# Patent

## Title
Modified isoprene synthase

## Abstract

The present application relates to a modified isoprene synthase that has an isoprene synthetic activity and has at least one mutation of an amino acid residue in the amino acid sequence of SEQ ID NO: 4, an amino acid sequence having one or several amino acid substitutions, deletions, insertions or additions in the amino acid sequence of SEQ ID NO: 4, or an amino acid sequence having 90% or more identity to the amino acid sequence of SEQ ID NO: 4. The modified isoprene synthase is useful for preparing isoprene monomers in improved yields.

## Background
CROSS REFERENCES TO RELATED APPLICATIONS
This application is a continuation of International Patent Application No. PCT/JP2014/080980, filed on Nov. 21, 2014, and claims priority to Japanese Patent Application No. 2013-242261, filed on Nov. 22, 2013, both of which are incorporated herein by reference in their entireties.


BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates to modified isoprene synthases, polynucleotides which encode such an isoprene synthase, and methods of producing isoprene with such an isoprene synthase.
Discussion of the Background
Natural rubbers are very important raw materials in the tire industry and rubber industries. While demands for rubbers will expand in motorization mainly in developing countries in future, increase of farm plantations is not easy due to regulation to deforestation and competition with palms. Thus, it is predicted that the increase of natural rubber yields is difficult to be anticipated and the balance of demands and supplies will become tight. Synthesized polyisoprene is available as a material in place of the natural rubber, and its raw material monomer, isoprene (2-methyl-1,3-butadiene), is obtained by extracting from a C5 fraction obtained by cracking of naphtha. However in recent years, with lightening in the field of crackers, the production amount of isoprene has tended to decrease, and its supply has been apprehended. Also in recent years, due to strong influence of variation in oil prices, establishment of a system for inexpensively producing isoprene derived from non-oil resource has been required for stably securing an isoprene monomer.
For such a demand, methods of producing the isoprene monomer using a transformant obtained by integrating an isolated isoprene synthase gene derived from kudzu or poplar and its mutant into a bacterium for fermentation production, and the like have been disclosed (see Japanese Laid-Open Publication No. 2011-505841, Japanese Laid-Open Publication No. 2011-518564, US Patent Application Publication No. 2011/0076743, US Patent Application Publication No. 2013/0045891, US Patent Application Publication No. 2013/0295632, US Patent Application Publication No. 2013/0330709, US Patent Application Publication No. 2013/0330796, US Patent Application Publication No. 2013/0295632, US Patent Application Publication No. 2011/0045563, US Patent Application Publication No. 2011/0039323, International Publication WO 2013/016591, Kesselmeier J. et al., Journal of Atmospheric Chemistry, vol. 33, pages 23-88, 1999, Monson R. K. et al., Plant Physiol., vol. 98, pages 1175-1180, 1992, and Kuzma J. et al., Plant Physiol., vol. 101, pages 435-440, 1993, all of which are incorporated herein by reference in their entireties).
There remains, however, a need for improved transformants.
SUMMARY OF THE INVENTION
Accordingly, it is one object of the present invention to provide novel isoprene synthases.
It is another object of the present invention to provide novel polynucleotides which encode such an isoprene synthase.
It is another object of the present invention to provide novel methods of producing isoprene with such an isoprene synthase.
It is another object of the present invention to achieve a high productivity of isoprene monomer by using a further improved enzyme.
It is another object of the present invention to provide an enzyme and the like useful for establishing an excellent isoprene monomer production system
These and other objects, which will become apparent during the following detailed description, have been achieved by the inventors' discovery of a modified isoprene synthase having an excellent isoprene monomer productivity by mutating an amino acid residue of isoprene synthase derived from Mucuna (Mucuna bracteata).
Namely, the present invention is as follows.
(1) A modified isoprene synthase that has a mutation(s) of an amino acid residue(s) corresponding to one or more amino acid residues selected from the following:
S2, F31, L35, L67, I90, V97, L114, Q123, D124, V125, K127, R128, K130, D131, G134, C137, V144, V187, R202, L224, L247, S248, L249, T257, K259, R264, D265, R266, E269, C286, K292, T298, I300, D301, Y304, D305, E312, F316, E321, V325, I328, C338, L340, C370, E371, C373, E379, S383, K386, I388, A390, Y394, S401, S402, G404, V405, L414, C416, C440, R444, N447, R458, T461, T462, T466, E471, C480, K481, R484, K492, V499, P505, F508, I518, S519, H520, C521, Y523, and G530 in any amino acid sequence of
(a) the amino acid sequence of SEQ ID NO:4,
(b) an amino acid sequence having one or several amino acid substitutions, deletions, insertions or additions in the amino acid sequence of SEQ ID NO:4, or
(c) an amino acid sequence having 90% or more identity to the amino acid sequence of SEQ ID NO:4,
and has an isoprene synthetic activity.
(2) The modified isoprene synthase according to (1), wherein said mutation is selected from the group consisting of S2A, F31E, F31K, L35E, L35K, L67E, 190E, V97E, L114E, Q123C, D124E, V125E, K127D, K127E, K127N, K127R, R128K, K130G, D131C, G134P, C137E, C137I, C137L, C137M, C137S, V144E, V187E, R202D, R202N, L224E, L247D, L247E, L247Q, S248E, S248K, S248R, L249E, L249K, L249R, L249T, T257L, K259D, K259E, K259N, K259Q, K259R, R264F, R264M, R264T, D265E, D265N, D265Q, D265R, R266N, R266Q, E269D, E269I, E269Y, C286V, C286N, K292L, T298I, I300N, D301R, Y304F, D305R, E312I, E312R, F316E, E321D, V325K, I328E, C338V, C338L, L340K, C370E, C370N, C370K, C370V, E371D, C373V, C373Y, E379T, S383I, K386R, I388C, A390C, Y394F, S401T, S402L, G404A, G404M, V405C, L414C, C416E, C440S, R444T, N447L, N447R, R458Q, T461R, T462M, T462S, T466F, T466C, T466W, T466M, T466Y, T466H, T466P, T466Q, T466N, T466A, E471C, C480N, C480Y, C480V, K481E, R484K, K492E, V499I, P505H, F508C, F508Q, F508R, I518C, I518S, S519N, H520N, C521N, C521S, C521V, C521E, C521I, Y523I, Y523L, and G530K.
(3) The modified isoprene synthase according to (1) or (2), further having a signal sequence at N-terminus.
(4) The modified isoprene synthase according to (3), which has a mutation(s) of an amino acid residue(s) corresponding to one or more amino acid residues selected from the following:
S45, F74, L78, L110, I133, V140, L157, Q166, D167, V168, K170, R171, K173, D174, G177, C180, V187, V230, R245, L267, L290, S291, L292, T300, K302, R307, D308, R309, E312, C329, K335, T341, I343, D344, Y347, D348, E355, F359, E364, V368, I371, C381, L383, C413, E414, C416, E422, S426, K429, I431, A433, Y437, S444, S445, G447, V448, L457, C459, C483, R487, N490, R501, T504, T505, T509, E514, C523, K524, R527, K535, V542, P548, F551, I561, S562, H563, C564, Y566, and G573 in any amino acid sequence of
(d) the amino acid sequence of SEQ ID NO:2,
(e) an amino acid sequence having one or several amino acid substitutions, deletions, insertions or additions in the amino acid sequence of SEQ ID NO:2, or
(f) an amino acid sequence having 90% or more identity to the amino acid sequence of SEQ ID NO:2,
and has an isoprene synthetic activity.
(5) The modified isoprene synthase according to (4), wherein said mutation is selected from the group consisting of S45A, F74E, F74K, L78E, L78K, L110E, I133E, V140E, L157E, Q166C, D167E, V168E, K170D, K170E, K170N, K170R, R171K, K173G, D174C, G177P, C180E, C180I, C180L, C180M, C180S, C180M, V187E, V230E, R245D, R245N, L267E, L290D, L290E, L290Q, S291E, S291K, S291R, L292E, L292K, L292R, L292T, T300L, K302D, K302E, K302N, K302Q, K302R, R307F, R307M, R307T, D308E, D308N, D308Q, D308R, R309N, R309Q, E312D, E312I, E312Y, C329V, C329N, K335L, T341I, I343N, D344R, Y347F, D348R, E355I, E355R, F359E, E364D, V368K, I371E, C381V, C381L, L383K, C413E, C413N, C413K, C413V, E414D, C416V, C416Y, E422T, S426I, K429R, I431C, A433C, Y437F, S444T, S445L, G447A, G447M, V448C, L457C, C459E, C483S, R487T, N490L, N490R, R501Q, T504R, T505M, T505S, T509F, T509C, T509W, T509M, T509Y, T509H, T509P, T509Q, T509N, T509A, E514C, C523N, C523Y, C523V, K524E, R527K, K535E, V542I, P548H, F551C, F551Q, F551R, I561C, I561S, S562N, H563N, C564N, C564S, C564V, C564E, C564I, Y566I, Y566L, and G573K.
(6) A polynucleotide encoding the modified isoprene synthase according to any one of (1) to (5).
(7) An expression vector comprising the polynucleotide according to (6).
(8) A host cell comprising an expression unit of a polynucleotide encoding the modified isoprene synthase according to any one of (1) to (5).
(9) The host cell according to (8), wherein said host cell has an ability to synthesize dimethylallyl diphosphate via a methylerythritol phosphate pathway.
(10) The host cell according to (9), wherein said host cell is an Escherichia coli. 
(11) The host cell according to any one of (8) to (10), wherein said host cell has an ability to synthesize dimethylallyl diphosphate via both a mevalonate pathway and a methylerythritol phosphate pathway.
(12) The host cell according to (8), wherein said host cell is a microorganism belonging to the genus Corynebacterium, the genus Pantoea, the genus Enterobacter or the genus Saccharomyces. 
(13) A method for producing a modified isoprene synthase, comprising producing the modified isoprene synthase using the host cell according to any one of (8) to (12).
(14) A method for producing a modified isoprene monomer, comprising producing the isoprene monomer from dimethylallyl diphosphate in the presence of the modified isoprene synthase according to any one of (1) to (5).
(15) The method according to (14), wherein the isoprene monomer is produced by cultivation of the host cell according to any one of (8) to (12) in a medium.
(16) The method according to (15), wherein the dimethylallyl diphosphate is supplied from a carbon source in medium by cultivation of said host cell.
(17) A method for producing an isoprene polymer, comprising (I) and (II):
(I) producing an isoprene monomer by the method according to any one of (14) to (16), and
(II) polymerizing the isoprene monomer to form the isoprene polymer.
(18) A polymer derived from an isoprene monomer produced by the method according to any one of (14) to (16).
(19) A rubber composition comprising the polymer according to (18).
(20) A tire produced by the use of the rubber composition according to (19).
According to the present invention, an excellent isoprene monomer production system can be established.



