76/172, 52/138/172, 53/76/202, 53/172, 76, 76/119, 76/119/172, 76/172/202, 119/138/172, 119/172, 138/202, 172/202, and 202, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

    3. The engineered adenylate kinase of claim 1, wherein said polypeptide sequence of said engineered adenylate kinase has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 4, and wherein said polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions selected from 42, 1/2/104, 16, 29, 41, 46, 49, 50, 51, 61, 65, 72, 74, 76, 77, 79, 81, 108, 110, 127, 152, 191, 214, 218, and 222, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 4.

    4. The engineered adenylate kinase of claim 1, wherein said polypeptide sequence of said engineered adenylate kinase has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 230, and wherein said polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions selected from 16, 16/29/49/104/108/191/218, 16/29/49/104/108/210, 16/29/49/104/191, 16/29/49/104/191/218, 16/29/49/108, 16/29/49/108/191, 16/29/49/108/210, 16/29/49/191, 16/29/49/191/210, 16/29/76/210, 16/29/104/108/191/218, 16/29/104/210, 16/29/108/191, 16/49, 16/49/76/104/191, 16/49/104/108, 16/49/104/108/191, 16/49/104/108/210, 16/49/104/191, 16/49/104/210, 16/49/108/210, 16/49/108/218, 16/49/191, 16/49/191/210, 16/81/104, 16/104/191/210, 16/108, 16/108/191/210, 16/108/218, 16/191/210, 29, 29/42/49/77/81/108, 29/42/76/77/104/191/210, 29/42/76/104/108, 29/42/104/108/191/210, 29/42/104/108/191/218, 29/42/108, 29/42/108/191, 29/42/108/191/210, 29/42/108/210, 29/49/76/77/81/191/210, 29/49/77/81/104/108/191, 29/49/81/108, 29/49/104/108, 29/49/104/108/191, 29/49/104/108/191/210, 29/49/104/108/191/210/218, 29/49/104/108/210, 29/49/104/191, 29/49/104/191/210, 29/49/108/191, 29/49/108/191/210, 29/49/108/191/210/218, 29/49/108/191/218, 29/49/108/210, 29/49/191, 29/49/191/210, 29/49/191/210/218, 29/49/210/215, 29/76/191/210, 29/104, 29/104/108, 29/104/108/191/210, 29/104/108/210, 29/104/191, 29/104/191/210, 29/104/191/210/218, 29/104/210, 29/108, 29/108/191, 29/108/191/210, 29/108/191/210/218, 29/108/191/218, 29/108/210, 29/191/210, 42/49/76/81/108/210, 42/49/108/191/210/218, 42/77/108/191, 42/108/191/210, 49, 49/76/77/81/104/191/210, 49/76/81/104/108, 49/76/108/191, 49/76/108/191/210, 49/81/104/108, 49/81/108, 49/104/108, 49/104/108/180/191, 49/104/108/191, 49/104/108/191/210, 49/104/108/210, 49/104/191, 49/104/191/210, 49/104/218, 49/108, 49/108/191, 49/108/191/210, 49/108/191/210/218, 49/108/210, 49/191, 49/191/210, 49/210, 76/77/81/108/191, 76/77/81/108/191/210, 76/77/81/210/218, 76/81/108, 76/81/108/191/218, 77/81/108/191, 104/108/191, 104/108/191/210, 104/108/191/210/218, 104/108/210, 104/108/218, 104/191, 104/191/210, 108/191, 108/191/210, 108/191/218, and 108/210, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 230.

    5. The engineered adenylate kinase of claim 1, wherein said polypeptide sequence of said engineered adenylate kinase has at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NO: 230, and wherein said polypeptide sequence of said engineered adenylate kinase comprises at least one substitution or substitution set at one or more positions selected from 16, 16/29, 16/29/51/110/191, 16/29/51/191, 16/29/51/214, 16/29/119/191, 16/29/119/191/214, 16/29/191, 16/51/107, 16/51/107/110/214, 16/51/110/202/214, 16/51/191/202, 16/51/191/202/214, 16/51/214, 16/107/110/119, 16/107/110/119/191/202/214, 16/107/110/191, 16/107/191/214, 16/110/119, 16/110/191, 16/191, 16/191/202, 16/214, 29, 29/46/79/107/110/202/214, 29/46/110/202/214, 29/46/110/214, 29/46/191, 29/51/107/110/191, 29/51/107/110/191/214, 29/51/107/110/202/214, 29/51/107/119/191, 29/51/110/191/202, 29/51/119/191/214, 29/51/191, 29/51/191/202, 29/51/191/214, 29/74/79/107/214, 29/74/107/191, 29/74/191, 29/107/119/191, 29/110/119/191, 29/119, 29/191/214, 51, 51/107/110, 51/107/110/119, 51/107/110/191, 51/107/110/191/214/218, 51/107/119/191/214, 51/107/214, 51/110/191, 51/110/214, 51/191, 51/191/202/214, 51/191/214, 51/202, 51/214, 74/79/107/110/191/202, 107/110/119/191, 107/110/119/207/214, 107/110/123/191/202, 110/191/202/214, 119, 119/191, 191/202, and 191/214, wherein the amino acid positions of said polypeptide sequence are numbered with reference to SEQ ID NO: 230.

    6. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase comprises a polypeptide sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the sequence of at least one engineered adenylate kinase variant set forth in Tables 2-1, 2-2, 3-1, and/or 3-2.

    7. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase comprises a variant engineered adenylate kinase set forth in SEQ ID NOs: 4 and/or SEQ ID NO: 230.

    8. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase comprises a polypeptide sequence that is at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the sequence of at least one engineered adenylate kinase variant set forth in the even numbered sequences of SEQ ID NOs: 4-848.

    9. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase comprises a polypeptide sequence set forth in at least one of the even numbered sequences of SEQ ID NOs: 4-848.

    10. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase comprises at least one improved property compared to wild-type Saccharomyces cerevisiae adenylate kinase.

    11. The engineered adenylate kinase of claim 10, wherein said improved property comprises improved activity on a substrate.

    12. The engineered adenylate kinase of claim 11, wherein said substrate comprises 2′F-ara-adeno sine-5′-(1-thio)-monophosphate (F-thioAMP) and/or Sp-2′ F-ara-adenosine-5′ -(1-thio)-triphosphate (F-thioATP).

    13. The engineered adenylate kinase of claim 10, wherein said improved property comprises improved production Sp-2′F-ara-adenosine-5′-(1-thio)-diphosphate (F-thioADP).

    14. The engineered adenylate kinase of claim 1, wherein said engineered adenylate kinase is purified.

    15. A composition comprising at least one engineered adenylate kinase of claim 1.

    16. A polynucleotide sequence encoding at least one engineered adenylate kinase of claim 1.

    17. A polynucleotide sequence encoding at least one engineered adenylate kinase, said polynucleotide sequence comprises at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NOs: 3 and/or 229, wherein the polynucleotide sequence of said engineered adenylate kinase comprises at least one substitution at one or more positions.

    18. A polynucleotide sequence encoding at least one engineered adenylate kinase or a functional fragment thereof comprising at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to SEQ ID NOs: 3 and/or 229.

    19. The polynucleotide sequence of claim 16, wherein said polynucleotide sequence is operably linked to a control sequence.

    20. The polynucleotide sequence of claim 16, wherein said polynucleotide sequence is codon optimized.

    21. The polynucleotide sequence of claim 16, wherein said polynucleotide sequence comprises a polynucleotide sequence set forth in the odd numbered sequences of SEQ ID NOs: 3-847.

    22. An expression vector comprising at least one polynucleotide sequence of claim 16.

    23. A host cell comprising at least one expression vector of claim 22.

    24. A host cell comprising at least one polynucleotide sequence of claim 16.

    25. A method of producing an engineered adenylate kinase in a host cell, comprising culturing the host cell of claim 23, under suitable conditions, such that at least one engineered adenylate kinase is produced.

    26. The method of claim 25, further comprising recovering at least one engineered adenylate kinase from the culture and/or host cell.

    27. The method of claim 25, further comprising the step of purifying said at least one engineered adenylate kinase.

    Description

    DETAILED DESCRIPTION OF THE INVENTION

    [0133] The present invention provides engineered adenylate kinase (AdK) enzymes, polypeptides having AdK activity, and polynucleotides encoding these enzymes, as well as vectors and host cells comprising these polynucleotides and polypeptides. Methods for producing AdK enzymes are also provided. The present invention further provides compositions comprising the AdK enzymes and methods of using the engineered AdK enzymes. The present invention finds particular use in the production of pharmaceutical compounds.

    [0134] In some embodiments, the present invention provides enzymes suitable for the production of cyclic dinucleotides, such as cGAMP. The present invention was developed in order to address the potential use of enzymes to produce these cyclic dinucleotides. In some embodiments, the present invention provides enzymes that are useful in producing compounds that result in methods for the in vitro enzymatic synthesis of the non-natural cyclic dinucleotide of compound (1).

    Compound (1)

    [0135] ##STR00001##

    [0136] In some embodiments, the present invention provides engineered enzymes suitable for the production of nucleoside diphosphates. In some embodiments, the present invention provides engineered enzymes suitable for the production of nonnatural nucleoside diphosphates. In some embodiments, the nonnatural nucleoside diphosphate is a thio and/or fluorinated nucleoside diphosphate. In some embodiments, the nonnatural nucleoside diphosphate is Sp-2′Fluoro-ara-adenosine-5′-(1-thio)-diphosphate (F-thioADP or compound (5)).

    [0137] In some embodiments, the engineered enzymes produce nucleoside diphosphates. In some embodiments, the nucleoside diphosphates are substrates for an acetate kinase that produces nucleoside triphosphates. In some embodiments, the engineered enzymes produce nucleoside diphosphates as precursor compounds to nucleoside triphosphates. In some embodiments, the present invention provides enzymes that are useful in producing compounds for the in vitro enzymatic synthesis of the non-natural nucleoside diphosphate of compound (5). In some embodiments, the present invention provides enzymes that are useful in producing compound (5), which is converted through in vitro enzymatic synthesis to the non-natural cyclic dinucleotide of compound (1).

    [0138] Nonnatural derivatives of cGAMP, including compound (1), are being investigated in cancer therapy. cGAMP, a cyclic dinucleotide, is known to function as a second messenger that stimulates innate immunity through the endoplasmic reticulum sensor STING. cGAMP activation of STING was demonstrated to have an anti-tumor effect in mice through induction of production of interferon and stimulation of dendritic cells (Li et al., Sci. Rep. 6:19049 [2016]) cGAMP is produced in response to double-stranded DNA (dsDNA) by cyclic GMP-AMP synthase (cGAS) (Gao et al., Cell. 153:1094-1107 [2013]), which functions as a cellular sensor of foreign nucleic acids. cGAS activity requires binding of dsDNA, with single-stranded (ssDNA) or RNA ligands producing only weak or no activity, respectively. Binding to dsDNA induces conformational changes in cGAS to the active enzyme state (Kranzusch et al., Cell Rep. 3(5): 1362-1368 [2013]).

    [0139] Several cGAS crystal structures have been generated, including murine and human cGAS. These crystal structures reveal several conserved domains, including a nucleotidyltransferase core, a zinc finger domain, and a C-terminal domain (Gao et al., Cell. 153(5): 1094-1107 [2013]; Kranzusch et al., Cell Rep. 3(5): 1362-1368 [2013]). In addition to bound dsDNA, cGAS requires a divalent metal cation (typically Mn.sup.2+ or Mg.sup.2+) for activity. cGAS is capable of producing several diastereomeric forms of cGAMP, depending on whether (s) or (r) nucleoside triphosphates are used as substrates. The desired diastereomeric form is (r,r) (compound (1)), which is produced by cGAS conversion of Sp-3′Fluoro-3′-deoxyguanosine-5′-(1-thio)-triphosphate (F-thioGTP or compound (2)) and Sp-2′Fluoro-ara-adenosine-5′-1-thio-triphosphate (F-thioATP or compound (3)).

    ##STR00002##

    [0140] The substrates for cGAS, compound (2) and compound (3), are generated by guanylate kinase and adenylate kinase, respectively, together with acetate kinase (AcK), which recycles F-thioATP and converts the nucleoside diphosphate products of guanylate kinase and adenylate kinase to nucleoside triphosphates, see Scheme 2.

    ##STR00003##

    [0141] In the first step, AdK converts Sp-2′Fluoro-ara-adenosine-5′-(1-thio)-monophosphate (F-thioAMP or compound (4)) to Sp-2′Fluoro-ara-adenosine-5′-(1-thio)-diphosphate (F-thioADP or compound (5)) using F-thioATP, compound (3), as the phosphate donor. Two molecules of F-thioADP , compound (5), are generated for each substrate molecule of F-thioAMP, compound (4). One F-thioADP (5) is recycled by AcK to F-thioATP (3), which is consumed by the reaction. The same AcK subsequently transforms the second F-thioADP (5) using acetyl phosphate as the phosphate donor to the final product F-thioATP (3); see Scheme 3, below.

    ##STR00004##

    [0142] Adenylate kinase is a cellular housekeeping enzyme that catalyzes the conversion of ATP and AMP to two molecules of ADP through phosphoryl group transfer. Several crystal structures of AdK have been solved, including yeast (Abele et al., Protein Sci. 4(7):1262-71. [1995]) and E. coli (Muller et al., J Mol Biol. 224(1):159-77 [1992]; among many others), to reveal a core structure with flexible ATP and AMP binding domains. AdK is essential to maintaining cellular energy balance and has been demonstrated to be essential for yeast cell viability and stress response (Tukenmez et al., PLoS One. 11:e0163115 [2016]). AdK undergoes a conformational change upon binding of ATP that allows for selectivity over the related substrate GTP (Rogne et al., PNAS. 115(12): 3012-3017 [2018]).

    [0143] However, the wild-type adenylate kinases (AdK) possesses only limited activity and diasetereoselectivity towards conversion of the non-natural substrate ofF-thioAMP (4) to F-thioADP (5) using F-thioATP (3) as the phosphate donor. Therefore, AdK enzymes with improved activity and diasetereoselectivity are necessary to generate F-thioADP (5), a precursor to compound (1). Engineered AdKs that have improved activity and that operate under typical industrial conditions and/or as part of multi-enzyme systems are necessary. The present invention addresses this need and provides engineered AdKs that are suitable for use in these and other reactions under industrial conditions.

    Engineered AdK Polypeptides

    [0144] The present invention provides engineered AdK polypeptides, polynucleotides encoding the polypeptides, methods of preparing the polypeptides, and methods for using the polypeptides. Where the description relates to polypeptides, it is to be understood that it also describes the polynucleotides encoding the polypeptides. In some embodiments, the present invention provides engineered, non-naturally occurring AdK enzymes with improved properties as compared to wild-type AdK enzymes.

    [0145] In some embodiments, the present invention provides engineered adenylate kinases, wherein the engineered adenylate kinases comprise polypeptide sequences that are at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to SEQ ID NO: 4 and/or 230. In some embodiments, the engineered adenylate kinase comprises a variant engineered adenylate kinase set forth in SEQ ID NO: 230.

    [0146] In some additional embodiments, the present invention provides engineered adenylate kinases, wherein the engineered adenylate kinases comprise polypeptide sequences that are at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the sequence of at least one engineered adenylate kinase variant set forth in Table 2-1, 2-2, 3-1, and/or 3-2.

    [0147] The present invention also provides engineered adenylate kinases wherein the engineered adenylate kinases comprise polypeptide sequences that are at least 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to the sequence of at least one engineered adenylate kinase variant set forth in the even numbered sequences of SEQ ID NOs: 4-848.

