Carotenoid and amino acid biosynthesis using recombinant corynebacterium glutamicum
11312981 · 2022-04-26
Assignee
Inventors
Cpc classification
C12Y114/13129
CHEMISTRY; METALLURGY
C12N9/0071
CHEMISTRY; METALLURGY
C12N9/0073
CHEMISTRY; METALLURGY
C12P23/00
CHEMISTRY; METALLURGY
C12P13/08
CHEMISTRY; METALLURGY
C12Y114/11
CHEMISTRY; METALLURGY
International classification
C12P13/08
CHEMISTRY; METALLURGY
Abstract
The present invention provides a method of producing astaxanthin and lysine in recombinant gram-positive bacteria comprising a nucleic acid sequence encoding for a crtZ-protein from F. pelagi and comprises a nucleic acid sequence encoding for a crtW-protein.
Claims
1. A process for the preparation of astaxanthin and lysine in recombinant C. glutamicum, wherein the genome of said recombinant C. glutamicum comprises a deletion in the endogenous crtR, crtY and crtEb genes, and wherein said recombinant C. glutamicum has been genetically modified to introduce crtE, crtB, and crtl genes from C. glutamicum, a crtY from P. ananatis, at least one recombinant gene encoding a crtZ-protein from F. pelagi, B. bacteroides, S. astaxanthinifaciens, or B. vesicularis, and at least one recombinant gene encoding a crtW-protein from F. pelagi, B. aurantiaca, S. astaxanthinifaciens, B. bacteroides, or B. vesicularis.
2. The process according to claim 1, wherein the gene encoding the crtZ-protein comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1, 13, 15 and 17, or wherein the crtZ-protein encoded by the gene encoding the crtZ-protein has an amino acid sequence selected from the group consisting of SEQ ID NO: 2, 14, 16 and 18.
3. The process according to claim 2, wherein the gene encoding the crtZ-protein comprises the nucleic acid sequence of SEQ ID NO: 1.
4. The process according to claim 1, wherein the gene encoding the crtW-protein comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 3, 5, 7, 9, 11, 19 and 21.
5. The process according to claim 1, wherein the crtW-protein encoded by the gene encoding the crtW-protein comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 4, 6, 8, 10, 12, 20 and 22.
6. The process according to claim 1, wherein said recombinant C. glutamicum comprises a first promoter which is operably linked to the gene encoding the crtZ-protein.
7. The process according to claim 6, wherein said recombinant C. glutamicum comprises a second promoter which is operably linked to the gene encoding the crtW-protein.
8. The process according to claim 7, wherein the first promoter is induced by a first inducing compound and the second promoter is induced by a second inducing compound, wherein the first and second inducing compounds are not the same inducing compound.
9. The process according to claim 7, wherein the second promoter is a constitutively expressing promoter.
10. The process according to claim 7, wherein induction of the first promoter and induction of the second promoter occur at different times.
11. The process according to claim 7, wherein induction of promoter activity of the first promoter occurs at the beginning of the cultivation, in the exponential growth phase within the first 6 hours.
12. The process according to claim 7, wherein the first promoter and the second promoter are constitutively expressing promoters.
13. The process according to claim 1, wherein said recombinant C. glutamicum has a deletion in the endogenous sugR and IdhA genes.
Description
FIGURES
(1)
(2)
(3)
(4)
(5)
(6) DECA LYS1 (5 a and b: deletion of crtR),
(7) DECA LYS2 (5 c (primer NW29 OP1-E and crtE-B) and d (primer NW29 OP1-E and NW30 OP1-F): insertion of crtEBI),
(8) DECA BETA LYS (5 e: insertion of crtY.sub.Pa),
(9) LYC LYS (5 f: deletion of genes crtYe, crtYf and crtEb since they are part of an operon),
(10) BETA LYS (5 g and h: insertion of crt Y.sub.Fp),
(11) CAN LYS (5 i: insertion of pSH1_crtW1.sub.Fp),
(12) ZEA LYS (5 j: insertion of pECXT_crtZ.sub.Fp),
(13) ASTA LYS (5 k: BETALYS (pECXT99a_crtZFp) (pSH1-crtWFp).
(14)
(15)
DETAILED DESCRIPTION
(16) It was surprisingly found that the use of recombinant C. glutamicum wherein in the genome of said recombinant C. glutamicum crtR, crtYe and crtYf and crtEb were deleted and crtEBI, crtYe, and at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtZ-protein (crtZ-nucleic acid sequence), preferably from F. pelagi (crtZ.sub.Fp-nucleic acid sequence), at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtW-protein (crtW-nucleic acid sequence), preferably from F. pelagi (crtW.sub.Fp-nucleic acid sequence), B. aurantiaca (crtW.sub.Ba-nucleic acid sequence) or S. astaxanthinifaciens (crtW.sub.Sa-nucleic acid sequence) were introduced in a process for the production of astaxanthin and lysine yields not only higher amounts of said substance compared to processes with recombinant C. glutamicum known in the art but also an increased production of lysine.
(17) One aspect of the present invention refers to a recombinant gram-positive bacterium, preferably C. glutamicum, wherein the genome of said bacterium was modified in that it comprises deletions of crtR, crtYe and crtYf from said bacterium, preferably from C. glutamicum, and crtEb, respectively, and introduction of crtEBI, introduction of crtY.sub.Pa and introduction of at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtZ-protein (crtZ-nucleic acid sequence), preferably from F. pelagi (crtZ.sub.Fp-nucleic acid sequence), at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtW-protein (crtW-nucleic acid sequence), preferably from F. pelagi (crtW.sub.Fp-nucleic acid sequence), B. aurantiaca (crtW.sub.Ba-nucleic acid sequence) or S. astaxanthinifaciens (crtW.sub.Sa-nucleic acid sequence).
(18) In one preferred embodiment, in said recombinant gram-positive bacterium according to the invention, preferably C. glutamicum, the genes crtYe, crtYf and crtEb are replaced by said crtZ-nucleic acid sequence, preferably a crtZ.sub.Fp-nucleic acid sequence, and nucleic acid sequence encoding for a crtW-protein (crtW-nucleic acid sequence), preferably from F. pelagi (crtW.sub.Fp-nucleic acid sequence), B. aurantiaca (crtW.sub.Ba-nucleic acid sequence) or S. astaxanthinifaciens (crtW.sub.Sa-nucleic acid sequence) in at least one recombinant sequence.
(19) In one preferred embodiment, said recombinant bacterium according to the invention comprises only one recombinant sequence, which comprises a crtZ.sub.Fp-nucleic acid sequence, and a crtW-nucleic acid sequence, preferably crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence.
(20) Another aspect of the present invention refers to a method to produce astaxanthin and lysine in recombinant gram-positive bacterium according to the invention such as recombinant C. glutamicum, wherein said bacterium comprises a crtZ-nucleic acid sequence, preferably a crtZ.sub.Fp-nucleic acid sequence, and comprises a crtW-nucleic acid sequence, preferably crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence, in at least one recombinant sequence.
(21) Yet another aspect of the present invention refers to a method to produce astaxanthin and lysine in recombinant C. glutamicum according to the invention, wherein said recombinant C. glutamicum comprises a recombinant sequence, which comprises a crtZ-nucleic acid sequence, preferably a crtZ.sub.Fp-nucleic acid sequence, and a crtW-nucleic acid sequence, preferably a crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence.
(22) Especially preferred is a method according to the invention or a bacterium according to the invention, wherein a crtZ-nucleic acid sequence, preferably a crtZ.sub.Fp-nucleic acid sequence, and a crtW-nucleic acid sequence, preferably crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence, are each expressed and corresponding crtZ-protein and crtW-protein are produced.
(23) In one preferred embodiment, said crtZ-nucleic acid sequence and said crtW-nucleic acid sequence being each part of a recombinant sequence, preferably being part of one recombinant sequence, are each individually operatively linked to a promotor.
(24) In a preferred embodiment, the method of the invention further comprises the step of obtaining astaxanthin and lysine.
(25) In a particular embodiment, recombinant crtW- and/or crtZ-nucleic acid sequences may be expressed from a non-native or heterologous promoter (i.e. a promoter which is heterologous to a crtW- and/or crtZ-nucleic acid sequence, i.e. is not the native crtW- or crtZ-gene promoter of the host bacterium, e.g., C. glutamicum) and particularly a strong, non-native or heterologous promoter. Thus, in this embodiment the crtW- or crtZ-nucleic acid sequences are not used with their native promoter. A crtW- or crtZ-nucleic acid sequence may be introduced which is under the control of a non-native promoter.
(26) The use of a non-native promoter may advantageously have the effect of relieving the crtW- or crtZ-nucleic acid sequences of transcriptional repression, as at least some of any repressive elements will be located in the native promoter region. By replacing the native promoter with a non-native promoter devoid of repressive elements responsive to the effects of pathway products, the crtW- or crtZ-nucleic acid sequence will be at least partly relieved of transcriptional repression.
(27) The invention, in one preferred embodiment, may thus provide a method wherein a crtW- and/or a crtZ-nucleic acid sequence is expressed which is not subject to transcriptional repression, e.g. by a product of the astaxanthin pathway or by a repressor of the endogenous crtW- or crtZ-nucleic acid sequence.
(28) In a preferred embodiment, the non-native promoter in view of a crtZ-nucleic acid sequence of C. glutamicum and a crtW-nucleic acid sequence of C. glutamicum is nevertheless native to C. glutamicum.