BRIEF DESCRIPTION OF THE DRAWINGS
A more complete appreciation of the invention and many of the attendant advantages thereof will be readily obtained as the same become better understood by reference to the following detailed description when considered in connection with the accompanying drawings, wherein:
FIG. 1 shows the amounts of isoprene generated per unit weight of dry leaves from various plants.
FIG. 2 shows the amounts of isoprene generated per total protein mass extracted from leaves of various plants.
FIG. 3 shows an outline of mevalonic acid pathway downstream and its surrounding region in chromosome fixation.
FIG. 4 shows an outline of mevalonic acid pathway downstream and its surrounding region controlled by a tac promoter on a chromosome.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
The present invention provides a modified isoprene synthase.
Isoprene synthase is an enzyme that converts dimethylallyl diphosphate into isoprene. The modified isoprene synthase of the present invention can be derived from Mucuna. The isoprene synthase derived from Mucuna is a protein encoded by an amino acid sequence of SEQ ID NO:4 (a mature protein in which a signal sequence has been removed) or a protein encoded by an amino acid sequence of SEQ ID NO:2 (a protein having the signal sequence). The isoprene synthase derived from Mucuna may delete a methionine residue artificially added to an N-terminus of the amino acid sequence of SEQ ID NO:4.
In one embodiment, the modified isoprene synthase of the present invention can be a mutant of isoprene synthase having no signal sequence at the N-terminus. The isoprene synthase having no signal sequence at N-terminus is one comprising any amino acid sequence of:
(a) the amino acid sequence of SEQ ID NO:4;
(b) an amino acid sequence having one or several amino acid substitutions, deletions, insertions or additions in the amino acid sequence of SEQ ID NO:4; or
(c) an amino acid sequence having 90% or more identity to the amino acid sequence of SEQ ID NO:4;
and having an isoprene synthetic activity.
In the present invention, the term isoprene synthetic activity refers to an activity to convert dimethylallyl diphosphate into isoprene (the same shall apply hereinafter).
The modified isoprene synthase of the present invention may have the signal sequence at the N-terminus. In another embodiment, the modified isoprene synthase of the present invention is a mutant of isoprene synthase having the signal sequence at the N-terminus. Examples of the signal sequence may include transit signal sequences such as a chloroplast transit signal sequence (e.g., a sequence composed of amino acid residues at positions 1 to 44 in the amino acid sequence of SEQ ID NO:2) and secretory signal sequences. Examples of the isoprene synthase having the signal sequence at the N-terminus may include those that have a mutation(s) of an amino acid residue(s) corresponding to one or more amino acid residues selected from the followings in any amino acid sequence of
(d) the amino acid sequence of SEQ ID NO:2;
(e) an amino acid sequence having one or several amino acid substitutions, deletions, insertions or additions in the amino acid sequence of SEQ ID NO:2; or
(f) an amino acid sequence having 90% or more identity to the amino acid sequence of SEQ ID NO:2;
and have an isoprene synthetic activity.
The isoprene synthase of each of the above (b) and (d) may comprise a mutation (e.g., substitution, deletion, insertion, and addition) of one or several amino acid residues. The number of mutation is, for example, 1 to 50, preferably 1 to 40, more preferably 1 to 30, still more preferably 1 to 20, and most preferably 1 to 10 (e.g., 1, 2, 3, 4, or 5).
The isoprene synthase of each of the above (c) and (f) may comprise an amino acid sequence having 90% or more identity to the amino acid sequences represented by SEQ ID NO:4 and SEQ ID NO:2. The amino acid sequence percent identity may be preferably 92% or more, more preferably 95% or more, further preferably 97% or more, and most preferably 98% or more, or 99% or more.
The identity of the amino acid sequences can be determined, for example, using the algorithm BLAST (Pro. Natl. Acad. Sci. USA, 90, 5873 (1993) which is incorporated herein by reference in its entirety) by Karlin and Altschul, and the FASTA algorithm (Methods Enzymol., 183, 63 (1990) which is incorporated herein by reference in its entirety) by Pearson. The program referred to as BLASTP was developed based on the algorithm BLAST (see http(colon)//www(dot)ncbi(dot)nlm(dot)nih(dot)gov). Thus, the identity of the amino acid sequences may be calculated using this program with default setting. Also, for example, a numerical value obtained by calculating similarity as a percentage at a setting of “unit size to compare=2” using the full length of a polypeptide portion encoded in ORF with the software GENETYX Ver. 7.0.9 from Genetyx Corporation employing the Lipman-Pearson method may be used as the identity of the amino acid sequences. Alternatively, the homology may be a value (Identity) calculated using a parameter of default setting (Gap penalty=10, Extend penalty=0.5, Matrix=EBLOSUM62) in a NEEDLE program (J Mol Biol 1970; 48: 443-453, which is incorporated herein by reference in its entirety) search. The lowest value among the values derived from these calculations may be employed as the identity of the amino acid sequences.
A position of an amino acid residue into which a mutation can be introduced in the amino acid sequence of any of the above (b), (c), (d), and (f) is known to those skilled in the art, and, for example, an additional mutation can be introduced with reference to an alignment of amino acid sequences. Specifically, a person skilled in the art can recognize a correlation between structure and function, since a person skilled in the art can 1) compare the amino acid sequences of multiple homologs (known isoprene synthases), 2) clarify regions that are relatively conserved and regions that are not relatively conserved, and then 3) predict regions capable of playing a functionally important role and regions incapable of playing a functionally important role from the regions that are relatively conserved and the regions that are not relatively conserved, respectively.
When the additional mutation of the amino acid residue is substitution, the substitution of the amino acid residue may be conservative substitution. The term “conservative substitution” refers to substitution of a certain amino acid residue with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains are well-known in the art. Examples of such families may include amino acids having a basic side chain (e.g., lysine, arginine, histidine), amino acids having an acidic side chain (e.g., aspartic acid, glutamic acid), amino acids having a non-charged polar side chain (e.g., asparagine, glutamine, serine, threonine, tyrosine, cysteine), amino acids having a non-polar side chain (e.g., glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), amino acids having a branched side chain at position β (e.g., threonine, valine, isoleucine), amino acids having an aromatic side chain (e.g., tyrosine, phenylalanine, tryptophan, histidine), amino acids having a hydroxyl group-containing (e.g., alcoholic, phenolic) side chain (e.g., serine, threonine, tyrosine), and amino acids having a sulfur-containing side chain (e.g., cysteine, methionine). Preferably, the conservative substitution of the amino acids may be the substitution between aspartic acid and glutamic acid, the substitution among arginine, lysine and histidine, the substitution between tryptophan and phenylalanine, the substitution between phenylalanine and valine, the substitution among leucine, isoleucine and alanine, and the substitution between glycine and alanine.
In the modified isoprene synthase of the present invention, at least one amino acid residue is mutated so as to improve an amount of isoprene to be produced. Examples of mutations of amino acid residues may include substitution, deletion, addition and insertion, and the substitution is preferred. An amino acid residue to be mutated is L-alanine (A), L-asparagine (N), L-cysteine (C), L-glutamine (Q), L-isoleucine (I), L-leucine (L), L-methionine (M), L-phenylalanine (F), L-proline (P), L-serine (S), L-threonine (T), L-tryptophan (W), L-tyrosine (Y), L-valine (V), L-aspartic acid (D), L-glutamic acid (E), L-arginine (R), L-histidine (H) or L-lysine (K) that is a naturally occurring L-α-amino acid, or glycine (G). When the mutation is substitution, addition or insertion, an amino acid residue after the substitution, addition or insertion corresponds to the amino acid residue to be mutated as described above. Hereinafter, “L” and “a” may be omitted in description of amino acids.
The modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the amount of isoprene to be produced may comprise the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S2, F31, L35, L67, I90, V97, L114, Q123, D124, V125, K127, R128, K130, D131, G134, C137, V144, V187, R202, L224, L247, S248, L249, T257, K259, R264, D265, R266, E269, C286, K292, T298, I300, D301, Y304, D305, E312, F316, E321, V325, I328, C338, L340, C370, E371, C373, E379, S383, K386, I388, A390, Y394, S401, S402, G404, V405, L414, C416, C440, R444, N447, R458, T461, T462, T466, E471, C480, K481, R484, K492, V499, P505, F508, I518, S519, H520, C521, Y523, and G530 in the amino acid sequences of (a) to (c) above. Because the amino acid sequences of (a) to (c) above may have the signal sequence at the N-terminus and may have the mutation such as deletion and substitution, the above position can alter depending on the presence or absence of the signal sequence and its length, the presence or absence of the mutation, and the like. For example, when the amino acid sequences of (a) to (c) above having the signal sequence at the N-terminus are the amino acid sequences of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the amount of isoprene to be produced may comprise the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S45, F74, L78, L110, I133, V140, L157, Q166, D167, V168, K170, R171, K173, D174, G177, C180, V187, V230, R245, L267, L290, S291, L292, T300, K302, R307, D308, R309, E312, C329, K335, T341, I343, D344, Y347, D348, E355, F359, E364, V368, I371, C381, L383, C413, E414, C416, E422, S426, K429, I431, A433, Y437, S444, S445, G447, V448, L457, C459, C483, R487, N490, R501, T504, T505, T509, E514, C523, K524, R527, K535, V542, P548, F551, I561, S562, H563, C564, Y566, and G573 in the amino acid sequences of (d) to (f) above. The modified isoprene synthase of the present invention may comprise a plurality of (e.g., 1 to 10, 1 to 5, 1 to 3, or 1 or 2) the mutations at above positions in combination. A mutation of an amino acid residue(s) in certain embodiments described later may also comprise a plurality of the same mutations as above at positions described above.
In one embodiment, the mutation of the amino acid residue for improving the amount of isoprene to be produced is introduced so that an isoprene synthetic activity is enhanced relative to the isoprene synthase derived from Mucuna (hereinafter referred to as isoprene synthase before modification if necessary). Examples of the mutation of the amino acid residue for enhancing the isoprene synthetic activity may include mutations of amino acid residues corresponding to one or more amino acid residues selected from F31, L35, L67, I90, V97, D124, V125, K127, R128, K130, D131, G134, C137, R202, L247, S248, L249, T257, K259, R264, D265, R266, E269, C286, K292, T298, D301, D305, E312, F316, E321, V325, I328, L340, C370, E371, C373, E379, S383, K386, A390, S401, S402, G404, R444, N447, R458, T461, T462, E471, C480, K481, R484, K492, V499, P505, F508, I518, S519, H520, C521, Y523, and G530 in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the amount of isoprene to be produced may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from F74, L78, L110, I133, V140, D167, V168, K170, R171, K173, D174, G177, C180, R245, L290, S291, L292, T300, K302, R307, D308, R309, E312, C329, K335, T341, D344, D348, E355, F359, E364, V368, I371, L383, C413, E414, C416, E422, S426, K429, A433, S444, S445, G447, R487, N490, R501, T504, T505, E514, C523, K524, R527, K535, V542, P548, F551, I561, S562, H563, C564, Y566, and G573 in the amino acid sequence of (d) to (f) above. The extent of enhancement of the isoprene synthetic activity of the modified isoprene synthase relative to the isoprene synthase before the modification (e.g., SEQ ID NO:4 or SEQ ID NO:2) is not particularly limited as long as the activity is enhanced relative to that of the isoprene synthase before the modification, and is, for example, 1.1 fold or more, preferably 1.2 fold or more, more preferably 1.3 fold or more, still more preferably 1.5 fold or more, and most preferably 2 fold or more.
More specifically, the modified isoprene synthase comprising a mutation of an amino acid residue for enhancing the isoprene synthetic activity may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from F31E, F31K, L35E, L35K, L67E, 190E, V97E, D124E, V125E, K127D, K127E, K127N, K127R, R128K, K130G, D131C, G134P, C137E, C137I, C137L, C137M, C137S, R202D, R202N, L247D, L247E, L247Q, S248E, S248K, S248R, L249E, L249K, L249R, L249T, T257L, K259D, K259E, K259N, K259Q, K259R, R264F, R264M, R264T, D265E, D265N, D265Q, D265R, R266N, R266Q, E269D, E269I, E269Y, C286N, K292L, T298I, D301R, D305R, E312I, E312R, F316E, E321D, V325K, I328E, L340K, C370V, E371D, C373Y, E379T, K386R, A390C, S401T, S402L, G404A, G404M, R444T, N447L, N447R, R458Q, T461R, T462M, E471C, C480N, C480Y, K481E, R484K, K492E, V499I, P505H, F508C, F508Q, F508R, I518C, I518S, S519N, H520N, C521N, Y523I, Y523L, and G530K in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the amount of isoprene to be produced may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from F74E, F74K, L78E, L78K, L110E, I133E, V140E, D167E, V168E, K170D, K170E, K170N, K170R, R171K, K173G, D174C, G177P, C180E, C180I, C180L, C180M, C180S, R245D, R245N, L290D, L290E, L290Q, S291E, S291K, S291R, L292E, L292K, L292R, L292T, T300L, K302D, K302E, K302N, K302Q, K302R, R307F, R307M, R307T, D308E, D308N, D308Q, D308R, R309N, R309Q, E312D, E312I, E312Y, C329N, K335L, T341I, D344R, D348R, E355I, E355R, F359E, E364D, V368K, I371E, L383K, C413V, E414D, C416Y, E422T, K429R, A433C, S444T, S445L, G447A, G447M, R487T, N490L, N490R, R501Q, T504R, T505M, E514C, C523N, C523Y, K524E, R527K, K535E, V542I, P548H, F551C, F551Q, F551R, I561C, I561S, S562N, H563N, C564N, Y566I, Y566L, and G573K in the amino acid sequence of (d) to (f) above.
In another embodiment, the mutation of amino acid residue for improving the amount of isoprene to be produced is introduced so that enzyme stability is improved relative to the isoprene synthase before the modification. Improvement of the enzyme stability can be confirmed, for example, by comparing an accumulation rate of isoprene by the modified isoprene synthase with that by the isoprene synthase before the modification, as described later in the examples. Examples of the mutations of amino acid residues for improving the enzyme stability may include the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S2, V97, L114, Q123, V125, D131, C137, V144, V187, L224, C286, T298, I300, C338, C370, C373, S383, I388, A390, V405, L414, C416, C440, E471, C480, K481, I518, and C521 in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the enzyme stability may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S45, V140, L157, Q166, V168, D174, C180, V187, V230, L267, C329, T341, I343, C381, C413, C416, S426, I431, A433, V448, L457, C459, C483, E514, C523, K524, I561, and C564 in the amino acid sequences of (d) to (f) above. The extent of the improvement of the enzyme stability of the modified isoprene synthase relative to the isoprene synthase before the modification (e.g., SEQ ID NO:4 or SEQ ID NO:2) is not particularly limited as long as the enzyme stability is improved relative to the isoprene synthase before the modification, and is, for example, 1.1 fold or more, preferably 1.3 fold or more, more preferably 1.5 fold or more, still more preferably 2 fold or more, and most preferably 3 fold or more.
More specifically, the modified isoprene synthase comprising a mutation of an amino acid residue for improving the enzyme stability may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S2A, V97E, L114E, Q123C, V125E, D131C, C137E, C137I, C137M, C137S, V144E, V187E, L224E, C286V, C286N, T298I, I300N, C338V, C338L, C370V, C370E, C370N, C370K, C373V, C373Y, S383I, I388C, A390C, V405C, L414C, C416E, C440S, E471C, C480N, C480V, C480Y, K481E, I518C, C521E, C521I, C521S, C521N, and C521V in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the enzyme stability may those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from S45A, V140E, L157E, Q166C, V168E, D174C, C180E, C180I, C180M, C180S, V187E, V230E, L267E, C329V, C329N, T341I, I343N, C381V, C381L, C413V, C413E, C413N, C413K, C416V, C416Y, S426I, I431C, A433C, V448C, L457C, C459E, C483S, E514C, C523N, C523V, C523Y, K524E, I561C, C564E, C564I, C564S, C564N, and C564V in the amino acid sequences of (d) to (f) above.
In still another embodiment, the mutation of the amino acid residue for improving the amount of isoprene to be produced is introduced so that the amount of isoprene to be produced in a host is improved relative to that by the isoprene synthase before the modification. The improvement of the amount of isoprene to be produced in the host is accomplished, for example, by enhancing the isoprene synthetic activity and/or improving the enzyme stability. Examples of the mutation of the amino acid residue for improving the amount of isoprene to be produced in the host may include mutations of amino acid residues corresponding to one or more amino acid residues selected from Y304, Y394, T462, and T466 in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising the mutation of the amino acid residue for improving the amount of isoprene to be produced in the host may be those comprising mutations of amino acid residues corresponding to one or more amino acid residues selected from Y347, Y437, T505, and T509 in the amino acid sequences of (d) to (f) above. The extent of the improvement of the amount of isoprene to be produced by the modified isoprene synthase in the host relative to that by the isoprene synthase before the modification (e.g., SEQ ID NO: 4 or SEQ ID NO:2) is not particularly limited as long as the amount of isoprene to be produced in the host is improved relative to that by the isoprene synthase before the modification, and is, for example 1.02 fold or more, preferably 1.05 fold or more, more preferably 1.07 fold or more, still more preferably 1.1 fold or more, and most preferably 1.15 fold or more.
More specifically, the modified isoprene synthase comprising the mutation of the amino acid residue for improving the amount of isoprene to be produced in the host may be those comprising a mutation(s) of an amino acid residue(s) corresponding to one or more amino acid residues selected from Y304F, Y394F, T462S, T466F, T466C, T466W, T466M, T466Y, T466H, T466P, T466Q, T466N, and T466A in the amino acid sequences of (a) to (c) above. Alternatively, when the amino acid sequence of (a) to (c) above having the signal sequence at the N-terminus is the amino acid sequence of (d) to (f) above, the modified isoprene synthase of the present invention comprising a mutation of an amino acid residue for improving the amount of isoprene to be produced in the host may be those comprising the mutation(s) of the amino acid residue(s) corresponding to one or more amino acid residues selected from Y347F, Y437F, T505S, T509F, T509C, T509W, T509M, T509Y, T509H, T509P, T509Q, T509N, and T509A in the amino acid sequences of (d) to (f) above.
The modified isoprene synthase of the present invention may have another peptide component (e.g., a tag moiety) at C-terminus or N-terminus. Examples of the other peptide component which may be added to the modified isoprene synthase of the present invention may include peptide components that make purification of an objective protein easy (e.g., tag moieties such as histidine tag and Strep-tag II; proteins commonly used for the purification of an objective protein, such as glutathione-S-transferase and a maltose binding protein), peptide components that enhance solubility of an objective protein (e.g., Nus-tag), peptide components that work as a chaperon (e.g., a trigger factor), and peptide components as a protein or a protein domain having another function or a linker linking them.
The present invention also provides a polynucleotide encoding the modified isoprene synthase of the present invention. The polynucleotide of the present invention may be DNA or RNA, but is preferably DNA.
The modified isoprene synthase of the present invention can be prepared using a transformant of the present invention that expresses the modified isoprene synthase of the present invention, or using a cell-free system, and the like. The transformant of the present invention can be made, for example, by making an expression vector of the present invention and then transforming a host cell with this expression vector.
The present invention provides an expression vector. The expression vector of the present invention comprises a polynucleotide of the present invention or a polynucleotide encoding a protein of the present invention.
Examples of the expression vector of the present invention may include cellular system vectors that express the protein in a host or cell-free system vectors that utilize a protein translation system. The expression vector may also be a plasmid, a viral vector, a phage, an integrative vector, or an artificial chromosome. The integrative vector may be a vector of a type entirely incorporated into genome in a host cell. Alternatively, the integrative vector may be a vector of a type in which only a portion (e.g., an expression unit described later) of which is incorporated into the genome in the host cell. The expression vector may further be a DNA vector or an RNA vector.
A known expression vector suitable for a host is used as the cellular system vector. Examples thereof may include ColE-based plasmids typified by pBR322 derivatives, pACYC-based plasmid having a p15A origin, pSC-based plasmids, and F factor-derived mini F plasmids such as Bac-based plasmids in Escherichia coli (E. coli). In addition, expression vectors having a tryptophan promoter such as trc and tac, a lac promoter, a T7 promoter, a T5 promoter, a T3 promoter, an SP6 promoter, an arabinose inducible promoter, a cold shock promoter, a tetracycline inducible promoter, or the like may also be included.
Examples of the cell-free system vector may include an expression vector having the T7 promoter and an expression vector having the T3 promoter included in the cellular system vectors; vectors such as pEU-based plasmids having an SP6 promoter or the T7 promoter for synthesizing a wheat protein in the cell-free system, and the like.
In protein synthesis using the cell-free system vector, first cDNA of an objective protein is transcribed to synthesize mRNA using a transcription system. Such a transcription system may include a known system where cDNA is transcribed using RNA polymerase. Examples of the RNA polymerase may include T7 RNA polymerase.
Then, mRNA is translated to synthesize the protein using a cell-free protein synthesis system that is a translation system. This system includes ribosome, a translation initiation factor, a translation extension factor, a dissociation factor, amino-acyl tRNA synthetase, and the like, which are elements necessary for the translation. Such a protein translation system may include an Escherichia coli extract, a rabbit reticulocyte extract, and a wheat germ extract.
Further, a rearrangement type cell-free protein synthesis system consisting of factors obtained by independently purifying elements necessary for the above translation may be included.
Protein synthesis using the cellular system vector will be described layer in Transformants.
A protein synthesized using the cellular system vector or the cell-free system vector may be purified. A purification method may include methods using salting out and various chromatographic methods. When an expression vector is designed to express a tag sequence such as a histidine tag attached at the N-terminus or C-terminus of an objective protein, a purification method by an affinity column using a substance such as nickel or cobalt having affinity for this tag is employed. In addition, the purity of the protein of the present invention can be enhanced by purifying with appropriate combination of ion-exchange chromatography, gel filtration chromatography, and the like.
The expression vector of the present invention further comprises a homologous promoter or a heterologous promoter operably linked to the above polynucleotide. The term “homologous promoter” refers to a natural promoter of an isoprene synthase gene derived from Mucuna. The term “heterologous promoter” refers to promoters other than the natural promoter of the isoprene synthase gene derived from Mucuna. Therefore, examples of the heterologous promoter may include promoters of genes derived from Mucuna other than the isoprene synthase gene derived from Mucuna, promoters derived from organisms other than Mucuna (e.g., microorganisms, animals, insects, and plants), promoters derived from viruses, and artificially synthesized promoters. A promoter commonly used for production of a foreign protein may also be used as the heterologous promoter.
The expression vector of the present invention may further comprise a terminator downstream of the above polynucleotide. Examples of such a terminator may include a T7 terminator, a fd phage terminator, a T4 terminator, a terminator of a tetracycline resistant gene, and a terminator of an Escherichia coli trpA gene.
The expression vector of the present invention may further comprise a ribosome binding site (e.g., Shine-Dalgarno sequence) upstream of an initiation codon.
The expression vector of the present invention may further comprise a polynucleotide encoding a drug resistant gene. Examples of the drug resistant gene may include resistant genes to drugs such as tetracycline, ampicillin, kanamycin, hygromycin, and phosphinothricin.
The expression vector of the present invention may further comprise one or more regions that allow for homologous recombination with genome of a host cell when introduced into the host cell. For example, the expression vector of the present invention may be designed such that an expression unit comprising the polynucleotide of the present invention is located between a pair of homologous regions (e.g., homology arm homologous to a certain sequence in host genome, loxP, FRT). The expression unit refers to a unit that comprises a given polynucleotide to be expressed and a promoter (e.g., homologous promoter, heterologous promoter) operably linked thereto and allows for transcription of the polynucleotide. The expression unit may further comprise elements such as the terminator, the ribosome binding site and the drug resistant gene described above.
The transformant of the present invention is a host cell that can produce the modified isoprene synthase of the present invention or can express the polynucleotide of the present invention to produce the modified isoprene synthase. Specifically, the transformant of the present invention is a host cell comprising the expression unit comprising the polynucleotide of the present invention. Examples of the host cell comprising the expression unit comprising the polynucleotide of the present invention may include a host cell in which the expression vector of the present invention has been entirely introduced and a host cell in which the expression unit in the expression vector of the present invention has been introduced into its genome. The host cell is not particularly limited as long as it can express the modified isoprene synthase of the present invention. The host cell may be homogeneous or heterogeneous to the modified isoprene synthase of the present invention and the polynucleotide of the present invention, but is preferably heterogeneous. The host cell may also be homogeneous or heterogeneous to the above promoter, but is preferably heterogeneous. Examples of the host cell may include animal cells, plant cells, insect cells and microbial cells, and are preferably the microbial cells. More preferably, the host cell used for the present invention is a bacterial cell or a fungal cell. The bacterial cell may be Gram-positive or Gram-negative.
Examples of the gram-positive bacterium may include bacteria belonging to the genera Bacillus, Listeria, Staphylococcus, Streptococcus, Enterococcus, Clostridium, Corynebacterium, and Streptomyces. Bacteria belonging to the genera Bacillus and Corynebacterium are preferable.
Examples of the bacteria belonging to the genus Bacillus may include Bacillus subtilis, Bacillus anthracis, and Bacillus cereus. Bacillus subtilis is more preferable.
Examples of the bacteria belonging to genus the Corynebacterium may include Corynebacterium glutamicum, Corynebacterium efficiens, and Corynebacterium callunae. Corynebacterium glutamicum is more preferable.
Examples of the gram-negative bacterium may include bacteria belonging to the genera Escherichia, Pantoea, Salmonella, Vivrio, Serratia, and Enterobacter. The bacteria belonging to the genera Escherichia, Pantoea and Enterobacter are preferable.
Escherichia coli is preferable as the bacteria belonging to the genus Escherichia. 
Examples of the bacteria belonging to the genus Pantoea may include Pantoea ananatis, Pantoea stewartii, Pantoea agglomerans, and Pantoea citrea. Pantoea ananatis and Pantoea citrea are preferable. Strains exemplified in EP 0 952 221, which is incorporated herein by reference in its entirety, may be used as the bacteria belonging to the genus Pantoea. Examples of representative strains of the bacteria belonging to genus Pantoea may include Pantoea ananatis AJ13355 strain (FERM BP-6614) and Pantoea ananatis AJ13356 strain (FERM BP-6615), both of which are disclosed in EP 0 952 221, which is incorporated herein by reference in its entirety.
Examples of the bacteria belonging to the genus Enterobacter may include Enterobacter agglomerans and Enterobacter aerogenes. Enterobacter aerogenes is preferable. The bacterial strains exemplified in EP 0 952 221, which is incorporated herein by reference in its entirety, may be used as the bacteria belonging to the genus Enterobacter. Examples of representative strains of the bacteria belonging to the genus Enterobacter may include Enterobacter agglomerans ATCC12287 strain, Enterobacter aerogenes TACC 13048 strain, Enterobacter aerogenes NBRC 12010 strain (Biotechnol. Bioeng., 2007 Mar. 27; 98(2): 340-348, which is incorporated herein by reference in its entirety), and Enterobacter aerogenes AJ110637 (FERM BP-10955). The Enterobacter aerogenes AJ110637 strain was deposited to International Patent Organism Depositary (IPOD), National Institute of Advanced Industrial Science and Technology (AIST) (Chuo No. 6, Higashi 1-1-1, Tsukuba City, Ibaraki Pref., JP, Postal code 305-8566) as of Aug. 22, 2007, with the deposit number of FERM P-21348 and was transferred to the international deposition based on Budapest Treaty on Mar. 13, 2008, and the receipt number FERM BP-10955 was given thereto.
Examples of the fungus may include microorganisms belonging to the genera Saccharomyces, Schizosaccharomyces, Yarrowia, Trichoderma, Aspergillus, Fusarium, and Mucor. The microorganisms belonging to the genera Saccharomyces, Schizosaccharomyces, Yarrowia, or Trichoderma are preferable.