    [0148] The present invention further provides engineered adenylate kinases, wherein said engineered adenylate kinases comprise at least one improved property compared to wild-type Saccharomyces cerevisiae adenylate kinase. In some embodiments, the improved property comprises improved activity on a substrate. In some further embodiments, the substrate comprises 2′F-ara-adenosine-5′-(1-thio)-monophosphate (F-thioAMP or compound (4)) and/or Sp-2′F-ara-adenosine-5′-(1-thio)-triphosphate (F-thioATP or compound (3)). In some additional embodiments, the improved property comprises improved production of compound Sp-2′F-ara-adenosine-5′-(1-thio)-diphosphate (F-thioADP or compound (5)). hi yet some additional embodiments, the engineered adenylate kinase is purified. The present invention also provides compositions comprising at least one engineered adenylate kinase provided herein.

    [0149] As will be appreciated by the skilled artisan, in some embodiments, one or a combination of residue differences above that is selected can be kept constant (i.e., maintained) in the engineered adenylate kinases as a core feature, and additional residue differences at other residue positions incorporated into the sequence to generate additional engineered adenylate kinase polypeptides with improved properties. Accordingly, it is to be understood for any engineered adenylate kinase containing one or a subset of the residue differences above, the present invention contemplates other engineered adenylate kinases that comprise the one or subset of the residue differences, and additionally one or more residue differences at the other residue positions disclosed herein.

    [0150] In some embodiments, the engineered adenylate kinase polypeptide is capable of converting the substrate compound to product compound with at least 1.2 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, or more activity relative to the activity of the reference polypeptide of SEQ ID NO: 4 and/or 230. In some embodiments, the engineered adenylate kinase polypeptide capable of converting the substrate compound to product compound with at least 1.2 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 60 fold, 70 fold, 80 fold, 90 fold, 100 fold, or more activity relative to the activity of the reference polypeptide of SEQ ID NO: 4 and/or 230, comprises an amino acid sequence having one or more features selected from improved stereoselectivity, improved activity, improved specific activity, and/or improved thermostability.

    [0151] In some embodiments, the engineered adenylate kinase polypeptide is capable of converting the substrate compound to product compound with at least 1.2 fold the activity relative to SEQ ID NO: 4 and/or 230, and comprises an amino acid sequence selected from the even-numbered sequences in the following range: SEQ ID NO: 4-848.

    [0152] In some embodiments, the engineered adenylate kinase polypeptide is capable of converting the substrate compound to product compound with at least 2 fold the activity relative to SEQ ID NO: 4 and/or 230, and comprises an amino acid sequence having one or more residue differences as provided herein (as compared to SEQ ID NO: 4 and/or 230, as applicable).

    [0153] In some embodiments, the engineered adenylate kinase polypeptide capable of converting the substrate compound to product compound with at least 2 fold the activity relative to SEQ ID NO: 4 and/or 230, comprises an amino acid sequence selected from: the even-numbered sequences in the following range: SEQ ID NO: 4-848.

    [0154] In some embodiments, the engineered adenylate kinase polypeptide is capable of converting at least 50% or more, 60% or more, 70% or more, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more, 94% or more, or 95% or more of substrate compound to product compound in 120 h or less, 72 h or less, 48 h or less, 24h or less, or 3 h or less, at a substrate loading of about 100 g/L, about 40 g/L, or about 20 g/L under HTP assay conditions, under SFP assay conditions, or DSP assay conditions. In some embodiments, the engineered adenylate kinase polypeptide is capable of converting at least 95% or more of substrate compound to product compound in 3 h or less at a substrate loading of about 40 g/L under SFP Assay conditions at about 30° C.

    [0155] In some embodiments, the engineered polypeptide having adenylate kinase activity, comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to one of the even-numbered sequences in the following range: SEQ ID NO: 4-848, and the amino acid residue differences as compared to SEQ ID NO: 4 and/or 230, present in any one of the even-numbered sequences in the following range: SEQ ID NO: 4-848, as provided in Tables 2.1, 2.2, 3.1 and/or 3.2.

    [0156] In addition to the residue positions specified above, any of the engineered adenylate kinase polypeptides disclosed herein can further comprise other residue differences relative to SEQ ID NO: 4 and/or 230, at other residue positions (i.e., residue positions other than those included in any of the even-numbered sequences in the following range: SEQ ID NO: 4-848). Residue differences at these other residue positions can provide for additional variations in the amino acid sequence without adversely affecting the ability of the polypeptide to carry out the conversion of substrate to product. Accordingly, in some embodiments, in addition to the amino acid residue differences present in any one of the engineered adenylate kinase polypeptides selected from the even-numbered sequences in the following range: SEQ ID NO: 4-848, the sequence can further comprise 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40, 1-45, or 1-50 residue differences at other amino acid residue positions as compared to the SEQ ID NO: 4 and/or 230. In some embodiments, the number of amino acid residue differences as compared to the reference sequence can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45 or 50 residue positions. In some embodiments, the number of amino acid residue differences as compared to the reference sequence can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, or 25 residue positions. The residue difference at these other positions can be conservative changes or non-conservative changes. In some embodiments, the residue differences can comprise conservative substitutions and non-conservative substitutions as compared to adenylate kinase polypeptide of SEQ ID NO: 4 and/or 230.

    [0157] In some embodiments, the present invention also provides engineered polypeptides that comprise a fragment of any of the engineered adenylate kinase polypeptides described herein that retains the functional activity and/or improved property of that engineered adenylate kinase. Accordingly, in some embodiments, the present invention provides a polypeptide fragment capable of converting substrate compound to product compound under suitable reaction conditions, wherein the fragment comprises at least about 80%, 90%, 95%, 96%, 97%, 98%, or 99% of a full-length amino acid sequence of an engineered adenylate kinase polypeptide of the present invention, such as an exemplary engineered adenylate kinase polypeptide selected from the even-numbered sequences in the following range: SEQ ID NO: 4-848.

    [0158] In some embodiments, the engineered adenylate kinase polypeptide can have an amino acid sequence comprising a deletion in any one of the engineered adenylate kinase polypeptide sequences described herein, such as the exemplary engineered polypeptides of the even-numbered sequences in the following range: SEQ ID NO: 4-848. Thus, for each and every embodiment of the engineered adenylate kinase polypeptides of the invention, the amino acid sequence can comprise deletions of one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, up to 20% of the total number of amino acids, or up to 30% of the total number of amino acids of the adenylate kinase polypeptides, where the associated functional activity and/or improved properties of the engineered adenylate kinase described herein are maintained. In some embodiments, the deletions can comprise 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, or 1-50 amino acid residues. In some embodiments, the number of deletions can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, or 50 amino acid residues. In some embodiments, the deletions can comprise deletions of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, or 25 amino acid residues.

    [0159] In some embodiments, the engineered adenylate kinase polypeptide herein can have an amino acid sequence comprising an insertion as compared to any one of the engineered adenylate kinase polypeptides described herein, such as the exemplary engineered polypeptides of the even-numbered sequences in the following range: SEQ ID NO: 4-848. Thus, for each and every embodiment of the adenylate kinase polypeptides of the invention, the insertions can comprise one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, 20 or more amino acids, 30 or more amino acids, 40 or more amino acids, or 50 or more amino acids, where the associated functional activity and/or improved properties of the engineered adenylate kinase described herein is maintained. The insertions can be to amino or carboxy terminus, or internal portions of the adenylate kinase polypeptide.

    [0160] In some embodiments, the engineered adenylate kinase polypeptide herein can have an amino acid sequence comprising a sequence selected from the even-numbered sequences in the following range: SEQ ID NO: 4-848, and optionally one or several (e.g., up to 3, 4, 5, or up to 10) amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1- 45, or 1-50 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, or 50 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the amino acid sequence has optionally 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, or 25 amino acid residue deletions, insertions and/or substitutions. In some embodiments, the substitutions can be conservative or non-conservative substitutions.

    [0161] In the above embodiments, the suitable reaction conditions for the engineered polypeptides may be as described in the Examples.

    [0162] In some embodiments, the polypeptides of the present invention are fusion polypeptides in which the engineered polypeptides are fused to other polypeptides, such as, by way of example and not limitation, antibody tags (e.g., myc epitope), purification sequences (e.g., His tags for binding to metals), and cell localization signals (e.g., secretion signals). Thus, the engineered polypeptides described herein can be used with or without fusions to other polypeptides.

    [0163] It is to be understood that the polypeptides described herein are not restricted to the genetically encoded amino acids. In addition to the genetically encoded amino acids, the polypeptides described herein may be comprised, either in whole or in part, of naturally occurring and/or synthetic non-encoded amino acids. Certain commonly encountered non-encoded amino acids of which the polypeptides described herein may be comprised include, but are not limited to: the D-stereomers of the genetically-encoded amino acids; 2,3-diaminopropionic acid (Dpr); α-aminoisobutyric acid (Aib); ϵ-aminohexanoic acid (Aha); δ-aminovaleric acid (Ava); N-methylglycine or sarcosine (MeGly or Sar); ornithine (Orn); citrulline (Cit); t-butylalanine (Bua); t-butylglycine (Bug); N-methylisoleucine (MeIle); phenylglycine (Phg); cyclohexylalanine (Cha); norleucine (Nle); naphthylalanine (Nal); 2-chlorophenylalanine (Oct); 3-chlorophenylalanine (Mcf); 4-chlorophenylalanine (Pcf); 2-fluorophenylalanine (Off); 3-fluorophenylalanine (Mff); 4-fluorophenylalanine (Pff); 2-bromophenylalanine (Obi); 3-bromophenylalanine (Mbf); 4-bromophenylalanine (Pbf); 2-methylphenylalanine (Omf); 3-methylphenylalanine (Mmf); 4-methylphenylalanine (Pmf); 2-nitrophenylalanine (Onf); 3-nitrophenylalanine (Mnf); 4-nitrophenylalanine (Pnf); 2-cyanophenylalanine (Oct); 3-cyanophenylalanine (Mcf); 4-cyanophenylalanine (Pcf); 2-trifluoromethylphenylalanine (Otf); 3-trifluoromethylphenylalanine (Mtf); 4-trifluoromethylphenylalanine (Ptf); 4-aminophenylalanine (Pat); 4-iodophenylalanine (Pif); 4-aminomethylphenylalanine (Pamf); 2,4-dichlorophenylalanine (Opef); 3,4-dichlorophenylalanine (Mpcf); 2,4-difluorophenylalanine (Opff); 3,4-difluorophenylalanine (Mpff); pyrid-2-ylalanine (2pAla); pyrid-3-ylalanine (3pAla); pyrid-4-ylalanine (4pAla); naphth-l-ylalanine (1nAla); naphth-2-ylalanine (2nAla); thiazolylalanine (taAla); benzothienylalanine (bAla); thienylalanine (tAla); furylalanine (fAla); homophenylalanine (hPhe); homotyrosine (hTyr); homotryptophan (hTrp); pentafluorophenylalanine (5f0; styrylkalanine (sAla); authrylalanine (aAla); 3,3-diphenylalanine (Dfa); 3-amino-5-phenypentanoic acid (Afp); penicillamine (Pen); 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic); β-2-thienylalanine (Thi); methionine sulfoxide (Mso); N(w)-nitroarginine (nArg); homolysine (hLys); phosphonomethylphenylalanine (pmPhe); phosphoserine (pSer); phosphothreonine (pThr); homoaspartic acid (hAsp); homoglutanic acid (hGlu); 1-aminocyclopent-(2 or 3)-ene-4 carboxylic acid; pipecolic acid (PA), azetidine-3-carboxylic acid (ACA); 1-aminocyclopentane-3-carboxylic acid; allylglycine (aGly); propargylglycine (pgGly); homoalanine (hAla); norvaline (nVal); homoleucine (hLeu), homovaline (hVal); homoisoleucine (hIle); homoarginine (hArg); N-acetyl lysine (AcLys); 2,4-diaminobutyric acid (Dbu); 2,3-diaminobutyric acid (Dab); N-methylvaline (MeVal); homocysteine (hCys); homoserine (hSer); hydroxyproline (Hyp) and homoproline (hPro). Additional non-encoded amino acids of which the polypeptides described herein may be comprised will be apparent to those of skill in the art (See e.g., the various amino acids provided in Fasman, CRC Practical Handbook of Biochemistry and Molecular Biology, CRC Press, Boca Raton, FL, pp. 3-70 [1989], and the references cited therein, all of which are incorporated by reference). These amino acids may be in either the L- or D-configuration.

    [0164] Those of skill in the art will recognize that amino acids or residues bearing side chain protecting groups may also comprise the polypeptides described herein. Non-limiting examples of such protected amino acids, which in this case belong to the aromatic category, include (protecting groups listed in parentheses), but are not limited to: Arg(tos), Cys(methylbenzyl), Cys (nitropyridinesulfenyl), Glu(δ-benzylester), Gln(xanthyl), Asn(N-δ-xanthyl), His(bom), His(benzyl), His(tos), Lys(fmoc), Lys(tos), Ser(O-benzyl), Thr (O-benzyl) and Tyr(O-benzyl).

    [0165] Non-encoding amino acids that are conformationally constrained of which the polypeptides described herein may be composed include, but are not limited to, N-methyl amino acids (L-configuration); 1-aminocyclopent-(2 or 3)-ene-4-carboxylic acid; pipecolic acid; azetidine-3-carboxylic acid; homoproline (hPro); and 1-aminocyclopentane-3-carboxylic acid.

    [0166] In some embodiments, the engineered polypeptides can be in various forms, for example, such as an isolated preparation, as a substantially purified enzyme, whole cells transformed with gene(s) encoding the enzyme, and/or as cell extracts and/or lysates of such cells. The enzymes can be lyophilized, spray-dried, precipitated or be in the form of a crude paste, as further discussed below.

    [0167] In some embodiments, the engineered polypeptides can be provided on a solid support, such as a membrane, resin, solid carrier, or other solid phase material. A solid support can be composed of organic polymers such as polystyrene, polyethylene, polypropylene, polyfluoroethylene, polyethyleneoxy, and polyacrylamide, as well as co-polymers and grafts thereof. A solid support can also be inorganic, such as glass, silica, controlled pore glass (CPG), reverse phase silica or metal, such as gold or platinum. The configuration of a solid support can be in the form of beads, spheres, particles, granules, a gel, a membrane or a surface. Surfaces can be planar, substantially planar, or non-planar. Solid supports can be porous or non-porous, and can have swelling or non-swelling characteristics. A solid support can be configured in the form of a well, depression, or other container, vessel, feature, or location.

    [0168] In some embodiments, the engineered polypeptides having adenylate kinase activity of the present invention can be immobilized on a solid support such that they retain their improved activity, selectivity, and/or other improved properties relative to the reference polypeptide of SEQ ID NO: 4 and/or 230. In such embodiments, the immobilized polypeptides can facilitate the biocatalytic conversion of the substrate compounds or other suitable substrates to the product and after the reaction is complete are easily retained (e.g., by retaining beads on which polypeptide is immobilized) and then reused or recycled in subsequent reactions. Such immobilized enzyme processes allow for further efficiency and cost reduction. Accordingly, it is further contemplated that any of the methods of using the adenylate kinase polypeptides of the present invention can be carried out using the same adenylate kinase polypeptides bound or immobilized on a solid support.

