CPMV enhancer elements
11884929 ยท 2024-01-30
Assignee
Inventors
Cpc classification
C12N7/045
CHEMISTRY; METALLURGY
C12N15/8251
CHEMISTRY; METALLURGY
International classification
Abstract
An expression enhancer comprising a CPMV 5UTR nucleotide sequence consisting of X nucleotides (CMPVX), where X=160, 155, 150, or 114 of SEQ ID NO:1, or consisting of a nucleotide sequence comprising from about 80% to 100% sequence similarity with CMPVX, where X=160, 155, 150, or 114 of SEQ ID NO:1 SEQ ID NO:1 is provided. The expression enhancer may further comprise a stuffer sequence fused to the 3 end of the 5UTR nucleotide sequence (CMPVX+, where X=160, 155, 150, or 114 of SEQ ID NO:1). The stuffer sequence may comprise one or more plant kozak sequences. Plants comprising the expression enhancer and methods using the expression enhancer are also described
Claims
1. A nucleic acid molecule comprising: a first portion consisting of nucleotides 1-160 of SEQ ID NO:1 having a substitution of G115A, a second portion comprising a plant Kozak sequence, a multiple cloning site, or a combination of a plant Kozak sequence and a multiple cloning site, the second portion positioned 3 to the first portion, and a third portion encoding a heterologous protein of interest, the third portion positioned 3 to the second portion, wherein the nucleic acid molecule does not comprise nucleotides 161-509of SEQ ID NO:4.
2. The nucleic acid molecule of claim 1, wherein the second portion is a multiple cloning site.
3. The nucleic acid molecule of claim 1, wherein the second portion is a plant Kozak sequence.
4. The nucleic acid molecule of claim 1, wherein the second portion is a multiple cloning site and a plant Kozak sequence, wherein the multiple cloning site is positioned 3 to the first portion and the plant Kozak sequence is positioned 3 to the multiple cloning site.
5. The nucleic acid molecule of claim 1, wherein the plant Kozak sequence is selected from the group consisting of: TABLE-US-00024 caA(A/C)a; aaA(A/C)a; aa(A/G)(A/C)a; AGAAA; AGACA; AGGAA; AAAAA; AAACA; AAGCA; AAGAA; AAAGAA; and AAAGAA.
6. The nucleic acid molecule of claim 1, wherein the first portion and the second portion together consist of the nucleotide sequence of SEQ ID NO: 2.
7. The nucleic acid molecule of claim 1, wherein the first portion and the second portion together consist of the nucleotide sequence of SEQ ID NO: 75.
8. The nucleic acid molecule of claim 1, wherein the heterologous protein of interest is a viral protein or an antibody.
9. The nucleic acid molecule of claim 8, wherein the viral protein is an influenza hemagglutinin (HA) selected from the group consisting of H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, H16, and influenza type B hemagglutinin.
10. The nucleic acid molecule of claim 9, wherein the influenza hemagglutinin (HA) is a chimeric HA, wherein a native trans-membrane domain of the HA is replaced with a heterologous trans-membrane domain.
11. A plant expression system comprising the nucleic acid molecule of claim 1 or a vector comprising the nucleic acid molecule of claim 1.
12. The plant expression system of claim 11, further comprising a regulatory region operatively linked to the nucleic acid molecule of claim 1.
13. The plant expression system of claim 12, wherein the regulatory region is selected from the group a plastocyanin promoter, a CaMV 35S promoter, a 2x CaMV35S promoter, a CAS promoter, a RbcS promoter, a Ubi promoter, and an actin promoter.
14. The plant expression system of claim 11, wherein the nucleic acid molecule or vector further comprises a comovirus 3 UTR.
15. The plant expression system of claim 11, wherein the nucleic acid molecule or vector further comprises a suppressor of silencing.
16. The plant expression system of claim 15, wherein the suppressor of silencing is selected from the group HcPro and p19.
17. A method of producing a protein of interest in a plant or in a portion of a plant comprising, introducing into the plant or in the portion of a plant the plant expression system of claim 11, and incubating the plant or the portion of a plant under conditions that permit expression of the heterologous protein of interest.
18. A plant or portion of a plant transiently transfected or stably transformed with the plant expression system of claim 11.
19. The nucleic acid molecule of claim 1, wherein the second portion further comprises a linker, a polylinker, a recombination site, or a combination thereof.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
(1) These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein:
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DETAILED DESCRIPTION
(25) The present invention relates to the expression of proteins of interest in plants. The present invention also provides methods and compositions for the production of proteins of interest in plants.
(26) In the description that follows, a number of terms are used extensively, the following definitions are provided to facilitate understanding of various aspects of the invention. Use of examples in the specification, including examples of terms, is for illustrative purposes only and is not intended to limit the scope and meaning of the embodiments of the invention herein.
(27) As used herein, the use of the word a or an when used herein in conjunction with the term comprising may mean one, but it is also consistent with the meaning of one or more, at least one and one or more than one. The term about refers to an approximately +/10% variation from a given value. The term plurality, means more than one, for example, two or more, three or more, four or more, and the like.
(28) The present invention provides an expression enhancer comprising a CPMV 5 untranslated region (UTR), CPMVX, comprising X nucleotides of SEQ ID NO:1, where X=160, 155, 150, or 114 of SEQ ID NO:1, or a sequence that comprises between 80% to 100% sequence similarity with CPMVX, where X=160, 155, 150, or 114 of SEQ ID NO:1. This expression enhancer is generally referred to as CPMVX (see
(29) The CPMVX enhancer sequence may further be fused to a stuffer sequence, wherein the CMPVX comprises X nucleotides of SEQ ID NO:1, where X=160, 155, 150, or 114 of SEQ ID NO:1, or a sequence that comprises between 80 to 100% sequence similarity with CPMVX, where X=160, 155, 150, or 114 of SEQ ID NO:1, and the stuffer sequence comprises from 1-100 nucleotides fused to the 3 end of the CMPVX sequence. For example, the stuffer sequence may comprise from about 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, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 nucleotides, or any number of nucleotides therebetween.
(30) If the CMPVX sequence comprises a stuffer fragment, then this expression enhancer may be referred to as CPMVX+(see
(31) The stuffer sequence may be modified by truncation, deletion, or replacement of the native CMPV5UTR sequence that is located 3 to nucleotide 160. The modified stuffer sequence may be removed, replaced, truncated or shortened when compared to the initial or unmodified (i.e. native) stuffer sequence associated with the 5UTR (as described in Sainsbury F., and Lomonossoff G. P., 2008, Plant Physiol. 148: pp. 1212-1218). The stuffer sequence may comprise a one or more restriction sites (polylinker, multiple cloning site, one or more cloning sites), one or more plant kozak sequences, one or more linker sequences, one or more recombination sites, or a combination thereof. For example, which is not to be considered limiting, a stuffer sequence may comprise in series, a multiple cloning site of a desired length fused to a plant kozak sequence. The stuffer sequence does not comprise a nucleotide sequence from the native 5UTR sequence that is positioned 3 to nucleotide 160 of the native CPMV 5UTR, for example nucleotides 161 to 512 as shown in
(32) The expression enhancer CPMVX, or CPMVX+, may be operatively linked at the 5end of the enhancer sequence with a regulatory region that is active in a plant, and operatively linked to a nucleotide sequence of interest at the 3end of the expression enhancer (
(33) Expression systems to produce one or more proteins of interest in a plant using either CMPVX or CPMVX+ are also provided. The expression systems described herein comprise an expression cassette comprising CPMVX, or a sequence that comprises 80% sequence similarity with CPMVX, and optionally, a stuffer sequence fused to CMPVX (CPMVX+). The expression cassette comprising CMPVX or CMPVX+, may further comprise a regulatory region that is active in a plant that is operatively linked to the 5end of the expression enhancer. A nucleotide sequence of interest may be operatively linked to the 3end of the expression cassette so that when introduced within a plant, expression of the nucleotide sequence of interest within a plant host is achieved.
(34) Plant cells, plant tissues, whole plants, inoculum, nucleic acids, constructs comprising nucleotide sequences of interest encoding proteins of interest, expression cassettes or expression systems comprising CPMVX or CPMVX+ as described herein, and methods of expressing a protein of interest in plants are also provided.
(35) With reference to
(36) The nucleotide sequence of interest may be fused (operatively linked) to the enhancer sequence comprising a plant regulatory region, using a variety of approaches. For example, which are not to be considered limiting: 1) A nucleotide sequence of interest encoding a protein of interest may be fused to the 3 end of the expression enhancer immediately after the 5UTR sequence, for example CPMVX, where X=160, 155, 150, 114 nucleotides of SEQ ID NO:1. In this example, the nucleotide sequence of interest is fused to the 5UTR without a multiple cloning site, and the nucleotide sequence of interest may include at its 5 end a plant kozak sequence immediately upstream from an ATG initiation site of the nucleotide sequence of interest (see
(37) The overall result using any of the above methods, is a construct (or expression cassette) comprising a plant regulatory region in operative association (operatively linked) with a CPMV 5UTR sequence comprising nucleotides X, where X=160, 155, 150, 114 of SEQ ID NO:1 (or an enhancer sequence that comprises 80% sequence similarity with CPMV 5UTR sequence), the 3 end of the CPMV 5UTR sequence is fused to the 5 end of a plant kozak sequence, the 3 end of the plant kozak sequence fused and adjacent to the 5 end of the nucleotide sequence of interest comprising an ATG initiation sequence. The construct may, or may not, comprise a multiple cloning site located between the 5UTR and the plant kozak sequence. The construct may further comprise a 3 untranslated region (UTR) sequence, for example, a comovirus 3UTR, or a plastocyanin 3 UTR, and a terminator sequence, for example a NOS terminator, operatively linked to the 3end of the nucleotide sequence of interest (see
(38) A plant expression system comprising a nucleic acid comprising a regulatory region, operatively linked with one or more than one expression enhancer as described herein (e.g. CPMVX), and a nucleotide sequence of interest. is also provided. Furthermore, a nucleic acid comprising a promoter (regulatory region) sequence, operatively linked with an expression enhancer comprising a CPMV 5UTR and a modified or deleted stuffer sequence (e.g. CPMVX+) and a nucleotide sequence of interest is described. The nucleic acid may further comprise a sequence encoding a 3UTR, for example a comovirus 3 UTR, or a plastocyanin 3 UTR, and a terminator sequence, for example a NOS terminator, so that the nucleotide sequence of interest is inserted upstream from the 3UTR.
(39) By operatively linked it is meant that the particular sequences interact either directly or indirectly to carry out an intended function, such as mediation or modulation of expression of a nucleic acid sequence. The interaction of operatively linked sequences may, for example, be mediated by proteins that interact with the operatively linked sequences.
(40) Expression enhancer(s), enhancer sequence(s) or enhancer element(s), as referred to herein, include sequences derived from, or that share sequence similarity with, portions of the CPMV 5UTR from the RNA-2 genome segment. An enhancer sequence can enhance expression of a downstream heterologous open reading frame (ORF) to which they are attached.
(41) The term 5UTR or 5 untranslated region or 5 leader sequence refers to regions of an mRNA that are not translated. The 5UTR typically begins at the transcription start site and ends just before the translation initiation site or start codon (usually AUG in an mRNA, ATG in a DNA sequence) of the coding region. The length of the 5UTR may be modified by mutation for example substitution, deletion or insertion of the 5UTR. The 5UTR may be further modified by mutating a naturally occurring start codon or translation initiation site such that the codon no longer functions as start codon and translation may initiate at an alternate initiation site.