(29) The introduced sequences may be modified to render them relieved of transcriptional repression, e.g. by mutating or deleting recognition elements for transcriptional repressors or by using expression control elements (e.g. promoters) which are not subject to transcriptional regulation by the transcriptional regulator(s) which normally control expression of the crtW-gene and/or crtZ-nucleic acid sequence, e.g. which control expression in their native situation, for example transcriptional repressors being products of the astaxanthin pathway. The endogenous crtW- and/or crtZ-nucleic acid sequence may alternatively or additionally be modified in this way, or by addition of a stronger promoter. Thus, mutagenesis (including both random and targeted) may for example be used to mutate the endogenous control or regulatory elements so as to increase expression of the endogenous crtW- and/or crtZ-nucleic acid sequence (e.g. increase transcription and/or translation). Alternatively, the organism may be engineered to introduce additional or alternative regulatory elements.
(30) In yet another preferred embodiment, the C. glutamicum used for producing a recombinant C. glutamicum strain in regard of crtW and crtZ according to the present invention is GRLys1ΔsugRΔIdhA, a modified strain of MB001 (ATCC13032) known from Pérez-García, Peters-Wendisch and Wendisch, 2016.
(31) Especially preferably, the expression, preferably overexpression, of a recombinant crtZ.sub.Fp-nucleic acid sequence and a recombinant crtW-nucleic acid sequence, preferably a crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence, results in the production, preferably overproduction, of a crtZ.sub.Fp-protein encoded by said crtZ.sub.Fp-nucleic acid sequence and the production, preferably overproduction, of a crtW-protein, preferably a crtW.sub.Fp-protein, crtW.sub.Ba-protein or crtW.sub.Sa-protein, encoded by said crtW-nucleic acid sequence, preferably a crtW.sub.Fp-nucleic acid sequence, crtW.sub.Ba-nucleic acid sequence or crtW.sub.Sa-nucleic acid sequence, respectively.
(32) In yet another preferred embodiment, the crtZ.sub.Fp-nucleic acid sequence is SEQ ID NO.: 1 or is
(33) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 1, or
(34) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 1 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 2 and which amino acid sequence shows crtZ activity.
(35) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW.sub.Fp is SEQ ID NO.: 3 or SEQ ID NO.: 5 or is
(36) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 3 or 5, respectively, or
(37) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 3 or 5, respectively, under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 4 or 6, respectively, and which amino acid sequence shows crtW activity.
(38) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW.sub.Ba is SEQ ID NO.: 7 or is
(39) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 7, or
(40) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 7 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 8 and which amino acid sequence shows crtW activity.
(41) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW.sub.Sa is SEQ ID NO.: 9, or is
(42) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 9, or
(43) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 9 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 10 and which amino acid sequence shows crtW activity.
(44) Yet another aspect of the present invention refers to a method to produce astaxanthin and lysine comprising the step of cultivating recombinant gram-positive bacterium, preferably C. glutamicum according to the invention, under conditions that a recombinant crtZ.sub.Fp-protein resulting from a recombinant crtZ.sub.Fp-nucleic acid sequence described herein is overproduced and a recombinant crtW-protein, preferably a crtW.sub.Fp-, crtW.sub.Sa-, crtW.sub.Ba-protein resulting from a crtW-nucleic acid sequence described herein, is overproduced simultaneously, at different times or at overlapping times in said bacterium. As non-limiting examples for “simultaneously overproduced” recombinant proteins are, e.g., proteins which encoding nucleotide sequences are both individually operatively linked to a constitutively expressing promotor. A non-limiting example for “overproduced at different times” recombinant proteins are, e.g., proteins of which one encoding nucleotide sequences is operatively linked to a substance 1 (e.g. methanol) induced promotor and another encoding nucleotide sequence is operatively linked to a substance 2 (e.g. glucose) induced promotor and the inducing substances are provided to the bacterium at different times. A non-limiting example for overproduced “at overlapping times” recombinant proteins are, e.g., a protein which encoding nucleotide sequence is operatively linked to a substance 1 (e.g. methanol) induced promotor and a protein which encoding nucleotide sequence is operatively linked to a constitutively expressing promotor and the inducing substance is provided to the bacterium only for a specific time period.
(45) Yet another aspect of the present invention refers to a method to produce astaxanthin and lysine comprising the steps of introducing into a gram-positive bacterium according to the invention, preferably a C. glutamicum, a crtZ.sub.Fp-nucleic acid sequence according to the invention and a crtW-nucleic acid sequence, preferably a crtW.sub.Fp-, crtW.sub.Sa-, crtW.sub.Ba-nucleic acid sequence; and cultivating the gram-positive bacterium, preferably C. glutamicum, under conditions that crtZ.sub.Fp-protein is overproduced and crtW-protein, preferably a crtW.sub.Fp-, crtW.sub.Sa-, crtW.sub.Ba-protein, is overproduced.
(46) Preferably, both nucleic acid sequences encoding for a crtZ-protein and encoding for a crtW-protein, respectively, are introduced into the gram-positive bacterium, preferably C. glutamicum, simultaneously, e.g. both sequences being comprised in a plasmid which is introduced into C. glutamicum.
(47) The skilled person is aware how to transform plasmid into cells, e.g. by electroporation or heat-shock methods, by methods known in the art (see, e.g., Heider et al, supra).
(48) Methods for introducing nucleic acids and vectors into microorganisms are well known and widely described in the literature. The choice of method may depend on the microorganism used. As described in Heider et al., 2014 (supra), methods for introducing genes into C. glutamicum and suitable plasmids etc. for use in such methods are known and available in the art.
(49) Preferably, each recombinant nucleic acid sequence encoding for a crtZ.sub.Fp-protein and encoding for a crtW-protein, respectively, is individually operatively linked to a promotor. More preferably, at least one promotor, even more preferably, each promotor individually operatively linked to a recombinant crtZ.sub.Fp-nucleic acid sequence (promotor 1) and a crtW-nucleic acid sequence, preferably a crtW.sub.Fp-, crtW.sub.Sa-, or crtW.sub.Ba-nucleic acid sequence, respectively, (promotor 2), is a constitutively expressing promotor, preferably a constitutively expressing strong promotor.
(50) The use of promotors leads, when activated or constitutively expressing, to an overexpression of the operatively linked nucleic acid sequence and results in the overproduction of the encoded recombinant protein.
(51) One preferred embodiment refers a process according to the invention or a recombinant bacterium according to the invention comprises a recombinant crtZ-nucleic acid sequence, wherein the crtZ-protein encoding nucleic acid sequence is a nucleic acid sequence according to SEQ ID NO.: 1, or is
(52) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 1, or
(53) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 1 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 2 and which amino acid sequence shows crtZ activity.
(54) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW is SEQ ID NO.: 3 or SEQ ID NO.: 5 or is
(55) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 3 or 5, respectively, or
(56) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 3 or 5, respectively, under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 4 or 6, respectively, and which amino acid sequence shows crtW activity.
(57) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW is SEQ ID NO.: 7 or is
(58) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 7, or
(59) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 7 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 8 and which amino acid sequence shows crtW activity.
(60) In yet another preferred embodiment, the source for a nucleic acid sequence encoding for crtW is SEQ ID NO.: 9, or is
(61) a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 9, or
(62) a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 9 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 10 and which amino acid sequence shows crtW activity.
(63) (Sequence) “identity” may be assessed by any convenient method. However, for determining the degree of sequence identity between sequences, computer programs that make multiple alignments of sequences are useful, for instance Clustal W (Thompson et al, (1994) Nucleic Acids Res., 22: 4673-4680). Furthermore, the Dali server at the European Bioinformatics institute offers structure-based alignments of protein sequences (Holm (1993) J. Mol. Biol., 233: 123-38; Holm (1995) Trends Biochem. Sci., 20: 478-480; Holm (1998) Nucleic Acid Res., 26: 316-9).
(64) Yet another preferred embodiment refers to a method or a recombinant C. glutamicum wherein in the genome of the recombinant C. glutamicum
(65) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW.sub.Fp+pEC-XT-crtZ.sub.Fp,
(66) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW2.sub.Fp+pEC-XT-crtZ.sub.Fp,
(67) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW.sub.Sa+pEC-XT-crtZ.sub.Fp, or
(68) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW.sub.Sa+pEC-XT-crtZ.sub.Fp,
(69) more preferably the recombinant C. glutamicum is recombinant C. glutamicum GRLys1ΔsugRΔIdhA with the following modifications
(70) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW1.sub.Fp+pEC-XT-crtZ.sub.Fp,
(71) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW2.sub.Fp+pEC-XT-crtZ.sub.Fp,
(72) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW.sub.Sa+pEC-XT-crtZ.sub.Fp, or
(73) crtR, crtY from C. glutamicum and crtEb were deleted and the genome comprises crtEBI, crtY.sub.Pa, and pSH1_crtW.sub.Ba+pEC-XT-crtZ.sub.Fp.
(74) Even more preferred, the recombinant C. glutamicum is recombinant C. glutamicum ASTA LYS as described herein (i.e. BETALYS (pECXT99A-crtZFp)(XpSH1-crtWFp).
(75) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein the recombinant crtW-nucleic acid sequence is a crtW.sub.Fp-, crtW.sub.Sa-, or crtW.sub.Ba-nucleic acid sequence, more preferably a crtW.sub.Ba-nucleic acid sequence.
(76) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein said recombinant bacterium, preferably C. glutamicum, comprises a recombinant nucleic acid sequence encoding for a promotor 1 which is operatively linked to a crtZ.sub.Fp-nucleic acid sequence.
(77) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein said recombinant bacterium, preferably C. glutamicum, comprises a recombinant nucleic acid sequence encoding for a promotor 2 which is operatively linked to a crtW-nucleic acid sequence, preferably a crtW.sub.Fp-, crtW.sub.Sa-, or crtW.sub.Ba-nucleic acid sequence.