    [0169] Methods of enzyme immobilization are well-known in the art. The engineered polypeptides can be bound non-covalently or covalently. Various methods for conjugation and immobilization of enzymes to solid supports (e.g., resins, membranes, beads, glass, etc.) are well known in the art (See e.g., Yi et al., Proc. Biochem., 42(5): 895-898 [2007]; Martin et al., Appl. Microbiol. Biotechnol., 76(4): 843-851 [2007]; Koszelewski et al., J. Mol. Cat. B: Enzymatic, 63: 39-44 [2010]; Truppo et al., Org. Proc. Res. Dev., published online: dx.doi.org/10.1021/op200157c; Hermanson, Bioconjugate Techniques, 2.sup.nd ed., Academic Press, Cambridge, Mass. [2008]; Mateo et al., Biotechnol. Prog., 18(3):629-34 [2002]; and “Bioconjugation Protocols: Strategies and Methods,” In Methods in Molecular Biology, Niemeyer (ed.), Humana Press, New York, N.Y. [2004]; the disclosures of each which are incorporated by reference herein). Solid supports useful for immobilizing the engineered adenylate kinases of the present invention include but are not limited to beads or resins comprising polymethacrylate with epoxide functional groups, polymethacrylate with amino epoxide functional groups, styrene/DVB copolymer or polymethacrylate with octadecyl functional groups. Exemplary solid supports useful for immobilizing the engineered adenylate kinase polypeptides of the present invention include, but are not limited to, chitosan beads, Eupergit C, and SEPABEADs (Mitsubishi), including the following different types of SEPABEAD: EC-EP, EC-HFA/S, EXA252, EXE119 and EXE120.

    [0170] In some embodiments, the polypeptides described herein are provided in the form of kits. The enzymes in the kits may be present individually or as a plurality of enzymes. The kits can further include reagents for carrying out the enzymatic reactions, substrates for assessing the activity of enzymes, as well as reagents for detecting the products. The kits can also include reagent dispensers and instructions for use of the kits.

    [0171] In some embodiments, the kits of the present invention include arrays comprising a plurality of different adenylate kinase polypeptides at different addressable position, wherein the different polypeptides are different variants of a reference sequence each having at least one different improved enzyme property. In some embodiments, a plurality of polypeptides immobilized on solid supports are configured on an array at various locations, addressable for robotic delivery of reagents, or by detection methods and/or instruments. The array can be used to test a variety of substrate compounds for conversion by the polypeptides. Such arrays comprising a plurality of engineered polypeptides and methods of their use are known in the art (See e.g., WO2009/008908A2).

    [0172] Recombinant polypeptides can be produced using any suitable methods known in the art. Genes encoding the wild-type polypeptide of interest can be cloned in vectors, such as plasmids, and expressed in desired hosts, such as E. coli, etc. Variants of recombinant polypeptides can be generated by various methods known in the art. Indeed, there is a wide variety of different mutagenesis techniques well known to those skilled in the art. In addition, mutagenesis kits are also available from many commercial molecular biology suppliers. Methods are available to make specific substitutions at defined amino acids (site-directed), specific or random mutations in a localized region of the gene (regio-specific), or random mutagenesis over the entire gene (e.g., saturation mutagenesis). Numerous suitable methods are known to those in the art to generate enzyme variants, including but not limited to site-directed mutagenesis of single-stranded DNA or double-stranded DNA using PCR, cassette mutagenesis, gene synthesis, error-prone PCR, shuffling, and chemical saturation mutagenesis, or any other suitable method known in the art. Mutagenesis and directed evolution methods can be readily applied to enzyme-encoding polynucleotides to generate variant libraries that can be expressed, screened, and assayed. Any suitable mutagenesis and directed evolution methods find use in the present invention and are well known in the art (See e.g., U.S. Pat. Nos. 5,605,793, 5,811,238, 5,830,721, 5,834,252, 5,837,458, 5,928,905, 6,096,548, 6,117,679, 6,132,970, 6,165,793, 6,180,406, 6,251,674, 6,265,201, 6,277,638, 6,287,861, 6,287,862, 6,291,242, 6,297,053, 6,303,344, 6,309,883, 6,319,713, 6,319,714, 6,323,030, 6,326,204, 6,335,160, 6,335,198, 6,344,356, 6,352,859, 6,355,484, 6,358,740, 6,358,742, 6,365,377, 6,365,408, 6,368,861, 6,372,497, 6,337,186, 6,376,246, 6,379,964, 6,387,702, 6,391,552, 6,391,640, 6,395,547, 6,406,855, 6,406,910, 6,413,745, 6,413,774, 6,420,175, 6,423,542, 6,426,224, 6,436,675, 6,444,468, 6,455,253, 6,479,652, 6,482,647, 6,483,011, 6,484,105, 6,489,146, 6,500,617, 6,500,639, 6,506,602, 6,506,603, 6,518,065, 6,519,065, 6,521,453, 6,528,311, 6,537,746, 6,573,098, 6,576,467, 6,579,678, 6,586,182, 6,602,986, 6,605,430, 6,613,514, 6,653,072, 6,686,515, 6,703,240, 6,716,631, 6,825,001, 6,902,922, 6,917,882, 6,946,296, 6,961,664, 6,995,017, 7,024,312, 7,058,515, 7,105,297, 7,148,054, 7,220,566, 7,288,375, 7,384,387, 7,421,347, 7,430,477, 7,462,469, 7,534,564, 7,620,500, 7,620,502, 7,629,170, 7,702,464, 7,747,391, 7,747,393, 7,751,986, 7,776,598, 7,783,428, 7,795,030, 7,853,410, 7,868,138, 7,783,428, 7,873,477, 7,873,499, 7,904,249, 7,957,912, 7,981,614, 8,014,961, 8,029,988, 8,048,674, 8,058,001, 8,076,138, 8,108,150, 8,170,806, 8,224,580, 8,377,681, 8,383,346, 8,457,903, 8,504,498, 8,589,085, 8,762,066, 8,768,871, 9,593,326, 9,665,694, 9,684,771, and all related US, as well as PCT and non-US counterparts; Ling et al., Anal. Biochem., 254(2):157-78 [1997]; Dale et al., Meth. Mol. Biol., 57:369-74 [1996]; Smith, Ann. Rev. Genet., 19:423-462 [1985]; Botstein et al., Science, 229:1193-1201 [1985]; Carter, Biochem. J., 237:1-7 [1986]; Kramer et al., Cell, 38:879-887 [1984]; Wells et al., Gene, 34:315-323 [1985]; Minshull et al., Curr. Op. Chem. Biol., 3:284-290 [1999]; Christians et al., Nat. Biotechnol., 17:259-264 [1999]; Crameri et al., Nature, 391:288-291 [1998]; Crameri, et al., Nat. Biotechnol., 15:436-438 [1997]; Zhang et al., Proc. Nat. Acad. Sci. U.S.A., 94:4504-4509 [1997]; Crameri et al., Nat. Biotechnol., 14:315-319 [1996]; Stemmer, Nature, 370:389-391 [1994]; Stemmer, Proc. Nat. Acad. Sci. USA, 91:10747-10751 [1994]; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767; and WO 2009/152336, all of which are incorporated herein by reference).

    [0173] In some embodiments, the enzyme clones obtained following mutagenesis treatment are screened by subjecting the enzyme preparations to a defined temperature (or other assay conditions) and measuring the amount of enzyme activity remaining after heat treatments or other suitable assay conditions. Clones containing a polynucleotide encoding a polypeptide are then isolated from the gene, sequenced to identify the nucleotide sequence changes (if any), and used to express the enzyme in a host cell. Measuring enzyme activity from the expression libraries can be performed using any suitable method known in the art (e.g., standard biochemistry techniques, such as HPLC analysis).

    [0174] After the variants are produced, they can be screened for any desired property (e.g., high or increased activity, or low or reduced activity, increased thermal activity, increased thermal stability, and/or acidic pH stability, etc.). Any suitable reaction conditions find use in the present invention. In some embodiments, methods are used to analyze the improved properties of the engineered polypeptides to carry out the phosphorylation reaction. In some embodiments, the reaction conditions are modified with regard to concentrations or amounts of engineered AdK, substrate(s), buffer(s), solvent(s), pH, conditions including temperature and reaction time, and/or conditions with the engineered AdK polypeptide immobilized on a solid support, as further described below and in the Examples.

    [0175] In some embodiments, additional reaction components or additional techniques are utilized to supplement the reaction conditions. In some embodiments, these include taking measures to stabilize or prevent inactivation of the enzyme, reduce product inhibition, and/or shift reaction equilibrium to desired product formation.

    [0176] In some further embodiments, any of the above described processes for the conversion of substrate compound to product compound can further comprise one or more steps selected from: extraction, isolation, purification, crystallization, filtration, and/or lyophilization of product compound(s). Methods, techniques, and protocols for extracting, isolating, purifying, and/or crystallizing the product(s) from biocatalytic reaction mixtures produced by the processes provided herein are known to the ordinary artisan and/or accessed through routine experimentation. Additionally, illustrative methods are provided in the Examples below.

    Engineered AdK Polynucleotides Encoding Engineered Polypeptides, Expression Vectors and Host Cells

    [0177] The present invention provides polynucleotides encoding the engineered enzyme polypeptides described herein. In some embodiments, the polynucleotides are operatively linked to one or more heterologous regulatory sequences that control gene expression to create a recombinant polynucleotide capable of expressing the polypeptide. In some embodiments, expression constructs containing at least one heterologous polynucleotide encoding the engineered enzyme polypeptide(s) is introduced into appropriate host cells to express the corresponding enzyme polypeptide(s).

    [0178] As will be apparent to the skilled artisan, availability of a protein sequence and the knowledge of the codons corresponding to the various amino acids provide a description of all the polynucleotides capable of encoding the subject polypeptides. The degeneracy of the genetic code, where the same amino acids are encoded by alternative or synonymous codons, allows an extremely large number of nucleic acids to be made, all of which encode an engineered enzyme (e.g., AdK) polypeptide. Thus, the present invention provides methods and compositions for the production of each and every possible variation of enzyme polynucleotides that could be made that encode the enzyme polypeptides described herein by selecting combinations based on the possible codon choices, and all such variations are to be considered specifically disclosed for any polypeptide described herein, including the amino acid sequences presented in the Examples (e.g., in the various Tables).

    [0179] In some embodiments, the codons are preferably optimized for utilization by the chosen host cell for protein production. For example, preferred codons used in bacteria are typically used for expression in bacteria. Consequently, codon optimized polynucleotides encoding the engineered enzyme polypeptides contain preferred codons at about 40%, 50%, 60%, 70%, 80%, 90%, or greater than 90% of the codon positions in the full length coding region.

    [0180] In some embodiments, the enzyme polynucleotide encodes an engineered polypeptide having enzyme activity with the properties disclosed herein, wherein the polypeptide comprises an amino acid sequence having at least 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identity to a reference sequence selected from the SEQ ID NOs provided herein, or the amino acid sequence of any variant (e.g., those provided in the Examples), and one or more residue differences as compared to the reference polynucleotide(s), or the amino acid sequence of any variant as disclosed in the Examples (for example 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acid residue positions). In some embodiments, the reference polypeptide sequence is selected from SEQ ID NOs: 4 and 230.

    [0181] In some embodiments, the polynucleotides are capable of hybridizing under highly stringent conditions to a reference polynucleotide sequence selected from any polynucleotide sequence provided herein, or a complement thereof, or a polynucleotide sequence encoding any of the variant enzyme polypeptides provided herein. In some embodiments, the polynucleotide capable of hybridizing under highly stringent conditions encodes an enzyme polypeptide comprising an amino acid sequence that has one or more residue differences as compared to a reference sequence.

    [0182] In some embodiments, an isolated polynucleotide encoding any of the engineered enzyme polypeptides herein is manipulated in a variety of ways to facilitate expression of the enzyme polypeptide. In some embodiments, the polynucleotides encoding the enzyme polypeptides comprise expression vectors where one or more control sequences is present to regulate the expression of the enzyme polynucleotides and/or polypeptides. Manipulation of the isolated polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector utilized. Techniques for modifying polynucleotides and nucleic acid sequences utilizing recombinant DNA methods are well known in the art. In some embodiments, the control sequences include among others, promoters, leader sequences, polyadenylation sequences, propeptide sequences, signal peptide sequences, and transcription terminators. In some embodiments, suitable promoters are selected based on the host cells selection. For bacterial host cells, suitable promoters for directing transcription of the nucleic acid constructs of the present disclosure, include, but are not limited to promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (See e.g., Villa-Kamaroff et al., Proc. Natl Acad. Sci. USA 75: 3727-3731 [1978]), as well as the tac promoter (See e.g., DeBoer et al., Proc. Natl Acad. Sci. USA 80: 21-25 [1983]). Exemplary promoters for filamentous fungal host cells, include, but are not limited to promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (See e.g., WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof. Exemplary yeast cell promoters can be from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are known in the art (See e.g., Romanos et al., Yeast 8:423-488 [1992]).

    [0183] In some embodiments, the control sequence is also a suitable transcription terminator sequence (i.e., a sequence recognized by a host cell to terminate transcription). In some embodiments, the terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the enzyme polypeptide. Any suitable terminator which is functional in the host cell of choice finds use in the present invention. Exemplary transcription terminators for filamentous fungal host cells can be obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease. Exemplary terminators for yeast host cells can be obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are known in the art (See e.g., Romanos et al., supra).

    [0184] In some embodiments, the control sequence is also a suitable leader sequence (i.e., a non-translated region of an mRNA that is important for translation by the host cell). In some embodiments, the leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the enzyme polypeptide. Any suitable leader sequence that is functional in the host cell of choice finds use in the present invention. Exemplary leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase, and Aspergillus nidulans triose phosphate isomerase. Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

    [0185] In some embodiments, the control sequence is also a polyadenylation sequence (i.e., a sequence operably linked to the 3′ terminus of the nucleic acid sequence and which, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA). Any suitable polyadenylation sequence which is functional in the host cell of choice finds use in the present invention. Exemplary polyadenylation sequences for filamentous fungal host cells include, but are not limited to the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are known (See e.g., Guo and Sherman, Mol. Cell. Bio., 15:5983-5990 [1995]).

    [0186] In some embodiments, the control sequence is also a signal peptide (i.e., a coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded polypeptide into the cell's secretory pathway). In some embodiments, the 5′ end of the coding sequence of the nucleic acid sequence inherently contains a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the secreted polypeptide. Alternatively, in some embodiments, the 5′ end of the coding sequence contains a signal peptide coding region that is foreign to the coding sequence. Any suitable signal peptide coding region which directs the expressed polypeptide into the secretory pathway of a host cell of choice finds use for expression of the engineered polypeptide(s). Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions that include, but are not limited to those obtained from the genes for Bacillus NC1B 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are known in the art (See e.g., Simonen and Palva, Microbiol. Rev., 57:109-137 [1993]). In some embodiments, effective signal peptide coding regions for filamentous fungal host cells include, but are not limited to the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulase, and Humicola lanuginosa lipase. Useful signal peptides for yeast host cells include, but are not limited to those from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase.

    [0187] In some embodiments, the control sequence is also a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a polypeptide. The resultant polypeptide is referred to as a “proenzyme,” “propolypeptide,” or “zymogen.” A propolypeptide can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide. The propeptide coding region may be obtained from any suitable source, including, but not limited to the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Saccharomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophila lactase (See e.g., WO 95/33836). Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the propeptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the propeptide region.

    [0188] In some embodiments, regulatory sequences are also utilized. These sequences facilitate the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those that cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In prokaryotic host cells, suitable regulatory sequences include, but are not limited to the lac, tac, and trp operator systems. In yeast host cells, suitable regulatory systems include, but are not limited to the ADH2 system or GAL1 system. In filamentous fungi, suitable regulatory sequences include, but are not limited to the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase promoter.