Examples of the microorganisms belonging to the genus Saccharomyces may include Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, and Saccharomyces oviformis. Saccharomyces cerevisiae is preferable.
Schizosaccharomyces pombe is preferable as a microorganism belonging to the genus Schizosaccharomyces. 
Yarrowia lypolytica is preferable as a microorganism belonging to the genus Yarrowia. 
Examples of the microorganisms belonging to the genus Trichoderma may include Trichoderma harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, and Trichoderma viride. Trichoderma reesei is preferable.
In addition, the host used for the present invention is not particularly limited as long as the host has an ability to synthesize dimethylallyl diphosphate (DMAPP) via a mevalonate (MVA) pathway and/or a methylerythritol phosphate (MEP) pathway that are involved in synthesis of dimethylallyl diphosphate that is a substrate of the isoprene synthase, and may be an insect cell, an animal cell, a plant cell, and so forth.
In the transformant of the present invention, the pathway to synthesize dimethylallyl diphosphate (DMAPP) that is the substrate of the isoprene synthase may be further enhanced. For such an enhancement, an expression unit that expresses an isopentenyl-diphosphate delta isomerase having an ability to convert isopentenyl diphosphate (IPP) into dimethylallyl diphosphate (DMAPP) may be introduced into the transformant of the present invention by the above-described expression vector. An expression unit that expresses one or more enzymes involved in the mevalonate pathway and/or methylerythritol phosphate pathway associated with formation of IPP and/or DMAPP may also be introduced into the transformant of the present invention by the above-described expression vector. The expression unit for such an enzyme may further include a plurality of enzymes (e.g., one, two, three, or four or more) involved in the mevalonate pathway and/or the methylerythritol phosphate pathway, and may be, for example, an expression vector for polycistronic mRNA. The origin of the one or more enzymes involved in the mevalonate pathway and/or the methylerythritol phosphate pathway may be homologous or heterologous to the host. When the origin of the enzyme involved in the mevalonate pathway and/or the methylerythritol phosphate pathway is heterologous to the host, for example, the host may be a bacterium as described above (e.g., Escherichia coli) and the enzyme involved in the mevalonate pathway may be derived from a fungus (e.g., Saccharomyces cerevisiae). In addition, when the host inherently produces the enzyme involved in the methylerythritol phosphate pathway, the expression vector to be introduced into the host may express an enzyme involved in the mevalonate pathway.
Examples of isopentenyl-diphosphate delta isomerase (EC: 5.3.3.2) may include Idi1p (ACCESSION ID NP_015208), AT3G02780 (ACCESSION ID NP_186927), AT5G16440 (ACCESSION ID NP_197148) and Idi (ACCESSION ID NP_417365).
Examples of the enzymes involved in the mevalonate (MVA) pathway may include mevalonate kinase (EC: 2.7.1.36; example 1, Erg12p, ACCESSION ID NP_013935; example 2, AT5G27450, ACCESSION ID NP_001190411), phosphomevalonate kinase (EC: 2.7.4.2; example 1, Erg8p, ACCESSION ID NP_013947; example 2, AT1G31910, ACCESSION ID NP_001185124), diphosphomevalonate decarboxylase (EC: 4.1.1.33; example 1, Mvd1p, ACCESSION ID NP_014441; example 2, AT2G38700, ACCESSION ID NP_181404; example 3, AT3G54250, ACCESSION ID NP_566995), acetyl-CoA-C-acetyltransferase (EC: 2.3.1.9; example 1, Erg10p, ACCESSION ID NP_015297; example 2, AT5G47720, ACCESSION ID NP_001032028; example 3, AT5G48230, ACCESSION ID NP_568694), hydroxymethylglutaryl-CoA synthase (EC: 2.3.3.10; example 1, Erg13p, ACCESSION ID NP_013580; example 2, AT4G11820, ACCESSION ID NP_192919; example 3, MvaS, ACCESSION ID AAG02438), hydroxymethylglutaryl-CoA reductase (EC: 1.1.1.34; example 1, Hmg2p, ACCESSION ID NP_013555; example 2, Hmg1p, ACCESSION ID NP_013636; example 3, AT1G76490, ACCESSION ID NP_177775; example 4, AT2G17370, ACCESSION ID NP_179329, EC: 1.1.1.88, example, MvaA, ACCESSION ID P13702), and acetyl-CoA-C-acetyltransferase/hydroxymethylglutaryl-CoA reductase (EC: 2.3.1.9/1.1.1.34, example, MvaE, ACCESSION ID AAG02439).
Examples of the enzymes involved in the methylerythritol phosphate (MEP) pathway may include 1-deoxy-D-xylulose-5-phosphate synthase (EC: 2.2.1.7, example 1, Dxs, ACCESSION ID NP_414954; example 2, AT3G21500, ACCESSION ID NP_566686; example 3, AT4G15560, ACCESSION ID NP_193291; example 4, AT5G11380, ACCESSION ID NP_001078570), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (EC: 1.1.1.267; example 1, Dxr, ACCESSION ID NP_414715; example 2, AT5G62790, ACCESSION ID NP_001190600), 4-diphosphocytidyl-2-C-methyl-D-erythritol synthase (EC: 2.7.7.60; example 1, IspD, ACCESSION ID NP_417227; example 2, AT2G02500, ACCESSION ID NP_565286), 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (EC: 2.7.1.148; example 1, IspE, ACCESSION ID NP_415726; example 2, AT2G26930, ACCESSION ID NP_180261), 2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase (EC: 4.6.1.12; example 1, IspF, ACCESSION ID NP_417226; example 2, AT1G63970, ACCESSION ID NP_564819), 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate synthase (EC: 1.17.7.1; example 1, IspG, ACCESSION ID NP_417010; example 2, AT5G60600, ACCESSION ID NP_001119467), and 4-hydroxy-3-methyl-2-butenyl diphosphate reductase (EC: 1.17.1.2; example 1, IspH, ACCESSION ID NP_414570; example 2, AT4G34350, ACCESSION ID NP_567965).
Introduction of the expression unit, in which the gene is incorporated, into the host (transformation) can be carried out using known methods regarding the expression vector. Examples of such a method may include a competent cell method using a microbial cell treated with calcium and an electroporation method. The gene may be introduced by infecting the microbial cell with a phage vector rather than the plasmid vector.
Further, a gene encoding the enzyme involved in the mevalonate pathway or the methylerythritol phosphate pathway that synthesizes dimethylallyl diphosphate that is the substrate of the isoprene synthase may also be introduced into the transformant of the present invention.
Examples of such an enzyme may include 1-deoxy-D-xylose-5-phosphate synthase that converts a pyruvate and D-glycelaldehyde-3-phosphate into 1-deoxy-D-xylose-5-phosphate, and isopentyl diphosphate isomerase that converts isopentenyl diphosphate into dimethylallyl diphosphate.
The protein of the present invention may be extracted or purified from the transformant of the present invention, and isoprene may be produced by culturing the transformant that expresses the protein of the present invention.
Method of Producing Isoprene Monomer and Isoprene Polymer
The present invention provides a method of producing an isoprene monomer. The method of producing an isoprene monomer of the present invention includes producing an isoprene monomer from dimethylallyl diphosphate in the presence of the protein of the present invention.
The method of producing the isoprene monomer of the present invention is not particularly limited as long as it is performed under the presence of the protein of the present invention, and it can be performed, for example, by utilizing an enzyme reaction system that uses the protein itself of the present invention (e.g., purified protein) or by culturing the transformant of the present invention that produces the protein of the present invention. Preferably, the method is performed by culturing the transformant of the present invention. When the transformant of the present invention is used in the method of producing the isoprene monomer of the present invention, dimethylallyl diphosphate that is a raw material of the isoprene monomer is efficiently supplied from a carbon source in a culture medium by the transformant of the present invention. The transformant of the present invention produces the isoprene monomer mainly as an outgas from the carbon source in the culture medium. Thus, the isoprene monomer is recovered by collecting gas produced from the transformant. Dimethylallyl diphosphate that is the substrate of the isoprene synthase is synthesized from the carbon source in the culture medium via the mevalonate pathway or the methylerythritol phosphate pathway in the host.
The culture medium for culturing the transformant of the present invention preferably contains the carbon source to be converted into isoprene. The carbon source may include carbohydrates such as monosaccharides, disaccharides, oligosaccharides, and polysaccharides; invert sugars obtained by hydrolyzing sucrose; glycerol; compounds having one carbon atom (hereinafter referred to as a C1 compound) such as methanol, formaldehyde, formate, carbon monoxide, and carbon dioxide; oils such as corn oil, palm oil and soybean oil; acetate; animal fats; animal oils; fatty acids such as saturated fatty acids and unsaturated fatty acids; lipids; phospholipids; glycerolipids; glycerine fatty acid esters such as monoglyceride, diglyceride and triglyceride; polypeptides such as microbial proteins and plant proteins; renewable carbon sources such as hydrolyzed biomass carbon sources; yeast extracts, or combinations thereof. For a nitrogen source, inorganic ammonium salts such as ammonium sulfate, ammonium chloride, and ammonium phosphate, organic nitrogen such as hydrolyzed soybeans, ammonia gas, ammonia water, and the like can be used. It is desirable to include required substances such as vitamin B1 and L-homoserine, or yeast extract and the like in an appropriate amount as an organic trace nutrient source. In addition thereto, potassium phosphate, magnesium sulfate, iron ion, manganese ion, and the like may be added in small amounts if necessary. The culture medium used in the present invention may be a natural medium or a synthesized medium as long as the culture medium contains a carbon source, a nitrogen source, inorganic ions, and optionally other organic trace ingredients.
Examples of the monosaccharides may include triose such as ketotriose (dihydroxyacetone) and aldotriose (glyceraldehyde); tetrose such as ketotetrose (erythrulose) and aldotetrose (erythrose, threose); pentose such as ketopentose (ribulose, xylulose), aldopentose (ribose, arabinose, xylose, lyxose) and deoxysaccharide (deoxyribose); hexose such as ketohexose (psychose, fructose, sorbose, tagatose), aldohexose (allose, altrose, glucose, mannose, gulose, idose, galactose, tallose), and deoxysaccharide (fucose, fucrose, rhamnose); and heptose such as sedoheptulose. C6 sugars such as fructose, mannose, galactose and glucose; and C5 sugars such as xylose and arabinose are preferable.
Examples of the disaccharides may include sucrose, lactose, maltose, trehalose, turanose, and cellobiose. Sucrose and lactose are preferable.
Examples of the oligosaccharides may include trisaccharides such as raffinose, melezitose and maltotriose; tetrasaccharides such as acarbose and stachyose; and other oligosaccharides such as fructooligosaccharide (FOS), galactooligosaccharide (GOS) and mannan-oligosaccharide (MOS).
Examples of the polysaccharides may include glycogen, starch (amylose, amylopectin), cellulose, dextrin, and glucan (β1,3-glucan). Starch and cellulose are preferable.
Examples of the microbial protein may include polypeptides obtainable from a yeast or bacterium. Examples of the plant protein may include polypeptides obtainable from soybean, corn, canola, Jatropha, palm, peanut, sunflower, coconut, mustard, cotton seed, palm kernel oil, olive, safflower, sesame, and linseed.
Examples of the lipid may include substances containing one or more saturated or unsaturated fatty acids of C4 or more.
The oil is preferably a lipid that contains one or more saturated or unsaturated fatty acids of C4 or more and is liquid at room temperature, and examples of the oil may include lipids obtainable from soybean, corn, canola, Jatropha, palm, peanut, sunflower, coconut, mustard, cotton seed, Palm kernel oil, olive, safflower, sesame, linseed, oily microbial cells, Chinese tallow tree, and a combination of two or more thereof.
Examples of the fatty acid may include compounds represented by a formula RCOOH (“R” represents a hydrocarbon group).
The unsaturated fatty acid is a compound having at least one double bond between two carbon atoms in “R”, and examples of the unsaturated fatty acid may include oleic acid, vaccenic acid, linoleic acid, palmitelaidic acid and arachidonic acid.
The saturated fatty acid is a compound where the “R” is a saturated aliphatic group, and examples of the saturated fatty acid may include docosanoic acid, eicosanoic acid, octadecanoic acid, hexadecanoic acid, tetradecanoic acid, and dodecanoic acid.
Among them, those containing one or more C2 to C22 fatty acids are preferable as the fatty acid, and those containing C12 fatty acid, C14 fatty acid, C16 fatty acid, C18 fatty acid, C20 fatty acid and C22 fatty acid are more preferable.
The carbon source may include salts and derivatives of these fatty acids and salts of these derivatives. Examples of the salt may include lithium salts, potassium salts, and sodium salts.
Examples of the carbon source may also include combinations of carbohydrate such as glucose with the lipid(s), the oil(s), the fats, the fatty acid(s) and glycerin fatty acid(s) ester(s).
Examples of the renewable carbon source may include hydrolyzed biomass carbon sources.
Examples of the biomass carbon source may include cellulose-based substrates such as waste materials of woods, papers and pulps, leafy plants, and fruit pulps; and partial plants such as stalks, grain particles, roots, and tubers.
Examples of the plants to be used as the biomass carbon source may include corn, wheat, rye, sorghum, triticale, rice, millet, barley, cassava, legumes such as peas, potato, sweet potato, banana, sugar cane, and tapioca.
When the renewable carbon source such as biomass is added to the culture medium, the carbon source is preferably pretreated. Examples of the pretreatment may include an enzymatic pretreatment, a chemical pretreatment, and a combination of the enzymatic pretreatment and the chemical pretreatment.
It is preferred that the renewable carbon source is entirely or partially hydrolyzed before being added to the culture medium.
Examples of the carbon source may also include a yeast extract and a combination of the yeast extract with the other carbon source such as glucose. The combination of the yeast extract with the C1 compound such as carbon dioxide and methanol is preferable.
In the method of culturing the transformant according to the present invention, it is preferable that the cell is cultured in a standard medium containing saline and nutrients.
The culture medium is not particularly limited, and examples of the culture medium may include ready-made general media that are commercially available such as Luria Bertani (LB) broth, Sabouraud dextrose (SD) broth, and yeast medium (YM) broth. The medium suitable for the cultivation of the specific host can be selected appropriately for the use.
It is desirable to include appropriate minerals, salts, supplemental elements, buffers, and ingredients known for those skilled in the art to be suitable for the cultivation and to facilitate the production of isoprene in addition to the appropriate carbon source in the cell medium.
It is preferable to add the sugar, a metal salt, an antimicrobial substance, and the like to the medium in order to maintain the expression of the protein of the present invention in the transformant of the present invention.
The culture condition for the transformant of the present invention is not particularly limited as long as the protein of the present invention can be expressed, and a standard cell culture condition can be used.
The culture temperature is preferably 20 to 37° C., the gas composition is preferably about 6 to about 84% of CO2 concentration, and the pH value is preferably about 5 to about 9.
It is preferable that the culturing is performed under an aerobic, oxygen-free, or anaerobic condition depending on a nature of the host.
Examples of methods of culturing the transformant include a method using a known fermentation method such as a batch cultivation method, a feeding cultivation method, or a continuous cultivation method.
In the batch cultivation method, a medium composition is added at start of the fermentation, the host is inoculated in the medium composition, and the transformant is cultured while pH and an oxygen concentration are controlled.
In the cultivation of the transformant by the batch cultivation method, the growth of the transformant starts from a mild induction phase, passes through a logarithmic growth phase and finally goes to a stationary phase in which a growth speed is reduced or stopped. Isoprene is produced by the transformant in the logarithmic growth phase and the stationary phase.
In the feeding cultivation method, in addition to the above batch method, the carbon source is gradually added according to the progress of a fermentation process. The feeding cultivation method is effective when the amount of the carbon source is to be restricted in the medium because metabolism of the transformant tends to be reduced due to catabolite suppression. The feed cultivation can be performed using a restricted amount or an excessive amount of the carbon source such as glucose.
In the continuous cultivation method, a certain amount of the medium is continuously supplied to a bioreactor at a constant rate while the same amount of the medium is removed. In the continuous cultivation method, the culture can be kept constantly at a high concentration and the transformant in the culture medium is generally in the logarithmic growth phase.
The nutrition can be supplemented by entirely or partly exchanging the medium appropriately, and accumulation of metabolic byproducts that potentially have adverse effects on the growth of the transformant, and the accumulation of dead cells can be prevented.
Examples of the promoter possessed by the expression vector or expression unit of the present invention may include a constitutive promoter or an inducible promoter. When the expression vector or the expression unit of the present invention has the inducible promoter such as a lac promoter, the expression of the protein of the present invention may be induced by, for example, adding IPTG (isopropyl-β-thiogalactopyranoside) into the culture medium.
Examples of the method of evaluating the amount of isoprene monomer produced by culturing the transformant of the present invention may include a method in which a gas phase is collected by a headspace method and this gas phase is analyzed by gas chromatography.
In detail, the isoprene monomer in a headspace which is obtained by culturing the transformant in a sealed vial with shaking the culture medium is analyzed by standard gas chromatography. Then, an area calculated by a curve measured by gas chromatography is converted into the amount of the isoprene monomer produced with the transformant using a standard curve.
Examples of the method of collecting the isoprene monomer obtained by culturing the transformant of the present invention may include gas stripping, fractional distillation, or dissociation of the isoprene monomer adsorbed to a solid phase by heat or vacuum, or extraction with a solvent.
In the gas stripping, isoprene gas is continuously removed from the outgas. Such removal of the isoprene gas can be performed by various methods. Examples of the removal may include adsorption to a solid phase, separation into a liquid phase, and a method in which the isoprene gas is directly condensed.
The isoprene monomer can be collected by a single step or multiple steps. When the isoprene monomer is collected by the single step, the isoprene monomer is converted into the liquid phase simultaneously with separating the isoprene monomer from the outgas. The isoprene monomer can also be directly condensed from the outgas to make the liquid phase. When the isoprene monomer is collected by the multiple stages, the isoprene monomer is separated from off-gas and subsequently converted into the liquid phase. For example, the isoprene monomer is adsorbed to a solid phase, and extracted from the solid phase with the solvent.
Exemplary methods of collecting the isoprene monomer may comprise further purifying the isoprene monomer. Examples of the purification may include separation from a liquid phase extract by distillation and various chromatographic methods.
The protein of the present invention is more excellent in ability to produce isoprene than conventional isoprene synthase. Thus, the isoprene monomer can be produced efficiently using the transformant that expresses the protein of the present invention.
The present invention further provides a method of producing an isoprene polymer. The method of producing the isoprene polymer according to the present invention comprises the following (I) and (II):
(I) producing an isoprene monomer by the method of the present invention; and
(II) polymerizing the isoprene monomer to form an isoprene polymer.
The step (I) can be performed in the same manner as in the method of producing the isoprene monomer according to the present invention described above. The polymerization of the isoprene monomer in the step (II) can be performed by any method such as addition polymerization known in the art (e.g., synthesis methods in organic chemistry).
The rubber composition of the present invention comprises a polymer derived from isoprene produced by a method for producing isoprene according to the present invention. The polymer derived from isoprene may be a homopolymer (i.e., isoprene polymer) or a heteropolymer comprising isoprene and one or more monomer units other than the isoprene (e.g., a copolymer such as a block copolymer). Preferably, the polymer derived from isoprene is a homopolymer (i.e., isoprene polymer) produced by a method for producing isoprene polymer according to the present invention. The rubber composition of the present invention may further comprise one or more polymers other than the above polymer, one or more rubber components, and/or other components. The rubber composition of the present invention can be manufactured using a polymer derived from isoprene. For example, the rubber composition of the present invention can be prepared by mixing a polymer derived from isoprene with one or more polymers other than the above polymer, one or more rubber components, and/or other components such as a reinforcing filler, a crosslinking agent, a vulcanization accelerator, and an antioxidant.
The tire of the present invention is manufactured using the rubber composition of the present invention. The rubber composition of the present invention may be applied to any portion of the tire without limitation, which may be selected as appropriate depending on the application thereof. For example, the rubber composition of the present invention may be used in a tread, a base tread, a sidewall, a side reinforcing rubber and a bead filler of a tire. The tire can be manufactured by a conventional method. For example, a carcass layer, a belt layer, a tread layer, which are composed of unvulcanized rubber, and other members used for the production of usual tires may be successively laminated on a tire molding drum, then the drum may be withdrawn to obtain a green tire. Thereafter, the green tire may be heated and vulcanized in accordance with an ordinary method, to thereby obtain a desired tire (e.g., a pneumatic tire).
Other features of the invention will become apparent in the course of the following descriptions of exemplary embodiments which are given for illustration of the invention and are not intended to be limiting thereof.
EXAMPLES
Example 1: Design of Modified Enzyme of Isoprene Synthase (IspS) (1) and Analysis of Modified Enzyme of Isoprene Synthase Using Crude Purification Solution
(1-1) Design of Modified Enzyme of IspS
For efficient screening of modified enzymes, rational modification was carried out exploiting information on steric structure. A gene of IspSM that was isoprene synthetase derived from Mucuna was utilized as an isoprene synthase (IspS) gene. IspSM is an enzyme encoded by a gene where a chloroplast transit signal was deleted in the IspS gene derived from Mucuna (its nucleotide and amino acid sequences are represented by SEQ ID NO:1 and SEQ ID NO:2, respectively) and its codon usage was optimized for E. coli. A nucleotide sequence of a polynucleotide encoding IspSM and an amino acid sequence of IspSM are represented by SEQ ID NO:3 and SEQ ID NO:4, respectively. Since a steric structure of IspSM is unknown, a model structure of IspSM was acquired by a homology modeling method using a steric structure of the isoprene synthase derived from Populus×canescnes (PDB code: 3n0g) as a template.
Two points were focused on in high functionality of IspS. A first one is to improve affinity between IspS and a dimethylallyl pyrophosphate (DMAPP) molecule that is a substrate thereof. According to the reference of Schnitzler (J. P. Schnitzler et al, Planta., 2005, 222, 777, which is incorporated herein by reference in its entirety), a Km value between IspS derived from Populus×canescnes and DMAPP that is the substrate thereof is known to be of the order of mM. A substrate affinity in a common enzymatic reaction is of the order of μM. Thus, it was thought that there was room to improve the substrate affinity of IspS. In general, it is known that affinity and specificity between an enzyme and a substrate can be altered by modifying an amino acid residue(s) present in the vicinity of a substrate binding site (Practical Application of Protein Engineering, edited by Kimitsuna Watanabe et al., CMC Publishing, which is incorporated herein by reference in entirety). Thus, in order to improve the affinity between IspS and DMAPP, a residue positioned in the vicinity of a DMAPP binding site was subjected to modification. Hereinafter, this line is referred to as Concept (1). A second one is to enhance stability of IspS. It is known that the stability of an enzyme is closely associated with a steric structure of an enzyme molecule. From the model structure of IspS derived from Mucuna (IspSM), it has been predicted that IspSM has no intermolecular disulfide bond in its molecule and has a highly hydrophobic region on its molecular surface. As reported in the reference (e.g., M. Matsumura et al, Nature, 1989, 342, 291-293, which is incorporated herein by reference in its entirety), it is known that an enzyme is further stabilized by modifying a free Cys residue and introducing a hydrophilic residue to the molecular surface. It has been suggested from the model structure that an N terminal region of IspS does not form a constant structure. From this, it has been anticipated that the stability of IspS can be enhanced by modifying the N-terminal region itself and altering the number of residues. The report of Ray Fall et al. has suggested that IspS forms a dimer upon expressing its function. Thus, it has been anticipated that a dimer structure can be stabilized by focusing on an intermolecular interaction of IspS with one another (GM. Silver et al, J. Biol. Chem., 1995, 270, 13010, which is incorporated herein by reference in its entirety).
Hereinafter, the modification of the free Cys residue and optimization of the vicinity of the free Cys residue are referred to as Concept (2), as well as introduction of the hydrophilic residue to the molecular surface, optimization of the N-terminal residue of IspS and stabilization of the dimeric structure of the IspS molecule are referred to as Concept (3).
(1-1-1) Amino Acids after Modification
Amino acids were selected from acidic residues (D, E), basic residues (R, K), neutral residues (N, Q), hydrophilic residues (M, S) and aromatic residues (Y, F) with focusing on two points. For a first point, amino acids that were close to amino acids before the modification in bulkiness were selected with reference to the truth table for physicochemical natures of amino acids (e.g., M. J. Zvelebil et al, J. Mol. Biol., 1987, 195, 57, which is incorporated herein by reference in its entirety) and BLOSSUM table that were indicators of amino acid homology (S. Henikoff et al, Proc. Natl. Acad. USA., 1992, 89, 10915, which is incorporated herein by reference in its entirety). For a second point, information on steric structure was visually inspected and when a space filling rate in the vicinity of a modified residue is low, amino acids suitable for filling the space were selected.
(1-1-2) Selection of Residues to be Modified
In Concept (1), amino acid residues, a side chain of which was directed toward a DMAPP molecule were selected as subjects for modification among amino acid residues present within the shortest 7 Å from total atoms composing the DMAPP molecule in the model steric structure of IspSM. Modified enzymes in Concept (1) correspond to modified enzymes of numbers 1 to 88 shown in Table 1-1.
Then, in Concept (2), all nine Cys residues present as free thiol (i.e., C137, C286, C338, C370, C373, C440, C446, C480, C521) were selected as subjects for the modification. Also a case where the modification of the Cys residue had not worked successfully was supposed, and amino acid residues positioned in the vicinity of free thiol and in the distance capable of making a hydrogen bond with the residue were also selected as subjects for the modification. Modified enzymes in Concept (2) correspond to modified enzymes of numbers 89 to 178 shown in Table 1-2.
Finally in Concept (3), Val residues that were present on the molecular surface and were hydrophobic and in particular potentially brought about no large change in the steric structure in the model steric structure of IspSM were selected as subjects for the modification. It has been described that N-terminal residues are involved in resistance to protease and substitution thereof with an amino acid such as Gly having a small side chain enhances the resistance (A. Bachmair et al, Science, 234, 179-186(1986) and J. W. Tobias et al, Science, 254, 1374-1377(1991), both of which are incorporated herein by reference in their entireties). Thus, Gly and Ala and the like were selected and modified according to the reference information. Further, for the stabilization by dimerization of an IspS molecule, residues present in a dimer interface and capable of forming a disulfide bond were selected from the information on steric structure. Modified enzymes in Concept (3) correspond to modified enzymes of numbers 179 to 211 shown in Table 1-3.
(1-2) Construction of Plasmid for Expressing Modified Enzyme of IspSM
A plasmid for expressing the isoprene synthase derived from Mucuna in a large amount was constructed by the following procedures. For a vector portion, PCR with pCold-TF (supplied from TaKaRa Bio, catalog #3365, sequence information: GenBank/EMBL/DDBJ accession ID AB213654) as a template was carried out using synthesized oligonucleotides shown in pCold-TF PCR primer 1 and pCold-TF PCR primer 2 as primers. PCR with pUC57-IspSM [see (Reference Example 3-3)] as the template was carried out using IspSM primer 1 and IspSM primer 2 as the primers. PrimeStar HS (supplied from TaKaRa Bio, catalog #R010A) was used as polymerase for PCR method, and a reaction solution was prepared according to a composition attached to the kit. A cycle of 95° C. for 10 seconds, 55° C. for 5 seconds, and 72° C. for 6 minutes was used as a reaction condition, and the cycle was repeated 30 times. These resulting DNA fragments were ligated using In-Fusion HD Cloning Kit (supplied from Clontech, catalog #639648). The constructed plasmid was designated as pCold-TF-IspSM (SEQ ID NO:9). The polynucleotide consisting of the nucleotide residues at positions 1663 to 3318 in the nucleotide sequence of SEQ ID NO:9 encodes IspSM.
Primers Used for PCR