(42) The 5UTR from nucleotides 1-160 of the CPMV RNA-2 sequence (SEQ ID NO: 1), starts at the transcription start site to the first in frame initiation start codon (at position 161), which serve as the initiation site for the production of the longer of two carboxy coterminal proteins encoded by a wild-type comovirus genome segment. Furthermore a third initiation site at (or corresponding to) position 115 in the CPMV RNA-2 genomic sequence may also be mutated, deleted or otherwise altered. It has been shown that removal of AUG 115 in addition to the removal of AUG 161 enhances expression when combined with an incomplete M protein (Sainsbury and Lomonossoff, 2008, Plant Physiology; 148: 1212-1218; WO 2009/087391; which are incorporated herein by reference).
(43) The expression enhancer may comprise a CPMV 5 untranslated region (UTR) comprising nucleotides from X of SEQ ID NO:1, where X=160, 155, 150, or 114 of SEQ ID NO:1 (CPMVX), or a sequence that comprises 80% sequence similarity with CPMVX (where X=160, 155, 150, or 114 of SEQ ID NO:1; see
(44) The CPMVX enhancer sequence may also be fused to a stuffer sequence, for example a multiple cloning site (MCS), or an MCS linked to a plant kozak sequence, wherein the CMPVX comprises nucleotides from X of SEQ ID NO:1, where X=160, 155, 150, or 114 of SEQ ID NO:1, or a sequence that comprises 80% sequence similarity with CPMVX (where X=160, 155, 150, or 114 of SEQ ID NO:1), and exhibits the property of enhancing the expression of nucleotide sequence encoding a heterologous open reading frame operatively linked to the expression enhancer, when compared to the expression of the same sequence encoding a heterologous open reading frame operatively linked to the prior art CPMV HT enhancer sequence comprising an incomplete M protein (as described in Sainsbury F., and Lomonossoff G. P., 2008, Plant Physiol. 148: pp. 1212-1218; which is incorporated herein by reference). The stuffer sequence comprises from 0-500 nucleotides fused to the 3 end of the CMPVX sequence. Preferably, the stuffer sequence comprises an multiple cloning site (MCS), or an MCS linked to a plant kozak sequence, and does not include an M protein. If the CMPVX sequence comprises a stuffer fragment (without an M protein), then this expression enhancer may be referred to as CPMVX+ (see
(45) The expression enhancer CPMVX, where X=160, consists of nucleotides 1-160 of SEQ ID NO: 1:
(46) TABLE-US-00001 (SEQIDNO:1) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagtaca
(47) If the expression enhancer consists of nucleotide 1-160 of SEQ ID NO:1 (CPMV160), then a nucleotide sequence of interest with or without a 5plant kozak sequence located at the 5 end adjacent to an initiation sequence (ATG), may be fused to the 3 end of the 5UTR (after nucleotide 160 of SEQ ID NO:1), so that the overall construct resembles that as shown in
(48) The expression enhancer may comprise CPMVX+, where X=160. A non-limiting example of such an enhancer is CPMV160+(see
(49) TABLE-US-00002 (SEQIDNO:2) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagtaca gggcccaataccgcggA 181
(50) Examples of constructs using SEQ ID NO:2 as an expression enhancer include constructs 1800, 1897, 1880, 2168, 2188, 1937, 1977, 2050, 2060, 1975, 1893, 2100, 2109, 2120, 2129 (see Examples 3, and 5-18, respectively).
(51) As would be evident to one of skill in the art, any multiple cloning site (MCS), or an MCS of different length (either shorter or longer) may used in place of the sequence at nucleotides 161-176 of SEQ ID NO:2. Furthermore, the plant kozak sequence of SEQ ID NO:2 (shown at nucleotides 177-181) may be any plant kozak sequence, including but not limited, one of the sequences selected from SEQ ID NO's:5-17 (also see
(52) The expression enhancer CPMVX, may include an A in position 115 (115A), so that CMPVX, 115A, where X=160, 155 or 150, comprises the sequence of the wild-type CPMV RNA2 genome (see WO 2009/087391, which is incorporated herein by reference, for the complete sequence of the wild type CPMV RNA-2 genome segment). An example of an expression enhancer CPMVX, 115A is CPMV160, 115A, as defined by SEQ ID NO: 69 (the A is shown in bold and underline):
(53) TABLE-US-00003 (SEQIDNO:69) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagtaca
(54) The expression enhancer CPMVX+, may also include an A in position 115 (115A), so that CMPVX+, 115A, where X=160, 155 or 150, comprises the sequence of the wild-type CPMV RNA2 genome (WO 2009/087391, which is incorporated herein by reference). A non-limiting example of an expression enhancer CPMVX+, 115A is CPMV160+, 115A, as defined by SEQ ID NO: 75 (the A is shown in bold and underline):
(55) TABLE-US-00004 (SEQIDNO:75) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagtaca gggcccaataccgcggA 181
(56) As noted above for SEQ ID NO:2, any MCS, or an MCS of different length, may used in place of the MCS sequence of SEQ ID NO:75, and the plant kozak sequence may be any plant kozak sequence.
(57) If the expression enhancer consists of nucleotide 1-155 of SEQ ID NO:1 (CPMV155):
(58) TABLE-US-00005 (SEQIDNO:24) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcggcacca,
then a nucleotide sequence of interest with a plant kozak sequence located at the 5 end, adjacent an initiation sequence (ATG), may be fused to the 3 end of the 5UTR (after nucleotide 155 of SEQ ID NO:1), so that the overall construct resembles that as shown in
(59) The expression enhancer may comprise CPMV155+, comprising the sequence of SEQ ID NO:72 (5UTR: nucleotide 1-155; multiple cloning site in italics nucleotides 156-171; plant kozak sequence in caps and bold, nucleotides 172-176):
(60) TABLE-US-00006 (SEQIDNO:72) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagggcc caataccgcggAGAAA
(61) As noted above for CPMV160+(SEQ ID NO:2), any MCS, including an MCS's of different length, may used in place of the MCS sequence of SEQ ID NO:72, and the plant kozak sequence may be any plant kozak sequence.
(62) The expression enhancer CPMV155, may include an A in position 115 (115A), so that CMPV155, 115A comprises the sequence of the wild-type CPMV RNA2 genome (see WO 2009/087391, which is incorporated herein by reference), as defined by SEQ ID NO: 70 (A is bolded and underlined):
(63) TABLE-US-00007 (SEQIDNO:70) 1 tattaaaatcttaataggttttgataaaagcgaacgtggg gaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctct cttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcggcacca
(64) The expression enhancer CPMV155+, may also include an A in position 115 (115A), so that CMPV155+, 115a comprises the sequence of the wild-type CPMV RNA2 genome (WO 2009/087391, which is incorporated herein by reference), as defined by SEQ ID NO: 76 (the A is shown in bold and underline):
(65) TABLE-US-00008 (SEQIDNO:76) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagggcccaataccgcggA 181
(66) As noted above for SEQ ID NO:2, any MCS, or an MCS of different length, may used in place of the MCS sequence of SEQ ID NO:76, and the plant kozak sequence may be any plant kozak sequence.
(67) If the expression enhancer consists of nucleotide 1-150 of SEQ ID NO:1 (CPMV150):
(68) TABLE-US-00009 (SEQIDNO:27) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcgg,
then a nucleotide sequence of interest with a plant kozak sequence located at the 5 end, adjacent an initiation sequence (ATG), may be fused to the 3 end of the 5UTR (after nucleotide 150 of SEQ ID NO:1), so that the overall construct resembles that as shown in
(69) The expression enhancer may comprise CPMV150+, comprising the sequence of SEQ ID NO:73 (5UTR: nucleotide 1-150; multiple cloning site in italics nucleotides 156-166; plant kozak sequence in caps and bold, nucleotides 167-171):
(70) TABLE-US-00010 (SEQIDNO:73) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcgtgagc 121 gatcttcaacgttgtcagatcgtgcttcgggggcccaataccgcggAGAAA
(71) As noted above for CPMV160+(SEQ ID NO:2), any MCS, including an MCS's of different length, may used in place of the MCS sequence of SEQ ID NO:73, and the plant kozak sequence may be any plant kozak sequence.
(72) The expression enhancer CPMV150, may include an A in position 115 (115A), so that CMPV150, 115A comprises the sequence of the wild-type CPMV RNA2 genome (see WO 2009/087391, which is incorporated herein by reference) as defined by SEQ ID NO: 71 (the A is shown in bold and underline):
(73) TABLE-US-00011 (SEQIDNO:71) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcgg
(74) The expression enhancer CPMV150+, may also include an A in position 115 (115A), so that CMPV150+, 115A comprises the sequence of the wild-type CPMV RNA2 genome (WO 2009/087391, which is incorporated herein by reference), as defined by SEQ ID NO: 77 (the A is shown in bold and underline):
(75) TABLE-US-00012 (SEQIDNO:77) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcatgagc 121 gatcttcaacgttgtcagatcgtgcttcgggggcccaataccgcggA 181
(76) As noted above for SEQ ID NO:2, any MCS, or an MCS of different length, may used in place of the MCS sequence of SEQ ID NO:77, and the plant kozak sequence may be any plant kozak sequence.
(77) If the expression enhancer consists of nucleotide 1-114 of SEQ ID NO:1:
(78) TABLE-US-00013 (SEQIDNO:68) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgc
then a nucleotide sequence of interest with a plant kozak sequence located at the 5 end, adjacent an initiation sequence (ATG), may be fused to the 3 end of the 5UTR (after nucleotide 114 of SEQ ID NO:1), so that the overall construct resembles that as shown in
(79) The expression enhancer may comprise CPMV114+, comprising the sequence of SEQ ID NO:74 (5UTR: nucleotide 1-114; multiple cloning site in italics nucleotides 115-130; plant kozak sequence in caps and bold, nucleotides 131-135):
(80) TABLE-US-00014 (SEQIDNO:74) 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgcgggccc 121 aataccgcggAGAAA
(81) As noted above for CPMV160+(SEQ ID NO:2), any MCS, including an MCS's of different length, may used in place of the MCS sequence of SEQ ID NO:73, and the plant kozak sequence may be any plant kozak sequence.
(82) The expression enhancer may also comprise nucleotides 1-160 of SEQ ID NO: 1, fused with a plant kozak sequence located downstream from position 160 of SEQ ID NO:1. The plant kozak sequence may be located immediately adjacent to nucleotide 160 of SEQ ID NO:1, or the expression enhancer may comprise a stuffer fragment of about 0 to about 500 nucleotides, or any amount therebetween, located immediately adjacent to nucleotide 160 of SEQ ID NO:1 (CPMVX+) and the plant kozak sequence linked to 3 end of the stuffer fragment. The stuffer fragment may comprise a multiple cloning site (MCS) of from about 4 to 100 nucleotides or any amount therebetween, and a nucleotide sequence of interest comprising a plant kozak sequence and a corresponding cloning site at its 5 end may be operatively linked to the CMPVX expression enhancer using the MCS, or the stuffer fragment may comprise a multiple cloning site of from about 4 to 100 nucleotides fused to a plant kozak sequence, and a nucleotide sequence of interest may be fused to the expression enhancer immediately downstream of the plant kozak sequence. Preferably, the stuffer fragment does not comprise a sequence encoding an M protein.