    [0189] In another aspect, the present invention is directed to a recombinant expression vector comprising a polynucleotide encoding an engineered enzyme polypeptide, and one or more expression regulating regions such as a promoter and a terminator, a replication origin, etc., depending on the type of hosts into which they are to be introduced. In some embodiments, the various nucleic acid and control sequences described herein are joined together to produce recombinant expression vectors which include one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the enzyme polypeptide at such sites. Alternatively, in some embodiments, the nucleic acid sequence of the present invention is expressed by inserting the nucleic acid sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In some embodiments involving the creation of the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.

    [0190] The recombinant expression vector may be any suitable vector (e.g., a plasmid or virus), that can be conveniently subjected to recombinant DNA procedures and bring about the expression of the enzyme polynucleotide sequence. The choice of the vector typically depends on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids.

    [0191] In some embodiments, the expression vector is an autonomously replicating vector (i.e., a vector that exists as an extra-chromosomal entity, the replication of which is independent of chromosomal replication, such as a plasmid, an extra-chromosomal element, a minichromosome, or an artificial chromosome). The vector may contain any means for assuring self-replication. In some alternative embodiments, the vector is one in which, when introduced into the host cell, it is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, in some embodiments, a single vector or plasmid, or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, and/or a transposon is utilized.

    [0192] In some embodiments, the expression vector contains one or more selectable markers, which permit easy selection of transformed cells. A “selectable marker” is a gene, the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers include, but are not limited to the dal genes from Bacillus subtilis or Bacillus licheniformis, or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol or tetracycline resistance. Suitable markers for yeast host cells include, but are not limited to ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in filamentous fungal host cells include, but are not limited to, amdS (acetamidase; e.g., from A. nidulans or A. orzyae), argB (ornithine carbamoyltransferases), bar (phosphinothricin acetyltransferase; e.g., from S. hygroscopicus), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase; e.g., from A. nidulans or A. orzyae), sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof.

    [0193] In another aspect, the present invention provides a host cell comprising at least one polynucleotide encoding at least one engineered enzyme polypeptide of the present invention, the polynucleotide(s) being operatively linked to one or more control sequences for expression of the engineered enzyme enzyme(s) in the host cell. Host cells suitable for use in expressing the polypeptides encoded by the expression vectors of the present invention are well known in the art and include but are not limited to, bacterial cells, such as E. coli, Vibrio fluvialis, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, BHK, 293, and Bowes melanoma cells; and plant cells. Exemplary host cells also include various Escherichia coli strains (e.g., W3110 (ΔfhuA) and BL21). Examples of bacterial selectable markers include, but are not limited to the dal genes from Bacillus subtilis or Bacillus licheniformis, or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol, and/or tetracycline resistance.

    [0194] In some embodiments, the expression vectors of the present invention contain an element(s) that permits integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome. In some embodiments involving integration into the host cell genome, the vectors rely on the nucleic acid sequence encoding the polypeptide or any other element of the vector for integration of the vector into the genome by homologous or nonhomologous recombination.

    [0195] In some alternative embodiments, the expression vectors contain additional nucleic acid sequences for directing integration by homologous recombination into the genome of the host cell. The additional nucleic acid sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). To increase the likelihood of integration at a precise location, the integrational elements preferably contain a sufficient number of nucleotides, such as 100 to 10,000 base pairs, preferably 400 to 10,000 base pairs, and most preferably 800 to 10,000 base pairs, which are highly homologous with the corresponding target sequence to enhance the probability of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding nucleic acid sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombination.

    [0196] For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacterial origins of replication are P15A ori or the origins of replication of plasmids pBR322, pUC19, pACYC177 (which plasmid has the P15A ori), or pACYC184 permitting replication in E. coli, and pUB110, pE194, or pTA1060 permitting replication in Bacillus. Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6. The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (See e.g., Ehrlich, Proc. Natl. Acad. Sci. USA 75:1433 [1978]).

    [0197] In some embodiments, more than one copy of a nucleic acid sequence of the present invention is inserted into the host cell to increase production of the gene product. An increase in the copy number of the nucleic acid sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleic acid sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleic acid sequence, can be selected for by cultivating the cells in the presence of the appropriate selectable agent.

    [0198] Many of the expression vectors for use in the present invention are commercially available. Suitable commercial expression vectors include, but are not limited to the p3xFLAGTM™ expression vectors (Sigma-Aldrich Chemicals), which include a CMV promoter and hGH polyadenylation site for expression in mammalian host cells and a pBR322 origin of replication and ampicillin resistance markers for amplification in E. coli. Other suitable expression vectors include, but are not limited to pBluescriptII SK(−) and pBK-CMV (Stratagene), and plasmids derived from pBR322 (Gibco BRL), pUC (Gibco BRL), pREP4, pCEP4 (Invitrogen) or pPoly (See e.g., Lathe et al., Gene 57:193-201 [1987]).

    [0199] Thus, in some embodiments, a vector comprising a sequence encoding at least one variant adenylate kinase is transformed into a host cell in order to allow propagation of the vector and expression of the variant adenylate kinase(s). In some embodiments, the variant adenylate kinases are post-translationally modified to remove the signal peptide, and in some cases may be cleaved after secretion. In some embodiments, the transformed host cell described above is cultured in a suitable nutrient medium under conditions permitting the expression of the variant adenylate kinase(s). Any suitable medium useful for culturing the host cells finds use in the present invention, including, but not limited to minimal or complex media containing appropriate supplements. In some embodiments, host cells are grown in HTP media. Suitable media are available from various commercial suppliers or may be prepared according to published recipes (e.g., in catalogues of the American Type Culture Collection).

    [0200] In another aspect, the present invention provides host cells comprising a polynucleotide encoding an improved adenylate kinase polypeptide provided herein, the polynucleotide being operatively linked to one or more control sequences for expression of the adenylate kinase enzyme in the host cell. Host cells for use in expressing the adenylate kinase polypeptides encoded by the expression vectors of the present invention are well known in the art and include but are not limited to, bacterial cells, such as E. coli, Bacillus megaterium, Lactobacillus kefir, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, BHK, 293, and Bowes melanoma cells; and plant cells. Appropriate culture media and growth conditions for the above-described host cells are well known in the art.

    [0201] Polynucleotides for expression of the adenylate kinase may be introduced into cells by various methods known in the art. Techniques include among others, electroporation, biolistic particle bombardment, liposome mediated transfection, calcium chloride transfection, and protoplast fusion. Various methods for introducing polynucleotides into cells are known to those skilled in the art.

    [0202] In some embodiments, the host cell is a eukaryotic cell. Suitable eukaryotic host cells include, but are not limited to, fungal cells, algal cells, insect cells, and plant cells. Suitable fungal host cells include, but are not limited to, Ascomycota, Basidiomycota, Deuteromycota, Zygomycota, Fungi imperfecti. In some embodiments, the fungal host cells are yeast cells and filamentous fungal cells. The filamentous fungal host cells of the present invention include all filamentous forms of the subdivision Eumycotina and Oomycota. Filamentous fungi are characterized by a vegetative mycelium with a cell wall composed of chitin, cellulose and other complex polysaccharides. The filamentous fungal host cells of the present invention are morphologically distinct from yeast.

    [0203] In some embodiments of the present invention, the filamentous fungal host cells are of any suitable genus and species, including, but not limited to Achlya, Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Cephalosporium, Chrysosporium, Cochliobolus, Corynascus, Cryphonectria, Cryptococcus, Coprinus, Coriolus, Diplodia, Endothia, Fusarium, Gibberella, Gliocladium, Humicola, Hypocrea, Myceliophthora, Mucor, Neurospora, Penicillium, Podospora, Phlebia, Piromyces, Pyricularia, Rhizomucor, Rhizopus, Schizophyllum, Scytalidium, Sporotrichum, Talaromyces, Thermoascus, Thielavia, Trametes, Tolypocladium, Trichoderma, Verticillium, and/or Volvariella, and/or teleomorphs, or anamorphs, and synonyms, basionyms, or taxonomic equivalents thereof.

    [0204] In some embodiments of the present invention, the host cell is a yeast cell, including but not limited to cells of Candida, Hansenula, Saccharomyces, Schizosaccharomyces, Pichia, Kluyveromyces, or Yarrowia species. In some embodiments of the present invention, the yeast cell is Hansenula polymorpha, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Saccharomyces diastaticus, Saccharomyces norbensis, Saccharomyces kluyveri, Schizosaccharomyces pombe, Pichia pastoris, Pichia finlandica, Pichia trehalophila, Pichia kodamae, Pichia membranaefaciens, Pichia opuntiae, Pichia thermotolerans, Pichia salictaria, Pichia quercuum, Pichia pijperi, Pichia stipitis, Pichia methanolica, Pichia angusta, Kluyveromyces lactis, Candida albicans, or Yarrowia lipolytica.

    [0205] In some embodiments of the invention, the host cell is an algal cell such as Chlamydomonas (e.g., C. reinhardtii) and Phormidium (P. sp. ATCC29409).

    [0206] In some other embodiments, the host cell is a prokaryotic cell. Suitable prokaryotic cells include, but are not limited to Gram-positive, Gram-negative and Gram-variable bacterial cells. Any suitable bacterial organism finds use in the present invention, including but not limited to Agrobacterium, Alicyclobacillus, Anabaena, Anacystis, Acinetobacter, Acidothermus, Arthrobacter, Azobacter, Bacillus, Bifidobacterium, Brevibacterium, Butyrivibrio, Buchnera, Campestris, Campylobacter, Clostridium, Corynebacterium, Chromatium, Coprococcus, Escherichia, Enterococcus, Enterobacter, Erwinia, Fusobacterium, Faecalibacterium, Francisella, Flavobacterium, Geobacillus, Haemophilus, Helicobacter, Klebsiella, Lactobacillus, Lactococcus, Ilyobacter, Micrococcus, Microbacterium, Mesorhizobium, Methylobacterium, Methylobacterium, Mycobacterium, Neisseria, Pantoea, Pseudomonas, Prochlorococcus, Rhodobacter, Rhodopseudomonas, Rhodopseudomonas, Roseburia, Rhodospirillum, Rhodococcus, Scenedesmus, Streptomyces, Streptococcus, Synecoccus, Saccharomonospora, Staphylococcus, Serratia, Salmonella, Shigella, Thermoanaerobacterium, Tropheryma, Tularensis, Temecula, Thermosynechococcus, Thermococcus, Ureaplasma, Xanthomonas, Xylella, Yersinia and Zymomonas. In some embodiments, the host cell is a species of Agrobacterium, Acinetobacter, Azobacter, Bacillus, Bifidobacterium, Buchnera, Geobacillus, Campylobacter, Clostridium, Corynebacterium, Escherichia, Enterococcus, Erwinia, Flavobacterium, Lactobacillus, Lactococcus, Pantoea, Pseudomonas, Staphylococcus, Salmonella, Streptococcus, Streptomyces, or Zymomonas. In some embodiments, the bacterial host strain is non-pathogenic to humans. In some embodiments the bacterial host strain is an industrial strain. Numerous bacterial industrial strains are known and suitable in the present invention. In some embodiments of the present invention, the bacterial host cell is an Agrobacterium species (e.g., A. radiobacter, A. rhizogenes, and A. rubi). In some embodiments of the present invention, the bacterial host cell is an Arthrobacter species (e.g., A. aurescens, A. citreus, A. globiformis, A. hydrocarboglutamicus, A. mysorens, A. nicotianae, A. paraffineus, A. protophonniae, A. roseoparqffinus, A. sulfureus, and A. ureafaciens). In some embodiments of the present invention, the bacterial host cell is a Bacillus species (e.g., B. thuringensis, B. anthracis, B. megaterium, B. subtilis, B. lentus, B. circulans, B. pumilus, B. lautus, B.coagulans, B. brevis, B. firmus, B. alkaophius, B. licheniformis, B. clausii, B. stearothermophilus, B. halodurans, and B. amyloliquefaciens). In some embodiments, the host cell is an industrial Bacillus strain including but not limited to B. subtilis, B. pumilus, B. licheniformis, B. megaterium, B. clausii, B. stearothermophilus, or B. amyloliquefaciens. In some embodiments, the Bacillus host cells are B. subtilis, B. licheniformis, B. megaterium, B. stearothermophilus, and/or B. amyloliquefaciens. In some embodiments, the bacterial host cell is a Clostridium species (e.g., C. acetobutylicum, C. tetani E88, C. lituseburense, C. saccharobutylicum, C. perfringens, and C. beijerinckii). In some embodiments, the bacterial host cell is a Corynebacterium species (e.g., C. glutamicum and C. acetoacidophilum). In some embodiments the bacterial host cell is an Escherichia species (e.g., E. coli). In some embodiments, the host cell is Escherichia coli W3110. In some embodiments, the bacterial host cell is an Erwinia species (e.g., E. uredovora, E. carotovora, E. ananas, E. herbicola, E. punctata, and E. terreus). In some embodiments, the bacterial host cell is a Pantoea species (e.g., P. citrea, and P. agglomerans). In some embodiments the bacterial host cell is a Pseudomonas species (e.g., P. putida, P. aeruginosa, P. mevalonii, and P. sp. D-01 10). In some embodiments, the bacterial host cell is a Streptococcus species (e.g., S. equisimiles, S. pyogenes, and S. uberis). In some embodiments, the bacterial host cell is a Streptomyces species (e.g., S. ambofaciens, S. achromogenes, S. avermitilis, S. coelicolor, S. aureofaciens, S. aureus, S. fungicidicus, S. griseus, and S. lividans). In some embodiments, the bacterial host cell is a Zymomonas species (e.g., Z. mobilis, and Z. lipolytica).

    [0207] Many prokaryotic and eukaryotic strains that find use in the present invention are readily available to the public from a number of culture collections such as American Type Culture Collection (ATCC), Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSM), Centraalbureau Voor Schimmelcultures (CBS), and Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL).

    [0208] In some embodiments, host cells are genetically modified to have characteristics that improve protein secretion, protein stability and/or other properties desirable for expression and/or secretion of a protein. Genetic modification can be achieved by genetic engineering techniques and/or classical microbiological techniques (e.g., chemical or UV mutagenesis and subsequent selection). Indeed, in some embodiments, combinations of recombinant modification and classical selection techniques are used to produce the host cells. Using recombinant technology, nucleic acid molecules can be introduced, deleted, inhibited or modified, in a manner that results in increased yields of adenylate kinase variant(s) within the host cell and/or in the culture medium. For example, knockout of Alp1 function results in a cell that is protease deficient, and knockout of pyr5 function results in a cell with a pyrimidine deficient phenotype. In one genetic engineering approach, homologous recombination is used to induce targeted gene modifications by specifically targeting a gene in vivo to suppress expression of the encoded protein. In alternative approaches, siRNA, antisense and/or ribozyme technology find use in inhibiting gene expression. A variety of methods are known in the art for reducing expression of protein in cells, including, but not limited to deletion of all or part of the gene encoding the protein and site-specific mutagenesis to disrupt expression or activity of the gene product. (See e.g., Chaveroche et al., Nucl. Acids Res., 28:22 e97 [2000]; Cho et al., Molec. Plant Microbe Interact., 19:7-15 [2006]; Maruyama and Kitamoto, Biotechnol Lett., 30:1811-1817 [2008]; Takahashi et al., Mol. Gen. Genom., 272: 344-352 [2004]; and You et al., Arch. Microbiol.,191:615-622 [2009], all of which are incorporated by reference herein). Random mutagenesis, followed by screening for desired mutations also finds use (See e.g., Combier et al., FEMS Microbiol. Lett., 220:141-8 [2003]; and Firon et al., Eukary. Cell 2:247-55 [2003], both of which are incorporated by reference).