pCold-TF PCR primer-1


(SEQ ID NO: 5)


5′-CCTACCTTCGATACCACCACTACC-3′


 


pCold-TF PCR primer-2


(SEQ ID NO: 6)


5′-TAGGTAATCTCTGCTTAAAAGCACAGAATC-3′


 


IspSM primer-1


(SEQ ID NO: 7)


5′-GGTAGTGGTGGTATCGAAGGTAGGATGTCCGCCGTTTCAAGCCA-3′


 


IspSM primer-2


(SEQ ID NO: 8)


5′-GATTCTGTGCTTTTAAGCAGAGATTACCTATTAGTTAATCGGGAACG


GGTCAA-3′






(1-3) Preparation of Expression Plasmid

A plasmid encoding the designed modified enzyme was acquired by the following methods. The plasmid pCold-TF-IspSM for expression prepared by the aforementioned method was used as a template, synthesized oligonucleotides for introducing an amino acid mutation shown in Tables 1-1 to 1-3 described later were prepared for each modified enzyme, and PCR was carried out using these oligonucleotides as primers. PrimeStar HS (supplied from TaKaRa Bio) was used as polymerase for the PCR method, and a reaction solution was prepared according to a composition attached to the kit. A cycle of 95° C. for 10 seconds, 55° C. for 5 seconds, and 72° C. for 6 minutes was used for PCR, and the cycle was repeated 30 times. The solution after PCR was digested with DpnI (Toyobo) at 37° C. for 2 hours. Subsequently, E. coli competent cells (Ecos competent cell DH-5α supplied from Nippon Gene, catalog #310-06231) were added thereto, and after heat shock at 42° C. for 45 seconds, seeded onto an LB plate, (a) 10 g/L of Bacto tryptone, (b) 5 g/L of yeast extract, (c) 10 g/L of NaCl, (d) 100 mg/L of ampicillin, (d) 30 g/L of agar, (a) and (b) from Becton Dickinson and Company, (c) and (d) from Nacalai Tesque, containing 100 mg/L of ampicillin (Nacalai Tesque). Stationary cultivation at 37° C. for 14 hours was carried out in the plate. Then, a formed colony was inoculated to 2 mL of an LB medium, (a) 10 g/L of Bacto tryptone, (b) 5 g/L of yeast extract, (c) 10 g/L of NaCl, (d) 100 mg/L of ampicillin, (a) and (b) from Becton Dickinson and Company, (c) and (d) from Nacalai Tesque, and cultured at 37° C. for 4 hours with shaking at 120 rpm. Microbial cells were collected by centrifugation at 14,000×g for one minute, and then pCold-TF-IspSM having the introduced mutation (hereinafter described as pCold-TF-mIspSM) was collected using Fastgene mini prep kit (Nippon Genetics). Subsequently, according to standard methods, a sequencing reaction by BigDye terminator ver3.1 (Applied Biosystems), and it was confirmed by a DNA sequencer 3130×1 (ABI) that the objective mutation had been introduced.
(1-4) Preparation of Modified Enzyme Crude Purified Solution
E. coli BL21 (DE3) (supplied from Life Technologies) was transformed with plasmid DNA of vector pCold-TF-mIspSM encoding the modified enzyme prepared in the aforementioned methods using the heat shock method. After the transformation, the cells were seeded on an LB plate, and the stationary cultivation was carried out at 37° C. for 14 hours. A formed colony was inoculated to 5 mL of the LB medium, and cultured at 37° C. for 4 hours with shaking at 120 rpm. Subsequently, 100 mL of the LB medium was added to a 250 ml volume Sakaguchi flask, the resulting cultured medium in total volume was inoculated thereto, and microbial cells were cultured at 37° C. with shaking at 120 ppm. When OD660 exceeded 1, IPTG (Nacalai Tesque) at a final concentration of 1 mM was added, and the cultivation with shaking at 120 ppm was carried out at 15° C. for 14 hours. Then, 30 mL of the resulting cultured medium was centrifuged at 5000×g for 10 minutes, and a supernatant was discarded. 1 mL of disruption buffer (50 mM sodium phosphate, 500 mM NaCl, pH 8.0, Nacalai Tesque) was added to microbial cells obtained here, which were then suspended. Subsequently, about 0.9 mL of beads for disruption (YBG01, diameter 0.1 mm) and 0.9 mL of the microbial cell suspension were placed in a 2 ml volume tube exclusive to a multibead shocker. And the microbial cells were disrupted in the multibead shocker (MB701 (S) model, Yasui Kikai) under a condition of 2500 rpm, 4° C. and 20 cycles of ON for 30 seconds and OFF for 30 seconds. Then, 200 mL of His-select nickel affinity gel (Sigma) was added to a 1.5 mL tube, resin was washed with the disruption buffer, and then, a disruption supernatant in total amount was added. After incubation at 4° C. for 14 hours, 1 mL of cleavage reaction buffer (25 mM tris-HCl, 10 mM MgCl2, pH 8.0) was added for washing. After tapping, centrifugation at 14,000×g for one minute was carried out, and a supernatant was discarded. The same manipulation was repeated one more time, then 200 μL of the cleavage reaction buffer was added, 1 μL of Factor Xa (Merck) was added, and the stationary cultivation was carried out at 4° C. for 14 hours. Subsequently, the centrifugation at 14,000×g for one minute was carried out, and a supernatant was collected to use as a crude purified solution of mIspSM.
(1-5) Comparison of Amounts of Isoprene Produced by Respective Modified Enzymes
On ice, 46 μL of the crude purified solution of each modified enzyme was placed in a 0.2 mL volume PCR tube (Nippon Genetics), and 4 μL of 40 mM DMAPP (Cayman, catalog #63180) was added thereto. After lightly tapping, a hole was made on a cap. Next, this tube was placed in a 20 mL vial (Perkin Elmer), and immediately tightly sealed with a cap for a head space vial with a butyl rubber septum (Perkin Elmer). A reaction for producing isoprene was carried out at 37° C. for 20 minutes. After cooling at 4° C. for 10 minutes, the reaction mixture was further incubated at room temperature for 10 minutes. After termination of the reaction, the concentration of isoprene in the head space of the vial was measured by gas chromatography based on the condition described in Reference Example (4-3). Measured by gas chromatography. In order to narrow down effective modified enzymes, an amount of isoprene converted by each modified enzyme was divided by an amount of isoprene converted by the isoprene synthase derived from Mucuna which deletes a chloroplast transit signal (hereinafter referred to as wild type IspSM as needed) to calculate a relative activity value. Their results are shown in Table 1-1 to Table 1-3. Of 211 modified enzymes analyzed, 116 modified enzymes lost their activity. Of the remaining modified enzymes, those having the relative activity value of 30% or more were assessed as promising modified enzymes, which were 68 modified enzymes. Their results are shown in Tables 2-1 and 2-2.







TABLE 1-1







Activity values of modified enzymes produced based on Concept (1)










Modified



No.
enzyme
Activity*












1
R264D
0%


2
R264Y
0%


3
R264I
0%


4
F294I
0%


5
F294Y
2%


6
F294R
13%


7
F294Q
0%


8
V297I
0%


9
V297F
0%


10
V297Y
0%


11
V297D
0%


12
T298I
236%


13
T298F
0%


14
T298Y
0%


15
T298D
0%


16
D301Q
0%


17
D301M
0%


18
D301Y
0%


19
D302E
2%


20
D302Q
0%


21
Y304E
0%


22
Y304Q
0%


23
Y304R
0%


24
Y304I
0%


25
Y304F
0%


26
D305Q
0%


27
D305K
0%


28
D305M
0%


29
D348E
185%


30
D348Q
0%


31
F376D
0%


32
F376R
0%


33
F376Q
29%


34
E379D
0%


35
E379R
0%


36
E379M
0%


37
S383I
35%


38
S383R
0%


39
S383E
10%


40
S383F
0%


41
S383M
220%


42
Y394Q
0%


43
Y394M
0%


44
A398I
0%


45
A398R
0%


46
A398E
0%


47
A398F
0%


48
A398S
0%


49
S401E
0%


50
S401N
0%


51
S401K
0%


52
S401F
0%


53
S401Y
0%


54
S402E
0%


55
S402N
0%


56
S402K
0%


57
S402F
0%


58
S402Y
0%


59
S402I
0%


60
S403E
0%


61
S403N
0%


62
S403K
0%


63
S403F
0%


64
S403Y
0%


65
F443I
0%


66
F443Y
2%


67
F443R
0%


68
R444K
0%


69
R444E
0%


70
R444Y
0%


71
N447S
0%


72
N447Q
0%


73
N447E
0%


74
T451S
5%


75
T451E
30%


76
T451N
0%


77
E455D
15%


78
E455Q
11%


79
E455M
5%


80
E460I
0%


81
E460R
0%


82
E460Q
0%


83
E460Y
5%


84
T462Q
9%


85
T462E
0%


86
T462S
23%


87
N463E
0%


88
N463Y
0%





*Activity value relative to wild type













TABLE 1-2







Activity values of Modified enzymes produced based on Concept (2)










Modified



No.
enzyme
Activity*












89
F129C
0%


90
D131C
124%


91
C137S
58%


92
C137M
70%


93
C137T
1%


94
C137I
164%


95
C137K
240%


96
C137E
208%


97
C286I
55%


98
C286V
1504%


99
C286E
0%


100
C286K
0%


101
C286N
56%


102
V290C
23%


103
V290S
0%


104
V290M
0%


105
V290T
0%


106
I300N
113%


107
F316C
0%


108
V320C
902%


109
C338L
90%


110
C338V
99%


111
C338F
0%


112
C338Y
1%


113
C338E
0%


114
C338K
0%


115
V346C
18%


116
V346S
39%


117
V346M
118%


118
V346T
0%


119
C370E
234%


120
C370K
85%


121
C370N
201%


122
C370V
255%


123
C373F
181%


124
C373Y
224%


125
C373W
0%


126
C373V
1391%


127
S399C
0%


128
V405E
40%


129
L414C
979%


130
C416E
157%


131
C416K
197%


132
C416F
0%


133
C416Y
123%


134
C416W
0%


135
C416I
0%


136
V436E
0%


137
R437E
0%


138
C440M
0%


139
C440S
231%


140
C440T
0%


141
C440I
0%


142
C440V
0%


143
I442E
0%


144
F443C
17%


145
C446E
26%


146
C446K
0%


147
C446N
52%


148
C446S
0%


149
C446Y
21%


150
C446I
5%


151
C446V
101%


152
S452C
52%


153
S464C
25%


154
I465C
2%


155
A479E
0%


156
A479K
0%


157
A479D
1%


158
C480D
4%


159
C480K
0%


160
C480Y
62%


161
C480R
6%


162
C480N
67%


163
C480V
42%


164
K481E
58%


165
K481D
0%


166
F508C
141%


167
M515C
0%


168
I518C
214%


169
S519C
11%


170
H520C
0%


171
C521E
265%


172
C521V
244%


173
C521K
0%


174
C521N
93%


175
C521S
102%


176
C521I
112%


177
C521V
244%


178
Y523C
0%





*Activity value relative to wild type













TABLE 1-3







Activity value of Modified enzymes produced base on Concept (3)









No.
Modified enzyme
Relative activity












179
S2K
0%


180
S2E
0%


181
S2G
0%


182
S2A
62%


183
V55E
45%


184
V76E
45%


185
V97E
75%


186
L114E
41%


187
V121E
0%


188
Q123C
69%


189
V125E
75%


190
V144E
60%


191
V187E
80%


192
V191E
40%


193
L224E
42%


194
V236E
40%


195
V270E
0%


196
V290E
0%


197
L313E
0%


198
V320E
0%


199
V346E
0%


200
L354E
0%


201
I388C
41%


202
I388C/Q123C
101%


203
I388C/N360C
40%


204
V400E
40%


205
V405C
35%


206
V436C
25%


207
R437C
0%


208
I442C
35%


209
E471C
145%


210
E471C/A390C
205%


211
L529E
0%
















TABLE 2-1







List of Modified enzymes exhibiting relative activity of 30% or more


(No. 1)










No.
Modified enzyme
Relative activity
Concept













1
C286V
1504%
(2)


2
C373V
1391%
(2)


3
L414C
979%
(2)


4
V320C
902%
(2)


5
C521E
265%
(2)


6
C370V
255%
(2)


7
C521V
244%
(2)


8
C137K
240%
(2)


9
T298I
236%
(1)


10
C370E
234%
(2)


11
C440S
231%
(2)


12
C373Y
224%
(2)


13
S383M
220%
(1)


14
I518C
214%
(2)


15
C137E
208%
(2)


16
E471C/A390C
205%
(3)


17
C370N
201%
(2)


18
C416K
197%
(2)


19
D348E
185%
(1)


20
C373F
181%
(2)


21
C137I
164%
(2)


22
C416E
157%
(2)


23
E471C
145%
(3)


24
F508C
141%
(2)


25
D131C
124%
(2)


26
C416Y
123%
(2)


27
V346M
118%
(2)


28
I300N
113%
(2)


29
C521I
112%
(2)


30
C521S
102%
(2)


31
C446V
101%
(2)


32
I388C/Q123C
101%
(3)


33
C338V
99%
(2)
















TABLE 2-2







List of Modified enzymes exhibiting relative activity of 30% or more


(No. 2)










No.
Modified enzyme
Relative activity
Concept













34
C521N
93%
(2)


35
C338L
90%
(2)


36
C370K
85%
(2)


37
V187E
80%
(3)


38
V97E
75%
(3)


39
V125E
75%
(3)


40
C137M
70%
(2)


41
Q123C
69%
(3)


42
C480N
67%
(2)


43
C480Y
62%
(2)


44
S2A
62%
(3)


45
V144E
60%
(3)


46
C137S
58%
(2)


47
K481E
58%
(2)


48
C286N
56%
(2)


49
C286I
55%
(2)


50
S452C
52%
(2)


51
C446N
52%
(2)


52
V55E
45%
(3)


53
V76E
45%
(3)


54
C480V
42%
(2)


55
L224E
42%
(3)


56
L114E
41%
(3)


57
I388C
41%
(3)


58
I388C/N360C
40%
(3)


59
V405E
40%
(2)


60
V191E
40%
(3)


61
V236E
40%
(3)


62
V400E
40%
(3)


63
V346S
39%
(2)


64
V405C
35%
(3)


65
I442C
35%
(3)


66
S383I
35%
(1)


67
T451E
30%
(1)









(1-6) Semi-Quantitative Evaluation of Ability of Modified Enzyme to Convert into Isoprene

The aforementioned comparison of the amounts of isoprene produced by respective modified enzymes is a qualitative analysis, and thus, an enzyme concentration of mIspSM is not controlled. Thus, for 36 of 68 promising modified enzymes, the crude purified solution of mIspSM was developed on 4 to 12% NuPAGE (Life Technologies, catalog #NPO323BOX), and a band derived from each modified enzyme was quantified as a band intensity using a gel analyzer (BioRad). The band intensity derived from each modified enzyme was divided by a band intensity derived from the wild type to calculate a relative intensity. An amount of isoprene converted from DMAPP by mIspSM for 20 minutes was quantified by the same method as in the aforementioned comparison of the amounts of isoprene produced by respective modified enzymes. Hereinafter, the amount of isoprene produced by the reaction for 20 minutes is referred to as an amount of isoprene produced in an early phase. Further, in order to evaluate the enzyme stability of mIspSM, an amount of isoprene produced for a long period of time was quantified and referred to as an ability to accumulate isoprene. In order to evaluate the ability to accumulate isoprene, a reaction mixture composed of 4 μL of crude purified mIspSM solution, 41 μL of reaction buffer (50 mM Tris-HCl, 20 mM MgCl2, pH 8.0) and 4 μL of 40 mM DMAPP was reacted at 37° C. for 17 hours. Subsequently, the produced isoprene was quantified by gas chromatography based on the condition described Reference Example (4-3). The resulting amount of isoprene produced in the early phase was divided by the band intensity to calculate a specific amount of isoprene produced in the early phase (Formula 1). The resulting ability to accumulate isoprene was divided by the band intensity to calculate a specific ability to accumulate isoprene (Formula 2). For the specific amount of isoprene produced in the early phase, a ratio was calculated so as to compare the modified enzymes with the wild type enzyme (Formula 3). For the specific ability to accumulate isoprene, a ratio was calculated so as to compare the modified enzymes with the wild type enzyme (Formula 4).

(Specific amount of isoprene produced in early phase)=(Amount of isoprene after reaction for 20 minutes)/(Band intensity)  Formula 1:

(Specific ability to accumulate isoprene)=(Amount of isoprene after reaction for 17 hours)/(Band intensity)  Formula 2:

(Ratio of modified enzyme to wild type for amount of isoprene produced in early phase)=(Formula 1 for modified enzyme)/(Formula 1 for wild type)  Formula 3:

(Ratio of modified enzyme to wild type for ability to accumulate isoprene)=(Formula 2 for modified enzyme)/(Formula 2 for wild type)  Formula 4:

The results are shown in Table 3. Those where the ratio of the modified enzyme to the wild type for the amount of isoprene produced in the early phase or the ratio of the modified enzyme to the wild type for the ability to accumulate isoprene was 1.1 fold or more were defined as effective modified enzymes. The modified enzymes where both ratios had increased were C446N, V97E, D131C, C137I, C137S, E471C/A390C, T298I, V125E, and I518C, the modified enzymes where only the ratio of the modified enzyme to the wild type for the ability to accumulate isoprene had increased were C521V, C521E, C480V, C286I, D348E, C370V, I300N, C521I, C286V, C137M, C137K, and C286N, and those where only the ratio of the modified enzyme to the wild type for the amount of isoprene produced in the early phase had increased were C480Y, C346M, C521N, and S383M.







TABLE 3







Ratio of mIspSM to wild type for activity and isoprene accumulation














Effective



Modified
Ratio for
Ratio for
modified


enzyme
activity*
accumulation*
enzyme
Effective function














C521V
0.9
22.5
Yes
Accum.*


C521E
0.3
16.7
Yes
Accum.*


C480V
0.7
9.4
Yes
Accum.*


C286I
0.8
7.4
Yes
Accum.*


D348E
0.2
6.3
Yes
Accum.*


C370V
0.9
5.8
Yes
Accum.*


C446N
1.3
5
Yes
Accum./Early pro.*


V97E
2.2
4.9
Yes
Accum./Early pro.*


I300N
0.9
4.7
Yes
Accum.*


C521I
0.4
4.5
Yes
Accum.*


C286V
0.7
4.5
Yes
Accum.*


D131C
2.4
4.2
Yes
Accum./Early pro.*


C137I
2.3
3.8
Yes
Accum./Early pro.*


C137M
0.4
3.4
Yes
Accum.*


C137S
1.8
2.9
Yes
Accum./Early pro.*


E471C/
1.3
2.3
Yes
Accum./Early pro.*


A390C


C137K
0.9
2.2
Yes
Accum.*


T298I
1.1
1.9
Yes
Accum./Early pro.*


V125E
1.2
1.5
Yes
Accum./Early pro.*


C286N
1
1.4
Yes
Accumulation


I518C
1.2
1.1
Yes
Accum./Early pro.*


S2A
0.9
1
No


L114E
0.4
0.9
No


C480N
0.5
0.9
No


C480Y
1.5
0.9
Yes
Early pro.*


V346M
1.1
0.9
Yes
Early pro.*


C521S
0.4
0.9
No


C373Y
0.3
0.9
No


C338L
0.9
0.8
No


Q123C
0.2
0.7
No


C521N
3.7
0.7
Yes
Early pro.*


K481E
1
0.7
No


L224E
0.1
0.6
No


V346S
0.4
0.5
No


C440S
0.4
0.4
No


S383M
1.1
0.4
Yes
Early pro.*





*Ratio for activity: Ratio of mIspSM to wild type for amount of isoprene produced in early phase


*Ratio for accumulation: Ratio of mIspSM to wild type for ability to accumulate isoprene


*Accum.: Ability of accumulation


*Early pro.: Amount of early production


“Yes” in columns for the effective modified enzyme indicates the effective modified enzyme where the value calculated in Formula 3 or Formula 4 is 1.1 folds or more in the modified enzyme as compared with the wild type.


“No” in columns for the effective modified enzyme indicates a non-effective modified enzyme where the value calculated in Formula 3 or Formula 4 is less than 1.1 folds in the modified enzyme as compared with the wild type. The ability of accumulation in columns for the effective function indicates that the value calculated in Formula 3 is 1.1 folds or more, and the amount of early production indicates that the value calculated in Formula 3 is 1.1 folds or more.






Example 2: Design of Modified Enzymes of Isoprene Synthase (IspS) and Analysis of Modified Enzymes of Isoprene Synthase by Fermentation Method Using Transformants
(2-1) Construction of Plasmid for Expressing Mutant IspSM
A mutation was introduced into an IspSM gene by the following procedures. PCR with pSTV-Ptac-IspSM as a template was carried out using primers for mutation introduction and PrimeStar polymerase (supplied from TaKaRa Bio). The nucleotide sequence of the polynucleotide encoding IspSM and its amino acid sequence are represented by SEQ ID NO:3 and 4, respectively as described in Example 1. A reaction solution was prepared according to a composition attached to the kit, and a cycle of 98° C. for 10 seconds, 54° C. for 20 seconds and 72° C. for 300 seconds was repeated 40 times. As a result, a PCR product of the IspSM gene having the introduced mutation was obtained. The resulting PCR product was purified followed by treatment with a restriction enzyme DpnI (TaKaRa Bio). E. coli JM109 was transformed with the PCR product after treatment with DpnI by a heat shock method, then applied onto an LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 16 to 24 hours. Subsequently, a transformant exhibiting resistance to chloramphenicol was obtained from the resulting plate. Plasmid extraction was carried out from the resulting transformant according to standard methods. Subsequently, in order to confirm that the mutation was introduced into an objective position as designed in the plasmid, a nucleotide sequence was analyzed by a sequencer. It was thus confirmed that amino acid substitution had occurred in the IspSM protein. Positions of the amino acid substitution in the IspSM protein and names for the plasmids for expressing mutant IspSM were described in Table 4.







TABLE 4







Positions of the amino acid substitution in the IspSM protein and names


for the plasmids for expressing mutant IspSM









Positions


Names for plasmids for expressing mutant
of amino acid substitution in


IspSM
IspSM protein





pSTV-Ptac-IspSM (Y304F)
Y304F


pSTV-Ptac-IspSM (Y394F)
Y394F


pSTV-Ptac-IspSM (T462S)
T462S


pSTV-Ptac-IspSM (T466F)
T466F


pSTV-Ptac-IspSM (T466C)
T466C


pSTV-Ptac-IspSM (T466W)
T466W


pSTV-Ptac-IspSM (T466M)
T466M


pSTV-Ptac-IspSM (T466Y)
T466Y


pSTV-Ptac-IspSM (T466H)
T466H


pSTV-Ptac-IspSM (T466P)
T466P


pSTV-Ptac-IspSM (T466Q)
T466Q


pSTV-Ptac-IspSM (T466N)
T466N


pSTV-Ptac-IspSM (T466A)
T466A









(2-2) Introduction of Plasmid for Expressing Mutant IspSM into Ptac-KKDyI Strain

Competent cells of MG1655 Ptac-KKDyI strain (see Reference Example (7-4)) were prepared, and then each of pSTV-Ptac-IspSM, pSTV-Ptac-IspSM (Y304F), pSTV-Ptac-IspSM (Y394F), pSTV-Ptac-IspSM (T462S), pSTV-Ptac-IspSM (T466F), pSTV-Ptac-IspSM (T466C), pSTV-Ptac-IspSM (T466W), pSTV-Ptac-IspSM (T466M), pSTV-Ptac-IspSM (T466Y), pSTV-Ptac-IspSM (T466H), pSTV-Ptac-IspSM (T466P), pSTV-Ptac-IspSM (T466Q), pSTV-Ptac-IspSM (T466N), or pSTV-Ptac-IspSM (T466A) was introduced thereto by an electroporation method. Culture medium containing the transformant was evenly applied onto an LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 16 to 24 hours. Subsequently, a transformant with resistance to chloramphenicol was obtained from the resulting plate. A strain where pSTV-Ptac-IspSM, pSTV-Ptac-IspSM (Y304F), pSTV-Ptac-IspSM (Y394F), pSTV-Ptac-IspSM (T462S), pSTV-Ptac-IspSM (T466F), pSTV-Ptac-IspSM (T466C), pSTV-Ptac-IspSM (T466W), pSTV-Ptac-IspSM (T466M), pSTV-Ptac-IspSM (T466Y), or pSTV-Ptac-IspSM (T466H) had been introduced into MG1655 Ptac-KKDyI strain was designated as Ptac-KKDyI/IspSM, Ptac-KKDyI/IspSM (Y304F), Ptac-KKDyI/IspSM (Y394F), Ptac-KKDyI/IspSM (T462S), Ptac-KKDyI/IspSM (T466F), Ptac-KKDyI/IspSM (T466C), Ptac-KKDyI/IspSM (T466W), Ptac-KKDyI/IspSM (T466M), Ptac-KKDyI/IspSM (T466Y), Ptac-KKDyI/IspSM (T466H), Ptac-KKDyI/IspSM (T466P), Ptac-KKDyI/IspSM (T466Q), Ptac-KKDyI/IspSM (T466N), or Ptac-KKDyI/IspSM (T466A).
(2-3) Comparison of Ability to Produce Isoprene in Strains Having Introduced Mutant IspSM
Each of the pSTV-Ptac-IspSM and the MG1655 Ptac-KKDyI strain having each introduced mutant IspSM were evenly applied onto an LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 18 hours. One loopful of microbial cells from the resulting plate was inoculated to 1 mL of M9 glucose medium (containing mevalonic acid) in a headspace vial (supplied from Perkin Elmer, 22 mL, CREAR CRIMP TOP VIAL cat#B0104236), and subsequently cultured with shaking for 24 hours. A composition of the M9 glucose medium (containing mevalonic acid) was described in Table 5. DMAPP (dimethylallyl diphosphate) is supplied from a carbon source (mevalonic acid) in the medium by culturing the above transformant in this medium. OD600 values at the end of the culture, amounts of produced isoprene, and relative values of production by Ptac-KKDyI/IspSM were described in Table 6. A concentration of isoprene in the headspace in the vial was measured by gas chromatography. A condition for the gas chromatography is described below.