(83) An example, which is not to be considered limiting, of a construct, comprising in series, a plant regulatory region fused to a CPMV 5UTR consisting of nucleotides 1-160 of SEQ ID NO:1, that is fused to a stuffer fragment is CPMV160+ as shown in
(84) Also shown in
(85) The expression enhancer may also comprise the expression enhancer CPMVX, where X=160, 155, 150, or 114 of SEQ ID NO: 1, in combination with a multiple cloning site (polylinker, restriction site; cloning site) fused to the 3 end of the 5UTR sequence, and lacking a plant kozak sequence (i.e. CPMVX+, where X=160, 155, 150, or 114 of SEQ ID NO: 1). In these cases the nucleic acid sequence encoding a protein of interest (nucleotide sequence of interest) to be joined to the enhancer, will comprises, in series from the 5 end to the 3 end of the nucleotide sequence of interest, a multiple cloning site (complimentary with that of the stuffer fragment; the stuffer fragment does not comprise any sequence encoding an M protein) fused to a plant kozak sequence located upstream from and adjacent to an ATG initiation site (transcriptional start site) of the nucleotide sequence of interest.
(86) The expression enhancer may further comprise one or more kozak consensus sequence or kozak sequence. Kozak sequences play a major role in the initiation of translation. The rate of translation can be optimized by ensuring that any mRNA instability sequences are eliminated from the transgene construct, and that the translational start site or initiation site matches the Kozak consensus for plants (Gutierrrez, R. A. et al., 1999, Trends Plant Sci. 4, 429-438; Kawaguchi, R. and Bailey-Serres, J., 2002, Curr. Opin. Plant Biol. 5, 460-465). The most highly conserved position in this motif is the purine (which is most often an A) three nucleotides upstream of the ATG codon, which indicates the start of translation (Kozak, M., 1987, J. Mol. Biol. 20:947-950, herein incorporated by reference). Plant Kozak consensus sequences are known in the art (see for example Rangan et al. Mol. Biotechnol., 2008, July 39(3), pp. 207-213). Both naturally occurring and synthetic Kozak sequences may be used in the expression enhancer or may be fused to the nucleotide sequence of interest as described herein.
(87) The plant kozak sequence may be any known plant kozak sequences (see for example L. Rangan et. al. Mol. Biotechnol., 2008, July 39(3), pp. 207-213), including, but not limited to the following plant consensus sequences:
(88) TABLE-US-00015 (SEQIDNO:5;plantkingdom) caA(A/C)a (SEQIDNO:6;dicots) aaA(A/C)a (SEQIDNO:7;arabidopsis) aa(A/G)(A/C)a
The plant kozak sequence may also be selected from the group of (see
(89) TABLE-US-00016 (SEQIDNO:8) AGAAA (SEQIDNO:9) AGACA (SEQIDNO:10) AGGAA (SEQIDNO:11) AAAAA (SEQIDNO:12) AAACA (SEQIDNO:13) AAGCA (SEQIDNO:14) AAGAA (SEQIDNO:15) AAAGAA (SEQIDNO:16) AAAAGAA (SEQIDNO:3;Consensussequence) (A/-)A(A/G)(A/G)(A/C)A.
(90) The expression enhancer may further comprise one or more restriction site(s) or restriction recognition site(s), multiple cloning site, MCS, cloning site(s) polylinker sequence or polylinker to facilitate the insertion of the nucleotide of interest into the plant expression system. Restrictions sites are specific sequence motifs that are recognized by restriction enzymes as are well known in the art. The expression enhancer may comprise one or more restriction sites or cloning sites that are located downstream (3) of the 5UTR. The one or more restriction sites or cloning sites may further be located up-stream (5) of one or more kozak sequences, and located between a 5 UTR and a kozak sequence. The polylinker sequence (multiple cloning site) may comprise any sequence of nucleic acids that are useful for adding and removing nucleic acid sequences, including a nucleotide sequence encoding a protein of interest, to the 3 end of the 5UTR. A polylinker sequence may comprise from 4 to about 100 nucleic acids, or any amount therebetween.
(91) The expression enhancer may also comprise the sequence of SEQ ID NO:1 in operative association with a plant regulatory region and a transcriptional start site (ATG) fused to a nucleotide sequence of interest (GOI), as shown in
(92) The 5UTR for use in the expression enhancer described herein (CPMVX or CPMVX+, where X=160, 155, 150 or 144), may be derived from a bipartite RNA virus, e.g. from the RNA-2 genome segment of a bipartite RNA virus such as a comovirus, provided that it exhibits 100%, 99%, 98%, 97%, 96%, 95%, 90%, 85% or 80% identity to the sequence as set forth in either SEQ ID NO's: 1 and 2. For example the enhancer sequence may have from about 80% to about 100% identity to the sequence of SEQ ID NO's: 1 and 2, or any amount therebetween, from about 90% to about 100% identity to the sequence of SEQ ID NO's: 1 and 2, or any amount therebetween, about 95% to about 100%, identity to the sequence of SEQ ID NO's: 1 and 2, or any amount therebetween, or about 98% to about 100%, identity to the sequence of SEQ ID NO's: 1 and 2, or any amount therebetween wherein the expression enhancer, when operatively linked to a plant regulatory region and a plant kozak sequence as described herein, increases the level of expression of a nucleotide sequence of interest that is operatively linked to the expression enhancer when compared to the level of expression of the nucleotide sequence of interest fused to the CMPV HT (SEQ ID NO:4; prior art enhancer sequence comprising an incomplete M protein as described in Sainsbury F., and Lomonossoff G. P., 2008, Plant Physiol. 148: pp. 1212-1218; which is incorporated herein by reference) using the same plant regulatory region.
(93) SEQ ID NO:4 comprises a CPMV HT expression enhancer as known in the prior art (e.g.
(94) TABLE-US-00017 SEQIDNO:4 1 tattaaaatcttaataggttttgataaaagcgaacgtggggaaacccgaaccaaaccttc 61 ttctaaactctctctcatctctcttaaagcaaacttctctcttgtctttcttgc gagc 121 gatcttcaacgttgtcagatcgtgcttcggcaccagtacaa
ttttctttcactgaagc 181 gaaatcaaagatctctttgtggacacgtagtgcggcgccattaaataacgtgtacttgtc 241 ctattcttgtcggtgtggtcttgggaaaagaaagcttgctggaggctgctgttcagcccc 301 atacattacttgttacgattctgctgactttcggcgggtgcaatatctctacttctgctt 361 gacgaggtattgttgcctgtacttctttcttcttcttcttgctgattggttctataagaa 421 atctagtattttctttgaaacagagttttcccgtggttttcgaacttggagaaagattgt 481 taagcttctgtatattctgcccaaatttgtcgggccc
(95) Constructs comprising CPMV HT are used herein as reference constructs, so that the expression levels of a nucleotide sequence of interest, or a product encoded by the nucleotide sequence of interest produced using a construct comprising CPMVX or CPMVX+, may be compared. Constructs 1391, 484, 489, 2140, 2130, 1039, 1067, 2072, 2074, 1445, 1454, 5001, 5002, 5021 and 5022 (see Examples 1 and 5-18, respectively) comprise the reference construct CPMV HT.
(96) As shown in
(97) H1 A/California/07/2009 (PDI-H1 Cal, or H1 A/California/07/2009): CPMV160+ based construct number 1897, CPMV HT based construct number 484 (see Example 5);
(98) H3 A/Victoria/361/2011 (PDI-H3 Vic, or H3 A/Victoria/361/2011): CPMV160+ based construct number 1800; CPMV HT based construct number 1391 (see Examples 1 and 2, respectively);
(99) H5 from Influenza A/Indonesia/5/2005 with a native signal peptide (WtSp-H5 Indo): CPMV160+ based construct number 1880; CPMV HT based construct number 489 (see Example 6);
(100) B/Wisconsin/1/2010 with deleted proteolytic loop and with a native signal peptide (WtSp-B Wis-PrL, or B/Wisconsin/1/2010): CPMV160+ based construct number 1975; CPMV HT based construct number 1445 (see Example 13);
(101) B Brisbane/60/08 with deleted proteolytic loop and with a PDI signal peptide (B Brisbane/60/08): CPMV160+ based construct number 1937; CMPV HT based construct number 1039 (see Example 9);
(102) B Brisbane/60/08+H1Tm, with deleted proteolytic loop fused to the transmembrane domain and cytoplasmic tail and with a PDI signal peptide (B Brisbane/60/08+H1Tm): CPMV160+ based construct number 1977; CMPV HT based construct 1067 (see Example 10),
(103) B Massachusetts/2/2012 2012 with deleted proteolytic loop and with a PDI signal peptide (B Massachusetts/2/2012 2012): CPMV160+ based construct number 2050; CPMV HT based construct number 2072 (see Example 11),
(104) B Massachusetts/2/2012+H1Tm with deleted proteolytic loop fused to the transmembrane domain and cytoplasmic tail and with a PDI signal peptide (B Massachusetts/2/2012+H1Tm): CPMV160+ based construct number 2060; CPMV HT based construct 2074 (see Example 12),
(105) B Wisconsin/1/2010+H1Tm with deleted proteolytic loop fused to the transmembrane domain and cytoplasmic tail and with the native signal peptide (B Wisconsin/1/2010+H1Tm): CPMV160+ based construct number 1893; CPMV HT based construct 1454 (see Example 14);
(106) Rituximab (Rituxan) under the control of CPMV-HT with a native or PDI signal peptide (CPMV-HT/wild-type SP and CPMV-HT/PDISP; construct numbers 5001 and 5002, respectively, see examples 15 and 16), or CPMV160+(CPMV160+/wile-typeSP and CPMV160+/PDISP; construct numbers 2100 and 2109, respectively, see example 15 and 16).
(107) In each case, the expression (determined as hemagglutination activity or rituximab (Rituxan) expression as the case may be) is increased in the CMPV160+ based construct when compared to that for the prior art CPMV based construct. Furthermore, several of the nucleotide sequences of interest encoded chimeric or modified proteins, for example comprising heterologous signal peptides (e.g. PDI), heterologous transmembrane domain cytoplasmic tail sequences (TDCT), and/or modified sequences including a deleted proteolytic loop (PrL).
(108) The increase in expression observed using CPMV160+ based constructs is also observed if the plant kozak sequence used in the CPMV160+ based constructs above is replaced with other plant kozak sequences for example, one of those plant kozak sequences defined in SEQ ID NO:8-16. For example, with reference to
(109) The terms percent similarity, or percent identity when referring to a particular sequence are used for example as set forth in the University of Wisconsin GCG software program, or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology, Ausubel et al., eds. 1995 supplement). Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, using for example the algorithm of Smith & Waterman, (1981, Adv. Appl. Math. 2:482), by the alignment algorithm of Needleman & Wunsch, (1970, J. Mol. Biol. 48:443), by the search for similarity method of Pearson & Lipman, (1988, Proc. Nat'l. Acad. Sci. USA 85:2444), by computerized implementations of these algorithms (for example: GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.).