    [0209] Introduction of a vector or DNA construct into a host cell can be accomplished using any suitable method known in the art, including but not limited to calcium phosphate transfection, DEAE-dextran mediated transfection, PEG-mediated transformation, electroporation, or other common techniques known in the art. In some embodiments, the Escherichia coli expression vector pCK100900i (See, U.S. Pat. No. 9,714,437, which is hereby incorporated by reference) finds use.

    [0210] In some embodiments, the engineered host cells (i.e., “recombinant host cells”) of the present invention are cultured in conventional nutrient media modified as appropriate for activating promoters, selecting transformants, or amplifying the adenylate kinase polynucleotide. Culture conditions, such as temperature, pH and the like, are those previously used with the host cell selected for expression, and are well-known to those skilled in the art. As noted, many standard references and texts are available for the culture and production of many cells, including cells of bacterial, plant, animal (especially mammalian) and archebacterial origin.

    [0211] In some embodiments, cells expressing the variant adenylate kinase polypeptides of the invention are grown under batch or continuous fermentations conditions. Classical “batch fermentation” is a closed system, wherein the compositions of the medium is set at the beginning of the fermentation and is not subject to artificial alternations during the fermentation. A variation of the batch system is a “fed-batch fermentation” which also finds use in the present invention. In this variation, the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is likely to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Batch and fed-batch fermentations are common and well known in the art. “Continuous fermentation” is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth. Continuous fermentation systems strive to maintain steady state growth conditions. Methods for modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology.

    [0212] In some embodiments of the present invention, cell-free transcription/translation systems find use in producing variant adenylate kinase(s). Several systems are commercially available and the methods are well-known to those skilled in the art.

    [0213] The present invention provides methods of making variant adenylate kinase polypeptides or biologically active fragments thereof. In some embodiments, the method comprises: providing a host cell transformed with a polynucleotide encoding an amino acid sequence that comprises at least about 70% (or at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) sequence identity to SEQ ID NO: 4 and/or 230, and comprising at least one mutation as provided herein; culturing the transformed host cell in a culture medium under conditions in which the host cell expresses the encoded variant adenylate kinase polypeptide; and optionally recovering or isolating the expressed variant adenylate kinase polypeptide, and/or recovering or isolating the culture medium containing the expressed variant adenylate kinase polypeptide. In some embodiments, the methods further provide optionally lysing the transformed host cells after expressing the encoded adenylate kinase polypeptide and optionally recovering and/or isolating the expressed variant adenylate kinase polypeptide from the cell lysate. The present invention further provides methods of making a variant adenylate kinase polypeptide comprising cultivating a host cell transformed with a variant adenylate kinase polynucleotide under conditions suitable for the production of the variant adenylate kinase polypeptide and recovering the adenylate kinase polypeptide. Typically, recovery or isolation of the adenylate kinase polypeptide is from the host cell culture medium, the host cell or both, using protein recovery techniques that are well known in the art, including those described herein. In some embodiments, host cells are harvested by centrifugation, disrupted by physical or chemical means, and the resulting crude extract retained for further purification. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including, but not limited to freeze-thaw cycling, sonication, mechanical disruption, and/or use of cell lysing agents, as well as many other suitable methods well known to those skilled in the art.

    [0214] Engineered adenylate kinase enzymes expressed in a host cell can be recovered from the cells and/or the culture medium using any one or more of the techniques known in the art for protein purification, including, among others, lysozyme treatment, sonication, filtration, salting-out, ultra-centrifugation, and chromatography. Suitable solutions for lysing and the high efficiency extraction of proteins from bacteria, such as E. coli, are commercially available under the trade name CelLytic B™ (Sigma-Aldrich). Thus, in some embodiments, the resulting polypeptide is recovered/isolated and optionally purified by any of a number of methods known in the art. For example, in some embodiments, the polypeptide is isolated from the nutrient medium by conventional procedures including, but not limited to, centrifugation, filtration, extraction, spray-drying, evaporation, chromatography (e.g., ion exchange, affinity, hydrophobic interaction, chromatofocusing, and size exclusion), or precipitation. In some embodiments, protein refolding steps are used, as desired, in completing the configuration of the mature protein. In addition, in some embodiments, high performance liquid chromatography (HPLC) is employed in the final purification steps. For example, in some embodiments, methods known in the art, find use in the present invention (See e.g., Parry et al., Biochem. J., 353:117 [2001]; and Hong et al., Appl. Microbiol. Biotechnol., 73:1331 [2007], both of which are incorporated herein by reference). Indeed, any suitable purification methods known in the art find use in the present invention.

    [0215] Chromatographic techniques for isolation of the adenylate kinase polypeptide include, but are not limited to reverse phase chromatography, high performance liquid chromatography, ion exchange chromatography, gel electrophoresis, and affinity chromatography. Conditions for purifying a particular enzyme will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity, molecular weight, molecular shape, etc., are known to those skilled in the art.

    [0216] In some embodiments, affinity techniques find use in isolating the improved adenylate kinase enzymes. For affinity chromatography purification, any antibody which specifically binds the adenylate kinase polypeptide may be used. For the production of antibodies, various host animals, including but not limited to rabbits, mice, rats, etc., may be immunized by injection with the adenylate kinase. The adenylate kinase polypeptide may be attached to a suitable carrier, such as BSA, by means of a side chain functional group or linkers attached to a side chain functional group. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (Bacillus Calmette Guerin) and Corynebacterium parvum.

    [0217] In some embodiments, the adenylate kinase variants are prepared and used in the form of cells expressing the enzymes, as crude extracts, or as isolated or purified preparations. In some embodiments, the adenylate kinase variants are prepared as lyophilisates, in powder form (e.g., acetone powders), or prepared as enzyme solutions. In some embodiments, the adenylate kinase variants are in the form of substantially pure preparations.

    [0218] In some embodiments, the adenylate kinase polypeptides are attached to any suitable solid substrate. Solid substrates include but are not limited to a solid phase, surface, and/or membrane. Solid supports include, but are not limited to organic polymers such as polystyrene, polyethylene, polypropylene, polyfluoroethylene, polyethyleneoxy, and polyacrylamide, as well as co-polymers and grafts thereof. A solid support can also be inorganic, such as glass, silica, controlled pore glass (CPG), reverse phase silica or metal, such as gold or platinum. The configuration of the substrate can be in the form of beads, spheres, particles, granules, a gel, a membrane or a surface. Surfaces can be planar, substantially planar, or non-planar. Solid supports can be porous or non-porous, and can have swelling or non-swelling characteristics. A solid support can be configured in the form of a well, depression, or other container, vessel, feature, or location. A plurality of supports can be configured on an array at various locations, addressable for robotic delivery of reagents, or by detection methods and/or instruments.

    [0219] In some embodiments, immunological methods are used to purify adenylate kinase variants. In one approach, antibody raised against a wild-type or variant adenylate kinase polypeptide (e.g., against a polypeptide comprising any of SEQ ID NO: 4 and/or 230, and/or a variant thereof, and/or an immunogenic fragment thereof) using conventional methods is immobilized on beads, mixed with cell culture media under conditions in which the variant adenylate kinase is bound, and precipitated. In a related approach, immunochromatography finds use.

    [0220] In some embodiments, the variant adenylate kinases are expressed as a fusion protein including a non-enzyme portion. In some embodiments, the variant adenylate kinase sequence is fused to a purification facilitating domain. As used herein, the term “purification facilitating domain” refers to a domain that mediates purification of the polypeptide to which it is fused. Suitable purification domains include, but are not limited to metal chelating peptides, histidine-tryptophan modules that allow purification on immobilized metals, a sequence which binds glutathione (e.g., GST), a hemagglutinin (HA) tag (corresponding to an epitope derived from the influenza hemagglutinin protein; See e.g., Wilson et al., Cell 37:767 [1984]), maltose binding protein sequences, the FLAG epitope utilized in the FLAGS extension/affinity purification system (e.g., the system available from Immunex Corp), and the like. One expression vector contemplated for use in the compositions and methods described herein provides for expression of a fusion protein comprising a polypeptide of the invention fused to a polyhistidine region separated by an enterokinase cleavage site. The histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromatography; See e.g., Porath et al., Prot. Exp. Purif., 3:263-281 [1992]) while the enterokinase cleavage site provides a means for separating the variant adenylate kinase polypeptide from the fusion protein. pGEX vectors (Promega) may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to ligand-agarose beads (e.g., glutathione-agarose in the case of GST-fusions) followed by elution in the presence of free ligand.

    [0221] Accordingly, in another aspect, the present invention provides methods of producing the engineered enzyme polypeptides, where the methods comprise culturing a host cell capable of expressing a polynucleotide encoding the engineered enzyme polypeptide under conditions suitable for expression of the polypeptide. In some embodiments, the methods further comprise the steps of isolating and/or purifying the enzyme polypeptides, as described herein.

    [0222] Appropriate culture media and growth conditions for host cells are well known in the art. It is contemplated that any suitable method for introducing polynucleotides for expression of the enzyme polypeptides into cells will find use in the present invention. Suitable techniques include, but are not limited to electroporation, biolistic particle bombardment, liposome mediated transfection, calcium chloride transfection, and protoplast fusion.

    Methods of Using the Engineered Adenylate Kinase Enzymes

    [0223] In some embodiments, the adenylate kinases described herein find use in processes for converting a suitable adenosine monophosphate substrate, such as F-thioAMP (4), to its corresponding adenosine diphosphate product, such as F-thioADP (5). Generally, the process for performing the phosphorylation reaction comprises contacting or incubating the substrate compound in presence of a co-substrate, such as an adenosine triphosphate, with an adenylate kinase polypeptide of the invention under reaction conditions suitable for formation of the diphosphate product, as shown in Scheme 3, above.

    [0224] In the embodiments provided herein and illustrated in the Examples, various ranges of suitable reaction conditions that can be used in the processes, include but are not limited to, substrate loading, co-substrate loading, reductant, divalent transition metal, pH, temperature, buffer, solvent system, polypeptide loading, and reaction time. Further suitable reaction conditions for carrying out the process for biocatalytic conversion of substrate compounds to product compounds using an engineered adenylate kinase polypeptide described herein can be readily optimized in view of the guidance provided herein by routine experimentation that includes, but is not limited to, contacting the engineered adenylate kinase polypeptide and substrate compound under experimental reaction conditions of concentration, pH, temperature, and solvent conditions, and detecting the product compound.

    [0225] Suitable reaction conditions using the engineered adenylate kinase polypeptides typically comprise a co-substrate, which is used stoichiometrically in the phosphorylation reaction. Generally, the co-substrate for adenylate kinases is adenosine triphosphate or F-thioATP. Other analogs of adenosine triphosphate that are capable of serving as co-substrates for adenylate kinases can be used. Because the co-substrate is used stoichiometrically, the co-substrate is present at an equimolar or higher amount than that of the substrate compound (i.e., the molar concentration of co-substrate is equivalent to or higher than the molar concentration of substrate compound). In some embodiments, the suitable reaction conditions can comprise a co-substrate molar concentration of at least 1 fold, 1.5 fold, 2 fold, 3 fold 4 fold or 5 fold or more than the molar concentration of the substrate compound. In some embodiments, the suitable reaction conditions can comprise a co-substrate concentration, particularly F-thioATP, of about 0.0005 M to about 2 M, 0.01 M to about 2 M, 0.1 M to about 2 M, 0.2 M to about 2 M, about 0.5 M to about 2 M, or about 1 M to about 2 M. In some embodiments, the reaction conditions comprise a co-substrate concentration of about 0.0001 M, 0.001 M, 0.01 M, 0.1 M, 0.2 M, 0.3 M, 0.4 M, 0.5 M, 0.6 M, 0.7 M, 0.8 M, 1 M, 1.5 M, or 2 M. In some embodiments, additional co-substrate can be added during the reaction.

    [0226] Substrate compound in the reaction mixtures can be varied, taking into consideration, for example, the desired amount of product compound, the effect of substrate concentration on enzyme activity, stability of enzyme under reaction conditions, and the percent conversion of substrate to product. In some embodiments, the suitable reaction conditions comprise a substrate compound loading of at least about 0.5 to about 200 g/L, 1 to about 200 g/L, 5 to about 150 g/L, about 10 to about 100 g/L, 20 to about 100 g/L or about 50 to about 100 g/L. In some embodiments, the suitable reaction conditions comprise a substrate compound loading of at least about 0.5 g/L, at least about 1 g/L, at least about 5 g/L, at least about 10 g/L, at least about 15 g/L, at least about 20 g/L, at least about 30 g/L, at least about 50 g/L, at least about 75 g/L, at least about 100 g/L, at least about 150 g/L or at least about 200 g/L, or even greater. The values for substrate loadings provided herein are based on the molecular weight of 2′F-thioAMP; however, it also contemplated that the equivalent molar amounts of various AMP analogues also can be used in the process.

    [0227] In carrying out the adenylate kinase mediated processes described herein, the engineered polypeptide may be added to the reaction mixture in the form of a purified enzyme, partially purified enzyme, whole cells transformed with gene(s) encoding the enzyme, as cell extracts and/or lysates of such cells, and/or as an enzyme immobilized on a solid support. Whole cells transformed with gene(s) encoding the engineered adenylate kinase enzyme or cell extracts, lysates thereof, and isolated enzymes may be employed in a variety of different forms, including solid (e.g., lyophilized, spray-dried, and the like) or semisolid (e.g., a crude paste). The cell extracts or cell lysates may be partially purified by precipitation (ammonium sulfate, polyethyleneimine, heat treatment or the like, followed by a desalting procedure prior to lyophilization (e.g., ultrafiltration, dialysis, etc.). Any of the enzyme preparations (including whole cell preparations) may be stabilized by crosslinking using known crosslinking agents, such as, for example, glutaraldehyde or immobilization to a solid phase (e.g., Eupergit C, and the like).

    [0228] The gene(s) encoding the engineered adenylate kinase polypeptides can be transformed into host cells separately or together into the same host cell. For example, in some embodiments one set of host cells can be transformed with gene(s) encoding one engineered adenylate kinase polypeptide and another set can be transformed with gene(s) encoding another engineered adenylate kinase polypeptide. Both sets of transformed cells can be utilized together in the reaction mixture in the form of whole cells, or in the form of lysates or extracts derived therefrom. In other embodiments, a host cell can be transformed with gene(s) encoding multiple engineered adenylate kinase polypeptide. In some embodiments the engineered polypeptides can be expressed in the form of secreted polypeptides, and the culture medium containing the secreted polypeptides can be used for the adenylate kinase reaction.

    [0229] In some embodiments, the improved activity and/or selectivity of the engineered adenylate kinase polypeptides disclosed herein provides for processes wherein higher percentage conversion can be achieved with lower concentrations of the engineered polypeptide. In some embodiments of the process, the suitable reaction conditions comprise an engineered polypeptide amount of about 1% (w/w), 2% (w/w), 5% (w/w), 10% (w/w), 20% (w/w), 30% (w/w), 40% (w/w), 50% (w/w), 75% (w/w), 100% (w/w) or more of substrate compound loading.

    [0230] In some embodiments, the engineered polypeptide is present at about 0.01 g/L to about 50 g/L; about 0.05 g/L to about 50 g/L; about 0.1 g/L to about 40 g/L; about 1 g/L to about 40 g/L; about 2 g/L to about 40 g/L; about 5 g/L to about 40 g/L; about 5 g/L to about 30 g/L; about 0.1 g/L to about 10 g/L; about 0.5 g/L to about 10 g/L; about 1 g/L to about 10 g/L; about 0.1 g/L to about 5 g/L; about 0.5 g/L to about 5 g/L; or about 0.1 g/L to about 2 g/L. In some embodiments, the adenylate kinase polypeptide is present at about 0.01 g/L, 0.05 g/L, 0.1 g/L, 0.2 g/L, 0.5 g/L, 1 g/L, 2 g/L, 5 g/L, 10 g/L, 15 g/L, 20 g/L, 25 g/L, 30 g/L, 35 g/L, 40 g/L, or 50 g/L.