TABLE 5





Composition of M9 glucose medium (containing mevalonic acid)


















Glucose
2.0 (g/L)



Na2HPO4
6.0 (g/L)



KH2PO4
3.0 (g/L)



NH4Cl
1.0 (g/L)



Mevalonic acid (ADEKA)
1.0 (g/L)



1M MgSO4 (autoclaved)
1.0 ml



1M CaCl2 (autoclaved)
0.1 ml










Chloramphenicol was added at a final concentration of 60 mg/L.

A total volume was adjusted to 1 L, and then filter sterilization was carried out.








TABLE 6







OD600 values, amounts of produced isoprene (mg/L), and relative


values as compared to production by Ptac-KKDyI/IspSM













Relative




Isoprene
valuea)




production
(Isoprene


Bacterial strain name
OD600
(mg/L)
production)





Ptac-KKDyI/IspSM
3.07 ± 0.09
38.94 ± 1.95
1.00


Ptac-KKDyI/IspSM(Y304F)
3.28 ± 0.09
40.03 ± 0.77
1.03


Ptac-KKDyI/IspSM(Y394F)
3.28 ± 0.09
40.25 ± 1.97
1.03


Ptac-KKDyI/IspSM(T462S)
3.64 ± 0.02
43.08 ± 1.48
1.10


Ptac-KKDyI/IspSM(T466F)
3.12 ± 0.06
48.65 ± 5.17
1.25


Ptac-KKDyI/IspSM(T466C)
3.22 ± 0.04
47.74 ± 2.47
1.23


Ptac-KKDyI/IspSM(T466W)
3.35 ± 0.04
47.01 ± 1.68
1.21


Ptac-KKDyI/IspSM(T466M)
3.32 ± 0.19
45.81 ± 2.51
1.18


Ptac-KKDyI/IspSM(T466Y)
3.11 ± 0.06
44.63 ± 3.03
1.15


Ptac-KKDyI/IspSM(T466H)
3.31 ± 0.10
42.74 ± 2.24
1.10


Ptac-KKDyI/IspSM(T466P)
3.38 ± 0.15
41.61 ± 3.10
1.07


Ptac-KKDyI/IspSM(T466Q)
3.23 ± 0.06
40.97 ± 2.35
1.05


Ptac-KKDyI/IspSM(T466N)
3.33 ± 0.16
39.74 ± 6.44
1.02


Ptac-KKDyI/IspSM(T466A)
3.32 ± 0.05
39.56 ± 3.60
1.02





a)A relative value is shown when an amount of isoprene produced by Ptac-KKDyI/IspSM is 1.






As a result, a larger amount (mg/L) of isoprene than that produced by Ptac-KKDyI/IspSM strain was observed in all of evaluated strains having the introduced mutant IspSM (Table 6).
Reference Example 1: Evaluation of Ability to Produce Isoprene in Plants
1-1) Measurement of Amount of Isoprene Formed Per Unit Weight of Dry Leaves
First, an amount of isoprene formed per 1 g of dry leaves in the plant was measured for evaluating an ability to produce isoprene in plants. Mucuna (Mucuna bracteata), Weeping willow (Salix babylonica), American sweetgum (Liquidambar styraciflua), Myrtle (Myrtus communis), and Kudzu (Pueraria lobata) were used as the plants.
In the measurement of an amount of formed isoprene, a gas replaceable desiccator (trade name: Vacuum Desiccator, manufactured by AS ONE Corporation) was housed in an incubator (trade name: Growth Chamber MLR-351H, manufactured by SANYO), and the incubator was set to a high temperature induction condition (an illuminance of 100 μmol E/m2/s at 40° C.) while a fan for stirring the gas, which was provided in the gas replaceable desiccator, was driven to stir an atmosphere in space in the gas replaceable desiccator. After the temperature of the atmosphere in the gas replaceable desiccator reached 40° C., a plant body of Mucuna planted in a planter was housed therein and kept for 3 hours in a state where the gas replaceable desiccator was sealed. Then, a gas component released from Mucuna was aspirated from the space in the gas replaceable desiccator by an aspiration pump through a silicon tube, an adsorption tube and a gas collection tube. Thereby, water vapor (water content) contained in the gas component released from Mucuna was adsorbed and separated in the adsorption tube, the gas component from which the water vapor had been separated was led to the gas collection tube, and the gas component was collected in the gas collection tube. Subsequently, isoprene contained in the gas component collected in the gas collection tube was quantitatively analyzed using gas chromatograph (trade name: GC-FID6890, manufactured by Agilent).
For the weight of dry leaves, a leaf area of a fresh individual leaf, and a dry weight when the fresh individual leaf is dried by a dryer at 80° C. for 8 hours establish a very good positive correlation. Thus, a formula for converting from the leaf area to the dry weight was derived, and the dry weight was estimated from the entire leaf area from the plant body of Mucuna used for the measurement of an amount of formed isoprene.
The amount of formed isoprene per 1 g of the dry leaf was obtained by dividing the amount of formed isoprene from the entire plant body of Mucuna by the estimated weight of the entire plant body.
As a result, it was demonstrated that Mucuna was excellent in amount of formed isoprene per unit weight of the dry leaf (FIG. 1).
1-2) Measurement of Amount of Formed Isoprene Per Amount of Total Protein
Then, the amount of formed isoprene per amount of total protein extracted from leaves of various plants was measured. Mucuna (samples 1 and 2), Weeping willow, American sweetgum, Myrtle, and Kudzu were used as the plants.
For extraction of the protein, a buffer solution (50 mM Tris-HCl, 20 mM MgCl, 5% glycerol, 0.02% TRITON® X100, pH 8.0) was made, and 10% POLYCLAR® AT, 20 mM DTT, protease complete tablet (one tablet/50 mL), and 1 mM benzamidine HCl (final concentrations, each) were added just before the use, and was used as a protein extraction buffer. 50 mL of the protein extraction buffer was added to 5 g of the sample, then the mixture was ground well in a cold mortar on ice and filtrated though doubly overlapped Miracloth. A filtrate was centrifuged at 12,000 G for 20 minutes and 40,000 G for 40 minutes to obtain a supernatant, and the supernatant was used as a crude extract.
Subsequently, this crude extract was fractionated with ammonium sulfate. Proteins precipitated in a range of 40% to 55% of final concentrations of ammonium sulfate were centrifuged at 40,000 G for 40 minutes, and an obtained pellet was re-dissolved in the protein extraction buffer to obtain an ammonium sulfate fraction.
A total (ammonium sulfate fraction) protein mass was calculated by measuring the ammonium sulfate fraction using Bradford assay. A Bradford reagent was reacted with the standard protein, bovine serum albumin, and absorbance at a wavelength of 595 nm was measured using a spectrophotometer. A standard curve for the protein was made using the obtained absorbance values. The absorbance at a wavelength of 595 nm was also measured in the ammonium sulfate fraction diluted to 50 times, and the amount of the total (ammonium sulfate fraction) protein was estimated from the standard curve for the standard protein.
In the measurement of the amount of formed isoprene, 100 μL of the crude extract or 100 μL of a crude enzyme solution boiled at 100° C. was placed in a 4 mL glass vial, and then 2 μL of a 0.5 M MgCl2 solution and 5 μL, of a 0.2 M DMAPP solution were added thereto. The vial was tightly closed with a screw cap with a septum, and then the vial was gently vortexed and set in an incubator at 40° C. After 0.5, 1 and 2 hours, 0.5 to 2 mL of a gas layer in a headspace was sampled by a gas-tight syringe, and the amount of formed isoprene was measured using gas chromatograph (trade name: GC-FID6890, manufactured by Agilent). The amount of formed isoprene using the crude enzyme after 0.5, 1 and 2 hours was calculated by subtracting a measured value in the case of using the crude enzyme solution boiled at 100° C. from a measured value in the case of using the crude enzyme. An enzymatic activity per 1 mg of the total protein (specific activity) was calculated from the amount of the formed isoprene per one hour. The amount of formed isoprene was measured with keeping the amount of DMAPP that was the substrate of the isoprene synthase constant.
As a result, it was demonstrated that Mucuna was excellent in amount of formed isoprene per amount of total protein (FIG. 2, Table 7). As described above, it was shown that Mucuna was excellent in ability to produce isoprene.







TABLE 7







Amount of formed isoprene per amount of total protein (index numbers relative to case of Kudzu)















1

Specific activity index (Value from



0 hour*
0.5 hour*
hour*
2 hours*
Kudzu was set to 1)
















Mucuna 1
0
16.947
61.895
160.632
16.87842808


Mucuna 2
0
0
183.587
449.514
47.23274141


American sweetgum
0
0
22.063
46.132
4.847325838


Weeping willow
0
0
9.756
24.39
2.562782389


Myrtle
0
0
0
27.451
2.884417358


Kudzu
0
0
6.662
9.517
1





*Unit is μg isoprene/mg protein






Reference Example 2: Cloning of Isoprene Synthase Gene Derived from Mucuna 
2-1) Evaluation of Sampling Time
Isoprene gas released from leaves of Mucuna illuminated with light for 1, 2, 3 and 5 hours at temperature of 40° C. was sampled and the amount of produced isoprene was quantified by gas chromatography described later, and production of 4, 8, 12 and 10 μg of isoprene/g DW leaf was confirmed. Thus, it was confirmed that an optimal light illumination time was 3 hours.
2-2) Extraction of Total RNA Lysis Solution
A total RNA was extracted from leaves of Mucuna with total RNA lysis solution according to the following procedures.
(1) The leaves of Mucuna illuminated with light for 3 hours at temperature of 40° C. were sampled.
(2) 100 mg of leaf tissue was pulverized in a mortar with rapidly freezing the leaf tissue with liquid nitrogen, then the leaf tissue together with the liquid nitrogen was dispensed in an RNA-free 2 mL Eppendorf tube, and the liquid nitrogen was gasified.
(3) To this Eppendorf tube, 450 μL of a dissolution buffer RLT (containing 2-mercaptoethanol) attached to RNEASY® Plant Kit (manufactured by Qiagen), and mixed vigorously with Vortex to obtain a leaf tissue lysate.
(4) This leaf tissue lysate was applied to Q1A shredder spin column attached to RNEASY® Plant Kit, and centrifuged at 15,000 rpm for 2 minutes.
(5) A supernatant alone of a column eluate was transferred to a new RNA-free 2 mL Eppendorf tube, then special grade ethanol in a half volume of the supernatant was added to the supernatant, and the obtained solution was mixed by pipetting to obtain about 650 μL of a solution.
(6) This solution was applied to RNEASY® spin column attached to RNEASY® Plant Kit, centrifuged at 10,000 rpm for 15 seconds, and a filtrate was discarded.
(7) 700 μL of RW1 buffer attached to RNEASY® Plant Kit was added to this RNEASY® spin column, centrifuged at 10,000 rpm for 15 seconds, and a filtrate was discarded.
(8) 500 μL of BPE buffer attached to RNEASY® Plant Kit was added to this RNEASY® spin column, centrifuged at 10,000 rpm for 15 seconds, and a filtrate was discarded.
(9) 500 μL of BPE buffer was again added to this RNEASY® spin column, centrifuged at 10,000 rpm for 2 minutes, and a filtrate was discarded.
(10) This RNEASY® spin column was set to a 2 mL collective tube attached to RNEASY® Plant Kit, centrifuged at 15,000 rpm for one minute, and a filtrate was discarded.
(11) This RNEASY® spin column was set to a 1.5 mL collective tube attached to RNEASY® Plant Kit.
(12) RNA-free distilled water attached to RNEASY® Plant Kit was directly added to a membrane of this RNEASY® spin column using a Pipetman, centrifuged at 10,000 rpm for one minute, and total RNA was collected. This step was repeated twice to obtain about 100 μg of total RNA.
2-3) Analysis of Nucleotide Sequence of Isoprene Synthase Gene Derived from Mucuna 
Quality of RNA in the extracted total RNA solution was checked using nano-chips for RNA provided by BioAnalyzer (Agilent Technologies, Inc.), and it was confirmed that the solution was not contaminated with genomic DNA and RNA was not decomposed in the solution.
This total RNA was converted into a double strand using reverse transcriptase, and then fragmented using a nebulizer. Nucleotide sequences of 198,179 fragments having a poly A sequence at a 3′ end were analyzed using 454 titanium FLX high performance sequencer (manufactured by Roche Applied Science). Overlapped sequences in the obtained fragment sequences were aligned to obtain 13,485 contig sequences. BLAST search was performed for these contig sequences, and 6 contig sequences having the homology (identity of nucleotide sequences) to registered and known isoprene synthase gene sequences from Kudzu and Poplar were extracted. These sequences were further analyzed in detail, and 3 sequences in these 6 contig sequences were found to be derived from the same gene. Thus, a partial sequence of the isoprene synthase gene derived from Mucuna was obtained. 5′ RACE was performed based on this partial sequence to obtain a full length nucleotide sequence of the isoprene synthase gene derived from Mucuna, which was represented by SEQ ID NO:1.
Reference Example 3: Preparation of Expression Plasmid for Isoprene Synthase Derived from Various Plants
3-1) Chemical Synthesis of Isoprene Synthase Derived from Pueraria montana Var. Lobata (Kudzu)
The nucleotide sequence and the amino acid sequence of the isoprene synthase derived from Pueraria montana var. lobata were already known (ACCESSION: AAQ84170: P. montana var. lobata isoprene synthase (IspS)). The amino acid sequence of the IspS protein derived from P. montana and the nucleotide sequence of its gene are represented by SEQ ID NO:10 and SEQ ID NO:11, respectively. The IspS gene was optimized for codon usage frequency in E. coli in order to efficiently express the IspS gene in E. coli, and further designed to cut off the chloroplast localization signal. The designed gene was designated as IspSK. A nucleotide sequence of IspSK is represented by SEQ ID NO:12. The IspSK gene was chemically synthesized, then cloned into pUC57 (manufactured by GenScript), and the resulting plasmid was designated as pUC5-IspSK.
3-2) Chemical Synthesis of Isoprene Synthase Derived from Populus alba×Populus tremula (Poplar)
The nucleotide sequence and the amino acid sequence of the isoprene synthase derived from P. alba×P. tremula were already known (ACCESSION: CAC35696: P. alba×P. tremula (Poplar) isoprene synthase). The amino acid sequence of the IspS protein derived from P. alba×P. tremula and the nucleotide sequence of its gene are represented by SEQ ID NO:13 and SEQ ID NO:14, respectively. An IspS gene that was optimized for the codon usage frequency in E. coli in the same manner as above and in which the chloroplast localization signal was cut off was designed and designated as IspSP. A nucleotide sequence of IspSP is represented by SEQ ID NO:15. The IspSP gene was chemically synthesized, then cloned into pUC57 (manufactured by GenScript), and the resulting plasmid was designated as pUC57-IspSP.
3-3) Chemical Synthesis of Isoprene Synthase Derived from Mucuna 
Based on the nucleotide sequence of the isoprene synthase derived from Mucuna, an IspS gene that was optimized for the codon usage frequency in E. coli was designed in the same manner as above. One in which the chloroplast localization signal had been conferred was designated as IspSM (L), and one in which the chloroplast localization signal had been cut off was designated as IspSM. Nucleotide sequences for IspSM (L) and IspSM are represented by SEQ ID NO:16 and SEQ ID NO:3, respectively. The IspSM gene and the IspSM (L) gene were chemically synthesized, then cloned into pUC57 (manufactured by GenScript), and the resulting plasmids were designated as pUC57-IspSM and pUC57-IspSM (L).
3-4) Construction of Expression Plasmid, pSTV28-Ptac-Ttrp
An expression plasmid pSTV28-Ptac-Ttrp for expressing IspS derived from various plants in E. coli was constructed. First, a DNA fragment comprising a tac promoter (synonym: Ptac) region (deBoer, et al., (1983) Proc. Natl. Acad. Sci. U.S.A., 80, 21-25) and a terminator region of tryptophan operon (synonym: Ttrp) derived from E. coli (Wu et al., (1978) Proc. Natl. Acad. Sci. U.S.A., 75, 442-5446) and having a KpnI site at a 5′ terminus and a BamHI site at a 3′ end was synthesized chemically (the nucleotide sequence of Ptac-Ttrp is represented by SEQ ID NO:17). The resulting Ptac-Ttrp DNA fragment was digested with KpnI and BamHI, and ligated to pSTV28 (manufactured by Takara Bio Inc.) similarly digested with KpnI and BamHI by a ligation reaction with DNA ligase. The resulting plasmid was designated as pSTV28-Ptac-Ttrp (its nucleotide sequence is represented by SEQ ID NO:18). This plasmid can amplify the expression of the IspS gene by cloning the IspS gene downstream of Ptac.
3-5) Construction of Plasmid for Expressing IspS Gene Derived from Various Plants
Plasmids for expressing the IspSK gene, the IspSP gene, the IspSM gene and the IspSM (L) gene in E. coli were constructed by the following procedure. PCR was performed with Prime Star polymerase (manufactured by Takara Bio Inc.) using synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:19 and 20 as primers with pUC57-IspSK as a template, synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:21 and 22 as primers with pUC57-IspSP as a template, synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:23 and 24 as primers with pUC57-IspSM as a template, or further synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:25 and 26 as primers with pUC57-IspSM (L) as a template. A reaction solution was prepared according to a composition attached to the kit, and a reaction at 98° C. for 10 seconds, 54° C. for 20 seconds and 68° C. for 120 seconds was performed in 40 cycles. As a result, a PCR product containing the IspSK gene, the IspSP gene, the IspSM gene or the IspSM (L) gene was obtained. Likewise, PCR was performed with Prime Star polymerase (manufactured by Takara Bio Inc.) using synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:27 and 28 as primers with pSTV28-Ptac-Ttrp as a template, A reaction solution was prepared according to a composition attached to the kit, and a reaction at 98° C. for 10 seconds, 54° C. for 20 seconds and 68° C. for 210 seconds was performed in 40 cycles. As a result, a PCR product containing pSTV28-Ptac-Ttrp was obtained. Subsequently, the purified IspSK gene, IspSP gene, IspSM gene, and IspSM (L) gene fragments were ligated to the PCR product for pSTV28-Ptac-Ttrp using In-Fusion HD Cloning Kit (manufactured by Clontech). The resulting plasmids for expressing the IspSK gene, the IspSP gene, IspSM gene and IspSM (L) gene were designated as pSTV28-Ptac-IspSK, pSTV28-Ptac-IspSP, pSTV28-Ptac-IspSM, and pSTV28-Ptac-IspSM (L), respectively.