(110) An example of an algorithm suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., (1977, Nuc. Acids Res. 25:3389-3402) and Altschul et al., (1990, J. Mol. Biol. 215:403-410), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. For example the BLASTN program (for nucleotide sequences) may use as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=4 and a comparison of both strands. For amino acid sequences, the BLASTP program may use as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (see URL: ncbi.nlm.nih.gov/).
(111) A nucleotide sequence interest that encodes a protein requires the presence of a translation initiation site or initiation site or translation start site or start site or start codon located upstream of the gene to be expressed. Such initiation sites may be provided either as part of an enhancer sequence or as part of a nucleotide sequence encoding the protein of interest.
(112) Expression cassette refers to a nucleotide sequence comprising a nucleic acid of interest under the control of, and operably (or operatively) linked to, an appropriate promoter or other regulatory elements for transcription of the nucleic acid of interest in a host cell.
(113) By proteolytic loop or cleavage site is meant the consensus sequence of the proteolytic site that is involved in precursor HA0 cleavage. Consensus or consensus sequence as used herein means a sequence (either amino acid or nucleotide sequence) that comprises the sequence variability of related sequences based on analysis of alignment of multiple sequences, for example, subtypes of a particular influenza HA0 sequence. Consensus sequence of the influenza HA0 cleavage site may include influenza A consensus hemagglutinin amino acid sequences, including for example consensus H1, consensus H3, consensus H5, or influenza B consensus hemagglutinin amino acid sequences, for example but not limited to B Florida, B Malaysia, B Wisconsin and B Massachusetts. Non limiting examples of sequences of the proteoloytic loop region are shown in FIGS. 15 and 18B of U.S. provisional application No. 61/806,227 (filed Mar. 28, 2013, which is incorporated herein by reference; also see Bianchi et al., 2005, Journal of Virology, 79:7380-7388; incorporated herein by reference).
(114) Residues in the proteolytic loop or cleavage site might be either mutated, for example but not limited to point mutation, substitution, insertion, or deletion. The term amino acid mutation or amino acid modification as used herein is meant to encompass amino acid substitutions, deletions, insertions, and modifications. Any combination of substitution, deletion, insertion, and modification can be made as described in U.S. provisional application No. 61/806,227 (filed Mar. 28, 2013, which is incorporated herein by reference) to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., reduced or abolished cleavage of the proteolytic loop or cleavage site by a protease.
(115) As described herein, there is provided a nucleic acid construct (expression system) comprising an expression enhancer sequence operatively linked to a nucleotide sequence of interest encoding a protein of interest. Also provided are plant expression systems comprising an enhancer sequence as described herein. Also provided is a plant expression system comprising a plant regulatory region, in operative association with an enhancer sequence that is operatively linked to a nucleotide sequence of interest, the nucleotide sequence of interest encoding a protein of interest. The enhancer sequence may be selected from any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, or a nucleotide sequence that exhibits 100%, 99%, 98%, 97%, 96%, 95%, 90%, 85% or 80% identity to the sequence as set forth in any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, wherein the expression enhancer, when operatively linked to a plant regulatory region and a plant kozak sequence as described herein, increases the level of expression of a nucleotide sequence of interest that is operatively linked to the expression enhancer when compared to the level of expression of the nucleotide sequence of interest fused to the CMPV HT (SEQ ID NO:4; prior art enhancer sequence comprising an incomplete M protein as described in Sainsbury F., and Lomonossoff G. P., 2008, Plant Physiol. 148: pp. 1212-1218; which is incorporated herein by reference) using the same plant regulatory region.
(116) The enhancer sequence of the present invention may be used to express a protein of interest in a host organism for example a plant. In this case, the protein of interest may also be heterologous to the host organism in question and introduced into the plant cells using transformation techniques know in the art. A heterologous gene in an organism may replace an endogenous equivalent gene, i.e. one which normally performs the same or a similar function, or the inserted sequence may be additional to the endogenous gene or other sequence.
(117) The enhancer sequence operatively linked to a nucleotide sequence of interest may also be operatively linked to promoter, or plant regulatory region, and a 3UTR and terminator sequences. The enhancer sequence may be defined by, for example, any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, or a nucleotide sequence that exhibits 100%, 99%, 98%, 97%, 96%, 95%, 90%, 85% or 80% identity to the sequence as set forth in any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77. Thus, the nucleotide sequence of interest is located between the enhancer sequence and the termination sequence (see
(118) The invention further provides an expression cassette comprising in series, a promoter or plant regulatory region, operatively linked to an expression enhancer sequence as described herein which is fused with a nucleotide sequence of interest, a 3UTR sequence, and a terminator sequence. The enhancer sequence may be defined by, for example, any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, or a nucleotide sequence that exhibits 100%, 99%, 98%, 97%, 96%, 95%, 90%, 85% or 80% identity to the sequence as set forth in any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77. Either the expression enhancer or the nucleotide sequence of interest may comprise a plant kozak sequence.
(119) As one of skill in the art would appreciate, the termination (terminator) sequence may be any sequence that is active the plant host, for example the termination sequence may be derived from the RNA-2 genome segment of a bipartite RNA virus, e.g. a comovirus, or the termination sequence may be a NOS terminator.
(120) The constructs of the present invention can further comprise a 3 untranslated region (UTR). A 3 untranslated region contains a polyadenylation signal and any other regulatory signals capable of effecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by effecting the addition of polyadenylic acid tracks to the 3 end of the mRNA precursor. Polyadenylation signals are commonly recognized by the presence of homology to the canonical form 5 AATAAA-3 although variations are not uncommon. Non-limiting examples of suitable 3 regions are the 3 transcribed non-translated regions containing a polyadenylation signal of Agrobacterium tumor inducing (Ti) plasmid genes, such as the nopaline synthase (Nos gene) and plant genes such as the soybean storage protein genes, the small subunit of the ribulose-1, 5-bisphosphate carboxylase gene (ssRUBISCO; U.S. Pat. No. 4,962,028; which is incorporated herein by reference), the promoter used in regulating plastocyanin expression (Pwee and Gray 1993; which is incorporated herein by reference). The termination (terminator) sequence may be obtained from the 3UTR of the alfalfa plastocyanin gene.
(121) By nucleotide (or nucleic acid) sequence of interest, or coding region of interest, it is meant any nucleotide sequence, or coding region (these terms may be used interchangeably) that is to be expressed within a host organism, for example a plant, to produce a protein of interest. Such a nucleotide sequence of interest may encode, but is not limited to, native or modified proteins, an industrial enzyme or a modified industrial enzyme, an agricultural protein or a modified agricultural protein, a helper protein, a protein supplement, a pharmaceutically active protein, a nutraceutical, a value-added product, or a fragment thereof for feed, food, or both feed and food use.
(122) The protein of interest may comprise a native, or a non-native signal peptide; the non-native signal peptide may be of plant origin. For example, the signal peptide may be a protein disulfide isomerase signal peptide (PDI). The native signal peptide may correspond to that of the protein of interest being expressed.
(123) The nucleotide sequence of interest, or coding region of interest may also include a nucleotide sequence that encodes a pharmaceutically active protein, for example growth factors, growth regulators, antibodies, antigens, and fragments thereof, or their derivatives useful for immunization or vaccination and the like. Such proteins include, but are not limited to a protein that is a human pathogen, a viral protein, for example but not limited to VLP-forming antigens, one or more proteins from Respiratory syncytial virus (RSV), Rotavirus, influenza virus, human immunodeficiency virus (HIV), Rabies virus, human papiloma virus (HPV), Enterovirus 71 (EV71), or interleukins, for example one or more than one of IL-1 to IL-24, IL-26 and IL-27, cytokines, Erythropoietin (EPO), insulin, G-CSF, GM-CSF, hPG-CSF, M-CSF or combinations thereof, interferons, for example, interferon-alpha, interferon-beta, interferon-gama, blood clotting factors, for example, Factor VIII, Factor IX, or tPA hGH, receptors, receptor agonists, antibodies for example but not limited to rituximab (Rituxan), neuropolypeptides, insulin, vaccines, growth factors for example but not limited to epidermal growth factor, keratinocyte growth factor, transformation growth factor, growth regulators, antigens, autoantigens, fragments thereof, or combinations thereof.
(124) The protein of interest may also include an influenza hemagglutinin (HA; see WO 2009/009876, which is incorporated herein by reference). HA is a homotrimeric membrane type I glycoprotein, generally comprising a signal peptide, an HA1 domain, and an HA2 domain comprising a membrane-spanning anchor site at the C-terminus and a small cytoplasmic tail. Nucleotide sequences encoding HA are well known and are available (see, for example, the BioDefense and Public Health Database (Influenza Research Database; Squires et al., 2008 Nucleic Acids Research 36:D497-D503) at URL: biohealthbase.org/GSearch/home.do?decorator=Influenza; or the databases maintained by the National Center for Biotechnology Information (see URL: ncbi.nlm.nih.gov), both of which are incorporated herein by reference).
(125) An HA protein may be of a type A influenza, a type B influenza, or is a subtype of type A influenza HA selected from the group of H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, and H16. In some aspects of the invention, the HA may be from a type A influenza, selected from the group H1, H2, H3, H5, H6, H7 and H9. Fragments of the HAs listed above may also be considered a protein of interest. Furthermore, domains from an HA type or subtype listed above may be combined to produce chimeric HA's (see for example WO2009/076778 which is incorporated herein by reference).
(126) Examples of subtypes comprising HA proteins include A/New Caledonia/20/99 (H1N1), A/Indonesia/5/2006 (H5N1), A/chicken/New York/1995, A/herring gull/DE/677/88 (H2N8), A/Texas/32/2003, A/mallard/1VIN/33/00, A/duck/Shanghai/1/2000, A/northern pintail/TX/828189/02, A/Turkey/Ontario/6118/68(H8N4), A/shoveler/Iran/G54/03, A/chicken/Germany/N/1949(H10N7), A/duck/England/56(H11N6), A/duck/Alberta/60/76(H12N5), A/Gull/Maryland/704/77(H13N6), A/Mallard/Gurjev/263/82, A/duck/Australia/341/83 (H15N8), A/black-headed gull/Sweden/5/99(H16N3), B/Lee/40, C/Johannesburg/66, A/PuertoRico/8/34 (H1N1), A/Brisbane/59/2007 (H1N1), A/Solomon Islands 3/2006 (H1N1), A/Brisbane 10/2007 (H3N2), A/Wisconsin/67/2005 (H3N2), B/Malaysia/2506/2004, B/Florida/4/2006, A/Singapore/1/57 (H2N2), A/Anhui/1/2005 (H5N1), A/Vietnam/1194/2004 (H5N1), A/Teal/HongKong/W312/97 (H6N1), A/Equine/Prague/56 (H7N7), A/HongKong/1073/99 (H9N2)).