    [0231] In some embodiments, the reaction conditions also comprise a divalent metal capable of serving as a cofactor in the reaction. Generally, the divalent metal co-factor is magnesium (i.e., Mg.sup.+2). The magnesium ion may be provided in various forms, such as magnesium chloride (MgCl.sub.2). While magnesium ion is the metal co-factor found in the naturally occurring adenylate kinase and functions efficiently in the engineered enzymes, it is to be understood that other divalent metals capable of acting as a co-factor can be used in the processes. In some embodiments, the reaction conditions can comprise a divalent metal cofactor, particularly Mg.sup.+2, at a concentration of about 1 mM to 100 mM, 1 mM to about 50 mM, 25 mM to about 35 mM, about 30 mM to about 60 mM or about 55 mM to about 65 mM. In some embodiments, the reaction conditions comprise a divalent metal co-factor concentration of about 1 mM, 10 mM, 20 mM, 30 mM, 40 mM, 50 mM, 60 mM, 70 mM, 80 mM, 90 mM, or 100 mM.

    [0232] During the course of the reaction, the pH of the reaction mixture may change. The pH of the reaction mixture may be maintained at a desired pH or within a desired pH range. This may be done by the addition of an acid or a base, before and/or during the course of the reaction. Alternatively, the pH may be controlled by using a buffer. Accordingly, in some embodiments, the reaction condition comprises a buffer. Suitable buffers to maintain desired pH ranges are known in the art and include, by way of example and not limitation, borate, phosphate, 2-(N-morpholino)ethanesulfonic acid (MES), 3-(N-morpholino) propanesulfonic acid (MOPS), acetate, triethanolamine, and 2-amino-2-hydroxymethyl-propane-1,3-diol (Tris), and the like. In some embodiments, the buffer is tris. In some embodiments of the process, the suitable reaction conditions comprise a buffer (e.g., tris) concentration of from about 0.01 to about 0.4 M, 0.05 to about 0.4 M, 0.1 to about 0.3 M, or about 0.1 to about 0.2 M. In some embodiments, the reaction condition comprises a buffer (e.g., tris) concentration of about 0.01, 0.02, 0.03, 0.04, 0.05, 0.07, 0.1, 0.12, 0.14, 0.16, 0.18, 0.2, 0.3, or 0.4 M.

    [0233] In the embodiments of the process, the reaction conditions can comprise a suitable pH. The desired pH or desired pH range can be maintained by use of an acid or base, an appropriate buffer, or a combination of buffering and acid or base addition. The pH of the reaction mixture can be controlled before and/or during the course of the reaction. In some embodiments, the suitable reaction conditions comprise a solution pH from about 4 to about 10, pH from about 5 to about 10, pH from about 5 to about 9, pH from about 6 to about 9, pH from about 6 to about 8. In some embodiments, the reaction conditions comprise a solution pH of about 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, or 10.

    [0234] In the embodiments of the processes herein, a suitable temperature can be used for the reaction conditions, for example, taking into consideration the increase in reaction rate at higher temperatures, and the activity of the enzyme during the reaction time period. Accordingly, in some embodiments, the suitable reaction conditions comprise a temperature of about 10° C. to about 60° C., about 10° C. to about 55° C., about 15° C. to about 60° C., about 20° C. to about 60° C., about 20° C. to about 55° C., about 25° C. to about 55° C., or about 30° C. to about 50° C. In some embodiments, the suitable reaction conditions comprise a temperature of about 10° C., 15° C., 20° C., 25° C., 30° C., 35° C., 40° C., 45° C., 50° C., 55° C., or 60° C. In some embodiments, the temperature during the enzymatic reaction can be maintained at a specific temperature throughout the course of the reaction. In some embodiments, the temperature during the enzymatic reaction can be adjusted over a temperature profile during the course of the reaction.

    [0235] In some embodiments, the reaction conditions can comprise a surfactant for stabilizing or enhancing the reaction. Surfactants can comprise non-ionic, cationic, anionic and/or amphiphilic surfactants. Exemplary surfactants, include by way of example and not limitation, nonyl phenoxypolyethoxylethanol (NP40), Triton X-100, polyoxyethylene-stearylamine, cetyltrimethylammonium bromide, sodium oleylamidosulfate, polyoxyethylene-sorbitanmonostearate, hexadecyldimethylamine, etc. Any surfactant that may stabilize or enhance the reaction may be employed. The concentration of the surfactant to be employed in the reaction may be generally from 0.1 to 50 mg/ml, particularly from 1 to 20 mg/ml.

    [0236] In some embodiments, the reaction conditions can include an antifoam agent, which aids in reducing or preventing formation of foam in the reaction solution, such as when the reaction solutions are mixed or sparged. Anti-foam agents include non-polar oils (e.g., minerals, silicones, etc.), polar oils (e.g., fatty acids, alkyl amines, alkyl amides, alkyl sulfates, etc.), and hydrophobic (e.g., treated silica, polypropylene, etc.), some of which also function as surfactants. Exemplary anti-foam agents include, Y-30® (Dow Corning), poly-glycol copolymers, oxy/ethoxylated alcohols, and polydimethylsiloxanes. In some embodiments, the anti-foam can be present at about 0.001% (v/v) to about 5% (v/v), about 0.01% (v/v) to about 5% (v/v), about 0.1% (v/v) to about 5% (v/v), or about 0.1% (v/v) to about 2% (v/v). In some embodiments, the anti-foam agent can be present at about 0.001% (v/v), about 0.01% (v/v), about 0.1% (v/v), about 0.5% (v/v), about 1% (v/v), about 2% (v/v), about 3% (v/v), about 4% (v/v), or about 5% (v/v) or more as desirable to promote the reaction.

    [0237] The quantities of reactants used in the kinase reaction will generally vary depending on the quantities of product desired, and concomitantly the amount of adenylate kinase substrate employed. Those having ordinary skill in the art will readily understand how to vary these quantities to tailor them to the desired level of productivity and scale of production.

    [0238] In some embodiments, the order of addition of reactants is not critical. The reactants may be added together at the same time to a solvent (e.g., monophasic solvent, biphasic aqueous co-solvent system, and the like), or alternatively, some of the reactants may be added separately, and some together at different time points. For example, the cofactor, co-substrate, adenylate kinase, and substrate may be added first to the solvent.

    [0239] The solid reactants (e.g., enzyme, salts, etc.) may be provided to the reaction in a variety of different forms, including powder (e.g., lyophilized, spray dried, and the like), solution, emulsion, suspension, and the like. The reactants can be readily lyophilized or spray dried using methods and equipment that are known to those having ordinary skill in the art. For example, the protein solution can be frozen at −80° C. in small aliquots, then added to a pre-chilled lyophilization chamber, followed by the application of a vacuum.

    [0240] For improved mixing efficiency when an aqueous co-solvent system is used, the adenylate kinase, and cofactor may be added and mixed into the aqueous phase first. The organic phase may then be added and mixed in, followed by addition of the adenylate kinase substrate and co-substrate. Alternatively, the adenylate kinase substrate may be premixed in the organic phase, prior to addition to the aqueous phase.

    [0241] The phosphorylation process is generally allowed to proceed until further conversion of substrate to phosphorylated product does not change significantly with reaction time (e.g., less than 10% of substrate being converted, or less than 5% of substrate being converted). In some embodiments, the reaction is allowed to proceed until there is complete or near complete conversion of substrate to product. Transformation of substrate to product can be monitored using known methods by detecting substrate and/or product, with or without derivatization. Suitable analytical methods include gas chromatography, HPLC, MS, and the like.

    [0242] In some embodiments of the process, the suitable reaction conditions comprise a substrate loading of at least about 5 g/L, 10 g/L, 20 g/L, 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, or more, and wherein the method results in at least about 50%, 60%, 70%, 80%, 90%, 95% or greater conversion of substrate compound to product compound in about 48 h or less, in about 36 h or less, in about 24 h or less, or in about 3 h or less.

    [0243] The engineered adenylate kinase polypeptides of the present invention when used in the process under suitable reaction conditions result in a diastereomeric excess of the Sp-2′F-thioADP product in at least 90%, 95%, 96%, 97%, 98%, 99%, or greater diastereomeric excess over the Rp-2′F-thioADP product.

    [0244] In further embodiments of the processes for converting substrate compound to product compound using the engineered adenylate kinase polypeptides, the suitable reaction conditions can comprise an initial substrate loading to the reaction solution which is then contacted by the polypeptide. This reaction solution is then further supplemented with additional substrate compound as a continuous or batchwise addition over time at a rate of at least about 1 g/L/h, at least about 2 g/L/h, at least about 4 g/L/h, at least about 6 g/L/h, or higher. Thus, according to these suitable reaction conditions, polypeptide is added to a solution having an initial substrate loading of at least about 20 g/L, 30 g/L, or 40 g/L. This addition of polypeptide is then followed by continuous addition of further substrate to the solution at a rate of about 2 g/L/h, 4 g/L/h, or 6 g/L/h until a much higher final substrate loading of at least about 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, 150 g/L, 200 g/L or more, is reached. Accordingly, in some embodiments of the process, the suitable reaction conditions comprise addition of the polypeptide to a solution having an initial substrate loading of at least about 20 g/L, 30 g/L, or 40 g/L followed by addition of further substrate to the solution at a rate of about 2 g/L/h, 4 g/L/h, or 6 g/L/h until a final substrate loading of at least about 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L or more, is reached. This substrate supplementation reaction condition allows for higher substrate loadings to be achieved while maintaining high rates of conversion of substrate to phosphorylated product of at least about 50%, 60%, 70%, 80%, 90% or greater conversion of substrate.

    [0245] In some embodiments, acetate kinase and acetyl phosphate recycle ADP to ATP. In some embodiments, acetate kinase and acetyl phosphate recycle an ADP analogue to an ATP analogue. In some embodiments, acetate kinase and acetyl phosphate recycle F-thioADP (5) to F-thioATP (3).

    [0246] In some embodiments of the processes, the reaction using an engineered adenylate kinase polypeptide can comprise the following suitable reaction conditions: (a) substrate loading at about 40 g/L; (b) about 0.031 g/L of the engineered polypeptide; (c) 400 mM acetyl phosphate; (d) about 2 g/L wild-type acetate kinase; (e) about 2 mM F-thioATP; (f) about 60 mM MgCl.sub.2; (g) a pH of about 7.5; (h) temperature of about 30° C.; and (i) reaction time of about 3 hrs.

    [0247] In some embodiments, additional reaction components or additional techniques are carried out to supplement the reaction conditions. These can include taking measures to stabilize or prevent inactivation of the enzyme, reduce product inhibition, shift reaction equilibrium to product formation.

    [0248] In further embodiments, any of the above described process for the conversion of substrate compound to product compound can further comprise one or more steps selected from: extraction; isolation; purification; and crystallization of product compound. Methods, techniques, and protocols for extracting, isolating, purifying, and/or crystallizing the product from biocatalytic reaction mixtures produced by the above disclosed processes are known to the ordinary artisan and/or accessed through routine experimentation. Additionally, illustrative methods are provided in the Examples below.

    [0249] Various features and embodiments of the invention are illustrated in the following representative examples, which are intended to be illustrative, and not limiting.

    Experimental

    [0250] The following Examples, including experiments and results achieved, are provided for illustrative purposes only and are not to be construed as limiting the present invention. Indeed, there are various suitable sources for many of the reagents and equipment described below. It is not intended that the present invention be limited to any particular source for any reagent or equipment item.

    [0251] In the experimental disclosure below, the following abbreviations apply: M (molar); mM (millimolar), uM and μM (micromolar); nM (nanomolar); mol (moles); gm and g (gram); mg (milligrams); ug and μg (micrograms); L and 1 (liter); ml and mL (milliliter); cm (centimeters); mm (millimeters); um and μm (micrometers); sec. (seconds); min(s) (minute(s)); h(s) and hr(s) (hour(s)); U (units); MW (molecular weight); rpm (rotations per minute); psi and PSI (pounds per square inch); ° C. (degrees Centigrade); RT and rt (room temperature); CV (coefficient of variability); CAM and cam (chloramphenicol); PMBS (polymyxin B sulfate); IPTG (isopropyl β-D-1-thiogalactopyranoside); LB (lysogeny broth); TB (terrific broth); SFP (shake flask powder); CDS (coding sequence); DNA (deoxyribonucleic acid); RNA (ribonucleic acid); nt (nucleotide; polynucleotide); aa (amino acid; polypeptide); E. coli W3110 (commonly used laboratory E. coli strain, available from the Coli Genetic Stock Center [CGSC], New Haven, Conn.); HTP (high throughput); HPLC (high pressure liquid chromatography); HPLC-UV (HPLC-Ultraviolet Visible Detector); 1H NMR (proton nuclear magnetic resonance spectroscopy); FIOPC (fold improvements over positive control); Sigma and Sigma-Aldrich (Sigma-Aldrich, St. Louis, Mo.; Difco) (Difco Laboratories, BD Diagnostic Systems, Detroit, Mich.); Microfluidics (Microfluidics, Westwood, Mass.); Life Technologies (Life Technologies, a part of Fisher Scientific, Waltham, Mass.); Amresco (Amresco, LLC, Solon, Ohio); Carbosynth (Carbosynth, Ltd., Berkshire, UK); Varian (Varian Medical Systems, Palo Alto, Calif.); Agilent (Agilent Technologies, Inc., Santa Clara, Calif.); Infors (Infors USA Inc., Annapolis Junction, Md.); and Thermotron (Thermotron, Inc., Holland, Mich.).

    EXAMPLE 1

    Production of Engineered Polypeptides in pCK110900

    [0252] The polynucleotide (SEQ ID NO: 1) encoding the polypeptide from Saccharomyces cerevisiae having adenylate kinase activity (SEQ ID NO: 2) with a n-terminal his tag was cloned into a pCK110900 vector system (See e.g., U.S. Pat. No. 9,714,437, which is hereby incorporated by reference in its entirety) and subsequently expressed in E. coli W3110 fhuA under the control of the lac promoter.

    [0253] In a 96-well format, single colonies were picked and grown in 190 μL LB containing 1% glucose and 30 μg/mL CAM, at 30° C. at 200 rpm with 85% humidity. Following overnight growth, 20 μof the grown cultures were transferred into a deep-well plate containing 380 μL of TB with 30 μg/mL CAM. The cultures were grown at 30° C. at 250 rpm with 85% humidity for approximately 2.5 hours. When the optical density (OD.sub.600) of the cultures reached 0.4-0.6, expression of the adenylate kinase gene was induced by addition of IPTG to a final concentration of 1 mM. Following induction, growth was continued for 18-20 hours at 30° C. at 250 rpm with 85% humidity. Cells were harvested by centrifugation at 4,000 rpm at 4° C. for 10 minutes and the media discarded. The cell pellets were stored at −80° C. until ready for use. Prior to performing the assay, cell pellets were resuspended in 400 μL of lysis buffer containing 10 mM Tris-HCl, pH 7.5, with 1 g/L lysozyme and 0.5 g/L PMBS. The plates were agitated with medium-speed shaking for 2 hours on a microtiter plate shaker at room temperature. The plates were then centrifuged at 4,000 rpm for 15 minutes at 4° C., and the clarified supernatants were used in the HTP assay reaction described below.