(78) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein the promotor 1 which is operatively linked to a crtZ.sub.Fp-nucleic acid sequence and the promotor 2 which is operatively linked to a crtW-nucleic acid sequence, preferably a crtW.sub.Fp-, crtW.sub.Sa-, or crtW.sub.Ba-nucleic acid sequence, are activated by different sources, e.g. one of both is constitutively expressing while the other is activated/induced, e.g. by IPTG or a saccharide such as xylitol or mannitol. The skilled person is well aware of further compound inducible promotors.
(79) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein promotor 2 is a constitutively expressing promotor.
(80) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein induction of promotor activity of promotor 1 and induction of promotor activity of promotor 2 occur at different times.
(81) Another preferred embodiment refers to a process according to the invention, wherein induction of promotor activity of promotor 1 occurs within the first 6 hours of the cultivation, in the exponential growth phase.
(82) Another preferred embodiment refers to a process according to the invention or a recombinant bacterium according to the invention, wherein promotor 1 and promotor 2 are constitutively expressing promotors.
(83) Another preferred embodiment refers to a process according to the invention, wherein the amount of astaxanthin is at least 0.5 mg/gCDW (cell dry weight), more preferably at least 0.75 mg/gCDW, even more preferably at least 0.8 mg/gCDW after 48 h of incubation at 30° C., e.g., in a 50 ml culture.
(84) Another preferred embodiment refers to a process according to the invention, wherein the concentration of astaxanthin after 48 h incubation at 30° C., e.g., in a 50 ml culture, is at least 1.6 mg/l, more preferably 2.45 mg/l, even more preferably at least 2.6 mg/l and the concentration of lysine is at least 9.2 mM, more preferably 13.8 mM, even more preferably at least 14.7 mM.
(85) Notably, all strains produced herein except of ASTA LYS (BETALYS (pECXT99A-crtZFp)(pSH1-crtWFp)) were not able to produce increased amounts of astaxanthin and lysine.
(86) Xylose and arabinose can be obtained from lignocelluloses by hydrolysis and these pentose sugars do not have competing uses in the food and feed industries. C. glutamicum wild type can neither utilize xylose nor arabinose, may be engineered for growth on these pentose sugars as sole and combined carbon sources (Meiswinkel et al., 2013; Schneider et al., 2011; Wendisch et al., 2016a). Example 4 shows that the use of different carbon sources for the production of β-carotene and lysine is possible.
(87) Accordingly, another aspect of the invention relates to a process for preparation of carotenoids, preferably astaxanthin and/or β-carotene, in recombinant C. glutamicum of the invention, preferably BETALYS, wherein arabinose is used as carbon source and wherein in the genome of said recombinant C. glutamicum araA, preferably as depicted in SEQ ID NO: 87, araB, preferably as depicted in SEQ ID NO: 88 and araD, preferably as depicted in SEQ ID NO: 89, is introduced. Another aspect of the invention relates to a process for preparation of carotenoids, preferably astaxanthin and/or β-carotene, in recombinant C. glutamicum of the invention, preferably BETALYS, wherein in the genome of said recombinant C. glutamicum xylA, preferably as depicted in SEQ ID NO: 90, and xylB, preferably as depicted in SEQ ID NO: 91, is introduced. A further aspect of the invention relates to a process for preparation of carotenoids, preferably astaxanthin and/or β-carotene, in recombinant C. glutamicum of the invention, preferably BETALYS, wherein arabinose and xylulose are used as carbon source and wherein in the genome of said recombinant C. glutamicum araA, preferably as depicted in SEQ ID NO: 87, araB, preferably as depicted in SEQ ID NO: 88, araD, preferably as depicted in SEQ ID NO: 89, xylA, preferably as depicted in SEQ ID NO: 90, and xylB, preferably as depicted in SEQ ID NO: 91, are introduced. Preferably, the introduced genes are operatively linked to a promotor.
(88) Another aspect of the present invention refers to a method and a strain for the production of lycopene and lysine, preferably a process for the preparation of lycopene in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh and crtR from C. glutamicum, crtYe, crtYf, crtEb were deleted, Ptuf-crtEcrtBcrtI was introduced. Preferably, the strain is LYC LYS as described herein.
(89) Yet another aspect of the present invention refers to a method and a strain for the production of decaprenoxanthin and lysine, preferably a process for the preparation of decaprenoxanthin in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh are deleted, or sugR and Idh and crtR are deleted, sugR and Idh and crtR are deleted and Ptuf-crtEcrtBcrtI is introduced, or sugR and Idh and crtR are deleted and Ptuf-crtEcrtBcrtI and Ptuf-crtY.sub.Pa is introduced. Preferably, the strain is selected from the group consisting of GRLYS1ΔsugRΔIdh), 2=DECA LYS1, 3=DECA LYS2 and 4=DECA-BETA LYS as described herein.
(90) Yet another aspect of the present invention refers to a method and a strain for the production of canthaxanthin and lysine, preferably a process for the preparation of canthaxanthin in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh and crtR from C. glutamicum, crtYe, crtYf, crtEb were deleted, Ptuf-crtEcrtBcrtI was introduced and crtW, preferably crtW.sub.Fp, are introduced. Preferably, the strain is CAN LYS.
(91) Yet another aspect of the present invention refers to a method and a strain for the production ozeaxanthin and lysine, preferably a process for the preparation of ozeaxanthin and lysine in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh and crtR from C. glutamicum, crtYe, crtYf, crtEb were deleted, Ptuf-crtEcrtBcrtI was introduced and crtZ, preferably crtZ.sub.Fp, are introduced. Preferably, the strain is ZEA LYS
(92) Yet another aspect of the present invention refers to a method and a strain for the production of β-carotene and lysine, preferably a process for the preparation of β-carotene and lysine in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh and crtR are deleted and Ptuf-crtEcrtBcrtI and Ptuf-crtY.sub.Pa is introduced or sugR and Idh and crtR and crtYe and crtYf and crtEb are deleted and Ptuf-crtEcrtBcrtI and Ptuf-crtY.sub.Pa is introduced. Preferably, the strain is DECA-BETA LYS or BETA LYS.
(93) Yet another aspect of the present invention refers to a method and a strain for the production of β-carotene, decaprenoxanthin and lysine preferably a process for the preparation of β-carotene, decaprenoxanthin and lysine in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum strain sugR and Idh and crtR are deleted and Ptuf-crtEcrtBcrtI and Ptuf-crtY.sub.Pa is introduced. Preferably, the strain is DECA-BETA LYS.
(94) The invention is also characterized by the following items:
(95) 1. A process for the preparation of astaxanthin and lysine in recombinant C. glutamicum, wherein in the genome of said recombinant C. glutamicum crtR, crtY from C. glutamicum and crtEb were deleted and crtEBI, crtYPa and at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtZ-protein (crtZ-nucleic acid sequence), preferably from F. pelagi (crtZFp-nucleic acid sequence) and at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtW-protein (crtW-nucleic acid sequence), preferably from F. pelagi (crtWFp-nucleic acid sequence), B. aurantiaca (crtWBa-nucleic acid sequence) or S. astaxanthinifaciens (crtWSa-nucleic acid sequence) were introduced.
2. The process according to item 1, wherein the crtZFp-nucleic acid sequence is SEQ ID NO.: 1, or
a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 1, or
a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 1 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 2 and which amino acid sequence shows crtZ activity.
3. The process according to item 2, wherein the crtZFp-nucleic acid sequence is SEQ ID NO.: 1.
4. The process according to item 1 or item 2, wherein the crtW-nucleic acid sequence is SEQ ID NO.: 3 or SEQ ID NO.: 5 or is
a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 3 or 5, respectively, or
a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 3 or 5, respectively, under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
is a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 4 or 6, respectively, and which amino acid sequence shows crtW activity; or
is SEQ ID NO.: 7 or is
a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 7, or a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 7 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 8 and which amino acid sequence shows crtW activity; or is SEQ ID NO.: 9, or
is a nucleic acid sequence having at least 80% identity as set forth with SEQ ID NO.: 9, or a nucleic acid sequence that hybridizes with the complement of a nucleic acid sequence according to SEQ ID NO.: 9 under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and wash conditions 2×SSC, 0.1% SDS, 65° C., followed by 0.1×SSC, 0.1% SDS, 65° C. (high stringency conditions), or
a nucleic acid sequence encoding for an amino acid sequence having at least 80% identity with SEQ ID NO.: 10 and which amino acid sequence shows crtW activity.
5. The process according to any one of the items 1 to 3, wherein the crtW-protein is of SEQ ID NO.: 4, 6, 8 or 10.
6. The process according to any of the preceding items, wherein said recombinant C. glutamicum comprises a nucleic acid sequence encoding for a promotor 1 which is operatively linked to a crtZFp-nucleic acid sequence according to item 2 or item 3.
7. The process according to any of the preceding items, wherein said recombinant C. glutamicum comprises a nucleic acid sequence encoding for a promotor 2 which is operatively linked to a crtWFp-, crtWBa-, or crtWSa-nucleic acid sequence according to item 4 or 5.
8. The process according to any one of the preceding items, wherein the promotor 1 and the promotor 2 are not induced by the same inducing compound.
9. The process according to any one of the preceding items, wherein promotor 2 is a constitutively expressing promotor.
10. The process according to any one of the preceding items, wherein induction of promotor activity of promotor 1 and induction of promotor activity of promotor 2 occur at different times.
11. The process according to any one of the preceding items, wherein induction of promotor activity of promotor 1 occurs at the beginning of the cultivation, in the exponential growth phase within the first 6 hours.
12. The process according to any one of items 1 to 7 and 8 to 10, wherein promotor 1 and promotor 2 are constitutively expressing promotors.
13. The process according to any one of the preceding items, wherein said recombinant C. glutamicum comprises the following modifications: deletion of sugR and deletion of LdhA, deletion of crtR insertion of crtEBI deletion of genes crtYe, crtYf and crtEb insertion of crt YPa, preferably as Ptuf-crtYPa, insertion of crtZFp, preferably as pECXT99a_crtZFp, insertion of crtWFp, preferably as pSH1-crtWFp.