(127) The HA protein may be an H1, H2, H3, H5, H6, H7 or H9 subtype. For example, the H1 protein may be from the A/New Caledonia/20/99 (H1N1), A/PuertoRico/8/34 (H1N1), A/Brisbane/59/2007 (H1N1), A/Solomon Islands 3/2006 (H1N1), A/California/04/2009 (H1N1) or A/California/07/2009 (H1N1) strain. The H3 protein may also be from the A/Brisbane 10/2007 (H3N2), A/Wisconsin/67/2005 (H3N2), A/Victoria/361/2011 (H3N2), A/Texas/50/2012 (H3N2), A/Hawaii/22/2012 (H3N2), A/New York/39/2012 (H3N2), or A/Perth/16/2009 (H3N2) strain. In a further aspect of the invention, the H2 protein may be from the A/Singapore/1/57 (H2N2) strain. The H5 protein may be from the A/Anhui/1/2005 (H5N1), A/Vietnam/1194/2004 (H5N1), or A/Indonesia/5/2005 strain. In an aspect of the invention, the H6 protein may be from the A/Teal/HongKong/W312/97 (H6N1) strain. The H7 protein may be from the A/Equine/Prague/56 (H7N7) strain, or H7 A/Hangzhou/1/2013, A/Anhui/1/2013 (H7N9), or A/Shanghai/2/2013 (H7N9) strain. In an aspect of the invention, the H9 protein is from the A/HongKong/1073/99 (H9N2) strain. In a further aspect of the invention, the HA protein may be from an influenza virus may be a type B virus, including B/Malaysia/2506/2004, B/Florida/4/2006, B/Brisbane/60/08, B/Massachusetts/2/2012like virus (Yamagata lineage), or B/Wisconsin/1/2010 (Yamagata lineage). Non-limiting examples of amino acid sequences of the HA proteins from H1, H2, H3, H5, H6, H7, H9 or B subtypes include sequences as described in WO 2009/009876, WO 2009/076778, WO 2010/003225 (which are incorporated herein by reference). The influenza virus HA protein may be H5 Indonesia.
(128) The HA may also be a chimeric HA, wherein a native transmembrane domain of the HA is replaced with a heterologous transmembrane domain. The transmembrane domain of HA proteins is highly conserved (see for example
(129) TABLE-US-00018 (SEQIDNO:78) iLXiYystvAiSslXlXXmlagXsXwmcs
(130) The HA may comprise a native, or a non-native signal peptide; the non-native signal peptide may be of plant origin. The native signal peptide may correspond to that of the hemagglutinin being expressed, or may correspond to a second hemagglutinin. Additionally, the signal peptide may be from a structural protein or hemagglutinin of a virus other than influenza. Non-limiting examples of a signal peptide that may be used is that of alfalfa protein disulfide isomerase (PDI SP; nucleotides 32-103 of Accession No. Z11499), or the patatin signal peptide (PatA SP; located nucleotides 1738-1806 of GenBank Accession number A08215). The nucleotide sequence of PatA SP for this accession number is:
(131) TABLE-US-00019 (SEQIDNO:79) ATGGCAACTACTAAAACTTTTTTAATTTTATTTTTTATGATATTAGCAACT ACTAGTTCAACATGTGCT
the amino acid sequence of patatin A signal peptide is:
(132) TABLE-US-00020 (SEQIDNO:80) MATTKTFLILFFMILATTSSTCA
(133) The present invention also provides nucleic acid molecules comprising sequences encoding an HA protein. The nucleic acid molecules may further comprise one or more regulatory regions operatively linked to the sequence encoding an HA protein. The nucleic acid molecules may comprise a sequence encoding an H1, H2, H3, H4, H5, H6, H7, H8, H9, H10, H11, H12, H13, H14, H15, H16 or HA from type B influenza. For example, the HA protein encoded by the nucleic acid molecule may be an H1, H2, H3, H5, H6, H7, H9 subtype an HA from type B. The H1 protein encoded by the nucleic acid may be from the A/New Caledonia/20/99 (H1N1), A/PuertoRico/8/34 (H1N1), A/Brisbane/59/2007 (H1N1), A/Solomon Islands 3/2006 (H1N1), A/California/04/2009 (H1N1) or A/California/07/2009 (H1N1) strain. The H3 protein encoded by the nucleic acid molecule may be from the A/Brisbane 10/2007 (H3N2), A/Wisconsin/67/2005 (H3N2), A/Victoria/361/2011 (H3N2), A/Texas/50/2012 (H3N2), A/Hawaii/22/2012 (H3N2), A/New York/39/2012 (H3N2), or A/Perth/16/2009 (H3N2) strain. The H2 protein encoded by the nucleic acid molecule may be from the A/Singapore/1/57 (H2N2) strain. The H5 protein encoded by the nucleic acid molecule A/Anhui/1/2005 (H5N1), A/Vietnam/1194/2004 (H5N1), or A/Indonesia/5/2005 strain. The H6 protein encoded by the nucleic acid molecule may be from the A/Teal/HongKong/W312/97 (H6N1) strain. The H7 protein encoded by the nucleic acid molecule may be from the A/Equine/Prague/56 (H7N7) strain, or H7 A/Hangzhou/1/2013, A/Anhui/1/2013 (H7N9), or A/Shanghai/2/2013 (H7N9) strain. Additional, the H9 protein encoded by the nucleic acid molecule may be from the A/HongKong/1073/99 (H9N2) strain. The HA protein encoded by the nucleic acid molecule may be from an influenza virus type B virus, including B/Malaysia/2506/2004, B/Florida/4/2006, B/Brisbane/60/08, B/Massachusetts/2/2012-like virus (Yamagata lineage), or B/Wisconsin/1/2010 (Yamagata lineage). Non-limiting examples of amino acid sequences of the HA proteins from H1, H2, H3, H5, H6, H7, H9 or B subtypes include sequences as described in WO 2009/009876, WO 2009/076778, WO 2010/003225 (which are incorporated herein by reference). The influenza virus HA protein may be H5 Indonesia.
(134) TABLE-US-00021 TABLE 1 Examples of constructs that have been prepared as described herein: CMPV-HT based constructs (constructs comprising SEQ ID NO: 4; prior art) Construct # SP.sup.1 Sequence of Interest Example 484 PDI.sup.2 H1 California 5 489 WT.sup.3 H5 Indonesia 6 2140 PDI H7 Hangzhou 7 2130 PDI H7 Hangzhou + H5 Indonesia TMCT.sup.4 8 1039 PDI B Brisbane(Prl) 9 1067 PDI B Brisbane(PrL) + Hi California TMCT 10 2072 PDI B Massachussetts (PrL) 11 2074 PDI B Massachussetts (PrL) + H1 California 12 TMCT 1445 WT B Wisconsin (PrL) 13 1454 WT B Wisconsin (PrL) + H1 California TMCT 14 5001 WT HC rituximab (Rituxan) 15 5002 PDI HC rituximab (Rituxin) 16 5021 WT LC rituximab (Rituxin) 17 5022 PDI LC rituximab (Rituxin) 18 Construct # SP Sequence of Interest Example CPMV160+ based constructs (constructs comprising SEQ ID NO: 2) 1800 PDI H3 Victoria 2 1897 PDI H1 California 5 1880 WT H5 Indonesia 6 2168 PDI H7 Hangzhou 7 2188 PDI H7 Hangzhou + H5 Indonesia TMCT 8 1937 PDI B Brisbane(Prl) 9 1977 PDI B Brisbane(PrL) + H1 California TMCT 10 2050 PDI B Massachussetts (PrL) 11 2060 PDI B Massachussetts (PrL) + H1 California 12 TMCT 1975 WT B Wisconsin (PrL) 13 1893 WT B Wisconsin (PrL) + H1 California TMCT 14 2100 WT HC rituximab (Rituxan) 15 2109 PDI HC rituximab (Rituxin) 16 2120 WT LC rituximab (Rituxin) 17 2129 PDI LC rituximab (Rituxin) 18 CPMV160 based constructs (constructs comprising SEQ ID NO: 1) 1935 PDI H3 Victoria 3 1885 WT H5 Indonesia 6 .sup.1SPsignal peptide .sup.2PDIalfalfa protein disulfide isomerise .sup.3WTwild type or native .sup.4TMCTtransmembrane domain and cytoplasmic tail
(135) If the nucleic acid sequence of interest encodes a product that is directly or indirectly toxic to the plant, then such toxicity may be reduced by selectively expressing the nucleotide sequence of interest within a desired tissue or at a desired stage of plant development.
(136) The coding region of interest or the nucleotide sequence of interest may be expressed in any suitable plant host which is either transformed or comprises the nucleotide sequences, or nucleic acid molecules, or genetic constructs, or vectors of the present invention. Examples of suitable hosts include, but are not limited to, Arabidopsis, agricultural crops including for example canola, Brassica spp., maize, Nicotiana spp., (tobacco) for example, Nicotiana benthamiana, alfalfa, potato, sweet potato (Ipomoea batatus), ginseng, pea, oat, rice, soybean, wheat, barley, sunflower, cotton, corn, rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), safflower (Carthamus tinctorius).
(137) The terms biomass and plant matter as used herein refer to any material derived from a plant. Biomass or plant matter may comprise an entire plant, or part of plant including the leaf, root, stem, flower, seed, it may also include any tissue of the plant, any cells of the plant, or any fraction of the plant, part or the plant, tissue or cell. Further, biomass or plant matter may comprise intracellular plant components, extracellular plant components, liquid or solid extracts of plants, or a combination thereof. Further, biomass or plant matter may comprise plants, plant cells, tissue, a liquid extract, or a combination thereof, from plant leaves, stems, fruit, roots or a combination thereof. A portion of a plant may comprise plant matter or biomass.
(138) By regulatory region regulatory element or promoter it is meant a portion of nucleic acid typically, but not always, upstream of the protein coding region of a gene, which may be comprised of either DNA or RNA, or both DNA and RNA. When a regulatory region is active, and in operative association, or operatively linked, with a gene of interest, this may result in expression of the gene of interest. A regulatory element may be capable of mediating organ specificity, or controlling developmental or temporal gene activation. A regulatory region includes promoter elements, core promoter elements exhibiting a basal promoter activity, elements that are inducible in response to an external stimulus, elements that mediate promoter activity such as negative regulatory elements or transcriptional enhancers. Regulatory region, as used herein, also includes elements that are active following transcription, for example, regulatory elements that modulate gene expression such as translational and transcriptional enhancers, translational and transcriptional repressors, upstream activating sequences, and mRNA instability determinants. Several of these latter elements may be located proximal to the coding region.
(139) In the context of this disclosure, the term regulatory element or regulatory region typically refers to a sequence of DNA, usually, but not always, upstream (5) to the coding sequence of a structural gene, which controls the expression of the coding region by providing the recognition for RNA polymerase and/or other factors required for transcription to start at a particular site. However, it is to be understood that other nucleotide sequences, located within introns, or 3 of the sequence may also contribute to the regulation of expression of a coding region of interest. An example of a regulatory element that provides for the recognition for RNA polymerase or other transcriptional factors to ensure initiation at a particular site is a promoter element. Most, but not all, eukaryotic promoter elements contain a TATA box, a conserved nucleic acid sequence comprised of adenosine and thymidine nucleotide base pairs usually situated approximately 25 base pairs upstream of a transcriptional start site. A promoter element may comprise a basal promoter element, responsible for the initiation of transcription, as well as other regulatory elements (as listed above) that modify gene expression.