    [0254] Shake-flask procedures can be used to generate engineered adenylate kinase polypeptide shake-flask powders (SFP), which are useful for secondary screening assays and/or use in the biocatalytic processes described herein. Shake flask powder (SFP) preparation of enzymes provides a more purified preparation (e.g., up to 30% of total protein) of the engineered enzyme, as compared to the cell lysate used in HTP assays and also allows for the use of more concentrated enzyme solutions. To start the cultures, a single colony of E. coli containing a plasmid encoding an engineered polypeptide of interest was inoculated into 50 mL LB with 30 μg/mL CAM and 1% glucose. The culture was grown overnight (at least 16 hours) in an incubator at 30° C., with shaking at 250 rpm. The grown culture was diluted into 250 mL of TB with 30 μg/mL CAM, in a 1L shakeflask, to a final OD.sub.600 of 0.02. The 250 mL culture was grown at 30° C. at 250 rpm for 2-3 hours until OD.sub.600 reached 0.6-0.8. Expression of the adenylate kinase gene was induced by addition of IPTG to a final concentration of 1 mM, and growth was continued for an additional 18-20 hours. Cells were harvested by transferring the culture into a pre-weighed centrifuge bottle, and then centrifuged at 4,000 rpm for 20 minutes at 4° C. The supernatant was discarded, and the remaining cell pellet was weighed. In some embodiments, the cells are stored at −80 ° C. until ready to use. For lysis, the cell pellet was resuspended in 30 mL of 10 mM Tris, pH 7.5 then centrifuged at 4,000 rpm for 20 minutes at 4° C. The supernatant was discarded, and the pellet was resuspended in 30 mL of cold 10 mM Tris, pH 7.5 with 6 mL/g per pellet. The resuspended cells were lysed using a 110L MICROFLUIDIZER® processor system (Microfluidics). Cell debris was removed by centrifugation at 10,000 rpm for 60 minutes at 4° C. The clarified lysate was collected, frozen at −80° C., and then lyophilized, using standard methods known in the art. Lyophilization of frozen clarified lysate provides a dry shake-flask powder comprising crude engineered polypeptide.

    EXAMPLE 2

    Evolution and Screening of Engineered Polypeptides Derived from SEQ ID NO: 4 for Improved Adenylate Kinase (AdK) Activity

    [0255] The engineered polynucleotide (SEQ ID NO: 3) encoding the polypeptide with adenylate kinase activity of SEQ ID NO: 4 was used to generate the engineered polypeptides of Table 2-1 and 2-2. These polypeptides displayed improved adenylate kinase activity under the desired conditions (e.g., the improvement in the conversion of the substrate 2′F-thioAMP to the production of the product, F-thioADP (5) with acetyl phosphate and acetate kinase (AcK) as the recycling system) as compared to the starting polypeptide. The engineered polypeptides having the amino acid sequences of even-numbered sequence identifiers were generated from the “backbone” amino acid sequence of SEQ ID NO: 4, as described below together with the HTP assay and analytical methods described in Table 2-3.

    [0256] Directed evolution began with the polynucleotide set forth in SEQ ID NO: 3. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to facilitate the recycling of ATP via ADP and acetyl phosphate (as measured via the conversion of 2′F-thioAMP substrate (4) to the F-thioATP (3) downstream product under ATP limited conditions).

    [0257] The enzyme assay was carried out in a 96-well deep-well (2 mL) plates, in 100 μL total volume/well, which included 5 μL HTP enzyme lysate and 95 μL of a master mix containing 55 mM F-thioAMP (4), 1 mM F-thioATP (3), 200 mM acetyl phosphate, 30 mM MgCl.sub.2, 2 g/L WT acetate kinase from Thermotoga maritima and MilliQ water. The reactions were performed by first aliquoting 95 μL of a master mix to each well. Then, the reactions were initiated by adding 5 μL HTP lysate. The reaction plate was heat-sealed and shaken at 500 rpm at 25° C. for 3 hours.

    [0258] After incubation (˜3 hours), 800 μL of MilliQ water were added to each well. For chiral analysis, HTP reactions were quenched with 1:1 volume equivalent of acetonitrile and shaken for 10 mins on tabletop shakers before centrifugation at 4,000 rpm for 10 mins at 4° C. to remove solids. The quenched reactions were diluted by transferring 20 μL of the supernatant into 180 μL of water in a new 96-well deep-well plate, then mixed and centrifuged at 4,000 rpm for 5 mins at 4° C. The eluent was used for UPLC analysis using the method described below in Table 2-3.

    [0259] Hit variants were grown in 250-mL shake flasks and enzyme powders generated. The activity of the enzyme powders was evaluated at 0.0625-2 g/L of the AdK SF Powder, 55 mM F-tAMP (5), 1 mM F-tATP (3), 200 mM Acetyl phosphate, 30 mM MgCl.sub.2, and 2 g/L acetate kinase. 100 μL of the reaction mix were incubated at 25-60° C. for 3 hours with shaking at 500 rpm using a similar assay as described above.

    TABLE-US-00001 TABLE 2-1 Adenylate Kinase Variant Activity Relative to SEQ ID NO: 4 Conversion Fold SEQ Improvement ID NO: Amino Acid Differences (Relative to (nt/aa) (Relative to SEQ ID NO: 4) SEQ ID NO: 4).sup.1 5/6 E34L/R35K/I51W/M76V/Q172R/T202A +++ 7/8 R35K/I51W/M76V/Q172R +++ 9/10 R35K/I51H/M76V/Q172R +++ 11/12 M76V/P119C/Q172R +++ 13/14 I51W/M76V/P119C +++ 15/16 R35K/I51W/M76V +++ 17/18 E34L/I51W/M76V +++ 19/20 M76V/P119C +++ 21/22 R35K/M76V/P119C/T138L/Q172R +++ 23/24 I51W/M76V/P119C/Q172R ++ 25/26 M76V/Q172R/T202A ++ 27/28 E34L/R35K/I51H/M76V ++ 29/30 R35K/I51W/M76V/T138L ++ 31/32 R35K/I51H/M76V/E131T ++ 33/34 E34L/R35K/A52R/M76V/P119C ++ 35/36 R35K/I51H/M76V/T138L ++ 37/38 R35K/I51H/A52R/K53I/M76V/ ++ P119C/Q172R/T202R 39/40 E34L/R35K/I51W/M76V ++ 41/42 R35K/M76V/P119C/T138L ++ 43/44 E34L/M76V/T138L/Q172R ++ 45/46 A52R/K53I/M76V/Q172R/T202A ++ 47/48 K53I/M76V/T202R ++ 49/50 E34L/R35K/I51W/P119C/Q172R ++ 51/52 E34L/I51H/P119C/T138L/Q172R ++ 53/54 R35K/M76V/P119C ++ 55/56 E34L/R35K/M76V/P119C/Q172R ++ 57/58 R35K/M76V ++ 59/60 R35K/I51H/P119C/T138L/Q172R ++ 61/62 E34L/I51H/A52R/K53I/M76V ++ 63/64 R35K/I51H/P119C/T138L ++ 65/66 M76V/Q172R/T202R ++ 67/68 R35K/I51H/P119C/Q172R ++ 69/70 A52R/M76V/Q172R ++ 71/72 E34L/I51H/K53I/M76V/Q172R ++ 73/74 R35K/I51W/P119C/Q172R ++ 75/76 E34L/R35K/M76V ++ 77/78 I51W/P119C/T138L ++ 79/80 E34L/R35K/I51W/P119C ++ 81/82 M76V + 83/84 R35K/I51W/Q172R/T202R + 85/86 I51W/P119C/Q172R/T202R + 87/88 R35K/I51W/T202R + 89/90 E34L/R35K/I51H/P119C + 91/92 P119C/T138L/Q172R + 93/94 R35K/I51W/P119C + 95/96 I51H/A52R/K53I/Q172R/T202R + 97/98 R35K/I51M/P119C/Q172R + 99/100 I51W/Q172R + 101/102 R35K/I51W/T202A + 103/104 E34L/R35N/K53I/M76V + 105/106 E34L/R35K/I51W/K53I/Q172R + 107/108 T138L/T202A + 109/110 E34L/T138L/Q172R + 111/112 R35K/M76V/Q172R + 113/114 R35N/A52R/K53I/P119C/T138L + 115/116 E34L/R35K/A52R/K53I/P119C/Q172R + 117/118 R35K/K53I/P119C/E131T/T202R + 119/120 R35K/I51W/Q172R + 121/122 R35K/P119C/Q172R + 123/124 R35N/I51W + 125/126 I51H/T138L + 127/128 E34L/I51W/T202R + 129/130 R35K/P119C/T138L + 131/132 R35K/K53I/P119C/T138L + 133/134 E34L/R35K/T138L/Q172R + 135/136 E34L/I51H/K53I/Q172R + 137/138 R35K/I51W + 139/140 E34L/R35K/I51W/Q172R + 141/142 I51W + 143/144 R35K/I51H/K53I/Q172R + 145/146 E34L/R35N/I51H/Q172R + 147/148 I51W/T138L + 149/150 I51W/K53I/Q172R + 151/152 R35K/I51H/Q172R + 153/154 R35K/T138L/Q172R + 155/156 E34L/I51H/K53I/T138L + 157/158 E34L/I51W + 159/160 I51H/K53I + 161/162 E34L/R35K/I51W + 163/164 I51W/K53I + 165/166 R35K/P119C + 167/168 E34L/R35K/I51W/K53I/T138L + 169/170 P119C/Q172R + 171/172 E34L/P119C/Q172R + 173/174 E34L/P119C + 175/176 R35N/I51H/K53I/T138L/Q172R + 177/178 R35K/Q172R/A186V + 179/180 Q172R/T202A + 181/182 E34L/R35K/I51M/Q172R + 183/184 E34L/R35K/I51H + 185/186 R35K/I51W/A52R/K53I/P119C + 187/188 R35K/I51M/T202A + 189/190 A52R/T138L/Q172R + 191/192 R35K/Q172R/T202A + 193/194 E34L/I51L/E131T + 195/196 E34L/R35K/K53I/T202A + 197/198 I51H/K53I/P119C + 199/200 R35K/I51M/K53I/T202R + 201/202 R35K/Q172R/T202R + 203/204 R35K/I51H/A52R/K53I + 205/206 R35K/Q172R + 207/208 R35K/I51H + 209/210 R35N/I51H + 211/212 E34L/R35K/P119C + 213/214 K53I/Q172R + 215/216 R35N/P119C + 217/218 T202A + 219/220 E34L/R35K/T138L + 221/222 I51H + 223/224 Q172R/T202R + 225/226 R35K/A52R/K53I/P119C + 227/228 R35N/I51M + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 4 and defined as follows: “+” 1.60 to 3.50, “++” >3.50, “+++” >6.00

    TABLE-US-00002 TABLE 2-2 Adenylate Kinase Variant Activity Relative to SEQ ID NO: 4 Amino Acid Conversion Fold Differences Improvement SEQ ID (Relative to (Relative to NO: (nt/aa) SEQ ID NO: 4) SEQ ID NO: 4).sup.1 229/230 A42G +++ 231/232 V77W ++ 233/234 K108F ++ 235/236 A61Q ++ 237/238 A61N ++ 239/240 M76V ++ 241/242 W218R ++ 243/244 A42R ++ 245/246 K108W ++ 247/248 I51G ++ 249/250 I51W ++ 251/252 I51T ++ 253/254 A29S ++ 255/256 V16A ++ 257/258 V77L ++ 259/260 L41V + 261/262 I51S + 263/264 M76A + 265/266 I51A + 267/268 W218S + 269/270 D74P + 271/272 S49M + 273/274 K108S + 275/276 K108Q + 277/278 V16T + 279/280 A61V + 281/282 M65V + 283/284 W218H + 285/286 M1H/H2M/P104Y + 287/288 K81T + 289/290 K108E + 291/292 Q191Y + 293/294 K152V + 295/296 K108D + 297/298 W218E + 299/300 A42S + 301/302 S72A + 303/304 S49V + 305/306 M79L + 307/308 L41T + 309/310 V77F + 311/312 M46K + 313/314 M46R + 315/316 D110E + 317/318 D74H + 319/320 Q191L + 321/322 P214V + 323/324 M79W + 325/326 K81Y + 327/328 M46Q + 329/330 L222R + 331/332 M46Y + 333/334 K127A + 335/336 K108R + 337/338 K81H + 339/340 L222S + 341/342 K81C + 343/344 Q50C + 345/346 K108V + 347/348 S72E + 349/350 D74N + 351/352 D74I + 353/354 D110R + 355/356 V77C + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 4 and defined as follows: “+” 1.50 to 3.00, “++” >3.00, “+++” >7.00

    TABLE-US-00003 TABLE 2-3 UPLC Parameters Instrument Thermo Fisher UltiMate 3000 Column Millipore Chromolith HighResolution RP-18 endcapped 25-4.6 mm HPLC column Gradient (A: 100 mM Triethylammonium acetate in water pH 7.0; B: acetonitrile Time (min) % B Mobile Phase 0.00 4.0 1.80 6.0 1.81 100.0 2.00 100.0 2.10 4.0 2.75 Flow Rate 1.5 mL/min Run time 2.75 min Peak F-thioAMP substrate (4) observed at ~0.690 min Retention F-thioATP (3) product observed at ~1.395 min Times F-thioGTP (2) product observed at ~1.596 min Column 45° C. Temperature Injection 5 μL Volume UV Detection 254 nm

    EXAMPLE 3

    Evolution and Screening of Engineered Polypeptides Derived from SEQ ID NO: 230 for Improved Adenylate Kinase (AdK) Activity

    [0260] The engineered polynucleotide (SEQ ID NO: 229) encoding the polypeptide with adenylate kinase activity of SEQ ID NO: 230 was used to generate the engineered polypeptides of Table 3-1 and 3-2. These polypeptides displayed improved adenylate kinase activity under the desired conditions (e.g., the improvement in the conversion of the substrate F-thioAMP (4) to the production of the product, F-thioADP (5) with acetyl phosphate and acetate kinase (AcK) as the recycling system) as compared to the starting polypeptide. The engineered polypeptides having the amino acid sequences of even-numbered sequence identifiers were generated from the “backbone” amino acid sequence of SEQ ID NO: 230, as described below together with the HTP assay and analytical methods described in Table 2-3.

    [0261] Directed evolution began with the polynucleotide set forth in SEQ ID NO: 229. Libraries of engineered polypeptides were generated using various well-known techniques (e.g., saturation mutagenesis, recombination of previously identified beneficial amino acid differences) and screened using HTP assay and analysis methods that measured the polypeptides ability to facilitate the recycling of ATP via ADP and acetyl phosphate (as measured via the conversion of F-thioAMP substrate (4) to the F-thioATP (3) downstream product under ATP limited conditions).

    [0262] The enzyme assay was carried out in a 96-well deep-well (2mL) plates, in 100 μL total volume/well, which included 5 μL HTP enzyme lysate and 95 μL of a master mix containing 110 mM 2′F-thioAMP (4), 2 mM F-thioATP (3), 400 mM acetyl phosphate, 60 mM MgCl.sub.2, 2 g/L WT acetate kinase from Thermotoga maritima and MilliQ water. The reactions were performed by first aliquoting 95 μL of a master mix to each well. Then, the reactions were initiated by adding 5 μL HTP lysate. The reaction plate was heat-sealed and shaken at 500 rpm at 30° C. for 3 hours.