TABLE 8







Primer sequences used for construction


of plasmids for expressing IspS genes derived


from various plants









Subject for
Sequence



amplification
name
Sequence (5′-)





IspSK
Ptac-
GATAACAATTTCACACAAT



IspS(K)F
AATTTTGTTTAACTTTAAG




AAGGAGATATAATGTGTGC




GACCTCTTCTCAATTTACT




CAG (SEQ ID NO: 19)


 


IspSK
IspS(K)R-
ACGGCCAGTGAATTCTTAG



MCSR
ACATACATCAGCTGGTTAA




TCGG




(SEQ ID NO: 20)


 


IspSP
Ptac-
GATAACAATTTCACACAAT



IspS(P)F
AATTTTGTTTAACTTTAAG




AAGGAGATATAATGTGCTC




TGTTTCTACCGAGAACGTT




TCC (SEQ ID NO: 21)


 


IspSP
IspS(P)R-
ACGGCCAGTGAATTCTTAA



MCSR
CGTTCGAACGGCAGAATCG




GTTCG




(SEQ ID NO: 22)


 


IspSM
Ptac-
GATAACAATTTCACACAAT



IspS(M)F
AATTTTGTTTAACTTTAAG




AAGGAGATATAATGTCCGC




CGTTTCAAGCCA




(SEQ ID NO: 23)


 


IspSM
IspS(M)R-
ACGGCCAGTGAATTCTTAG



MCSR
TTAATCGGGAACGGGT




(SEQ ID NO: 24)


 


IspSM(L)
Ptac-
GATAACAATTTCACACAAT



IspS(M(L))F
AATTTTGTTTAACTTTAAG




AAGGAGATATAATGGCTAC




CAACCCGTCCTGTCTGTCA




ACC (SEQ ID NO: 25)


 


IspSM(L)
IspS(M(L))R-
ACGGCCAGTGAATTCTCAG



MCSR
TTAATCGGGAACGGGT




(SEQ ID NO: 26)


 


pSTV28-
pSTV28-F
GTGTGAAATTGTTATCCGC


Ptac-Ttrp

TCACAATTCC




(SEQ ID NO: 27)


 


pSTV28-
pSTV28-R
GAATTCACTGGCCGTCGTT


Ptac-Ttrp

TTACAACG




(SEQ ID NO: 28)









Reference Example 4: Measurement of Enzymatic Activity of Isoprene Synthase Derived from Various Plants Using Crude Enzyme Extract Derived from E. coli 
4-1) Construction of E. coli MG1655 Strain Having Ability to Produce Isoprene
Competent cells of E. coli MG1655 strain (ATCC 700926) were prepared, and then pSTV28-Ptac-Ttrp, pSTV28-Ptac-IspSK, pSTV28-Ptac-IspSP, pSTV28-Ptac-IspSM, or further pSTV28-Ptac-IspSM (L) was introduced therein by an electroporation method. A suspension of the cells was evenly applied onto an LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 18 hours. Subsequently, transformants that were resistant to chloramphenicol were obtained from the resulting plate. A strain in which pSTV28-Ptac-Ttrp, pSTV28-Ptac-IspSK, pSTV28-Ptac-IspSP, pSTV28-Ptac-IspSM, or further pSTV28-Ptac-IspSM (L) was introduced into E. coli MG1655 strain were designated as MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP, MG1655/pSTV28-Ptac-IspSM, or further MG1655/pSTV28-Ptac-IspSM (L) strain, respectively.
4-2) Method of Preparing Crude Enzyme Extract
Microbial cells of MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP, MG1655/pSTV28-Ptac-IspSM, or MG1655/pSTV28-Ptac-IspSM (L) strain were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 18 hours. The microbial cells corresponding to 1⁄6 of the resulting plate were inoculated to a Sakaguchi flask in which 20 mL of LB containing 60 mg/L of chloramphenicol had been added, and cultured at 37° C. for 6 hours. The microbial cells from the culture medium were centrifuged at 5000 rpm at 4° C. for 5 minutes, and washed twice with ice-cold isoprene synthase buffer (50 mM Tris-HCl, pH 8.0, 20 mM MgCl2, 5% glycerol). The washed microbial cells were suspended in 1.8 mL of the same buffer. About 0.9 mL of beads for disruption (YBG01, diameter 0.1 mm) and 0.9 mL of the microbial cell suspension were placed in a 2 mL tube specific for a multibead shocker, and the microbial cells were disrupted using the multibead shocker manufactured by Yasui Kikai Corporation at 2500 rpm at 4° C. for 3 cycles of ON for 30 seconds/OFF for 30 seconds. After the disruption, the tube was centrifuged at 20,000 g at 4° C. for 20 minutes, and a supernatant was used as a crude enzyme extract.
4-3) Measurement of Isoprene Synthase Activity
The crude enzyme extract from MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP, MG1655/pSTV28-Ptac-IspSM, or MG1655/pSTV28-Ptac-IspSM (L) strain (containing 2 mg as amount of total protein) together with the isoprene buffer in a total volume of 0.5 mL was placed in a headspace vial (22 mL CLEAR CRIMP TOP VIAL (cat #B0104236) manufactured by Perkin Elmer), then 0.025 mL of a 0.5 M MgCl2 solution and 0.01 mL of a 0.2 M DMAPP (manufactured by Cayman, catalog No. 63180) solution were added thereto, and the mixture was lightly vortexed. Then immediately, the vial was tightly sealed with a cap with a butyl rubber septum for the headspace vial (CRIMPS (cat #B0104240) manufactured by Perkin Elmer), and kept at 37° C. for 2 hours.
After completion of the reaction, a concentration of isoprene in the headspace of the vial was measured by gas chromatography. An analysis condition for the gas chromatography will be described below.
Headspace sampler (manufactured by Perkin Elmer, Turbo Matrix 40)
Temperature for keeping vial warm: 40° C.
Time period for keeping vial warm: 30 minutes
Pressurization time: 3.0 minutes
Injection time: 0.02 minute
Needle temperature: 70° C.
Transfer temperature: 80° C.
Carrier gas pressure (high purity helium): 124 kPa
Gas chromatography (manufactured by Shimadzu Corporation, GC-2010 Plus AF)
Column (Rxi (registered trademark)−1 ms: length 30 m, internal diameter 0.53 mm, liquid phase film thickness 1.5 μm, cat #13370)
Column temperature: 37° C.
Pressure: 24.8 kPa
Column flow: 5 mL/minute
Influx method: Split 1:0 (actually measured 1:18)
Transfer flow: 90 mL
GC injection volume: 1.8 mL (transfer flow×injection time)
Injection volume of sample into column: 0.1 mL
Inlet temperature: 250° C.
Detector: FID (hydrogen 40 mL/minute, air 400 mL/minute, makeup gas helium 30 mL/minute)
Detector temperature: 250° C.
Preparation of Isoprene Standard Sample
A reagent isoprene (specific gravity 0.681) was diluted to 10, 100, 1000, 10000 and 100000 times with cold methanol to prepare standard solutions for addition. Subsequently, 1 μL of each standard solution for addition was added to a headspace vial in which 1 mL of water had been added, and used as a standard sample.
The amount of formed isoprene after the reaction of each microbial strain for 2 hours is described in Table 9.







TABLE 9







Amount of formed isoprene after reaction for 2 hours








Name of microbial strain
Amount of formed isoprene (mg/L)





MG1655/pSTV28-Ptac-Ttrp
0.10 ± 0.01


MG1655/pSTV28-Ptac-IspSK
0.45 ± 0.02


MG1655/pSTV28-Ptac-IspSM
28.93 ± 6.04 


MG1655/pSTV28-Ptac-IspSM(L)
5.06 ± 0.13


MG1655/pSTV28-Ptac-IspSP
0.10 ± 0.01









From the result in Table 9, the amount of formed isoprene was larger in order of MG1655/pSTV28-Ptac-IspSM, MG1655/pSTV28-Ptac-IspSM (L) and MG1655/pSTV28-Ptac-IspSK strains, and was almost equal in MG1655/pSTV28-Ptac-IspSP and MG1655/pSTV28-Ptac-Ttrp strains. From the above result, the crude enzyme extract from the strain introduced with the isoprene synthase derived from Mucuna exhibited the highest activity to form isoprene.
Reference Example 5: Effects of Introduction of Isoprene Synthase Derived from Various Plants on E. coli MG1655 Strain
From the result of the crude enzymatic activity in Reference Example 4, the highest activity was confirmed in the isoprene synthase derived from Mucuna that deleted the chloroplast localization signal. Thus, an ability to produce isoprene from glucose was compared in all isoprene synthase-introduced strains in which the chloroplast localization signal had been deleted. Microbial cells of MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP, or MG1655/pSTV28-Ptac-IspSM strain were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol, and cultured at 37° C. for 18 hours. One loopful of the microbial cells from the resulting plate was inoculated to 1 mL of M9 glucose medium in a headspace vial. The vial was tightly sealed with the cap with the butyl rubber septum for the headspace vial (CRIMPS (cat #B0104240) manufactured by Perkin Elmer), and the microbial cells were cultured at 30° C. for 24 hours using a reciprocal shaking cultivation apparatus (120 rpm). A composition of the M9 glucose medium is as described in Table 10.







TABLE 10





Composition of M9 glucose medium


















Glucose
1.0 g/L



Na2HPO4
6.0 g/L



KH2PO4
3.0 g/L



NaCl
0.5 g/L



NH4Cl
1.0 g/L



1M MgSO4 (autoclaved)
1.0 mL



1M CaCl2 (autoclaved)
0.1 mL










Further, chloramphenicol was added at a final concentration of 60 mg/L. The volume was adjusted to 1 L and the medium was then sterilized by filtration.

After completion of the cultivation, the concentration of isoprene in the headspace in the vial was measured by the gas chromatography. An OD value was also measured at 600 nm using a spectrophotometer (HITACHI U-2900). The concentration of isoprene and the OD value in each microbial strain at the time of completing the cultivation are described in Table 11.







TABLE 11







OD value, and amount (μg/L) of isoprene produced by MG1655/pSTV28-


Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP


and MG1655/pSTV28-Ptac-IspSM strains at the time of completing


cultivation











Amount (μg/L) of formed


Name of microbial strain
OD value
isoprene





MG1655/pSTV28-Ptac-Ttrp
1.68 ± 0.04
ND


MG1655/pSTV28-Ptac-IspSK
1.60 ± 0.09
43 ± 6


MG1655/pSTV28-Ptac-IspSM
1.45 ± 0.03
56 ± 7


MG1655/pSTV28-Ptac-IspSP
1.59 ± 0.07
26 ± 3









From the results in Table 11, it was found that the amount of produced isoprene was larger in order of MG1655/pSTV28-Ptac-IspSM, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSP and MG1655/pSTV28-Ptac-Ttrp strains. From the above results, the strain introduced with the isoprene synthase derived from Mucuna exhibited the highest activity to produce isoprene in the wild strains.
Reference Example 6: Effects of Introduction of Isoprene Synthase Derived from Various Plants on E. coli MG1655 Strain in which MEP (Methylerythritol) Pathway is Enhanced
6-1) Construction of Plasmid for Expressing dxs Gene (pMW219-dxs)
It was already reported that the amount of formed isoprene was enhanced (Appl. Microbiol. Biotechnol., (2011) 90, 1915-1922, which is incorporated herein by reference in its entirety), when the expression of a dxs (1-deoxy-D-xylulose-5-phosphate synthase) gene that constitutes the MEP pathway was enhanced in E. coli strain in which the isoprene synthase was introduced. Thus, it was confirmed whether an ability to produce isoprene was also different due to an origin of the isoprene synthase in the strain in which the expression of the dxs gene was enhanced. The entire genomic nucleotide sequence of E. coli K-12 strain was already shown (GenBank Accession No. U00096) (Science, (1997) 277, 1453-1474, which is incorporated herein by reference in its entirety). pMW219 (manufactured by Nippon Gene Co., Ltd.) was used for amplifying the gene. This plasmid can increase an expression level of an objective gene when isopropyl-β-thiogalactopyranoside (IPTG) is added by introducing the objective gene into a multicloning site. Synthesized oligonucleotides were synthesized from the nucleotide sequences represented by SEQ ID NOs:29 and 30 based on the nucleotide sequence of the dxs gene in the genomic nucleotide sequence of E. coli. Subsequently, PCR was performed with Prime Star polymerase (manufactured by Takara Bio Inc.) using the synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:29 and 30 as the primers with MR1655 strain genomic DNA as the template. A reaction solution was prepared according to the composition attached to the kit, and a reaction at 98° C. for 10 seconds, 54° C. for 20 seconds and 68° C. for 120 seconds was performed in 40 cycles. As a result, a PCR product containing the dxs gene was obtained. Likewise, PCR was performed with Prime Star polymerase (manufactured by Takara Bio Inc.) using the synthesized oligonucleotides consisting of the nucleotide sequences represented by SEQ ID NOs:31 and 32 as the primers with pMW219 as the template. A reaction solution was prepared according to the composition attached to the kit, and a reaction at 98° C. for 10 seconds, 54° C. for 20 seconds and 68° C. for 240 seconds was performed in 40 cycles. As a result, a PCR product containing pMW219 was obtained. Subsequently, the purified dxs gene fragment was ligated to the PCR product of pMW219 using In-Fusion HD Cloning Kit (manufactured by Clontech). The resulting plasmid for expressing the dxs gene was designated as pMW219-dxs.







TABLE 12







Primer sequences used for construction


of plasmid for expressing dxs gene










Sequence




name
Sequence (5′-)






dxs-F
CAGGAAACAGCTATGAGTTTTGA




TATTGCCAAATACCCGAC




(SEQ ID NO: 29)


 



dxs-R
GCTGCCACTCCTGCTATACTCGT




CATAC (SEQ ID NO: 30)


 



pMW219-F
CATAGCTGTTTCCTGTGTGAAAT




TGTTATC (SEQ ID NO: 31)


 



pMW219-R
AGCAGGAGTGGCAGCGAATTCGA




GCTCGGTACCCGGGGAT




(SEQ ID NO: 32)









6-2) Introduction of pMW219-dxs into E. coli MG1655 Strain Having Ability to Produce Isoprene

Competent cells of MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSM, or further MG1655/pSTV28-Ptac-IspSP strain were prepared, and pMW219-dxs was introduced therein by an electroporation method. The cells were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol and 50 mg/L of kanamycin hydrochloride, and the cells were cultured at 37° C. for 18 hours. Transformants that were resistant to chloramphenicol and kanamycin were obtained from the resulting LB plates. Strains in which pMW219-dxs had been introduced into MG1655/pSTV28-Ptac-Ttrp, MG1655/pSTV28-Ptac-IspSK, MG1655/pSTV28-Ptac-IspSM, or further MG1655/pSTV28-Ptac-IspSP strain were designated as MG1655/pSTV28-Ptac-Ttrp/pMW219-dxs, MG1655/pSTV28-Ptac-IspSK/pMW219-dxs, MG1655/pSTV28-Ptac-IspSM/pMW219-dxs, or further MG1655/pSTV28-Ptac-IspSP/pMW219-dxs strain, respectively.
6-3) Effects of Introduction of Isoprene Synthase Derived from Various Plants on E. coli MG1655 Strain in which Expression of DXS is Enhanced
MG1655/pSTV28-Ptac-Ttrp/pMW219-dxs, MG1655/pSTV28-Ptac-IspSK/pMW219-dxs, MG1655/pSTV28-Ptac-IspSM/pMW219-dxs, or further MG1655/pSTV28-Ptac-IspSP/pMW219-dxs strain were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol and 50 mg/L of kanamycin hydrochloride, and were cultured at 37° C. for 18 hours. Subsequently, the cultivation in the headspace vial was evaluated as described in Reference Example 5. The amount (μg/L) of produced isoprene and the OD value upon completion of the cultivation are described in Table 13.







TABLE 13







Amount (μg/L) of produced isoprene and OD value when the cultivation


was completed in various strains having enhanced isoprene synthase


which are prepared from E. coli MG1655 strain having enhanced


DXS as host











Amount




(μg/L) of




produced


Name of microbial strain
OD value
isoprene





MG1655/pSTV28-Ptac-Ttrp/pMW219-dxs
1.46 ± 0.04
ND


MG1655/pSTV28-Ptac-IspSK/pMW219-dxs
1.13 ± 0.02
101 ± 28


MG1655/pSTV28-Ptac-IspSM/pMW219-dxs
1.76 ± 0.06
126 ± 23


MG1655/pSTV28-Ptac-IspSP/pMW219-dxs
2.21 ± 0.12
 42 ± 17









From the results in Table 13, the amount of produced isoprene was larger in order of MG1655/pSTV28-Ptac-IspSM/pMW219-dxs, MG1655/pSTV28-Ptac-IspSK/pMW219-dxs, MG1655/pSTV28-Ptac-IspSP/pMW219-dxs and MG1655/pSTV28-Ptac-Ttrp/pMW219-dxs strains. From the above results, the strain introduced with the isoprene synthase derived from Mucuna also exhibited the highest ability to produce isoprene in the MEP pathway-enhanced strains.
Reference Example 7: Effects of Introduction of Isoprene Synthase Derived from Various Plants on E. coli MG1655 Strain in which MVA (Mevalonate) Pathway is Introduced
7-1) Cloning Gene Downstream of Mevalonate Pathway which is Derived from Yeast
A downstream region of the mevalonate pathway was obtained from Saccharomyces cerevisiae (WO2009076676, Saccharomyces Genome database http(colon)//www(dot)yeastgenome(dot)org/# Nucleic Acids Res., January 2012; 40: D700-D705, which are incorporated herein by reference in their entireties). An ERG12 gene encoding mevalonate kinase, an ERG8 gene encoding phosphomevalonate kinase, an ERG19 gene encoding diphosphomevalonate decarboxylase, and an IDI1 gene encoding isopentenyl-diphosphate delta isomerase were amplified by PCR with genomic DNA of S. cerevisiae as the template using the primer shown below (Table 14). Prime Star Max Premix sold by Takara Bio Inc. was used for a PCR enzyme, and the reaction was performed at 98° C. for 2 minutes and for 30 cycles of 98° C. for 10 seconds, 55° C. for 5 seconds and 72° C. for 5 seconds/kb. Cloning and construction of an expression vector were performed by introducing the PCR fragment into the pSTV28-Ptac-Ttrp vector (SEQ ID NO:18) treated with the restriction enzyme SmaI by an in-fusion cloning method. E. coli DH5α was transformed with the expression vector, clones having assumed sequence length from each gene were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The nucleotide sequences of these amplified genes and the amino acid sequences of the enzymes encoded by these genes are available on Saccharomyces Genome database http(colon)//www(dot)yeastgenome(dot)org/#.







TABLE 14







Primer sequences used for cloning of genes


downstream of mevalonate pathway











Amplified





gene
Sequence name
Sequence (5′-)






ERG12
MVK-IFS_5742-33-1
ACACAAGGAGACTCC





CATGTCATTACCGTT





CTTAACTTCT





(SEQ ID NO: 33)


 



ERG12
MVK-IFA_5742-33-2
GGAACTGGCGGCTCC





CGGGTTATTATGAAG





TCCATGGTAAATTCG





T





(SEQ ID NO: 34)


 



ERG8
PMK-IFS_5742-33-3
ACACAAGGAGACTCC





CATGTCAGAGTTGAG





AGCCTTCA





(SEQ ID NO: 35)


 



ERG8
PMK-IFA_5742-33-4
GGAACTGGCGGCTCC





CGGGTTATTATTTAT





CAAGATAAGTTTCCG





G





(SEQ ID NO: 36)


 



ERG19
MVD-IFS_5742-33-5
ACACAAGGAGACTCC





CATGACCGTTTACAC





AGCATCC





(SEQ ID NO: 37)


 



ERG19
MVD-IFA_5742-33-6
GGAACTGGCGGCTCC





CGGGTTATTATTCCT





TTGGTAGACCAGTCT





T





(SEQ ID NO: 38)


 



IDI1
yIDI-IFS_5742-33-7
ACACAAGGAGACTCC





CATGCCCCATGGTGC





AGTATC





(SEQ ID NO: 39)


 



IDI1
yIDI-IFA_5742-33-8
GGAACTGGCGGCTCC





CGGGTTATTATAGCA





TTCTATGAATTTGCC





TGTC





(SEQ ID NO: 40)









7-2) Construction of Artificial Operon Downstream of Mevalonate Pathway

A sequence in which the gene encoding the mevalonate kinase and the gene encoding the phosphomevalonate kinase were arranged in straight was constructed by the in-fusion cloning method. The ERG12 gene encoding the mevalonate kinase and the ERG8 gene encoding the phosphomevalonate kinase were amplified by PCR with genomic DNA from Saccharomyces cerevisiae as the template using the primers shown in Table 15. KOD plus sold by Toyobo was used for the PCR enzyme, and the reaction was performed at 94° C. for 2 minutes and for 30 cycles of 94° C. for 15 seconds, 45° C. for 30 seconds and 68° C. for 1 minute/kb. The cloning and the construction of an expression vector were performed by inserting the PCR fragment into pUC118 vector treated with the restriction enzyme SmaI by the in-fusion cloning method. E. coli JM109 was transformed with the expression vector, clones having assumed sequence length of each gene were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The produced plasmid was designated as pUC-mvk-pmk. The nucleotide sequence of pUC-mvk-pmk is represented by SEQ ID NO:41.







TABLE 15







Primer sequences used for ligating


mevalonate kinase and phosphomevalonate kinase









Amplified
Sequence



gene
name
Sequence (5′-)





ERG12
KKS1-6038-2-1
TCGAGCTCGGTACCC




ATGTCATTACCGTTC




TTAACTTCT




(SEQ ID NO: 42)


 


ERG12
KKA1-6038-2-2
TTAAGGGTGCAGGCC




TATCGCAAATTAGCT




TATGAAGTCCATGGT




AAATTCGT




(SEQ ID NO: 43)


 


ERG8
KKS2-6083-2-3
GGCCTGCACCCTTAA




GGAGGAAAAAAACAT




GTCAGAGTTGAGAGC




CTTCA




(SEQ ID NO: 44)


 


ERG8
KKA2-6083-2-4
CTCTAGAGGATCCCC




TTATTTATCAAGATA




AGTTTCCGG




(SEQ ID NO: 45)









A sequence in which a gene encoding diphosphomevalonate decarboxylase and a gene encoding isopentenyl-diphosphate delta isomerase were arranged in straight was constructed by the in-fusion cloning method. The ERG19 gene encoding the diphosphomevalonate decarboxylase and the IDI1 gene encoding the isopentenyl-diphosphate delta isomerase were amplified by PCR with genomic DNA of Saccharomyces cerevisiae as the template using the primers shown in Table 16. KOD plus sold by Toyobo was used for the PCR enzyme, and the reaction was performed at 94° C. for 2 minutes and for 30 cycles of 94° C. for 15 seconds, 45° C. for 30 seconds and 68° C. for 1 minute/kb, and then at 68° C. for 10 minutes. The cloning and the construction of an expression vector were performed by inserting the PCR fragment into TWV228 vector treated with the restriction enzyme SmaI by the in-fusion cloning method. E. coli DH5α was transformed with the expression vector, clones having assumed sequence length of each gene were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The produced plasmid was designated as pTWV-dmd-yidi. The nucleotide sequence of pTWV-dmd-yidi is represented by SEQ ID NO:46.







TABLE 16







Primer sequences used for ligating


diphosphomevalonate decarboxylase and


isopentenyl-diphosphate delta isomerase









Amplified
Sequence



gene
name
Sequence (5′-)





ERG19
DyIS1-6083-2-5
TCGAGCTCGGTACCC




ATGACCGTTTACACA




GCATCC




(SEQ ID NO: 47)


 


ERG19
DyIA1-6083-2-6
TTTTTTTACCTCCTA




AGGGCGATGCAGCGA




ATTGATCTTATTCCT




TTGGTAGACCAGTCT




T




(SEQ ID NO: 48)


 


IDI1
DyIS2-6083-2-7
TAGGAGGTAAAAAAA




AATGACTGCCGACAA




CAATAGTATGCCCCA




TGGTGCAGTATC




(SEQ ID NO: 49)


 


IDI1
DyIA2-6083-2-8
CTCTAGAGGATCCCC




TTATAGCATTCTATG




AATTTGCCTGTC




(SEQ ID NO: 50)









A sequence in which the gene encoding the mevalonate kinase, the gene encoding the phosphomevalonate kinase, the gene encoding the diphosphomevalonate decarboxylase and the gene encoding the isopentenyl-diphosphate delta isomerase were arranged in straight was constructed by the in-fusion cloning method. An expression vector in which these four enzyme genes were arranged in straight was constructed by amplifying the gene encoding the mevalonate kinase and the gene encoding the phosphomevalonate kinase by PCR with pUC-mvk-pmk as the template using the primers shown in Table 17 and amplifying the gene encoding the diphosphomevalonate decarboxylase and the gene encoding the isopentenyl-diphosphate delta isomerase by PCR with pTWV-dmd-yidi as the template using the primers shown in Table 17, followed by cloning the amplified products into pTrcHis2B vector by the in-fusion cloning method. Prime Star HS DNA polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 98° C. for 2 minutes followed by in 30 cycles of 98° C. for 10 seconds, 52° C. for 5 seconds and 72° C. for 1 minute/kb, and then at 72° C. for 10 minutes. The PCR fragment was inserted into pTrcHis2B vector treated with the restriction enzymes NcoI and PstI to construct the expression vector. E. coli JM109 was transformed with the expression vector, clones having an objective sequence length were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The constructed expression vector was designated as pTrc-KKDyI (β). The nucleotide sequence of pTrc-KKDyI (β) is represented by SEQ ID NO:51.