(140) There are several types of regulatory regions, including those that are developmentally regulated, inducible or constitutive. A regulatory region that is developmentally regulated, or controls the differential expression of a gene under its control, is activated within certain organs or tissues of an organ at specific times during the development of that organ or tissue. However, some regulatory regions that are developmentally regulated may preferentially be active within certain organs or tissues at specific developmental stages, they may also be active in a developmentally regulated manner, or at a basal level in other organs or tissues within the plant as well. Examples of tissue-specific regulatory regions, for example see-specific a regulatory region, include the napin promoter, and the cruciferin promoter (Rask et al., 1998, J. Plant Physiol. 152: 595-599; Bilodeau et al., 1994, Plant Cell 14: 125-130). An example of a leaf-specific promoter includes the plastocyanin promoter (see U.S. Pat. No. 7,125,978, which is incorporated herein by reference).
(141) An inducible regulatory region is one that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer. In the absence of an inducer the DNA sequences or genes will not be transcribed. Typically the protein factor that binds specifically to an inducible regulatory region to activate transcription may be present in an inactive form, which is then directly or indirectly converted to the active form by the inducer. However, the protein factor may also be absent. The inducer can be a chemical agent such as a protein, metabolite, growth regulator, herbicide or phenolic compound or a physiological stress imposed directly by heat, cold, salt, or toxic elements or indirectly through the action of a pathogen or disease agent such as a virus. A plant cell containing an inducible regulatory region may be exposed to an inducer by externally applying the inducer to the cell or plant such as by spraying, watering, heating or similar methods. Inducible regulatory elements may be derived from either plant or non-plant genes (e.g. Gatz, C. and Lenk, I. R. P., 1998, Trends Plant Sci. 3, 352-358; which is incorporated by reference). Examples, of potential inducible promoters include, but not limited to, tetracycline-inducible promoter (Gatz, C., 1997, Ann. Rev. Plant Physiol. Plant Mol. Biol. 48, 89-108; which is incorporated by reference), steroid inducible promoter (Aoyama, T. and Chua, N. H., 1997, Plant J. 2, 397-404; which is incorporated by reference) and ethanol-inducible promoter (Salter, M. G., et al, 1998, Plant Journal 16, 127-132; Caddick, M. X., et al, 1998, Nature Biotech. 16, 177-180, which are incorporated by reference) cytokinin inducible D36 and CKI1 genes (Brandstatter, I. and Kieber, J. J., 1998, Plant Cell 10, 1009-1019; Kakimoto, T., 1996, Science 274, 982-985; which are incorporated by reference) and the auxin inducible element, DRS (Ulmasov, T., et al., 1997, Plant Cell 9, 1963-1971; which is incorporated by reference).
(142) A constitutive regulatory region directs the expression of a gene throughout the various parts of a plant and continuously throughout plant development. Examples of known constitutive regulatory elements include promoters associated with the CaMV 35S transcript. (p35S; Odell et al., 1985, Nature, 313: 810-812), the rice actin 1 (Zhang et al, 1991, Plant Cell, 3: 1155-1165), actin 2 (An et al., 1996, Plant J., 10: 107-121), or tms 2 (U.S. Pat. No. 5,428,147, which is incorporated herein by reference), and triosephosphate isomerase 1 (Xu et. al., 1994, Plant Physiol. 106: 459-467) genes, the maize ubiquitin 1 gene (Cornejo et al, 1993, Plant Mol. Biol. 29: 637-646), the Arabidopsis ubiquitin 1 and 6 genes (Holtorf et al, 1995, Plant Mol. Biol. 29: 637-646), the tobacco translational initiation factor 4A gene (Mandel et al, 1995 Plant Mol. Biol. 29: 995-1004). the Cassava Vein Mosaic Virus promoter, pCAS, (Verdaguer et al., 1996); the promoter of the small subunit of ribulose biphosphate carboxylase, pRbcS: (Outchkourov et al., 2003), the pUbi (for monocots and dicots).
(143) As described herein, regulatory regions comprising enhancer sequences with demonstrated efficiency in leaf expression, have been found to be effective in transient expression. Without wishing to be bound by theory, attachment of upstream regulatory elements of a photosynthetic gene by attachment to the nuclear matrix may mediate strong expression. For example up to 784 from the translation start site of pea plastocyanin (U.S. Pat. No. 7,125,978, which is incorporated herein by reference) may be used mediate strong reporter gene expression.
(144) The term constitutive as used herein does not necessarily indicate that a nucleotide sequence under control of the constitutive regulatory region is expressed at the same level in all cell types, but that the sequence is expressed in a wide range of cell types even though variation in abundance is often observed.
(145) The expression constructs as described above may be present in a vector. The vector may comprise border sequences which permit the transfer and integration of the expression cassette into the genome of the organism or host. The construct may be a plant binary vector, for example a binary transformation vector based on pPZP (Hajdukiewicz, et al. 1994). Other example constructs include pBin19 (see Frisch, D. A., L. W. Harris-Haller, et al. 1995, Plant Molecular Biology 27: 405-409).
(146) If desired, the constructs of this invention may be further manipulated to include selectable markers. However, this may not be required. Useful selectable markers include enzymes that provide for resistance to chemicals such as an antibiotic for example, gentamycin, hygromycin, kanamycin, or herbicides such as phosphinothrycin, glyphosate, chlorosulfuron, and the like. Similarly, enzymes providing for production of a compound identifiable by colour change such as GUS (beta-glucuronidase), or luminescence, such as luciferase or GFP, may be used.
(147) A vector may also include a expression enhancer as described herein. The expression enhancer may be positioned on a T-DNA which also contains a suppressor of gene silencing and NPTII. The polylinker may also encode one or two sets of 6 Histidine residues to allow the inclusion of N- or C-terminal His-tags to the protein of interest to facilitate protein purification.
(148) Post-transcriptional gene silencing (PTGS) may be involved in limiting expression of transgenes in plants, and co-expression of a suppressor of silencing from the potato virus Y (HcPro) may be used to counteract the specific degradation of transgene mRNAs (Brigneti et al., 1998, EMBO J. 17, 6739-6746, which is incorporated herein by reference). Alternate suppressors of silencing are well known in the art and may be used as described herein (Chiba et al., 2006, Virology 346:7-14; which is incorporated herein by reference), for example but not limited to, TEV-p1/HC-Pro (Tobacco etch virus-p1/HC-Pro), BYV-p21, p19 of Tomato bushy stunt virus (TBSV p19; the construction of p19 is described in described in WO 2010/0003225, which is incorporated herein by reference), capsid protein of Tomato crinkle virus (TCV-CP), 2b of Cucumber mosaic virus; CMV-2b), p25 of Potato virus X (PVX-p25), p11 of Potato virus M (PVM-p11), p11 of Potato virus S (PVS-p11), p16 of Blueberry scorch virus, (BScV-p16), p23 of Citrus tristeza virus (CTV-p23), p24 of Grapevine leafroll-associated virus-2, (GLRaV-2 p24), p10 of Grapevine virus A, (GVA-p10), p14 of Grapevine virus B (GVB-p14), p10 of Heracleum latent virus (HLV-p10), or p16 of Garlic common latent virus (GCLV-p16).
(149) Therefore, one or more suppressors of silencing, for example, but not limited to, HcPro, TEV-p1/HC-Pro, BYV-p21, TBSV p19, TCV-CP, CMV-2b, PVX-p25, rgscam, B2 protein from FHV, the small coat protein of CPMV, and coat protein from TCV, PVM-p11, PVS-p11, BScV-p16, CTV-p23, GLRaV-2 p24, GBV-p14, HLV-p10, GCLV-p16, or GVA-p10 may be co-expressed along with the comovirus-based expression cassette, geminivirus-derived amplification element, and the nucleic acid sequence encoding the protein of interest to further ensure high levels of protein production within a plant.
(150) The constructs of the present invention can be introduced into plant cells using Ti plasmids, Ri plasmids, plant virus vectors, direct DNA transformation, micro-injection, electroporation, etc. For reviews of such techniques see for example Weissbach and Weissbach, Methods for Plant Molecular Biology, Academy Press, New York VIII, pp. 421-463 (1988); Geierson and Corey, Plant Molecular Biology, 2d Ed. (1988); and Miki and Iyer, Fundamentals of Gene Transfer in Plants. In Plant Metabolism, 2d Ed. D T. Dennis, D H Turpin, D D Lefebrve, D B Layzell (eds), Addison Wesly, Langmans Ltd. London, pp. 561-579 (1997). Other methods include direct DNA uptake, the use of liposomes, electroporation, for example using protoplasts, micro-injection, microprojectiles or whiskers, and vacuum infiltration. See, for example, Bilang, et al. (1991, Gene 100: 247-250), Scheid et al. (1991, Mol. Gen. Genet. 228: 104-112), Guerche et al. (1987, Plant Science 52: 111-116), Neuhause et al. (1987, Theor. Appl Genet. 75: 30-36), Klein et al., (2987, Nature 327: 70-73); Freeman et al. (1984, Plant Cell Physiol. 29: 1353), Howell et al. (1980, Science 208: 1265), Horsch et al. (1985, Science 227: 1229-1231), DeBlock et al., (1989, Plant Physiology 91: 694-701), Methods for Plant Molecular Biology (Weissbach and Weissbach, eds., Academic Press Inc., 1988), Methods in Plant Molecular Biology (Schuler and Zielinski, eds., Academic Press Inc., 1989), WO 92/09696, WO 94/00583, EP 331083, EP 175966, Liu and Lomonossoff (2002, J Virol Meth, 105:343-348), EP 290395; WO 8706614; U.S. Pat. Nos. 4,945,050; 5,036,006; and 5,100,792, U.S. patent application Ser. No. 08/438,666, filed May 10, 1995, and Ser. No. 07/951,715, filed Sep. 25, 1992, (all of which are hereby incorporated by reference).
(151) Transient expression methods may be used to express the constructs of the present invention (see D'Aoust et al., 2009, Methods in molecular biology, Vol 483, pages 41-50; Liu and Lomonossoff, 2002, Journal of Virological Methods, 105:343-348; which is incorporated herein by reference). Alternatively, a vacuum-based transient expression method, as described by Kapila et al., (1997, Plant Sci. 122, 101-108; which is incorporated herein by reference), or WO 00/063400, WO 00/037663 (which are incorporated herein by reference) may be used. These methods may include, for example, but are not limited to, a method of Agro-inoculation or Agro-infiltration, syringe infiltration, however, other transient methods may also be used as noted above. With Agro-inoculation, Agro-infiltration, or syringe infiltration, a mixture of Agrobacteria comprising the desired nucleic acid enter the intercellular spaces of a tissue, for example the leaves, aerial portion of the plant (including stem, leaves and flower), other portion of the plant (stem, root, flower), or the whole plant. After crossing the epidermis the Agr bacteria infect and transfer t-DNA copies into the cells. The t-DNA is episomally transcribed and the mRNA translated, leading to the production of the protein of interest in infected cells, however, the passage of t-DNA inside the nucleus is transient.