    [0263] After incubation (˜3 hours), 8004 of MilliQ water were added to each well. For chiral analysis, HTP reactions were quenched with 1:1 volume equivalent of acetonitrile and shaken for 10 mins on tabletop shakers before centrifugation at 4,000 rpm for 10 mins at 4° C. to remove solids. The quenched reactions were diluted by transferring 10 μL of the supernatant into 190 μL of water in a new 96-well deep-well plate, then mixed and centrifuged at 4,000 rpm for 5 mins at 4° C. The eluent was used for UPLC analysis using the method described in Table 2-3.

    [0264] Hit variants were grown in 250-mL shake flasks and enzyme powders generated. The activity of the enzyme powders was evaluated at 0.03125-1.0 g/L of the AdK SF Powder, 110mM F-tAMP (4), 2 mM F-tATP (3), 400 mM Acetyl phosphate, 60mM MgCl.sub.2 and 2 g/L acetate kinase. 100 μL of the reaction mix were incubated at 25-60° C. for 3hrs shaking at 500 rpm, using a similar assay as described above.

    TABLE-US-00004 TABLE 3-1 Adenylate Kinase Variant Activity Relative to SEQ ID NO: 230 Conversion Fold Improvement SEQ ID Amino Acid Differences (Relative to NO: (nt/aa) (Relative to SEQ ID NO: 230) SEQ ID NO: 230).sup.1 357/358 V16A/A29S/M76V/A210G +++ 359/360 A29S/S49M/P104Y/K108W +++ 361/362 V16A/A29S/S49M/P104Y/Q191L +++ 363/364 V16A/A29S/S49M/Q191L +++ 365/366 A29S/G42S/M76V/P104Y/K108S +++ 367/368 A29S/S49M/P104Y/Q191L/A210G +++ 369/370 A29S/K108W +++ 371/372 A29S/P104Y/K108W/A210G ++ 373/374 A29S/M76V/Q191Y/A210G ++ 375/376 V16A/A29S/S49M/Q191L/A210G ++ 377/378 A29S/S49M/K108E/Q191L ++ 379/380 A29S/K108S/A210G ++ 381/382 A29S/P104Y/Q191L ++ 383/384 A29S/S49M/Q191L/A210G ++ 385/386 A29S/S49M/P104Y/Q191Y ++ 387/388 A29S/S49M/A210G/A215S ++ 389/390 A29S/S49M/K108W/A210G ++ 391/392 A29S/S49A/K108W/A210G ++ 393/394 A29S/S49M/P104Y/K108W/A210G ++ 395/396 A29S/S49A/K108S/Q191L ++ 397/398 A29S/S49M/K108E/A210G ++ 399/400 A29S/K108E ++ 401/402 A29S/S49A/P104Y/K108S/Q191Y/ ++ A210G 403/404 A29S/P104Y/K108S ++ 405/406 A29S/S49M/K108E/Q191Y ++ 407/408 S49M/K108W ++ 409/410 A29S/S49M/K108E/Q191L/W218H ++ 411/412 A29S/S49A/Q191L ++ 413/414 S49M/M76V/K81Y/P104Y/K108W ++ 415/416 A29S/P104Y ++ 417/418 A29S/K108W/Q191L ++ 419/420 S49M/P104Y/K108S/Q191L ++ 421/422 A29S/G42S/M76V/V77W/P104Y/ ++ Q191L/A210G 423/424 A29S/S49M/P104Y/Q191Y/A210G ++ 425/426 A29S/S49A/P104Y/K108E ++ 427/428 V16A/A29S/P104Y/A210G ++ 429/430 A29S/K108W/Q191L/A210G ++ 431/432 A29S/P104Y/K108E ++ 433/434 V16A/A29S/S49M/P104Y/Q191Y ++ 435/436 A29S/S49M/K108W/Q191L ++ 437/438 A29S/P104Y/A210G ++ 439/440 M76V/K81Y/K108W ++ 441/442 A29S/K108E/A210G ++ 443/444 A29S/S49A/P104Y/K108E/Q191Y ++ 445/446 V16A/A29S/S49M/K108S/Q191L ++ 447/448 S49M/M76V/K108S/Q191L/A210G ++ 449/450 S49A/K108W/A210G ++ 451/452 S49M/K108W/Q191L ++ 453/454 S49M/P104Y/K108W/A210G ++ 455/456 P104Y/K108W/Q191L/A210G + 457/458 A29S/G42S/K108W + 459/460 A29S/Q191Y/A210G + 461/462 P104Y/K108W/Q191L + 463/464 V16A/S49A/P104Y/Q191L + 465/466 K108W/A210G + 467/468 S49M/Q191L + 469/470 V16A/S49M/Q191L + 471/472 K108W/Q191L + 473/474 M76V/V77W/K81Y/K108W/Q191L + 475/476 A29S/G42S/K108D/Q191L + 477/478 A29S/S49A/Q191Y/A210G/W218R + 479/480 V16A/S49M/M76V/P104Y/Q191Y + 481/482 S49M/K108W/A210G + 483/484 S49M/P104Y/W218H + 485/486 A29S/S49M/K81T/K108S + 487/488 A29S/S49M/P104Y/K108S/Q191Y/ + A210G/W218R 489/490 A29S/G42S/K108E/Q191L + 491/492 V16A/S49M/P104Y/K108S/Q191L + 493/494 A29S/P104Y/Q191L/A210G/W218H + 495/496 S49M/K108E/Q191L + 497/498 V16A/S49A + 499/500 S49M/P104Y/Q191L/A210G + 501/502 S49M/P104Y/K108E + 503/504 A29S/S49M/K108E/Q191Y/A210G + 505/506 A29S/K108E/Q191Y/A210G + 507/508 M76V/V77W/K81Y/A210G/W218R + 509/510 A29S/G42S/K108E/Q191L/A210G + 511/512 S49A/P104Y/K108W/Q191L + 513/514 A29S/Q191L/A210G + 515/516 K108W/Q191L/A210G + 517/518 P104Y/K108W/A210G + 519/520 S49M/K108W/Q191L/A210G + 521/522 A29S + 523/524 K108S/Q191L + 525/526 A29S/K108S/Q191L/A210G + 527/528 A29S/S49M/K108W/Q191L/W218H + 529/530 S49A/K108S + 531/532 S49A/K108S/Q191Y/A210G + 533/534 A29S/G42S/K108E/A210G + 535/536 S49M/P104Y/K108E/Q191L + 537/538 S49A/P104Y/K108S + 539/540 V16A/S49M/Q191Y/A210G + 541/542 A29S/P104Y/K108W/Q191Y/A210G + 543/544 S49M + 545/546 V16A/S49A/Q191Y + 547/548 A29S/G42S/P104Y/K108W/Q191L/ + A210G 549/550 V16A/S49M/P104Y/K108S + 551/552 V16A/K108S/W218H + 553/554 V16A/S49M/P104Y/A210G + 555/556 S49M/M76V/V77W/K81Y/P104Y/ + Q191L/A210G 557/558 V16A/P104Y/Q191L/A210G + 559/560 V16A/A29S/P104Y/K108S/Q191L/ + W218H 561/562 V16A/A29S/S49A/K108E/A210G + 563/564 S49M/P104Y/K108W/A180V/Q191Y + 565/566 S49A/K108E + 567/568 S49M/M76V/K108E/Q191Y + 569/570 S49A/K81T/K108W + 571/572 A29S/S49A/K108W/Q191L/A210G/ + W218R 573/574 S49M/P104Y/Q191Y + 575/576 K108S/Q191Y + 577/578 V16A/A29S/K108E/Q191L + 579/580 A29S/S49M/P104Y/K108W/Q191Y + 581/582 S49M/Q191Y + 583/584 S49M/Q191Y/A210G + 585/586 A29S/G42S/S49M/V77W/K81Y/K108D + 587/588 A29S/S49A/K108E/Q191Y/A210G/ + W218H 589/590 V16A/Q191Y/A210G + 591/592 A29S/K108W/Q191Y/W218H + 593/594 V16A/A29S/S49M/P104Y/Q191Y/ + W218H 595/596 S49M/K81T/K108W + 597/598 S49M/K108W/Q191Y/A210G + 599/600 P104Y/K108S/Q191Y/A210G + 601/602 S49M/K108E/Q191Y + 603/604 A29S/K108D + 605/606 A29S/S49A/P104Y/K108W/Q191Y/ + A210G 607/608 S49M/P104Y/K108E/Q191L/A210G + 609/610 P104Y/Q191L + 611/612 V16A/K108W + 613/614 P104Y/K108S/Q191Y/A210G/W218R + 615/616 V16A/A29S/S49M/P104Y/K108E/ + Q191L/W218R 617/618 K108W/Q191Y/A210G + 619/620 G42S/S49M/K108S/Q191Y/A210G/ + W218R 621/622 S49M/K108E/Q191L/A210G + 623/624 V16A/S49M/P104Y/K108W/A210G + 625/626 V16A/S49M/K108S/A210G + 627/628 V77W/K81Y/K108W/Q191L + 629/630 M76V/K81Y/K108W/Q191L/W218H + 631/632 K108E/Q191L + 633/634 V16A/A29S/S49M/K108W + 635/636 V16A/S49M/K108W/W218R + 637/638 G42S/K108W/Q191L/A210G + 639/640 V16A + 641/642 A29S/S49A/K108D/A210G + 643/644 K108E/Q191L/A210G + 645/646 S49A/P104Y/K108E/Q191L + 647/648 K108W/Q191Y/W218H + 649/650 S49A/K108E/A210G + 651/652 A29S/K108W/Q191Y/A210G/W218H + 653/654 S49M/A210G + 655/656 V16A/A29S/S49A/K108E/Q191Y + 657/658 A29S/P104Y/Q191Y/A210G + 659/660 S49A/K108E/Q191Y + 661/662 M76V/V77W/K81Y/K108S/Q191Y/ + A210G 663/664 V16A/A29S/S49M/P104Y/K108W/ + A210G 665/666 P104Y/K108E/W218R + 667/668 A29S/S49A/K108W/Q191Y/A210G/ + W218R 669/670 P104Y/K108W/Q191Y/A210G/W218H + 671/672 A29S/K108D/Q191Y/A210G + 673/674 A29S/S49M/K108D/A210G + 675/676 S49A/P104Y/Q191Y/A210G + 677/678 A29S/S49M/V77W/K81Y/P104Y/ + K108E/Q191Y 679/680 K108E/Q191Y + 681/682 K108E/A210G + 683/684 V16A/K81T/P104Y + 685/686 G42S/V77W/K108W/Q191L + 687/688 V16A/S49A/P104Y/K108W/Q191L + 689/690 V16A/A29S/S49A/K108D + 691/692 G42S/S49M/M76V/K81Y/K108E/ + A210G 693/694 P104Y/Q191L/A210G + 695/696 S49A/K108W/Q191Y/A210G/W218R + 697/698 A29S/S49M/M76V/V77W/K81Y/ + Q191Y/A210G 699/700 S49M/K81T/P104Y/K108S + 701/702 V16A/K108S/Q191L/A210G + 703/704 V16A/K108S/Q191Y/A210G + 705/706 A29S/G42S/P104Y/K108E/Q191Y/ + W218H .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 230 and defined as follows: “+” 3.00 to 6.00, “++” >6.00, “+++” >7.50

    TABLE-US-00005 TABLE 3-2 Adenylate Kinase Variant Activity Relative to SEQ ID NO: 230 Conversion Fold Improvement SEQ ID Amino Acid Differences (Relative to NO: (nt/aa) (Relative to SEQ ID NO: 230) SEQ ID NO: 230).sup.1 707/708 A29S/I51H/E107M/D110E/T202A/P214V +++ 709/710 A29S/P119C +++ 711/712 A29S/E107M/P119C/Q191Y +++ 713/714 A29S/D110E/P119C/Q191L +++ 715/716 V16A/A29S +++ 717/718 A29S/Q191L/P214V +++ 719/720 V16A/A29S/Q191L +++ 721/722 V16A/A29S/P119C/Q191L/P214V +++ 723/724 V16A/E107M/D110E/P119C/Q191L/ ++ T202A/P214V 725/726 A29S/D74I/Q191Y ++ 727/728 E107M/D110E/P119C/Q191L ++ 729/730 V16A/A29S/P119C/Q191Y ++ 731/732 V16A/E107M/Q191L/P214V ++ 733/734 A29S/D74I/M79L/E107M/P214V ++ 735/736 D110E/Q191L/T202A/P214V ++ 737/738 V16A/D110E/Q191L ++ 739/740 A29S/I51H/Q191Y/T202A ++ 741/742 V16A/D110E/P119C ++ 743/744 A29S ++ 745/746 V16A/P214V ++ 747/748 P119C/Q191L ++ 749/750 V16A/E107M/D110E/P119C ++ 751/752 E107M/D110E/P119C/G207V/P214V ++ 753/754 A29S/I51S/D110E/Q191Y/T202A ++ 755/756 V16A/E107M/D110E/Q191L ++ 757/758 A29S/I51S/Q191Y ++ 759/760 A29S/I51S/E107M/D110E/Q191Y ++ 761/762 I51S/E107M/P214V ++ 763/764 I51S/Q191L/T202A/P214V ++ 765/766 V16A/Q191L ++ 767/768 V16A/Q191Y/T202A ++ 769/770 A29S/I51H/E107M/P119C/Q191Y ++ 771/772 A29S/D74P/E107M/Q191L ++ 773/774 I51S/D110E/P214V ++ 775/776 A29S/I51H/E107M/D110E/Q191Y/P214V ++ 777/778 I51S/P214V + 779/780 I51S/E107M/D110E/Q191L + 781/782 I51S/Q191L/P214V + 783/784 A29S/151S/Q191Y/P214V + 785/786 I51S/E107M/D110E + 787/788 I51S/E107M/D110E/Q191L/P214V/W218R + 789/790 V16A + 791/792 I51S/E107M/D110E/P119C + 793/794 I51H/P214V + 795/796 I51S/T202A + 797/798 Q191L/T202A + 799/800 A29S/M46Y/M79L/E107M/D110E/ + T202A/P214V 801/802 A29S/M46K/D110E/T202A/P214V + 803/804 P119C + 805/806 I51S/Q191Y/T202A/P214V + 807/808 A29S/I51S/P119C/Q191Y/P214V + 809/810 V16A/A29S/I51S/P214V + 811/812 D741/M79L/E107M/D110E/Q191L/T202A + 813/814 Q191Y/P214V + 815/816 V16A/I51S/E107M + 817/818 V16A/I51H/Q191L/T202A + 819/820 V16A/I51S/D110E/T202A/P214V + 821/822 I51S/E107M/P119C/Q191Y/P214V + 823/824 I51S/Q191Y + 825/826 I51S + 827/828 I51S/Q191Y/P214V + 829/830 V16A/I51S/P214V + 831/832 V16A/A29S/I51H/Q191Y + 833/834 V16A/I51S/Q191L/T202A/P214V + 835/836 I51S/D110E/Q191Y + 837/838 V16A/A29S/I51S/D110E/Q191L + 839/840 V16A/I51S/E107M/D110E/P214V + 841/842 A29S/M46Y/D110E/P214V + 843/844 A29S/M46Y/Q191L + 845/846 E107M/D110E/A123V/Q191Y/T202A + 847/848 I51H/Q191L + .sup.1Levels of increased activity were determined relative to the reference polypeptide of SEQ ID NO: 230 and defined as follows: “+” 3.00 to 5.00, “++” >5.00, “+++” >8.00

    [0265] All publications, patents, patent applications, and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application, or other document were individually indicated to be incorporated by reference for all purposes.

    [0266] While various specific embodiments have been illustrated and described, it will be appreciated that various changes can be made without departing from the spirit and scope of the invention(s).