14. A recombinant C. glutamicum, wherein said recombinant C. glutamicum comprises a crtY-nucleic acid sequence, preferably a crtYPa-nucleic acid sequence, further comprises a crtZ-nucleic acid sequence, which is not from C. glutamicum, preferably a crtZFp-nucleic acid sequence, and further comprises a crtW-nucleic acid sequence, preferably a crtWFp-, crtWBa-, or crtWSa-nucleic acid sequence;
more preferably, in the genome of said recombinant C. glutamicum crtR, crtY from C. glutamicum and crtEb were deleted and crtEBI, crtYPa and at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtZ-protein, preferably from F. pelagi (crtZFp-nucleic acid sequence) and at least one recombinant sequence which comprises a nucleic acid sequence encoding for a crtW-protein, preferably from F. pelagi (crtWFp-nucleic acid sequence), B. aurantiaca (crtWBa-nucleic acid sequence) or S. astaxanthinifaciens (crtWSa-nucleic acid sequence) were introduced.
15. The recombinant C. glutamicum, according to item 15, wherein the nucleic acid sequence encoding for a crtZ-protein is a nucleic acid sequence according to item 2 or 3 and the nucleic acid sequence encoding for a crtW-protein is a nucleic acid sequence according to item 4 or 5.
EXAMPLES
Example 1: Co-Production of Astaxanthine and Lysine
(96) Agilent 1200 series HPLC system (Agilent Technologies) Autoclave DE-23 (Systec) Autoclave S. p. A. (Fedegari) Axio Lab.A1 (Zeiss) BioCapt MW Safe 2020 Biological Safety Cabinet (Thermo Scientific) Centrifuge 5417 R (Eppendorf) Centrifuge 5424 (Eppendorf) Centrifuge 5810 R (Eppendorf) DC Power Supply 5004 Ecotron (Infors HT) Gene Pulser Xcell™ (Biorad) Incubator (Memmert) Spectrophotometer ND-1000 (Nanodrop) Spectrophotometer V-1200 (VWR) Thermocycler FlexCycler (Biometra) Thermocycler T3000 (Biometra) Thermomixer comfort (Eppendorf) UV Transilluminator (UVP) Vortex Genie 2 (Scientific Industries) Waterbath 3042 (Köttermann)
(97) The chemicals used to prepare the buffers and solutions were obtained by AppliChem GmbH (Darmstadt), Carl Roth GmbH & Co. KG (Karisruhe), Merck KGaA (Darmstadt), Sigma-Aldrich GmbH (Taufkirchen) and VWR International GmbH (Darmstadt). The components and preparations for the buffers and solutions are listed in Table 1.
(98) TABLE-US-00002 TABLE 1 Buffers and solutions. Components, amounts and preparation of the used buffers and solutions Component End concentration RF1 RbCl 100 mM MnCl.sub.2 × 4 H.sub.2O 50 mM Potassium acetate 30 mM CaCl.sub.2 × 2 H.sub.2O 10 mM Glycerol 15% (w/v) adjust pH to 5.8 with 0.2 % acetic acid autoclave RF2 MOPS 10 mM RbCl 10 mM CaCl.sub.2 × 2 H.sub.2O 75 mM Glycerol 15% (w/v) adjust pH to 6.8 with NaOH autoclave EPB1 HEPES 20 mM Glycerol 5% (w/v) adjust pH to 7.2 with 2N NaOH autoclave EPB2 HEPES 5 mM Glycerol 15% (w/v) adjust pH to 7.2 with 2N NaOH autoclave 40% glucose Amount Glucose 400 g/l autoclave TAE End concentration Tris 40 mM Acetic acid 20 mM Na.sub.2EDTA 1 mM 1% Agarose Amount Agarose 10 g/l cook with 1 × TAE until solution is clear, store at 60° C. End concentration Gel Loading Buffer Na.sub.2EDTA 100 mM Glycerol 50% (w/v) Bromphenol blue 0.10% Xylene cyanol 0.20% Orange G 0.15% Component Borat Buffer Boronic acid 100 mM adjust pH to 7 with 30% NaOH Ethambutol dihydrochloride Ethambutol dihydrochloride 36 mM
Bioinformatic Tools: Clone Manager Version 9.0 (Sci-Ed)
(99) The components and preparations of the various media are listed in Table 2. To solve the components, deionized H.sub.2O was used. For the preparation of medium for plates, 16 g/l agar was added before autoclaving. To prepare media for organisms with antibiotic resistance, the antibiotics were added to the liquid media immediately before preparing the cultures. For producing plates with selective media, antibiotics were added before pouring the plates.
(100) In Table 3 the components of the solution for trace elements are listed. Table 4 contains the antibiotics and their used concentrations.
(101) TABLE-US-00003 TABLE 2 Media. Components, amounts and preparation of media Component Amount LB Medium Bacto tryptone 10 g/l Yeast extract 5 g/l NaCl 10 g/l autoclave BHIS Medium Brain Heart Infusion Medium 37 g/l autoclave Sorbitol 90 g/l autoclave BHIS 10% sucrose Medium Brain Heart Infusion Medium 37 g/l autoclave Sorbitol 90 g/l Sucrose 100 g/l autoclave CGXII (NH.sub.4).sub.2SO.sub.4 20 g/l Urea 5 g/l KH.sub.2PO.sub.4 1 g/l K.sub.2HPO.sub.4 1 g/l CaCl.sub.2 10 mg/l MgSO.sub.4 × 7 H.sub.2O 250 mg/l MOPS 42 g/l adjust pH to 7 with KOH autoclave Biotin (sterile) 0.2 mg/l PKS (sterile) 30 mg/l Carbon source (sterile) x g/l Trace elements (sterile) 1 ml/l
(102) TABLE-US-00004 TABLE 3 Trace elements. Components and amount to prepare trace elements used for CGXII medium Component Amount FeSO.sub.4 × 7 H.sub.2O 10 g/l MnSO.sub.4 × 7 H.sub.2O 10 g/l ZnSO.sub.4 × 7 H.sub.2O 1 g/l CuSO.sub.4 0.2 g/l NiCl.sub.2 × 6 H.sub.2O 20 g/l sterile filtrating
(103) TABLE-US-00005 TABLE 4 Antibiotics. Concentration of stock solution and end concentration of antibiotics used to prepare selective media Antibiotic Stock solution conc. [mg/ml] End conc. [μg/ml] Kanamycin 50 15/25 Nalidixic acid 50 50 Tetracycline 5 5
Oligonucleotides:
(104) The primers used for PCR were ordered from Metabion GmbH (Planegg/Steinkirchen) (Table 5).
(105) TABLE-US-00006 TABLE 5 Oligonucleotides. Name Sequence 5′ .fwdarw. 3′ crtY-A AAAAGGATCCAGTCGGCTTCAGCATCC (SEQ ID NO: 63) crtEb-DelD AAAACCCGGGATGTGTGGGAGGCTTCGC (SEQ ID NO: 64) IntY2 GAAGTCCAGGAGGACATACAATGCAACCGCATTAT GATCTG (SEQ ID NO: 65) IntY3 TCTTACTACTTGCGCTAGGTACAGTTAACGATGAG TCGTCATAATGG (SEQ ID NO: 66) NW23 P.sub.tuf-fw TGGCCGTTACCCTGCGAATG (SEQ ID NO: 67) crtl-sacI-rv TTTTGAGCTCTTAAGTCCGATCCACACTGT (SEQ ID NO: 68) cg0725_E GCGCGAAGATTTGATGGG (SEQ ID NO: 69) cg0725_F ACTTGTCACCACAGCACTAC (SEQ ID NO: 70) NW29 Op1-E TCGCACCATCTACGACAACC (SEQ ID NO: 71) NW30 Op1-F CTACGAAGCTGACGCCGAAG (SEQ ID NO: 72) crtE-B CCCATCCACTAAACTTAAACAGATTGTCATGCCAT TGTCCAT (SEQ ID NO: 73) crtE-Pstl-fw AAAACTGCAGGAAAGGAGGCCCTTCAGATGGACAA TGGCATGACAATC (SEQ ID NO: 74) NW31 Op2-E GTGGTGCTCGAGAACATAAG (SEQ ID NO: 75) NW32 Op2-F CGGTCACCCGTAACAATCAG (SEQ ID NO: 76) crtY-E TTGCACCTGCTGGATACGAA (SEQ ID NO: 77) crtEb-DelF AAAACAATGCGCAGCGCA (SEQ ID NO: 78) PD5 (pSH1-fw) ACCGGCTCCAGATTTATCAG (SEQ ID NO: 79) 582 (pSH1-rv, ATCTTCTCTCATCCGCCA pEKEx3-rv) (SEQ ID NO: 80) pECXT-fw AATACGCAAACCGCCTCTCC (SEQ ID NO: 81) pECXT-rv TACTGCCGCCAGGCAAATTC (SEQ ID NO: 82) cg0725_A GCAGGTCGACTCTAGAGGATCCCCGCGCGAAGATT TGATGGG (SEQ ID NO: 83) cg0725_D CCAGTGAATTCGAGCTCGGTACCCCTTGTCACCAC AGCACTACT (SEQ ID NO: 84) Pa_crtY-fw CTGCAGGTCGACTCTAGAGGAAAGGAGGCCCTTCA GATGCAACCGCATTATGATCTG (SEQ ID NO: 85) Pa_crtY-rv1 CGGTACCCGGGGATCTTAACGATGAGTCGTCATAA TGG (SEQ ID NO: 86) Sequences used to amplify genes. Sequence in italics = linker sequence for hybridization
Biological Material:
(106) The strains and plasmids used for growth experiments or constructing new strains are listed in Table 6 and 7. C. glutamicum GRLys1ΔsugRΔIdhA was used to construct further strains by deleting or inserting genes.