TABLE 17







Primer sequences used for amplifying


genes for constructing pTrc-KKDyI (β)









Template




plasmid
Sequence name
Sequence (5′-)





pUC-mvk-
KKDS2_6038-3-2
GAGGAATAAACCATG


pmk

TCATTACCGTTCTTA




ACTTCT




(SEQ ID NO: 52)


 


pUC-mvk-
KKMyIA_6038-2-9
AAGGGCGAATTCTGC


pmk

ATGCAGCTACCTTAA




GTTATTTATCAAGAT




AAGTTTCCGG




(SEQ ID NO: 53)


 


pTWV-dmd-
KMS_6038-6-1
GCAGAATTCGCCCTT


yidi

AAGGAGGAAAAAAAA




ATGACCGTTTACACA




GCATCC




(SEQ ID NO: 54)


 


pTWV-dmd-
KDyIA_6038-3-3
CCATATGGTACCAGC


yidi

TGCAGTTATAGCATT




CTATGAATTTGCCTG




TC




(SEQ ID NO: 55)









7-3) Fixation of Downstream Region of Mevalonate Pathway on Chromosome

The sequence in which the gene encoding the mevalonate kinase, the gene encoding the phosphomevalonate kinase, the gene encoding the diphosphomevalonate decarboxylase and the gene encoding the isopentenyl-diphosphate delta isomerase were arranged in straight was expressed on a chromosome. A glucose isomerase promoter was used for the expression of the gene, and a transcription termination region of aspA gene in E. coli was used for the termination of the transcription (WO2010/031062, which is incorporated herein by reference in its entirety). A translocation site of Tn7 was used as a chromosomal site to be fixed (Mol Gen Genet., 1981; 183 (2): 380-7, which is incorporated herein by reference in its entirety). A cat gene was used as a drug marker after the fixation of the chromosome. A Tn7 downstream region in the chromosome region to be fixed was amplified by PCR with genomic DNA of E. coli as the template using the primers shown in Table 18. Prime Star HS DNA polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 98° C. for 2 minutes followed by in 30 cycles of 98° C. for 10 seconds, 52° C. for 5 seconds and 72° C. for 1 minute/kb, and then at 72° C. for 10 minutes. A cat gene region containing a λ phage attachment site was amplified by PCR with pMW118-attL-Cm-attR plasmid as the template using the primers shown in Table 18 (WO2010/027022, which is incorporated herein by reference in its entirety). Prime Star HS DNA polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 95° C. for 3 minutes followed by in 2 cycles of 95° C. for 1 minute, 34° C. for 30 seconds and 72° C. for 40 seconds, 2 cycles of 95° C. for 30 seconds, 50° C. for 30 seconds and 72° C. for 40 seconds, and then at 72° C. for 5 minutes. A sequence downstream of the mevalonate pathway to which a promoter and a transcription termination region had been added (hereinafter abbreviated as KKDyI) was amplified with pTrc-KKDyI (β) as the template using the primers shown in Table 18. Prime Star HS DNA polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 98° C. for 2 minutes followed by in 30 cycles of 98° C. for 10 seconds, 52° C. for 5 seconds and 72° C. for 1 minute/kb, and then at 72° C. for 10 minutes. A vector was constructed using these PCR products and pMW219 treated with the restriction enzyme SmaI by the in-fusion cloning method. E. coli JM109 was transformed with the expression vector, clones having an objective sequence length were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The resulting plasmid was designated as pMW219-KKDyI-TaspA. The nucleotide sequence of pMW219-KKDyI-TaspA is represented by SEQ ID NO:56.
Subsequently, a Tn7 upstream region in the chromosome region to be fixed was amplified by PCR with the genomic DNA of E. coli as the template using the primers shown in Table 19. Prime Star HS DNA polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 98° C. for 2 minutes followed by in 30 cycles of 98° C. for 10 seconds, 52° C. for 5 seconds and 72° C. for 1 minute/kb, and then at 72° C. for 10 minutes. A vector was constructed using the PCR product and pMW219-KKDyI-TaspA treated with the restriction enzyme SalI by the in-fusion cloning method. E. coli JM109 was transformed with the expression vector, clones having an objective sequence length were selected, a plasmid was extracted according to standard methods, and its sequence was confirmed. The resulting plasmid was designated as pMW-Tn7-Pgi-KKDyI-TaspA-Tn7. The sequence of the constructed plasmid is represented by SEQ ID NO:57.
Subsequently, a chromosome having a region including the chloramphenicol resistance gene, the glucose isomerase promoter, the operon downstream of the mevalonate pathway, and the aspA gene transcription termination region was fixed using λ-Red method. A fragment for chromosome fixation was prepared by extracting the plasmid pMW-Tn7-Pgi-KKDyI-TaspA-Tn7 and then treating it with the restriction enzymes PvuI and SalI followed by purifying it. E. coli MG1655 containing a plasmid pKD46 having a temperature-sensitive replication capacity (hereinafter referred to as MG1655/pKD46) was used for the electroporation. The plasmid pKD46 (Proc. Natl. Acad. Sci. USA, 2000, vol. 97, No. 12, p 6640-6645, which is incorporated herein by reference in its entirety) contains a DNA fragment of total 2154 nucleotides (GenBank/EMBL Accession No. J02459, 31088th to 33241st) of λ phage containing λ Red system genes (λ, β, exo genes) controlled by an arabinose-inducible ParaB Promoter. After the electroporation, a colony that had acquired the resistance to chloramphenicol was obtained, subsequently genomic DNA was extracted, and it was confirmed by PCR using the primers shown in Table 20 that the objective region was fixed on the chromosome. Further, the sequence of the objective region was confirmed by confirming the sequence of the PCR fragment. The nucleotide sequence of the mevalonate pathway downstream and its proximal region fixed on the chromosome is represented by SEQ ID NO:58, and its construction outline is shown in FIG. 3. The resulting mutant was designated as MG1655 cat-Pgi-KKDyI.
The drug marker in MG1655 cat-Pgi-KKDyI was removed by the following procedure. Competent cells of MG1655 cat-Pgi-KKDyI was made, and then pMW-int-xis was introduced therein. pMW-int-xis is a plasmid containing a gene encoding integrase (Int) of the λ phage and a gene encoding excisionase (Xis) of the λ phage and having the temperature-sensitive replication capacity (WO2007/037460, JP Publication No. 2005-058827, which are incorporated herein by reference in their entireties).
The chloramphenicol-resistant gene located in a region sandwiched with attL and attR that are the attachment site of the λ phage is dropped off from the chromosome by introducing pMW-int-xis. As a result, it is known that the host loses the resistance to chloramphenicol. And, a chloramphenicol-sensitive strain was obtained from the resulting colony, and subsequently cultured on the LB medium at 42° C. for 6 hours. The cultured microbial cells were applied onto the LB plate medium to allow colonies to appear. A colony that had lost the resistance to ampicillin was selected from these colonies to remove the drug resistance. The mutant obtained as above was designated as MG1655 Pgi-KKDyI.







TABLE 18







Primers for making PCR fragments


used for construction of pMW219-KKDyI-TaspA










Template
Amplified
Sequence



DNA
region
name
Sequence (5′-)





E. coli
Tn7
Tn7dS_6038-7-1
TCGAGCTCGGTACCC


genome
downstream

TGTTTTTCCACTCTT





CGTTCACTTT





(SEQ ID NO: 59)


 


E. coli
Tn7
Tn7dA_6038-7-2
AGGCTTCATTTTAAT


genome
downstream

CAAACATCCTGCCAA





CTC





(SEQ ID NO: 60)


 


pMW-attL-
attL-cat-attR
Tn7dattLcmS_6038-
ATTAAAATGAAGCCT


Cm-attR

7-4
GCTTTTTTAT





(SEQ ID NO: 61)


 


pMW-attL-
attL-cat-attR
PgiattRcmA_6038-
GGCATCGTCAAGGGC


Cm-attR

7-5
CGCTCAAGTTAGTAT





AA





(SEQ ID NO: 62)


 


pTrc-
KKDyI
gi1.2-MVK-
GCCCTTGACGATGCC


KKDyI(β)

S_6038-7-6
ACATCCTGAGCAAAT





AATTCAACCACTAAT





TGTGAGCGGATAACA





CAAGGAGGAAACAGC





TATGTCATTACCGTT





CTTAACTTC





(SEQ ID NO: 63)


 


pTrc-
KKDyI
pMW-TaspA-
CTCTAGAGGATCCCC


KKDyI(β)

yIDIA_6038-7-7
GGCCCCAAGAAAAAA





GGCACGTCATCTGAC





GTGCCTTTTTTATTT





GTAGACGCGTTGTTA





TAGCATTCTATGAAT





TTGCCT





(SEQ ID NO: 64)
















TABLE 19







Primers for making PCR fragments used


for construction of pMW-Tn7-Pgi-KKDyI-TaspA-Tn7










Template
Amplified
Sequence



DNA
region
name
Sequence (5′-)





E. coli
Tn7
Tn7upSv02_
ATCCTCTAGAGTCGA


genome
upstream
6038-24-1
AAGAAAAATGCCCCG





CTTACG





(SEQ ID NO: 64)


 


E. coli
Tn7
Tn7upAv02_
ATGCCTGCAGGTCGA


genome
upstream
6038-24-2
CTGTCACAGTCTGGC





GAAACCG





(SEQ ID NO: 65)
















TABLE 20







PCR primers for confirming chromosome


fixation of mevalonate pathway downstream










Sequence name
Sequence (5′-)






Tn7v02-F_6038-22-5
ACGAACTGCTGTCGAAGGTT




(SEQ ID NO: 67)


 



Tn7v02-R_6038-22-6
GGTGTACGCCAGGTTGTTCT




(SEQ ID NO: 68)









7-4) Substitution of Promoter Downstream of Mevalonate Pathway on Chromosome

The promoter of the operon downstream of the mevalonate pathway on the chromosome was substituted by the λ-red method. A genomic fragment having attL-Tet-attR-Ptac was used as the template for PCR. This is one in which the tac promoter, and attL and attR that are the attachment sites for a tetracycline resistant drug marker and the λ, phage are aligned. This sequence is represented by SEQ ID NO:69. A PCR fragment was prepared using the promoter shown in Table 21. LA-Taq polymerase sold by Takara Bio Inc. was used for the PCR enzyme, and the reaction was carried out at 92° C. for 1 minute, then for 40 cycles of 92° C. for 10 seconds, 50° C. for 20 seconds and 72° C. for 1 minute/kb, and further at 72° C. for 7 minutes. The PCR product was purified. MG1655 Pgi-KKDyI containing the plasmid pKD46 (hereinafter referred to as MG1655 Pgi-KKDyI/pKD46) having the temperature-sensitive replication capacity was used for the electroporation. The plasmid pKD46 (Proc. Natl. Acad. Sci. USA, 2000, vol. 97, No. 12, p 6640-6645, which is incorporated herein by reference in its entirety) contains a DNA fragment of total 2154 nucleotides (GenBank/EMBL Accession No. J02459, 31088th to 33241st) of λ phage containing λ Red system genes (λ, β, exo genes) controlled by an arabinose-inducible ParaB Promoter. The plasmid pKD46 is required for incorporating the PCR product into MG1655 Pgi-KKDyI.
Competent cells for the electroporation were prepared as follows. MG1655 Pgi-KKDyI/pKD46 cultured in the LB medium containing 100 mg/L of ampicillin at 30° C. overnight were diluted to 100 times with 5 mL of LB medium containing ampicillin and L-arabinose (1 mM). The resulting cells in diluted suspension were grown until OD600 reached about 0.6 with ventilating at 30° C., and subsequently washed three times with ice-cold 10% glycerol solution to use for the electroporation. The electroporation was performed using 504 of the competent cells and about 100 ng of the PCR product. The cells after the electroporation in 1 mL of SOC medium (Molecular Cloning: Laboratory Manuals, 2nd Edition, Sambrook, J. et al., Cold Spring Harbor Laboratory Press (1989), which is incorporated herein by reference in its entirety) were cultured at 37° C. for one hour, and subjected to a plate culture on LB agar medium at 37° C. to select a chloramphenicol-resistant transformant. Subsequently, in order to remove the pKD46 plasmid, the transformant was subcultured on the LB agar medium containing tetracycline at 37° C. The ampicillin resistance was examined in the obtained colonies, and an ampicillin-resistant strain having no pKD46 was obtained. A mutant containing the tac promoter substitution that could be distinguished by the tetracycline-resistant gene was obtained. The obtained mutant was designated as MG1655 tet-Ptac-KKDyI.
The antibiotic marker was removed by the following procedure. Competent cells of MG1655 tet-Ptac-KKDyI were made, and then pMW-int-xis was introduced therein. pMW-int-xis is a plasmid containing the genes encoding integrase (Int) and excisionase (Xis) of the λ phage and having the temperature-sensitive replication capacity (WO2007/037460, JP Publication No. 2005-058827, which are incorporated herein by reference in their entireties). The tetracycline-resistant gene located in a region sandwiched with attL and attR that are the attachment site of the λ phage is dropped off from the chromosome by introducing pMW-int-xis. As a result, it is known that the host loses the resistance to tetracycline. Thus, a tetracycline-sensitive strain was obtained from the resulting colonies. Cells of this strain were cultured on the LB medium at 42° C. for 6 hours, and the cultured cells were applied onto the LB plate medium to allow colonies to appear. A clone that had lost the resistance to ampicillin was selected to remove the drug resistance. The resulting mutant was designated as MG1655 Ptac-KKDyI. The nucleotide sequence of the mevalonate pathway downstream and its proximal region controlled by the tac promoter on the chromosome is represented by SEQ ID NO:70, and its outline is shown in FIG. 4.







TABLE 21







Primers for making PCR fragments


for promoter substitution








Sequence name
Sequence (5′-)





APtacKKDyIv03_6038-36-5
gataaagtatcagtctgatttaa



ataagcgttgatattcagtcaat



tactgaagcctgatttttatac



(SEQ ID NO: 71)


 


SPtacKKDyIv02_6038-36-3
tcaccaaaaataataacctttcc



cggtgcagaagttaagaacggta



atgaCATggcagtctccttgtgt



ga (SEQ ID NO: 72)









7-5) Introduction of Isoprene Synthase Derived from Various Plants into MG1655 Ptac-KKDyI Strain

Competent cells of MG1655 Ptac-KKDyI strain were prepared, and then pSTV28-Ptac-Ttrp, pSTV28-Ptac-IspSK, pSTV28-Ptac-IspSM, or further pSTV28-Ptac-SP was introduced therein. The cells were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol, and the cells were cultured at 37° C. for 18 hours. Transformants that exhibited the chloramphenicol resistance were obtained from the resulting plate. A strain in which pSTV28-Ptac-Ttrp, pSTV28-Ptac-IspSK, pSTV28-Ptac-IspSM, or pSTV28-Ptac-IspSP had been introduced into MG1655 Ptac-KKDyI strain was designated as MG1655 Ptac-KKDyI/pSTV28-Ptac-Ttrp, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSK, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSM, or MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSP, respectively.
7-6) Effects of Introduction of Isoprene Synthase Derived from Various Plants on MG1655 Strain in which MVA Pathway is Enhanced
Microbial cells of MG1655 Ptac-KKDyI/pSTV28-Ptac-Ttrp, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSK, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSM, or further MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSP strain were evenly applied onto the LB plate containing 60 mg/L of chloramphenicol, and the cells were cultured at 37° C. for 18 hours. One loopful of the microbial cells from the resulting LB plate was inoculated to 1 mL of M9 glucose (containing mevalonic acid) medium in a headspace vial (22 mL CLEAR CRIMP TOP VIAL (cat #B0104236) manufactured by Perkin Elmer), and subsequently the cultivation was evaluated according to the method described in Reference Example 2. A composition of the M9 glucose (containing mevalonic acid) medium is described in Table 22. The amount of produced isoprene and the OD value upon completion of the cultivation are described in Table 23.







TABLE 22





Composition of M9 glucose (containing mevalonic acid) medium


















Glucose
2.0 g/L



Na2HPO4
6.0 g/L



KH2PO4
3.0 g/L



NaCl
0.5 g/L



NH4Cl
1.0 g/L



Mevalonic acid (manufactured by ADEKA)
1.0 g/L



1M MgSO4 (autoclaved)
1.0 mL



1M CaCl2 (autoclaved)
0.1 mL










Chloramphenicol was added at a final concentration of 60 mg/L.
A total volume was adjusted to 1 L, and the medium was sterilized by filtration.







TABLE 23







Amount (mg/L) of produced isoprene and OD value when cultivation


of MG1655 Ptac-KKDyI/pSTV28-Ptac-Ttrp, MG1655 Ptac-KKDyI/


pSTV28-Ptac-IspSK, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSM,


or further MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSP was completed











Amount (mg/L) of


Name of microbial strain
OD value
produced isoprene





MG1655 Ptac-KKDyI/pSTV28-Ptac-
2.08 ± 0.07
0.07 ± 0.01


Ttrp


MG1655 Ptac-KKDyI/pSTV28-Ptac-
2.48 ± 0.13
30.96 ± 3.04 


IspSK


MG1655 Ptac-KKDyI/pSTV28-Ptac-
2.48 ± 0.09
57.13 ± 15.00


IspSM


MG1655 Ptac-KKDyI/pSTV28-Ptac-
1.95 ± 0.09
0.52 ± 0.01


IspSP









From the results in Table 23, the amount of produced isoprene was larger in order of MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSM, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSK, MG1655 Ptac-KKDyI/pSTV28-Ptac-IspSP, and MG1655 Ptac-KKDyI/pSTV28-Ptac-Ttrp strains. From the above results, the strain introduced with the isoprene synthase derived from Mucuna also exhibited the highest ability to produce isoprene in the strains introduced with the MVA pathway.
Example 3: Selection and Modification of Amino Acids to be Subjected to Modification with Focusing on Specified Matter
(3-1) Selection and Modification of Amino Acids to be Subjected to Modification with Focusing on Interaction with Substrate
Hereinafter, amino acid residues are shown based on the amino acid sequence of SEQ ID NO:4. Residues that interacted with DMAPP that was the substrate were computed using the steric structure model constructed in Example 1 and simulation software Molgero Molecular Viewer (Molegro). As a result, an electromagnetic interaction with the substrate was predicted in total 47 residues of K259, R264, D265, R266, E269, K288, K292, F294, V297, D301, D302, D305, D311, E312, E321, K336, K367, E371, K374, F376, E379, K381, K386, K393, D396, S401, S402, S403, R437, F443, R444, N447, D448, E455, E457, R458, E460, E471, E476, K481, R484, E490, K492, K493, Y523, D533, and K541. Results obtained by computing using Molgero Molecular Viewer are shown in Table 24.
The higher activity value than that in the wild type was observed by modification of D131C in Example 1 (Table 1-2). Based on this result, the charged residues K127 and K130 that positioned in the vicinity of the D131 residue were selected and subjected to modification. Among the residues present in the vicinity of the substrate DMAPP, T451E, T451S, E455D, E455Q, E455M, T462Q, and T462S still retained their activity after the modification in Example 1 although their activity was reduced as compared with that in the wild type (Table 1-1). On the basis of this fact, T451, E455 and T462 were selected and subjected to modification. T461 and L407 present in the vicinity of these residues were selected and subjected to modification.
The amino acid residues after the modification were selected from acidic residues (D, E), basic residues (R, K), neutral residues (N, Q), hydrophilic residues (M, S) and aromatic residues (Y, F) with focusing on two points. A first one is bulkiness, and amino acids close to amino acids before the modification were selected with reference to the truth table for physicochemical natures of amino acids (e.g., M. J. Zvelebil et al, J. Mol. Biol., 1987, 195, 57, which is incorporated herein by reference in its entirety) and BLOSSUM table that was indicators of amino acid homology (S. Henikoff et al, Proc. Natl. Acad. USA., 1992, 89, 10915, which is incorporated herein by reference in its entirety). For a second point, the information on steric structure was visually inspected and when a space filling rate in the vicinity of an introduced modified residue is low, amino acids suitable for filling the space were selected.
(3-2) Selection of Amino Acid Residue to be Subjected to Modification and Modification Thereof with Focusing on Optimization of Cys Residues and Optimization of Surrounding Environment of Cys Residues
Based on optimization of Cys residues and optimization of surrounding environment of Cys residues, which was Concept shown in Example 1, 7 (C137, C286, C370, C373, C440, C480, C521) of total 9 Cys residues were substituted with Gly residues in order to alter motility of molecules in the vicinity of the Cys residue.
Surrounding residues that interacted with the Cys residue or surrounding residues capable of interacting with the Cys residue by modification were selected and subjected to the modification. With reference to the model structure, the presence of 22 residues of D131, L256, I299, Y304, F316, V320, E321, F376, S399, G404, V405, Y412, L414, V415, L449, S452, I465, P505, F508, I518, S519, and H520 was confirmed. These residues were modified in consideration of surrounding chemical environment.
(3-3) Selection of Amino Acid Residue to be Subjected to Modification and Modification Thereof with Focusing on Enhancement of Hydrophilicity on Enzyme Surface and Formation of Intermolecular Disulfide Bond
Among hydrophobic residues present on the molecular surface, Val residues (V106, V187, V289, V306, V325), Leu residues (L35, L67, L163, L310, L340, L377, L529) and Ile residues (I190, I328, I387, I388) not involved in packing, as well as Phe residues (F31, F129) and Gly residues (G528, G530) were selected and subjected to modification. Subsequently, Gly residues (G134, G135, G157, G160, G182) present on a loop were selected and substituted with Pro residues in order to control molecular motility. Next, residues present on a helix (D124, R128, L247, T257, R264, E269, K292, F294, V297, T298, G404, L407, F443, V499) were selected in order to enhance stability of an IspS molecule by stabilizing a helix structure. Finally, S162 for forming an intermolecular disulfide bond and R202 for forming an intramolecular disulfide bond were selected and substituted with Cys residue.
(3-4) Selection of Amino Acid Residues to be Subjected to Modification and Modification Thereof with Reference to Bornyl Synthase.
The substrate affinity of IspS derived from kudzu and poplar is known to be of the order of mM. From similarity on their primary sequences, the substrate affinity of IspSM was also predicted to be of the order of mM. On the other hand, bornyl synthase (EC5.5.1.8) having the similarity on their steric structure has a substrate affinity of the order of μM (Croteasu R. et al, J. Biol. Chem., 1986, 261(29), 13438-45, which is incorporated herein by reference in its entirety). As a result of comparing the model structure of IspSM with the steric structure of bornyl synthase, differences were observed in a J-K loop and an N-terminal region. In more detail, residues that interacted with the N-terminus of bornyl synthase were 5248 and R249, and they corresponded to 5248 and L249 on IspSM. Thus, these residues were substituted with K, E, R or T, and the formation of interaction with the N-terminus was examined.
(3-5) Method of Measuring Activity
Respective modified enzymes were prepared according to Example 1 (1-4) herein. The obtained crude purified solution was diluted to 0.026 mg/mL of protein with a solution composed of 25 mM Tris-HCl (pH 7.5) and 10 mM MgCl2. Subsequently, 10 μL of the crude purified solution was mixed with 0.1 mL of a substrate solution composed of 4 mM DMAPP, 25 mM Tris-HCl (pH 7.5) and 10 mM MgCl2. The mixed solution was incubated at 37° C. for 60 minutes to allow isoprene synthase to act upon DMAPP to produce isoprene and pyrophosphoric acid. Subsequently, 204 of 20 mg/mL activated charcoal suspension was mixed with the reaction solution, which was immediately transferred on ice to stop the reaction. The 20 mg/mL activated charcoal suspension was prepared by suspending activated charcoal powder washed with hydrochloric acid (Nacalai Tesque) in distilled water in 100 folds amount, then filtering it with glass filter, washing the residue by adding distilled water in 2000 folds amount with aspirating, and suspending its powder obtained by completely drying in a dryer at 60° C. in distilled water at a final concentration of 20 mg/mL. The mixed solution after stopping the reaction was centrifuged at 20,000×g at 4° C. for 10 minutes. A supernatant was diluted to one tenth with 0.1 M Tris-HCl (pH 7.5) and centrifuged again at ×g at 4° C. for 10 minutes. Then 50 μL of a supernatant was dispensed in each well in a 96-well plate (supplied from Sanplatec, #3719), and mixed with 50 μL of a chromogenic solution (Piper pyrophosphate assay kit, Life Technologies, #P22061). Subsequently, the mixture was incubated at 37° C. for 60 minutes, and then absorbance at 570 nm was measured using a plate reader (BioRad, Model 680). A solution composed of 0.1 M Tris-HCl (pH 7.5) and 1 mM MgCl2 was used as a blank in place of the enzyme solution. Simultaneously, a standard curve for pyrophosphoric acid concentrations was prepared using a series of solutions in which 50 μL of the chromogenic solution (Piper pyrophosphate assay kit, Life Technologies, #P22061) had been added to 0, 10, 20, 30, 40 or 50 μM pyrophosphoric acid solution dissolved in 0.1 M Tris-HCl (pH 7.5) and 2 mM MgCl2. The concentration of pyrophosphoric acid produced by each modified enzyme was calculated using a value obtained by correcting an actual measured value with a blank value and using the standard curve.
(3-6) Results
The activity was measured in total 292 mutants. Results are shown in Tables 25-1 to 25-6. The activity that was 1.1 fold or more higher than the activity in the wild type enzyme was observed in 79 modified enzymes (F31E, F31K, L35E, L35K, L67E, 190E, D124E, K127D, K127E, K127N, K127R, R128K, K130G, G134P, C137L, R202D, R202N, L247D, L247E, L247Q, S248E, S248K, S248R, L249E, L249K, L249R, L249T, T257L, K259D, K259E, K259N, K259Q, K259R, R264F, R264M, R264T, D265E, D265N, D265Q, D265R, R266N, R266Q, E269D, E269I, E269Y, K292L, D301R, D305R, E312I, E312R, F316E, E321D, V325K, I328E, L340K, E371D, E379T, K386R, S401T, S402L, G404A, G404M, R444T, N447L, N447R, R458Q, T461R, T462M, R484K, K492E, V499I, P505H, F508Q, F508R, I518S, S519N, H520N, Y523I, Y523L, G530K). In particular, modified enzymes F31K, K127E, C137L, L247D, L249E, S248K, L249R, L249T, R264F, F316E, G404M, Y523I, Y523L, and G530K were demonstrated to have high activity which was 3 folds or higher than the activity in the wild type enzyme. These effective modified enzymes are summarized as lists, and shown in Tables 26-1 and 26-2.