(152) Also considered part of this invention are transgenic plants, plant cells or seeds containing the gene construct of the present invention that may be used as a platform plant suitable for transient protein expression described herein. Methods of regenerating whole plants from plant cells are also known in the art (for example see Guerineau and Mullineaux (1993, Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy RRD ed) Oxford, BIOS Scientific Publishers, pp 121-148). In general, transformed plant cells are cultured in an appropriate medium, which may contain selective agents such as antibiotics, where selectable markers are used to facilitate identification of transformed plant cells. Once callus forms, shoot formation can be encouraged by employing the appropriate plant hormones in accordance with known methods and the shoots transferred to rooting medium for regeneration of plants. The plants may then be used to establish repetitive generations, either from seeds or using vegetative propagation techniques. Transgenic plants can also be generated without using tissue culture. Methods for stable transformation, and regeneration of these organisms are established in the art and known to one of skill in the art. Available techniques are reviewed in Vasil et al., (Cell Culture and Somatic Cell Genetics of Plants, VoI I, Il and III, Laboratory Procedures and Their Applications, Academic Press, 1984), and Weissbach and Weissbach, (Methods for Plant Molecular Biology, Academic Press, 1989). The method of obtaining transformed and regenerated plants is not critical to the present invention.
(153) If plants, plant portion or plant cell are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the Agrobacterium in a single transfection event the nucleic acids are pooled, and the bacterial cells transfected as described. Alternately, the constructs may be introduced serially. In this case, a first construct is introduced to the Agrobacterium as described, the cells grown under selective conditions (e.g. in the presence of an antibiotic) where only the singly transformed bacteria can grow. Following this first selection step, a second nucleic acid construct is introduced to the Agrobacterum as described, and the cells grown under doubly-selective conditions, where only the doubly-transformed bacteria can grow. The doubly-transformed bacteria may then be used to transform a plant, plant portion or plant cell as described herein, or may be subjected to a further transformation step to accommodate a third nucleic acid construct.
(154) Alternatively, if plants, a plant portion, or a plant cell are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the plant by co-infiltrating a mixture of Agrobacterium cells with the plant, plant portion, or plant cell, each Agrobacterium cell may comprise one or more constructs to be introduced within the plant. In order to vary the relative expression levels within the plant, plant portion or plant cell, of a nucleotide sequence of interest within a construct, during the step of infiltration, the concentration of the various Agrobacteria populations comprising the desired constructs may be varied.
(155) The present disclosure further provides a transgenic plant comprising the expression system as defined herein, wherein the heterologous nucleic acid of interest in the cassette is expressed at an enhanced level when compared to other analogous expression systems that lack one or more components of the expression system as described herein, for example CMPV HT (SEQ ID NO:4).
(156) The present disclosure further comprises a method for generating a protein of interest, comprising the steps of providing a plant, or plant part, that expresses the expression system as described herein, harvesting, at least, a tissue in which the protein of interest has been expressed and optionally, isolating the protein of interest from the tissue.
(157) Thus in various aspects, and without limitation, the invention provides: an expression enhancer, comprising a comovirus 5UTR selected from any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, or a.nucleotide sequence that exhibits 100%, 99%, 98%, 97%, 96%, 95%, 90%, 85% or 80% identity to the sequence as set forth in any one of SEQ ID NO's:1, 2, 24, 27, 68, 69 and 70-77, wherein the expression enhancer, when operatively linked to a plant regulatory region and a plant kozak sequence as described herein, increases the level of expression of a nucleotide sequence of interest that is operatively linked to the expression enhancer when compared to the level of expression of the nucleotide sequence of interest fused to the CMPV HT (SEQ ID NO:4; prior art enhancer sequence comprising an incomplete M protein as described in Sainsbury F., and Lomonossoff G. P., 2008, Plant Physiol. 148: pp. 1212-1218; which is incorporated herein by reference) using the same plant regulatory region. one or more expression systems comprising a comovirus-based expression enhancer or expression cassette as defined above, a promoter (regulatory region), optionally a polylinker, a kozak sequence, a nucleic acid encoding a protein of interest, and a terminator. methods of expressing a protein of interest, in a host organism such as a plant using one or more expression systems or vectors as described herein. host cells and organisms expressing proteins of interest from the one or more expression systems or vectors of the invention and methods of producing the hosts and organisms.
(158) TABLE-US-00022 TABLE2 listofsequences SEQ ID NO Description 1 CPMV160 2 CPMV160+ 3 Consensuskozaksequence (A/-)A(A/G)(A/G)(A/C)A 4 CPMVHT(priorart5UTR) 5 Consensusplantkingdomkozaksequence 6 Consensusdicotkozaksequence 7 ConsensusArabidopsiskozaksequence 8 kozaksequenceAGAAA 9 kozaksequenceAGACA 10 kozaksequenceAGGAA 11 kozaksequenceAAAAA 12 kozaksequenceAAACA 13 kozaksequenceAAGCA 14 kozaksequenceAAGAA 15 kozaksequenceAAAGAA 16 kozaksequenceAAAAGAA 17 IF-H3V36111.s14r 18 NucleotidesequenceofPDISP/H3Victoria. 19 Nucleotidesequenceofconstruct1191 20 Nucleotidesequenceofexpressioncassette number1391 21 AminoacidsequenceofPDISP/H3Victoria 22 IF**(SacII)-PDI.s1+4c 23 IF-H3V36111.s14r 24 CPMV155 25 Nucleotidesequenceofconstruct2171 26 Nucleotidesequenceofexpressioncassette number1800from2X35SpromotertoNOS terminator 27 CPMV150 28 IF-CPMV(fl5UTR)_SpPDI.c 29 Nucleotidesequenceofconstruct1190 30 Nucleotidesequenceofexpressioncassette number1935from2X35SpromotertoNOS terminator 31 IF-HT1*(Mprot)-PDI.c 32 IF-HT2*(Mprot)-PDI.c 33 IF-HT3*(Mprot)-PDI.c 34 IF-HT4*(Mprot)-PDI.c 35 IF-HT5*(Mprot)-PDI.c 36 IF-HT6*(Mprot)-PDI.c 37 IF-HT7*(Mprot)-PDI.c 38 IF-HT8*(Mprot)-PDI.c 39 NucleotidesequenceofPDISP/H1California 40 AminoacidsequenceofPDISP/H1California 41 NucleotidesequenceofnativeH5Indonesia 42 AminoacidsequenceofnativeH5Indonesia 43 NucleotidesequenceofPDISP/H7Hangzhou 44 AminoacidsequenceofPDISP/H7Hangzhou 45 NucleotidesequenceofPDISP/H7Hangzhou+H5 IndonesiaTMCT 46 AminoacidsequenceofPDISP/H7Hangzhou+H5 IndonesiaTMCT 47 NucleotidesequenceofPDISP/HABBrisbane (PrL) 48 AminoacidsequenceofPDISP/HABBrisbane (PrL) 49 NucleotidesequenceofPDISP/HABBrisbane (PrL)+H1CaliforniaTMCT 50 AminoacidsequenceofPDISP/HABBrisbane (PrL)+H1CaliforniaTMCT 51 NucleotidesequenceofPDISP/HAB Massachussetts(PrL) 52 AminoacidsequenceofPDISP/HAB Massachussetts(PrL) 53 NucleotidesequenceofPDISP/HAB Massachussetts(PrL)+H1CaliforniaTMCT 54 AminoacidsequenceofPDISP/HAB Massachussetts(PrL)+H1CaliforniaTMCT 55 NucleotidesequenceofHABWisconsin(PrL) 56 AminoacidsequenceofHABWisconsin(PrL) 57 NucleotidesequenceofHABWisconsin (PrL)+H1CaliforniaTMCT 58 AminoacidsequenceofHABWisconsin (PrL)+H1CaliforniaTMC 59 NucleotidesequenceofHCrituximab(Rituxan) 60 AminoacidsequenceofHCRituxan 61 NucleotidesequenceofPDISP/HCrituximab (Rituxan) 62 AminoacidsequenceofPDISP/HCrituximab (Rituxan) 63 NucleotidesequenceofLCrituximab(Rituxan) 64 AminoacidsequenceofLCrituximab(Rituxan) 65 NucleotidesequenceofPDISP/LCrituximab (Rituxan) 66 AminoacidsequenceofPDISP/LCrituximab (Rituxan) 67 IF-PDI.S1+3c 68 CPMV114 69 CPMV160,115A 70 CPMV155,115A 71 CPMV150,115A 72 CPMV155+ 73 CPMV150+ 74 CPMV114+ 75 CPMV160+,115A 76 CPMV155+,115A 77 CPMV150+,115A 78 Transmembranedomainconsensusaminoacid 79 Patatinsignalpeptide;nucleicacidsequence 80 Patatinsignalpeptide;aminoacidsequence
Example 12X35S/CPMV-HT/PDISP/H3 Victoria/NOS (Construct Number 1391)
(159) A sequence encoding H3 from Influenza A/Victoria/361/2011 in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/H3 Victoria) was cloned into 2X35S-CPMV-HT-NOS expression system (original CMPV-HT) using the following PCR-based method. A fragment containing the PDISP/H3 Victoria coding sequence was amplified using primers IF-PDI.S1+3c (
Example 22X35S/CPMV160+/PDISP/H3 Victoria/NOS (Construct Number 1800)
(160) A sequence encoding H3 from Influenza A/Victoria/361/2011 in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/H3 Victoria) was cloned into 2X35S/CPMV160+/NOS expression system (CPMV160+) using the following PCR-based method. A fragment containing the PDISP/H3 Victoria coding sequence was amplified using primers IF**(SacII)-PDI.s1+4c (
Example 32X35S/CPMV160/PDISP/H3 Victoria/NOS (Construct Number 1935)
(161) A sequence encoding H3 from Influenza A/Victoria/361/2011 in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/H3 Victoria) was cloned into 2X35S-CPMV160-NOS expression using the following PCR-based method. A fragment containing the PDISP/H3 Victoria coding sequence was amplified using primers IF-CPMV(fl5UTR)_SpPDI.c (
Example 4Variation of Sequence Between SacII Restriction Site and ATG of PDISP/H3 Victoria in 2X35S/CPMV160+/NOS Expression System (Constructs Number 1992 to 1999)
(162) Eight constructs comprising sequence variations between SacII restriction site and the ATG of PDISP/H3 Victoria in 2X35S/CPMV160+/NOS expression system were created using the same PCR-based method as for construct no 1800 (see Example 2) using a modified forward primer and keeping all other components the same. Variant HT1* to HT8* were amplified using the primers listed in
(163) IF-HT1*(Mprot)-PDI.c (
(164) IF-HT2*(Mprot)-PDI.c (
(165) IF-HT3*(Mprot)-PDI.c (
(166) IF-HT4*(Mprot)-PDI.c (
(167) IF-HT5*(Mprot)-PDI.c (
(168) IF-HT6*(Mprot)-PDI.c (
(169) IF-HT7*(Mprot)-PDI.c (
(170) IF-HT8*(Mprot)-PDI.c (
(171) to create construct no 1992 to 1999, respectively. Representations of plasmid 1992 is presented in
Example 52X35S/CPMV HT (Construct No 484) and 2X35S/CPMV160+(Construct No 1897) for PDISP/H1 California
(172) A coding sequence corresponding to H1 from Influenza A/California/7/2009 in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/H1 California) (
Example 62X35S/CPMV HT (Construct No 489), 2X35S/CPMV160+(Construct No 1880) and 2X35S/CPMV160 (Construct No 1885) for H5 Indonesia
(173) A coding sequence corresponding to native H5 from Influenza A/Indonesia/5/2005 (
Example 72X35S/CPMV HT (Construct No 2140) and 2X35S/CPMV160+(Construct No 2168) for PDISP-H7 Hangzhou