(107) TABLE-US-00007 TABLE 6 Strains used for this invention Source or Strain Relevant characteristics reference E. coli S17-1 hsdR Pro, Rec.sup.−, genome integrated Simon, RP4-2Tc::Mu Priefer Km::Tn7 and Puhler, 1983 C. glutamicum strains MB001 prophage cured, genome reduced Baumgart ATCC 13032 et al., 2013 GRLys1ΔsugRΔldhA ATCC 13032 with following Pérez- modifications: Δpck, pyc.sup.P458S, Garcia, hom.sup.V59A, 2 copies of lysC.sup.T311I, 2 Peters- copies of asd, 2 copies of dapA, 2 Wendisch copies of dapB, 2 copies of ddh, 2 and copies of lysA, 2 copies of lysE, Wendisch, in-frame deletion of prophages CGP1 2016 (cg1507-cg1524), CGP2 (cg1746- cg1752), CGP3 (cg1890-cg2071), in-frame deletion of sugR (cg2115) and ldhA (cg3219) DECA LYS1 crtR deletion mutant of this work GRLys1ΔsugRΔldhA DECA LYS2 DECA LYS1 derivative with genome this work integration of the artificial operon crtE, crtB, crt1 under control of the P.sub.tuf promoter DECA-BETA LYS DECA LYS2 derivative with genome this work integration of crtY.sub.Pa under control of the P.sub.tuf promoter LYC LYS crtY.sub.eY.sub.fEb deletion mutant of DECA this work LYS2 BETA LYS LYC LYS derivative with genome this work integration of crtY.sub.Pa under control of P.sub.tuf Promoter CAN LYS BETA LYS with plasmid this work pSH1_crtW1.sub.Fp ZEA LYS BETA LYS with plasmid this work pECXT_crtZ.sub.Fp ASTA LYS BETA4 (pECXT99A_crtZFp)(pSH1- this work crtWFp)
(108) TABLE-US-00008 TABLE 7 Plasmids invention Source or Plasmid/Vector Relevant characteristics reference pk19mobsacB- Km.sup.R, shuttle vector for E. coli and C. (Henke et ΔcrtR glutamicum to construct deletions and al., 2016) insertions in C. glutamicum; contains a construct to delete crtR pk19mobsacB-Int- Km.sup.R, shuttle vector for E. coli and C. (Henke et crtEBI glutamicum to construct deletions and al., 2016) insertions in C. glutamicum; contains a construct to insert the artificial operon crtEBI under control of P.sub.tuf promoter, additional ribosome binding site in front of crtB for the integration into the CGP2 cured region of C. glutamicum pk19mobsacB- Km.sup.R, shuttle vector for E. coli and C. (S. A. E. ΔcrtYEb glutamicum to construct deletions and Heider et insertions in C. glutamicum; contains a al., 2014) construct to delete crtY.sub.eY.sub.fEb pk19mobsacB-Int- Km.sup.R, shuttle vector for E. coli and C. (Henke et crtY.sub.Pa glutamicum to construct deletions and al., 2016) insertions in C. glutamicum; contains a construct to insert crtY of Pantoea ananatis under control of P.sub.tuf promoter into the cgp1 cured region of C. glutamicum pSH1_crtW1.sub.Fp Km.sup.R, P.sub.tuf, pHM519 oriV.sub.Cg, C. (Henke et glutamicum/E. coli expression shuttle al., 2016) vector, constitutive expression of crtW from Fulvimarina pelagi with artificial ribosome binding site PEC-XT99A_crtZ.sub.Fp Tet.sup.R, P.sub.trclacl.sup.q, pGA1 oriV.sub.Cg, C. (Henke et (pECXT_crtZ.sub.Fp) glutamicum/E. coli expression shuttle al., 2016) vector, IPTG-inducible expression of crtZ from Fulvimarina pelagi with artificial ribosome binding site
Cultivation:
(109) If not mentioned otherwise, Escherichia coli was cultivated in LB at 37° C. with an agitation of 180 rpm and Corynebacterium glutamicum was cultivated in BHIS at 30° C. and 120 rpm.
(110) Plasmid Isolation:
(111) To isolate plasmids from E. coli bacteria cells, 20 ml of an overnight culture were processed according to the GeneJET Plasmid Miniprep kit from Thermo Scientific. To elute the plasmids, the elution buffer was substituted with 50 μl MilliQ. Subsequently the concentration was determined by Spectrophotometer ND-1000 (Nanodrop).
(112) Competent E. coli Cells:
(113) A colony of E. coli S17-1 was cultivated in 5 ml LB and incubated overnight at 37° C. Two 500 ml flasks with 50 ml LB were inoculated with 1 ml of the overnight culture. The flasks were incubated for 2-3 hours until they reached an OD600 of 0.2-0.4. Afterwards the cultures were transferred to 50 ml Falcon tubes and incubated on ice for 10 minutes. Thereafter the cells were centrifuged for 20 minutes at 4000 rpm and 4° C. in a Centrifuge 5810 R (Eppendorf). The cells were washed in 30 ml ice-cooled RF1-Buffer and centrifuged for 7 minutes at 4000 rpm and 4° C. Afterwards the pellets were resuspended in 8 ml ice-cooled RF2-Buffer and incubated on ice for 10-15 minutes. 100 μl aliquots were frozen in liquid nitrogen and stored at −80° C.
(114) Transformation in E. coli Via Heat-Shock:
(115) Competent E. coli cells were thawed on ice. 50 ng plasmid DNA was added to the cells and incubated on ice for 15 minutes. Thereafter the heat-shock at 42° C. for 1.5 minutes occurred. Afterwards the cells were incubated on ice for 1 minute. 700 μl of LB medium was added. Cells were regenerated for 45-60 minutes at 37° C. and 450 rpm in a Thermomixer comfort (Eppendorf). The cells were plated on LB plates with the required antibiotics and incubated at 37° C.
(116) Colony-PCR:
(117) Colony-PCR was performed to verify if the transformation of a plasmid into a bacteria cell or a genomic integration/deletion was successful. For this process Taq-polymerase from NEB was used. For each PCR a forward and a reverse primer were added to the reaction mix, the list which primers were used for which plasmid or strain is listed in Table 5. The components of a single reaction mix and the parameters of the program for the PCR cycler can be seen in Table 8 and 9. To perform the PCR the Thermocycler FlexCycler or Thermocycler T3000 (Biometra) was used. After each PCR the samples were analysed by gel electrophoresis.
(118) TABLE-US-00009 TABLE 8 A single reaction mix for colony PCR. Components and used amounts Taq DNA polymerase reaction mix Components Volume [μl] MilliQ 15.5 10 × Thermo polymerase buffer 2 dNTPs (10 mM) 0.4 Forward primer (10 mM) 1 Reverse Primer (10 mM) 1 Taq-polymerase 0.04 Total volume 20
(119) TABLE-US-00010 TABLE 9 PCR program used for colony PCR with the rmocycler Colony-PCR program Initial denaturation 95° C. 5 min Denaturation 95° C. 20 s Annealing 58-65° C. 25 s Elongation 72° C. 60 s/kb 35 cycles Final Elongation 72° C. 5 min Storage 4° C. ∞
Gel Electrophoresis:
(120) To separate the DNA fragments on the basis of their size, gel electrophoresis was performed with 1% agarose gel (peqGOLD Universal Agarose, peqlab). Each sample was mixed with 5 μl 6× triple dye loading buffer and 9 μl of the sample were loaded on the gel. As a standard to compare the sizes of the fragments, 5 μl 1 kb ladder (NEB) were used. The gel was run at 100 V for 20-30 minutes and stained in an ethidium bromide bath (400 μl 1% ethidium bromide solution in 700 ml H2O) for 5-9 minutes. To analyse the gels, a UV transilluminator (UVP) was used.
(121) PCR Clean-Up:
(122) The kit DNA, RNA, and protein purification (Macherey-Nagel, Düren, Germany) was used to purify the amplified DNA fragments. The steps were performed according to the instructions, but instead of using the elution buffer of the kit, the fragments were eluted with 15 μl MilliQ. The concentration was measured by Spectrophotometer ND-1000 (Nanodrop) and the fragments were sequenced.
(123) Conjugation:
(124) Genomic integrations/deletions in the chromosome of C. glutamicum were carried out via homologous recombination events. With this method, genomic regions can be deleted or foreign DNA can be integrated by introducing the suicide vector pk19mobsacB (
(125) Two pre-cultures were inoculated, one with cells of the donor (E. coli S17-1 pk19mobsacB) in 50 ml LB with Km.sup.25 and one with cells of the recipient (C. glutamicum) in 50 ml BHIS. The flasks were incubated overnight. Two flasks with fresh media and appropriate antibiotics were inoculated, both to an OD.sub.600 of 0.1 and incubated until they reached an OD.sub.600 of 1-1.5. 50 ml of the recipient were transferred to a 50 ml Falcon tube and centrifuged for 10 minutes at 4000 rpm (Centrifuge 5810 R, Eppendorf). The cells were resuspended with 5 ml BHIS and aliquots of 800 μl were incubated at 50° C. for 9 minutes (Thermomixer comfort, Eppendorf).
(126) Two 15 ml Falcon tubes, each with 10 ml of the donor culture, were harvested and centrifuged for 10 minutes at 4000 rpm. The pellets were resuspended in 1 ml LB.
(127) 200 μl of the donor were added to each aliquot of the recipient and inverted gently. The tubes were centrifuged for 3 minutes at 3000 rpm (Centrifuge 5424, Eppendorf) and the pellets were resuspended by stirring carefully with a 1 ml pipette tip.
(128) Sterile cellulose acetate or cellulose nitrate filters were placed onto BHIS plates and the cell suspensions were pipetted onto the filters. The plates were incubated for 20 minutes under the sterile bench (Safe 2020 Biological Safety Cabinet, Thermo Scientific, Massachusetts, USA), in which the lids were left open for 12 minutes. Afterwards the plates were incubated at 30° C. for at least 20 hours. Then the filters were transferred to 15 ml Falcon tubes to remove the cells from the filters with 500 μl BHIS. The cell suspensions were centrifuged for 4 minutes at 4000 rpm and the supernatants were discarded. The pellets were resuspended and plated onto BHIS Km.sup.15 NaI.sup.50 plates and incubated for two days at 30° C. Colonies which grew on the plates were picked onto a fresh BHIS Km.sup.25 NaI.sup.50 plate to dispose of E. coli cells and were incubated overnight at 30° C. The new colonies were picked parallel, first onto a BHIS Km.sup.25 and then onto a BHIS Km.sup.25+10% sucrose plate and incubated overnight. Six Colonies which grew on BHIS Km.sup.25 but not on Km.sup.25+10% sucrose were streaked on BHIS 10% sucrose plates with a glass pipette and incubated for 2 days for the second recombination to occur. Colonies from these plates were parallel picked onto BHIS Km.sup.25 and BHIS 10% sucrose and incubated overnight. Cells which grew on BHIS 10% sucrose but not on BHIS Km.sup.25 were used to perform a colony-PCR to verify that the deletion or insertion was successful.
(129) Competent C. glutamicum Cells:
(130) A pre-culture of 5 ml BHIS with appropriate antibiotics and cell material of C. glutamicum was incubated overnight at 30° C. and an agitation of 120 rpm. Two flasks with 50 ml fresh BHIS with required antibiotics were inoculated with 1 ml of the pre-culture and incubated until they reached an OD600 of 0.6. To each flask, Ampicillin [1.5 μg/ml] was added and they were incubated for 1-1.5 hours. Afterwards the suspensions were transferred to 50 ml Falcon tubes and centrifuged for 7 min at 4000 rpm and 4° C. in a Centrifuge 5810 R (Eppendorf). The pellets were washed three times with 30 ml ice-cooled EPB1-Buffer and centrifuged as performed before. Thereafter the pellets were resuspended in 750 μl ice-cooled EPB2-Buffer and incubated for 10-15 minutes on ice. Aliquots of 150 μl were stored at −80° C.
(131) Transformation in C. glutamicum Via Electroporation:
(132) Competent C. glutamicum cells were thawed on ice. 500 ng of purified plasmid DNA was added to the cells and incubated for 15 minutes on ice. The cells were transferred into a pre-cooled sterile electroporation cuvette. The electroporation was performed with 2.5 kV, 200Ω and 25 μF with Gene Pulser Xcell™ (Biorad). Immediately after the electroporation the cells were transferred to a tube with 750 μl BHIS which was preheated to 46° C. The heat shock was performed at 46° C. for 6 minutes. Afterwards the regeneration occurred at 30° C. for 60-90 minutes with an agitation of 450 rpm in a Thermomixer comfort (Eppendorf). The cells were plated onto a BHIS plate with the required antibiotics and incubated for two days at 30° C.
(133) Growth Experiment with C. glutamicum:
(134) A pre-culture with 20 ml BHIS, 50 mM glucose, appropriate antibiotics and cell material was incubated overnight at 30° C. and 120 rpm. Cells for an OD600 of 1.1 in 50 ml were harvested and centrifuged for 7 min at 4000 rpm in a Centrifuge 5810 R (Eppendorf). Afterwards they were washed with 20 ml basic CGXII. To prepare the CGXII medium, 100 mM glucose, 1 mM IPTG and appropriate antibiotics were added. The pellet was resuspended with 50 ml of the CGXII medium and transferred to a 500 ml flask. The flask was incubated for 24-48 hours with an agitation of 120 rpm. The OD600 of the culture was measured at different time points. After 24, 32 or 36 hours the glucose content in the flask was measured with a glucose test strip DIABUR Test 5000 (Roche Diabetes Care Deutschland GmbH, Mannheim, Germany). At the end of the growth experiment, 2×1 ml from the flask were transferred to 2 ml Eppendorf tubes and centrifuged for 10 minutes at max rpm in a Centrifuge 5242 (Eppendorf). The supernatant was transferred to a 1.5 ml tube. The pellet and the supernatant were stored at −20° C. until further use.
(135) Carotenoid Extraction:
(136) The pellet was thawed at room temperature for 5 minutes and resuspended in 800 μl of methanol:acetone (7:3) with 0.05% BHT (2, 6-Di-tert-Butyl-4-methylphenol). The tube was incubated for 15 minutes in a 60° C. waterbath 3042 (Köttermann), while it was shaken every 5 minutes. After the incubation, the tube was centrifuged for 10 minutes at max rpm (Centrifuge 5424, Eppendorf). The supernatant was transferred to a fresh 2 ml tube. If the pellet was not colourless, another extraction round was performed. The supernatant was centrifuged for 15 minutes at max rpm and transferred to a fresh 2 ml tube. 500 μl were analysed by HPLC.
(137) Preparation of samples for amino acid analysis: The frozen supernatants were thawed at room temperature. Then they were centrifuged for 15 minutes at max rpm in a Centrifuge 5424 (Eppendorf) to spin down possible remaining cells and residues.
(138) 49 ml Borat Buffer were mixed with 0.5 ml 10 mM asparagine, 495 μl of this solution were transferred to a vial and 5 μl of the sample were added. Standards were prepared as prescribed in Table 10. The prepared sample and the standards were analysed by HPLC.
(139) TABLE-US-00011 TABLE 10 Preparation of standards of one amino acid. In each set of standards, there are H.sub.2O, asparagine as internal standard and one amino acid. In this case it is either glutamate or lysine. The total volume of each vial is 495 μl. Amino acid Volume [μl] (10 mM) 50 μM 100 μM 150 μM 200 μM 250 μM 300 μM 350 μM 400 μM Asparagine 5 5 5 5 5 5 5 5 Glutamate 2.5 5 7.5 10 12.5 15 17.5 20 Lysine 2.5 5 7.5 10 12.5 15 17.5 20 H.sub.2O 492.5 490 487.5 485 482.5 480 477.5 475 Total 495
(140) High performance liquid chromatography: The carotenoid extracts and supernatants with amino acids were analysed by high performance liquid chromatography (HPLC) using the Agilent 1200 series HPLC system (Agilent Technologies).
(141) Automatic precolumn derivatization with ortho-phthaldialdehyde (Georgi, Rittmann and Wendisch, 2005) was used to determine the amino acids. The column system consisted of a precolumn (LiChrospher 100 RP18 EC-5μ (40×4 mm), CS Chromatographie Service GmbH, Langerwehe, Germany) and a reversed-phase main column (LiChrospher 100 RP18 EC-5μ (125×4 mm), CS Chromatographie Service GmbH) which were used to separate the amino acids. A fluorescence detector (FLD G1321A, 1200 series, Agilent Technologies) was used to detect the amino acids (Pérez-Garcia, Peters-Wendisch and Wendisch, 2016) with excitation at 230 nm and emission at 450 nm (Peters-Wendisch et al., 2014). .sub.L-Asparagine was used as internal standard to quantify the amount of amino acid (Pérez-Garcia, Peters-Wendisch and Wendisch, 2016). The buffers used for this process were sodium acetate 0.1 M, pH 7.1, and methanol in a mixture of 4:1 (unpublished method from Pérez-Garcia 2016).
(142) To determine the carotenoids a diode array detector (DAD) was used to detect the UV/visible (Vis) spectrum. To quantify the carotenoids, every maximum of the extracted wavelength chromatogram at λ.sub.max 470 nm was integrated and the respective profiles of UV/Vis were analysed. For the standard calibration curve samples with different carotenoids and various concentrations were measured. The carotenoids were lycopene (Sigma-Aldrich), β-carotene (Sigma-Aldrich), canthaxanthin (Sigma-Aldrich), zeaxanthin (Sigma-Aldrich) and astaxanthin (Sigma-Aldrich). The stock solution [1 mg/ml] was dissolved in dichloromethane and different amounts of the solution were diluted in methanol:acetone (7:3) with 0.05% BHT to prepare the standards (Henke et al., 2016).
(143) 50 μl of the samples were run through a precolumn (LiChrospher 100 RP18 EC-5μ, (40×4 mm), CS-Chromatographie) and a reversed-phase main column (LiChrospher 100 RP18 EC-5, (125×4 mm), CS-Chromatographie). Buffers used were methanol (A) and methanol:water (9:1) (B). The gradient started with 0% of B at 0 minutes, increasing to 100% of B at 10 minutes and 100% of B at 32.5 minutes with a flow rate of 1.5 ml/min (Henke, unpublished method from Henke 2016).
(144) Strain Construction by Conjugation and Transformation:
(145) To construct new strains by conjugation, the various pk19mobsacB plasmids were transferred into S17-1 cells. The strain GRLys1ΔsugRΔIdhA was used as the initial strain. The first step was to delete the gene crtR (cg0725) which encodes a putative transcriptional regulator (Pfeifer et al., 2016) with the plasmid pk19mobsacB-ΔcrtR to construct the strain DECA LYS1 (GRLys1ΔsugRΔIdhAΔcrtR) (
(146) The gene crtY.sub.Pa was integrated into DECA LYS2 using the plasmid pk19mobsacB-Int-crtY.sub.Pa constructing DECA-BETA LYS (GRLys1ΔsugRΔIdhAΔcrtR-IntcrtEBI-IntcrtY.sub.Pa). To verify the genomic modification, the primers NW31 OP2-E and NW32 OP2-F were used for colony-PCR.