(174) A coding sequence corresponding to H7 from Influenza A/Hangzhou/1/2013 in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/H7 Hangzhou) (
Example 82X35S/CPMV HT (Construct No 2130) and 2X35S/CPMV160+(Construct No 2188) for PDISP/H7 Hangzhou+H5 Indonesia TMCT
(175) A chimer hemagglutinin coding sequence corresponding to the ectodomain of H7 from Influenza A/Hangzhou/1/2013 fused to the transmembrane domain and cytoplasmic tail (TMCT) of H5 from influenza A/Indonesia/5/2005 and with the signal peptide of alfalfa protein disulfide isomerase (PDISP/H7 Hangzhou+H5 Indonesia TMCT) (
Example 92X35S/CPMV HT (Construct No 1039) and 2X35S/CPMV160+(Construct No 1937) for PDISP/HA B Brisbane (PrL)
(176) A coding sequence corresponding to HA from Influenza B/Brisbane/60/2008 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013, which is incorporated herein by reference, for additional information re: deleted proteolytic loop regions in HA sequences) in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/HA B Brisbane (PrL)) (
Example 102X35S/CPMV HT (Construct No 1067) and 2X35S/CPMV160+(Construct No 1977) for PDISP/HA B Brisbane (PrL)+H1 California TMCT
(177) A chimer hemagglutinin coding sequence corresponding to the ectodomain of HA from Influenza B/Brisbane/60/08 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013, which is incorporated herein by reference, for additional information re: deleted proteolytic loop regions in HA sequences) fused to the transmembrane domain and cytoplasmic tail (TMCT) of H1 from influenza A/California/7/2009 and with the signal peptide of alfalfa protein disulfide isomerase (PDISP/HA B Brisbane (PrL)+H1 California TMCT) (
Example 112X35S/CPMV HT (Construct No 2072) and 2X35S/CPMV160+(Construct No 2050) for PDISP/HA B Massachussetts (PrL)
(178) A coding sequence corresponding to HA from Influenza B/Massachussetts/2/2012 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013 for additional information re: deleted proteolytic loop regions in HA sequences, which is incorporated herein by reference) in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/HA B Massachussetts (PrL)) (
Example 122X35S/CPMV HT (Construct No 2074) and 2X35S/CPMV160+(Construct No 2060) for PDISP/HA B Massachussetts (PrL)+H1 California TMCT
(179) A chimer hemagglutinin coding sequence corresponding to the ectodomain of HA from Influenza B/Massachussetts/2/2012 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013 for additional information re: deleted proteolytic loop regions in HA sequences, which is incorporated herein by reference) fused to the transmembrane domain and cytoplasmic tail (TMCT) of H1 from influenza A/California/7/2009 and with the signal peptide of alfalfa protein disulfide isomerase (PDISP/HA B Massachussetts (PrL)+H1 California TMCT) (FIG. 17A, SEQ ID NO: 53) was cloned into original CPMV-HT and CPMV160+ using the same PCR-based method as construct 1391 (see Example 1) and 1800 (see Example 2), respectively, but with modified PCR primers specifically designed for PDISP/HA B Massachussetts (PrL)+H1 California TMCT. The amino acid sequence of mature HA B Massachussetts (PrL)+H1 California TMCT fused with PDISP is presented in
Example 132X35S/CPMV HT (Construct No 1445), 2X35S/CPMV160+(Construct No 1820) and CPMV160 (Construct No 1975) for HA B Wisconsin (PrL)
(180) A coding sequence corresponding to HA from Influenza B/Wisconsin/1/2010 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013 for additional information re: deleted proteolytic loop regions in HA sequences, which is incorporated herein by reference) with his native signal peptide (HA B Wisconsin (PrL)) (
Example 142X35S/CPMV HT (Construct No 1454) and 2X35S/CPMV160+(Construct No 1893) for HA B Wisconsin (PrL)+H1 California TMCT
(181) A chimer hemagglutinin coding sequence corresponding to the ectodomain of HA from Influenza B/Wisconsin/2/2012 with deleted proteolytic loop (PrL) (see U.S. provisional application No. 61/806,227 Filed Mar. 28, 2013 for additional information re: deleted proteolytic loop regions in HA sequences, which is incorporated herein by reference) fused to the transmembrane domain and cytoplasmic tail (TMCT) of H1 from influenza A/California/7/2009 with the native signal peptide of HA B Wisconsin (HA B Wisconsin (PrL)+H1 California TMCT) (
Example 152X35S/CPMV HT (Construct No 5001) and 2X35S/CPMV160+(Construct No 2100) for HC Rituximab (Rituxan)
(182) A coding sequence corresponding to the heavy chain of monoclonal IgG1 antibody Rituximab (HC rituximab (Rituxan);
Example 162X35S/CPMV HT (Construct No 5002) and 2X35S/CPMV160+(Construct No 2109) for PDISP/HC Rituximab (Rituxan)
(183) A coding sequence corresponding to the heavy chain of monoclonal IgG1 antibody Rituximab in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/HC rituximab (Rituxan);
Example 172X35S/CPMV-HT (Construct No 5021) and 2X35S/CPMV160+(Construct No 2120) for LC Rituximab (Rituxan)
(184) A coding sequence corresponding to the light chain of monoclonal IgG1 antibody Rituximab (LC rituximab (Rituxan;
Example 182X35S/CPMV-HT (Construct No 5022) and 2X35S/CPMV160+(Construct No 2129) for PDISP/LC Rituximab (Rituxan)
(185) A coding sequence corresponding to the light chain of monoclonal IgG1 antibody Rituximab in which the native signal peptide has been replaced by that of alfalfa protein disulfide isomerase (PDISP/LC rituximab (Rituxan;
Example 19Agrobacterium Transfection
(186) Agrobacterium strain AGL1 was transfected by electroporation with the DNA constructs using the methods described by D'Aoust et al 2008 (Plant Biotechnology Journal 6:930-940). Transfected Agrobacterium were grown in YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (IVIES), 20 M acetosyringone, 50 g/ml kanamycin and 25 g/ml of carbenicillin pH5.6 to an OD.sub.600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl.sub.2 and 10 mM IVIES pH 5.6).
(187) Preparation of Plant Biomass, Inoculum and Agroinfiltration
(188) Nicotiana benthamiana plants were grown from seeds in flats filled with a commercial peat moss substrate. The plants were allowed to grow in the greenhouse under a 16/8 photoperiod and a temperature regime of 25 C. day/20 C. night. Three weeks after seeding, individual plantlets were picked out, transplanted in pots and left to grow in the greenhouse for three additional weeks under the same environmental conditions.
(189) Agrobacteria transfected with each construct were grown in a YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (MES), 20 M acetosyringone, 50 g/ml kanamycin and 25 g/ml of carbenicillin pH5.6 until they reached an OD.sub.600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl.sub.2 and 10 mM IVIES pH 5.6) and stored overnight at 4 C. On the day of infiltration, culture batches were diluted in 2.5 culture volumes and allowed to warm before use. Whole plants of N. benthamiana were placed upside down in the bacterial suspension in an air-tight stainless steel tank under a vacuum of 20-40 Torr for 2-min. Plants were returned to the greenhouse for a 2-6 day incubation period until harvest.
(190) Leaf Harvest and Total Protein Extraction
(191) Following incubation, the aerial part of plants was harvested, frozen at 80 C. and crushed into pieces. Total soluble proteins were extracted by homogenizing (Polytron) each sample of frozen-crushed plant material in 3 volumes of cold 50 mM Tris pH 8.0, 0.15 M NaCl, 0.1% Triton X-100 and 1 mM phenylmethanesulfonyl fluoride. After homogenization, the slurries were centrifuged at 10,000 g for 10 min at 4 C. and these clarified crude extracts (supernatant) kept for analyses.
Example 20Protein Analysis and Immunoblotting
(192) The total protein content of clarified crude extracts was determined by the Bradford assay (Bio-Rad, Hercules, Calif.) using bovine serum albumin as the reference standard. Proteins were separated by SDS-PAGE and electrotransferred onto polyvinylene difluoride (PVDF) membranes (Roche Diagnostics Corporation, Indianapolis, Ind.) for immunodetection. Prior to immunoblotting, the membranes were blocked with 5% skim milk and 0.1% Tween-20 in Tris-buffered saline (TBS-T) for 16-18h at 4 C.
(193) Immunoblotting was performed with a first incubation with a primary antibody (Table 4 presents the antibodies and conditions used for the detection of each HA), in 2 g/ml in 2% skim milk in TBS-Tween 20 0.1%. Secondary antibodies used for chemiluminescence detection were as indicated in Table 4, diluted as indicated in 2% skim milk in TBS-Tween 20 0.1%. Immunoreactive complexes were detected by chemiluminescence using luminol as the substrate (Roche Diagnostics Corporation).
(194) TABLE-US-00023 TABLE 4 Electrophoresis conditions, antibodies, and dilutions for immunoblotting of expressed proteins. HA Electrophoresis Primary Secondary subtype Influenza strain condition antibody Dilution antibody Dilution B B/Brisbane/60/2008 Non-reducing NIBSC 1:20000 Rabbit anti- 1:10000 10/146 sheep (JIR 313-035-045) B B/Wisconsin/1/2010 Non-reducing NIBSC 1:2000 Rabbit anti- 1:10000 07/356 sheep (JIR 313-035-045) B B/Massachussetts/2/2012 Non-reducing NIBSC 1:2000 Rabbit anti- 1:10000 07/356 sheep (JIR 313-035-045) H7 A/Hangzhou/1/2013 (H7N9)) Non-reducing ITC, IT- 1:5000 Goat anti- 1:5000 003-008M6 mouse (JIR 115-035-146) H3 A/Victoria/361/2011 Non-reducing TGA, AS400 1:20000 Rabbit anti- 1:10000 sheep (JIR 313-035-045) H1 A/Califomia/07/2009 (H1N1) Reducing NIB SC11/110 1 g/ml Rabbit anti- 1:7500 sheep (JIR 313-035-045 H5 A/Indonesia/05/2005 (H5N1) Reducing CBER, S-7858 1:4000 Rabbit anti- 1:10000 sheep (JIR 313-035-045) JIR: Jackson ImmunoResearch, West Grove, PA, USA; CBER: Center for Biologies Evaluation and Research, Rockville, MD, USA. Sino: Sino Biological inc., Beijing, China. TGA: Therapeutic Goods Administration, Australia. NIBSC: National Institute for Biological Standards and Control, United Kingdom ITC: Immune Technology Corp., New York, NY, USA
Example 21Hemagglutination Assay
(195) Hemagglutination assay was based on a method described by Nayak and Reichl (2004). Briefly, serial double dilutions of the test samples (100 L) were made in V-bottomed 96-well microtiter plates containing 100 L PBS, leaving 100 L of diluted sample per well. One hundred microliters of a 0.25% turkey red blood cells suspension (Bio Link Inc., Syracuse, N.Y.; for all B strains, H1, H5 and H7) or 0.5% guinea pig red blood cells suspension (for H3) were added to each well, and plates were incubated for 2h at room temperature. The reciprocal of the highest dilution showing complete hemagglutination was recorded as HA activity.
(196) All citations are hereby incorporated by reference.
(197) The present invention has been described with regard to one or more embodiments. However, it will be apparent to persons skilled in the art that a number of variations and modifications can be made without departing from the scope of the invention as defined in the claims.