(147) Starting from DECA LYS2, the genes crtY.sub.eY.sub.fEb (=crtY.sub.e crtY.sub.f and crtEb) were deleted creating the strain LYC LYS (GRLys1ΔsugRΔIdhAΔcrtR-IntcrtEBIΔcrtY.sub.eY.sub.fEb). To verify the deletion, the primers crtY-E and crtEb-DelF were used.
(148) The integration of crtY.sub.Pa in LYC LYS led to the strain BETA LYS (GRLys1ΔsugRΔIdhAΔcrtR-IntcrtEBIΔcrtY.sub.eY.sub.fEb-IntcrtY.sub.Pa). For this colony-PCR the primers NW31 OP2-E and NW32 OP2-F were used. The strain BETA LYS was used as the initial strain for transformation. The plasmids pSH1_crtW1.sub.Fp and pECXT_crtZ.sub.Fp were isolated from the strains E. coli DH5α pSH1_crtW.sub.Fp and E. coli DH5α pECXT_crtZ.sub.Fp.
(149) The vector pSH1_crtW1.sub.Fp was transferred into the competent BETA LYS cells by electroporation with Gene Pulser Xcell™ (Biorad) constructing the strain CAN LYS. For colony-PCR the standard vector primers for pSH1, PD5 (pSH1-fw) and 582 (pSH1-rv, pEKEx3-rv), were used.
(150) The plasmid pECXT_crtZ.sub.Fp was transferred into BETA LYS to create the strain ZEA LYS. To verify via colony-PCR the standard vector primers pECXT-fw and pECXT-rv, were used.
(151) After confirmation that the transformations were successful, the vector pECXT_crtZ.sub.Fp was transferred into CAN LYS resulting in ASTA LYS1.
(152) The plasmid pSH1_crtW1.sub.Fp was transferred into ZEA LYS to construct ASTA LYS2. The verification was made with the standard primers for each new added plasmid.
(153) Cultures for Production of Carotenoids and Glutamate:
(154) To produce glutamate in C. glutamicum there need to be specific conditions, e.g. biotin limitation or addition of ethambutol dihydrochloride (following called ethambutol or EMB). The strains tested were MB001, MB001ΔcrtR and ASTA1. Each strain was grown in different conditions (i) CGXII medium without further addition, serves as control, (ii) CGXII medium with EMB [50 μg/ml], (iii) biotin limitation. The pre-cultures were prepared with 50 ml BHIS, 50 mM glucose, appropriate antibiotics and cell material. They were incubated overnight.
(155) (i) Control: Cell suspension to inoculate a flask with 50 ml to an OD.sub.600 of 1.1 were centrifuged for 7 minutes at 4000 rpm and 4° C. (Centrifuge 5810 R, Eppendorf). The cells were resuspended in basic CGXII and centrifuged. The pellet was resuspended in CGXII medium with 100 mM glucose, appropriate antibiotics and 50 mM IPTG if required.
(156) (ii) EMB: The main culture was prepared as described in (i) but 50 μg/ml EMB were added to the flask before incubation.
(157) (iii) Biotin limitation: A second pre-culture was prepared with CGXII, 100 mM glucose, appropriate antibiotics and 50 mM IPTG if required. But instead of adding biotin with a concentration of 0.2 mg/ml, the concentration was 0.01 mg/ml. The flask was incubated overnight. The main culture was prepared as described in (i) with a concentration of biotin of 1 μg/ml.
(158) The flasks were incubated for 48 hours at 30° C. with an agitation of 120 rpm.
(159) Cultures for Production of Carotenoids and Lysine:
(160) Pre-cultures of the strains GRLys1ΔsugRΔIdhA, DECA LYS1, DECA LYS2, DECA-BETA LYS, LYC LYS, BETA LYS, CAN LYS, ZEA LYS and ASTA LYS were inoculated with 20 ml BHIS, 50 mM glucose (pre-cultivation) and appropriate antibiotics. The flasks were incubated overnight at 30° C. at 120 rpm. Cell suspension to inoculate a flask with 50 ml of the same medium (main cultivation) to an OD.sub.600 of 1.1 were centrifuged for 7 minutes at 4000 rpm and 4° C. (Centrifuge 5810 R, Eppendorf). The cells were washed with basic CGXII. The pellet was resuspended in CGXII medium with 100 mM glucose, appropriate antibiotics and 50 mM IPTG if required. The flasks were incubated for 48 hours at 30° C. and an agitation of 120 rpm.
(161) Establishment of a platform strain for the coproduction of carotenoids and lysine on the basis of a metabolically optimized lysine producer GRLys1ΔsugRΔIdhA: The strain GRLys1ΔsugRΔIdhA (Unthan et al., 2015) was used as a platform strain to construct the following strains which are able to produce carotenoids and lysine simultaneously.
(162) The almost white colour of GRLys1ΔsugRΔIdhA was changed to a pale yellow, when crtR, the gene encoding for the putative transcriptional regulator of carotenogenesis in C. glutamicum, was deleted, leading to the construction of the strain DECA LYS1 (
(163) Insertion of the artificial operon crtEBI lead to a stronger yellow pigmentation and to the construction of the strain DECA LYS2. The verification of the insertion was done by three colony-PCRs with the primer combinations NW29 Op1-E+crtE-B, NW29 Op1-E+NW30 OP1-F and crtE-Pstl-fw+NW30 OP1-F. This was necessary, as C. glutamicum naturally possesses an operon with the genes crtB and crtI. The combination NW29 and crtE-B lead to a 1,500 bp fragment. The fragment produced with the primers NW29 and NW30 had a size of 6,300 bp, while the combination crtE-fw and NW30 lead to a size of 4,800 bp. The colony-PCR verified the insertion of the artificial operon in the colonies 27, 29, 32 and 41 (
(164) When the lycopene cyclase crtY.sub.Pa (S. A. E. Heider et al., 2014) was integrated into the genome, the colour changed from yellow to orange in the strain DECA-BETA LYS. The fragments without the integrated gene are 2,100 bp while the fragments which contain the integration are about 3,800 bp (
(165) The strain LYC LYS contains the deletion of the genes crtYEb, encoding for the lycopene elongase and the C50 ε-cyclase (Krubasik, Kobayashi and Sandmann, 2001), leading to the accumulation of lycopene in the strain LYC LYS. The colonies 1, 12, 16, 21 and 22 among others had the size of 1,050 bp (
(166) BETA LYS had an orange pigmentation due to the production of the carotenoid β-carotene by the insertion of the gene crtY.sub.Pa. The DNA fragment had a size of 3,800 bp and the colonies 8, 11, 29 and 33 were used to make glycerol stocks (
(167) The transformation of the plasmids pSH1_crtW1.sub.Fp and pECXT_crtZ.sub.Fp lead to the synthesis of canthaxanthin in CAN LYS (
(168) The strains produced carotenoids and the values were analysed by HPLC (
(169) The strain GRLys1ΔsugRΔIdhA produced the highest amount of lysine, 24.79±1 mM (
(170) All in all, the simultaneous production of C40/C50 carotenoids and the amino acid lysine in one cultivation is possible with the strains used and constructed in this work.
(171) TABLE-US-00012 TABLE 11 Carotenoid production in growth experiment for carotenoids and lysine after 48 hours. The various strains with their corresponding carotenoids are listed, as well as the final OD.sub.600 after 48 hours and the production of the carotenoids in different units. Carotenoid Strain Carotenoid Final OD mg/g CDW mg/l mg/l*h GRLYS1ΔsugRΔldh Decaprenoxanthin 10.90 ± 0.26 0.05 ± 0 0.14 ± 0.00 >0.01 ± 0.00 DECA LYS1 Decaprenoxanthin 10.00 ± 0.49 1.41 ± 0.14 3.52 ± 0.27 0.07 ± 0.01 DECA LYS2 Decaprenoxanthin 13.00 ± 1.04 1.51 ± 0.12 4.94 ± 0.80 0.10 ± 0.02 DECA-BETA LYS Decaprenoxanthin 14.17 ± 0.47 0.54 ± 0.05 1.93 ± 0.20 0.04 ± 0.00 DECA-BETA LYS 3-carotene 14.17 ± 0.47 3.19 ± 0.31 11.26 ± 0.85 0.23 ± 0.02 LYC LYS Lycopene 14.60 ± 0.85 0.67 ± 0.1 2.44 ± 0.22 0.05 ± 0.00 BETA LYS 3-carotene 12.61 ± 0.65 3.77 ± 0.73 11.89 ± 2.30 0.25 ± 0.05 CAN LYS Canthaxanthin 11.45 ± 0.79 0.92 ± 0.11 2.62 ± 0.28 0.05 ± 0.01 ZEA LYS Zeaxanthin 11.76 ± 0.30 0.34 ± 0.02 0.99 ± 0.06 0.02 ± 0.00 ASTA LYS Astaxanthin 13.27 ± 1.01 0.84 ± 0.11 2.76 ± 0.21 0.06 ± 0.00
(172) TABLE-US-00013 TABLE 12 Production of lysine in the growth experiment for carotenoids and lysine. The strains, final OD.sub.600 and the lysine production in different units after 48 hours are listed. Strain Final OD Lysine [mM] Lysine [mg/l] GRLYS1ΔsugRΔldh 10.90 ± 0.26 24.79 ± 1.00 3624.31 ± 146.38 DECA LYS1 10.00 ± 0.49 16.16 ± 1.28 2362.94 ± 187.53 DECA LYS2 13.00 ± 1.04 18.61 ± 1.37 2720.20 ± 200.56 DECA-BETA LYS 14.17 ± 0.47 18.79 ± 0.19 2746.98 ± 28.43 LYC LYS 14.60 ± 0.85 16.14 ± 1.43 2359.92 ± 209.19 BETA LYS 16.57 ± 0.87 14.33 ± 0.46 2094.85 ± 67.44 CAN LYS 11.45 ± 0.79 14.40 ± 0.41 2104.47 ± 59.89 ZEA LYS 11.76 ± 0.30 17.29 ± 0.62 2527.49 ± 91.16 ASTA LYS 13.27 ± 1.01 15.93 ± 1.74 2328.24 ± 253.88
Example 2: Repetition of Experiments Leads to Similar Results
(173) The experiments were performed as described in Example 1 unless stated otherwise using the strains described in Example 1.
(174) First, the production of carotenoids was measured in different C. glutamicum strains. Table 13 shows the results. The highest amount of carotenoids was produced in the BETALYS strain with 11.6±0.94 mg/l carotenoids (β-carotene). ASTALYS showed a production of 3.15±0.58 mg/l astaxanthin, a value even higher than the one shown in Table 11 of Example 1.
(175) TABLE-US-00014 TABLE 13 Carotenoid production in lysine-coproducing C. glutamicum strains. Titer, yield and productivity of carotenoids from cultivation in CGXII (100 mM glucose) and 32 h. Decaprenoxanthin is given as β-carotene equivalents (GRLys1ΔsugRΔldhA and DECALYS2), lycopene (LYCLYS), β-carotene (BETALYS), zeaxanthin (ZEALYS, canthaxanthin (CAN LYS) and astaxanthin (ASTALYS). Means of three biological triplicates and standard deviations are given. Vol. prod. Yield Strain CDW [g/L] [mg/g CDW] [mg/L] [mg/L/h] [mg/g] GRLYS1ΔsugRΔldhA 3.48 ± 0.12 0.06 ± 0.03 0.20 ± 0.09 0.01 ± 0.00 0.01 ± 0.00 DECALYS1 3.58 ± 0.18 1.70 ± 0.11 6.10 ± 0.38 0.19 ± 0.01 0.34 ± 0.02 LYCLYS 4.02 ± 0.11 0.68 ± 0.11 2.74 ± 0.49 0.09 ± 0.02 0.15 ± 0.03 BETALYS 2.93 ± 0.13 3.96 ± 0.17 11.60 ± 0.94 0.36 ± 0.03 0.64 ± 0.05 ZEALYS 2.65 ± 0.10 0.49 ± 0.02 1.29 ± 0.02 0.04 ± 0.00 0.07 ± 0.00 CANLYS 2.69 ± 0.14 0.84 ± 0.05 2.26 ± 0.04 0.07 ± 0.00 0.13 ± 0.00 ASTALYS 3.16 ± 0.09 1.00 ± 0.18 3.15 ± 0.58 0.10 ± 0.02 0.17 ± 0.03
(176) The strain GRLys1ΔsugRΔIdhA produced the highest amount of lysine, 23.61±0.43 mM. The other strains produced less lysine, varying from 12.37±0.65 to 19.08±1.17 mM. The highest amount, apart from GRLys1ΔsugRΔIdhA, was produced by DECALYS1 with a concentration of 19.08±1.17 mM lysine. The data are listed in Table 14. ASTALYS produced lysine to a concentration of 16.2±1.31 mM, a value that is comparable to the one presented in Table 12 of Example 1.
(177) TABLE-US-00015 TABLE 14 Lysine production in carotenoid-coproducing C. glutamicum strains. Biomass, titers, volumetric productivity and yield are shown as mean values. Lysine Lysine Vol. prod. Yield Strain CDW [g/L] [mM] [g/L] [g/L/h] [g/g] GRLYS1ΔsugRΔldhA 3.48 ± 0.12 23.61 ± 0.43 3.45 ± 0.06 0.11 ± 0.00 0.19 ± 0.00 DECALYS1 3.58 ± 0.18 19.08 ± 1.17 2.79 ± 0.17 0.09 ± 0.01 0.15 ± 0.01 LYCLYS 4.02 ± 0.11 15.57 ± 0.46 2.27 ± 0.07 0.07 ± 0.00 0.13 ± 0.00 BETALYS 2.93 ± 0.13 12.37 ± 0.65 1.81 ± 0.10 0.06 ± 0.00 0.10 ± 0.01 ZEALYS 2.65 ± 0.10 16.92 ± 0.34 2.47 ± 0.07 0.08 ± 0.00 0.14 ± 0.00 CANLYS 2.69 ± 0.14 14.46 ± 0.94 2.11 ± 0.14 0.07 ± 0.00 0.12 ± 0.01 ASTALYS 3.16 ± 0.09 16.20 ± 1.31 2.37 ± 0.19 0.07 ± 0.00 0.13 ± 0.01
(178) These results further demonstrate that the simultaneous production of C40/C50 carotenoids and the amino acid lysine in one cultivation is possible with the strains used and constructed in this work.
Example 3: Fed-Batch Fermentation of C. glutamicum ASTALYS
(179) A bioreactor with a total volume of 20 L and a working volume of 15 L was used (MBR Bioreactor AG, Switzerland). It was equipped with three six-bladed Rushton turbines and four baffles. Operating pH and oxygen saturation in the medium (pO.sub.2) were followed by electrodes (Ingold, Germany). By automated addition of KOH (4 M) and phosphoric acid (10%) pH was kept at 7.0. Samples for quantification were taken by an autosampler and cooled down to 4° C. until use. Initial volume of the fermentation was 12 L with additional feeding volume of 3 L. Fermentation was carried out with 0.4 bar overpressure and aeration rate was set to 12 NL min.sup.−1. Stirrer speed was regulated in a cascade to maintain the oxygen saturation at 60% (Pérez-García et al., 2016). Antifoam was added manually to avoid foaming by the use of Struktol (1:10). The feeding profile was activated when the pO.sub.2 signal reached above 60% for the first time and stopped when it fell below 60%. Feed was pumped with 0.1 g min.sup.−1 resulting in low sugar concentrations during the whole feeding-phase and an oscillating pO.sub.2 signal around 60%. Moreover a cascade was included in the fermentation allowing a stirrer speeding up when pO.sub.2 fell below 30% until pO.sub.2 of 60% was reached again. The maximum stirring speed was set to 500 min.sup.−1 (Pérez-García et al., 2016). The process was inoculated with the cell pellet of 600 ml of an overnight culture grown at 30° C. and 120 rpm on a rotary shaker in complex medium containing 13.5 g L.sup.−1 soypeptone, 7 g L.sup.−1 yeast extract, 2.5 g L.sup.−1 NaCl, 2.3 g L.sup.−1 K.sub.2HPO.sub.4, 1.5 g L.sup.−1 KH.sub.2PO.sub.4, 0.25 g L.sup.−1 MgSO.sub.4 7H.sub.2O and 15 g L.sup.−1 D-glucose. The fermentation was performed in the same medium as for the pre-cultivation, however 20 g L.sup.−1 D-glucose were used. Feed-medium consisted of 400 g L.sup.−1 D-glucose as well as 232 g L.sup.−1 (NH.sub.4).sub.2SO.sub.4 (autoclaved separately) (Pérez-García et al., 2016).
(180) Coproduction of L-lysine and astaxanthin by metabolically engineered C. glutamicum strain ASTALYS was tested in a 20 L fermenter with a working volume of 15 L (
Example 4: Alternative Carbon Sources for Coproduction of β-Carotene and L-Lysine
(181) In order to test the possibility to coproduce carotenoids, such as β-carotene, with L-lysine from alternative carbon sources, C. glutamicum strain BETALYS was transformed with plasmids allowing for growth with xylose and arabinose, respectively: For the use of arabinose as carbon source, the strain was additionally transformed with the araBAD operon from E. coli (b0061-b0063) encoding for arabinose isomerase (AraA, SEQ ID NO: 87), ribulokinase (AraB, SEQ ID NO: 88) and ribulose-5-phosphate-4-epimerase (AraD, SEQ ID NO: 89). For xylulose as carbon source, the strain was transformed with xylose isomerase xylA from Xanthomonas campestris (XCC1758, SEQ ID NO: 90) and xylulokinase xylB from C. glutamicum (cg0147, SEQ ID NO: 91). Cells were grown in CGXII minimal medium with 10 g/L of either glucose, arabinose or xylose as sole carbon and energy source. The empty vector control strain BETALYS(pVWEx1) produced around 6 mg/L β-carotene and 1.7 g/L of L-lysine from glucose corresponding to yields of 0.6 mg/g and 0.17 g/g, respectively (
(182) Coproduction was achieved from both alternative carbon sources (Table 15). Production of β-carotene and L-lysine was decreased when arabinose (BETALYS (pVWEx1-araBAD)) was used as substrate. However, still 4.5 mg/L β-carotene and 1.2 g/L L-lysine were produced with yields of 0.45 mg/g and 0.12 g/g. With xylose as sole carbon source (BETALYS (pVWEx1-xalAb)), titers for the secreted and the cell-bound product were similar to cultivations with glucose as sole carbon source. With xylose, β-carotene titers of around 7 mg/L (corresponding to a yield of 0.7 mg/g xylose) and L-lysine titers of around 1.5 g/L (yield of 0.15 g/g) were obtained.
(183) TABLE-US-00016 TABLE 15 Coproduction of β-carotene and lysine overproducing C. glutamicum strains from non-food competitive substrates. Titers are shown as mean values. Strain β-carotene [mg/L] Lysine [g/L] BETALYS (pVWEx1) 6.0 ± 0.4 1.7 ± 0.1 BETALYS (pVWEx1-araBAD) 4.5 ± 0.3 1.2 ± 0.01 BETALYS (pVWEx1-xylAB) 7.0 ± 0.2 1.5 ± 0.01
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