TABLE 24







Results of computation by Molegro Molecular Viewer












Number
Residue
Total
EPair
EElec (r > 4.5)
EElec (r < 4.5)















1
R444
−22.5
−7.2
−3.6
−11.7


2
R264
−5.8
−1.9
−3.8


3
N447
−4.5
−4.5


4
S402
−3.6
−3.6


5
F376
−2.8
−2.8


6
S401
−2.5
−2.5


7
F294
−2.3
−2.3


8
R458
−2.3
0
−2.3


9
F443
−2
−2


10
S403
−1.6
−1.6


11
R266
−1.5
0
−1.5


12
K374
−0.9
0
−0.9


13
R437
−0.9
0
−0.9


14
K381
−0.9
0
−0.9


15
R484
−0.7
0
−0.7


16
K386
−0.7
0
−0.7


17
K393
−0.6
0
−0.6


18
K367
−0.6
0
−0.6


19
V297
−0.5
−0.5


20
K292
−0.4
0
−0.4


21
K493
−0.4
0
−0.4


22
Y523
−0.4
−0.4


23
K481
−0.4
0
−0.4


24
K259
−0.4
0
−0.4


25
K336
−0.3
0
−0.3


26
K541
−0.3
0
−0.3


27
K288
−0.3
0
−0.3


28
K492
−0.3
0
−0.3


29
D311
0.3
0
0.3


30
E471
0.4
0
0.4


31
E490
0.7
0
0.7


32
E321
0.7
0
0.7


33
E476
0.7
0
0.7


34
D265
0.7
0
0.7


35
E457
0.8
0
0.8


36
E312
0.8
0
0.8


37
D533
0.8
0
0.8


38
E371
0.8
0
0.8









EPair, EElec (r>4.5) and EElec (r<4.5) represent energy due to charge pairing, energy of electrostatic interaction that occurs in distance of 4.5 Å or more and energy of electrostatic interaction that occurs in distance within 4.5 Å, respectively. Total is defined as total sum of these energies. A blank column indicates that the energy was zero computationally.








TABLE 25-1







Activity changes in isoprene synthase mutants (No. 1)









Number
Mutation
Fold












1
K127R
2.3


2
K127E
3.4


3
K127D
2.4


4
K127N
1.4


5
K127Q
ND


6
K127Y
ND


7
K130D
ND


8
K130N
ND


9
K130Q
ND


10
K130Y
0.2


11
R202E
0.3


12
R202K
0.3


13
R202D
1.3


14
R202Q
0.7


15
R202N
1.3


16
W250E
0.2


17
W250D
ND


18
W250Q
ND


19
W250N
ND


20
K259R
1.8


21
K259E
2.5


22
K259D
2.3


23
K259Q
2  


24
K259N
1.5


25
D265E
1.4


26
D265Q
2.6


27
D265N
1.7


147
D131I
0.2


148
C137G
ND


149
C137L
3  


150
L256E
0.3


151
L256K
0.1


152
C286G
1  


153
I299E
ND


154
I299R
0.7


155
I299M
ND


156
Y304S
ND


157
Y304W
ND


158
F316S
0.5


159
F316E
3.1


160
F316N
ND


161
F316R
ND


162
V320M
ND


163
V320S
ND


164
V320I
ND


165
E321C
ND


166
E321S
1  


167
E321N
ND


168
C370G
ND


169
C373G
ND


170
F376I
ND


171
F376H
ND


172
F376Y
0.8


173
C388G
ND





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 25-2







Activity changes of isoprene synthase mutants (No. 2)









Number
Mutation
Fold












28
D265K
0.2


29
D265R
1.4


30
R266K
0.2


31
R266E
0.8


32
R266Q
1.2


33
R266N
2.6


34
K288R
0.3


35
K288Q
0.6


36
K288N
1  


37
K288E
0.8


38
F294L
0.6


39
F294W
ND


40
V297E
0.4


41
D301R
1.6


42
D301T
ND


43
D305R
1.2


44
D305T
ND


45
D311E
0.6


46
D311Q
0.6


47
D311N
0.4


48
D311K
0.5


49
D311R
0.7


50
D311I
0.6


51
E312D
0.2


52
E312Q
0.6


53
E312N
0.7


54
E312K
0.7


174
S399N
ND


175
S399M
ND


176
G404N
0.3


177
G404M
3  


178
V405N
0.9


179
V405M
0.5


180
Y412N
ND


181
Y412M
ND


182
L414N
0.6


183
L414M
ND


184
V415N
ND


185
V415M
ND


186
C416G
ND


187
C416M
ND


188
C416L
ND


189
L449N
0.4


190
L449I
0.5


191
S452E
ND


192
S452I
ND


193
S452N
0.8


194
I465S
0.4


195
I465N
ND


196
I465M
ND


197
C446G
ND


198
C480G
ND


199
P505Q
0.3


200
P505R
1  





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 25-3







Activity changes in isoprene synthase mutants (No. 3)









Number
Mutation
Fold












55
E312I
1.4


56
E312R
1.8


57
E321D
2.9


58
E321Q
0.5


59
E321N
0.5


60
E321K
0.5


61
E321R
0.9


62
E321I
0.7


63
K336D
0.5


64
K336Q
0.7


65
K336N
0.6


66
K336E
0.9


67
K336L
0.6


68
K367R
0.9


69
K367Q
0.6


70
K367E
0.5


71
E371D
1.3


72
E371Q
0.6


73
E371K
0.6


74
E371R
0.5


75
E371L
0.4


76
K374R
0.4


77
K374Q
0.6


78
K374N
0.6


79
K374E
1  


80
E379T
2.2


81
K381R
0.2


201
P505H
1.3


202
F508Q
1.8


203
F508R
1.2


204
F508H
0.3


205
I518S
2.1


206
I518N
0.6


207
I518L
0.3


208
S519M
ND


209
S519N
2.1


210
H520N
1.8


211
H520M
ND


212
C521G
ND


213
F31E
2.8


214
F31K
3.6


215
L35E
1.9


216
L35K
2.8


217
L67E
2.4


218
I90E
1.1


219
V106E
0.1


220
S122G
0.1


221
S122D
ND


222
S122E
ND


223
D124E
1.3


224
R128K
1.6


225
F129G
0.7


226
F129D
0.4


227
F129E
0.1





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 25-4







Activity changes in isoprene synthase mutants (No. 4)









Number
Mutation
Fold












82
K381Q
0.8


83
K381N
0.6


84
K381E
0.7


85
K381L
0.9


86
K386R
1.1


87
K386Q
1  


88
K386D
0.7


89
K393R
0.7


90
K393L
0.8


91
K393N
0.5


92
K393E
0.6


93
K393D
0.7


94
D396E
0.7


95
D396Q
0.2


96
D396N
0.4


97
D396K
0.3


98
D396R
0.4


99
S401R
0.9


100
S401T
2.2


101
S402L
1.2


102
S402W
ND


103
L407F
0.2


104
R437K
1  


105
R437E
0.4


106
R437L
0.5


107
F443L
0.8


108
F443W
0.5


228
K130G
2.2


229
G134P
1.1


230
G135P
0.5


231
G157P
0.3


232
G160P
0.3


233
S162C
0.6


234
L163E
ND


235
L163K
0.1


236
G182P
0.3


237
V187K
0.1


238
R202C
ND


239
L247E
1.6


240
L247D
4.8


241
L247Q
1.5


242
L247N
0.4


243
T257L
2.5


244
R264K
ND


245
R264M
2.9


246
R264F
3.5


247
R264T
1.3


248
E269Y
2.8


249
E269I
2.8


250
E269D
1.7


251
V289K
0.3


252
K292A
1  


253
K292I
0.7


254
K292L
1.3





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 25-5







Activity changes in isoprene synthase mutants (No. 5)









Number
Mutation
Fold





109
R444T
2.3


110
N447R
1.4


111
N447T
0.3


112
N447I
ND


113
N447W
0.5


114
N447Y
ND


115
N447L
1.1


116
D448E
0.9


117
D448L
0.8


118
D448K
0.8


119
T451Q
0.3


120
E455H
0.1


121
R458K
0.9


122
R458Q
1.2


123
R458N
0.5


124
R458E
0.5


125
R458D
0.4


126
T461R
1.3


127
T462M
2.1


128
E476R
0.5


129
R484K
1.3


130
R484Q
0.1


131
R484L
0.1


132
K492R
0.2


133
K492Q
0.1


134
K492L
0.3


135
K492E
1.1


255
F294I
0.6


256
V297L
0.8


257
T298V
0.9


258
T298L
1  


259
V306E
ND


260
V306K
ND


261
L310E
0.7


262
V325E
0.5


263
V325K
1.1


264
I328E
1.2


265
L340K
1.2


266
L377R
1  


267
I387K
ND


268
I388K
0.2


269
G404A
2.7


270
L407Y
ND


271
F443I
0.3


272
V499I
1.6


273
G528K
ND


274
G528E
ND


275
G528R
0.2


276
G528T
ND


277
L529K
ND


278
L529R
ND


279
L529T
ND


280
G530K
3  


281
G530E
0.1





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 25-6







Activity changes in isoprene synthase mutants (No. 6)









Number
Mutation
Fold












136
K492D
1


137
K493R
0.5


138
K493Q
0.8


139
K493L
0.8


140
K493E
0.5


141
K493D
0.3


142
Y523I
3.2


143
Y523L
3


144
Y523W
1


145
D131Q
0.1


146
D131S
0.1


282
G530R
ND


283
G530T
0.1


284
I96K
0.1


285
S248K
3.9


286
S248E
1.7


287
S248R
1.1


288
S248T
0.5


289
L249K
1.7


290
L249E
3.4


291
L249R
3.2


292
L249T
3.5





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.


ND (Not Detected): indicates that no significant activity was observed in the mutant enzyme.













TABLE 26-1







List of effective mutants (No. 1)









Number
Mutation
Fold












1
K127R
2.3


2
K127E
3.4


3
K127D
2.4


4
K127N
1.4


13
R202D
1.3


15
R202N
1.3


20
K259R
1.8


21
K259E
2.5


22
K259D
2.3


23
K259Q
2


24
K259N
1.5


25
D265E
1.4


26
D265Q
2.6


27
D265N
1.7


29
D265R
1.4


32
R266Q
1.2


33
R266N
2.6


41
D301R
1.6


43
D305R
1.2


55
E312I
1.4


56
E312R
1.8


57
E321D
2.9


71
E371D
1.3


80
E379T
2.2


86
K386R
1.1


100
S401T
2.2


101
S402L
1.2


201
P505H
1.3


202
F508Q
1.8


203
F508R
1.2


205
I518S
2.1


209
S519N
2.1


210
H520N
1.8


213
F31E
2.8


214
F31K
3.6


215
L35E
1.9


216
L35K
2.8


217
L67E
2.4


218
I90E
1.1


223
D124E
1.3


224
R128K
1.6


228
K130G
2.2


229
G134P
1.1


239
L247E
1.6


240
L247D
4.8


241
L247Q
1.5


243
T257L
2.5


245
R264M
2.9


246
R264F
3.5


247
R264T
1.3


248
E269Y
2.8


249
E269I
2.8


250
E269D
1.7


254
K292L
1.3





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.













TABLE 26-2







List of effective mutants (No. 2)









Number
Mutation
Fold












109
R444T
2.3


110
N447R
1.4


115
N447L
1.1


122
R458Q
1.2


126
T461R
1.3


127
T462M
2.1


129
R484K
1.3


135
K492E
1.1


142
Y523I
3.2


143
Y523L
3


149
C137L
3


159
F316E
3.1


177
G404M
3


263
V325K
1.1


264
I328E
1.2


265
L340K
1.2


269
G404A
2.7


272
V499I
1.6


280
G530K
3


285
S248K
3.9


286
S248E
1.7


287
S248R
1.1


289
L249K
1.7


290
L249E
3.4


291
L249R
3.2


292
L249T
3.5





Fold: Scale factor of activity change in mutant enzyme compared with wild type enzyme.






Example 4: Quantitative Evaluation of Ability of Modified Enzyme to Convert into Isoprene
Among 67 modified enzymes having the qualitative activity value of 30% or more relative to the wild type in Example 1 (1-5), 66 modified enzymes except C416K were evaluated for quantitative function. The function was specifically evaluated as follows. A concentration of each IspS mutant protein after simple purification was quantified by Bradford method. Subsequently, 1 μs of each IspS mutant was weighed and placed in a 0.2 mL volume PCR tube (Nippon Genetics) on ice. Then, 5 μL of reaction buffer (250 mM Tris-HCl, 200 mM MgCl2, pH 8.0) was added thereto, and sterilized water was added so as to make 45 μL solution together with the enzyme solution. After gently tapping, 5 μL of 40 mM DMAPP (Cayman, catalog #63180) was added and mixed. The mixture was left stand at 37° C. for 10 minutes or 17 hours, and then an amount of produced isoprene was measured by GC. A relative value of the enzyme activity of each modified enzyme relative to the wild type IspS was calculated by dividing the amount of isoprene produced by each modified enzyme by the amount isoprene produced by wild type IspS. The relative value for a reaction time of 10 minutes was defined as an activity, and the relative activity for the reaction time of 18 hours was defined as an accumulation ability. The results are shown in Tables 27-1 to 27-3. The modified enzymes that exhibited 1.1 or more of the activity or the accumulation ability were 43 modified enzymes of S2A, V97E, L114E, Q123C, V125E, D131C, C137E, C137I, C137M, C137S, V144E, V187E, L224E, C286V, C286N, T298I, I300N, C338V, C338L, C370V, C370E, C370N, C370K, C373V, C373Y, S383I, I388C/Q123C, V405C, L414C, C416E, C440S, E471C/A390C, C480N, C480Y, C480V, K481E, F508C, I518C, C521E, C521V, C521I, C521S, and C521N. The mutants that were evaluated as the effective modified enzymes in Example 1 (1-6), but effectiveness of which could not be reproduced in Tables 27-1 to 27-3 are C137K, C286I, V346M, D348E, S383M, and C446N.







TABLE 27-1







Activity evaluation of isoprene synthase mutants (No. 1)











Number
Mutant
Activity
Accumulation
Effective mutant














1
S2A
0.9
1.5
Yes


2
V55E
0
0.1


3
V76E
0
0.1


4
V97E
0.8
4.4
Yes


5
L114E
0.6
1.8
Yes


6
Q123C
0.6
3.3
Yes


7
V125E
0.8
2.7
Yes


8
D131C
1.6
1.3
Yes


9
C137K
0.4
0.4


10
C137E
1.1
3.4
Yes


11
C137I
0.6
1.2
Yes


12
C137M
1.5
5
Yes


13
C137S
0.7
2.2
Yes


14
V144E
0.6
1.5
Yes


15
V187E
0.3
1.8
Yes


16
V191E
0
0.1


17
L224E
0.7
3.3
Yes


18
V236E
0.3
0.3


19
C286V
0.5
4.6
Yes


20
C286N
1.6
3.8
Yes


21
C286I
0
0.2


22
T298I
1.2
1.9
Yes


23
I300N
0.6
3.6
Yes


24
V320C
0.3
0.7


25
C338V
0.7
4.2
Yes


26
C338L
0.2
1.1
Yes


27
V346M
0
0.1





Activity: Relative activity for reaction time of 10 minutes.


Accumulation: Relative activity for reaction time of 18 hours.













TABLE 27-2







Activity evaluation of isoprene synthase mutants (No. 2)











Number
Mutant
Activity
Accumulation
Effective mutant














28
V346S
0
0.1



29
D348E
0.5
0.4


30
C370V
1.4
6.1
Yes


31
C370E
0.5
3.2
Yes


32
C370N
0.5
3.4
Yes


33
C370K
0.5
6
Yes


34
C373V
0.5
2.2
Yes


35
C373Y
1.2
3.3
Yes


36
C373F
0
0.1


37
S383M
1
0.9


38
S383I
0.2
1.4
Yes


39
I388C/Q123C
1
1.7
Yes


40
I388C
0.3
0.5


41
I388C/N360C
0.2
0.3


42
V400E
0.1
0.1


43
V405E
0.5
0.3


44
V405C
0.8
1.5
Yes


45
L414C
0.5
1.7
Yes


46
C416E
0.9
1.5
Yes


47
C416Y
0.5
0.3


48
C440S
0.6
2.4
Yes


49
I442C
0
0.8


50
C446V
0.2
0.5


51
C446N
0.1
0.9


52
T451E
0
0.1


53
S452C
0.1
0.1


54
E471C/A390C
0.5
2
Yes





Activity: Relative activity for reaction time of 10 minutes.


Accumulation: Relative activity for reaction time of 18 hours.













TABLE 27-3







Activity evaluation of isoprene synthase mutants (No. 3)











Number
Mutant
Activity
Accumulation
Effective mutant














55
E471C
0.3
0.2



56
C480N
1.4
1.3
Yes


57
C480Y
0.8
2
Yes


58
C480V
1.1
4.4
Yes


59
K481E
1.3
5.4
Yes


60
F508C
2
0.3
Yes


61
I518C
0.4
2.9
Yes


62
C521E
1.6
9.4
Yes


63
C521V
0.7
2.4
Yes


64
C521I
0.5
1.4
Yes


65
C521S
1
1.8
Yes


66
C521N
0.5
1.9
Yes





Activity: Relative activity for reaction time of 10 minutes.


Accumulation: Relative activity for reaction time of 18 hours.






Example 5: Production of Polyisoprene
Isoprene is collected with a trap cooled with liquid nitrogen by passing the fermentation exhaust. Collected isoprene is mixed with 35 g of hexane (Sigma-Aldrich) and 10 g of silica gel (Sigma-Aldrich, catalog No. 236772) and 10 g of alumina (Sigma-Aldrich, catalog No. 267740) under a nitrogen atmosphere in 100 mL glass vessel that is sufficiently dried. Resulting mixture is left at room temperature for 5 hours. Then supernatant liquid is skimmed and is added into 50 ml glass vessel that is sufficiently dried.
Meanwhile, in a glove box under a nitrogen atmosphere, 40.0 μmol of tris[bis(trimethylsilyl)amido]gadolinium, 150.0 μmol of tributylaluminium, 40.0 μmol of bis[2-(diphenylphosphino)phenyl]amine, 40.0 μmol of triphenylcarbonium tetrakis(pentafluorophenyl)borate ((Ph3CBC6F5)4) are provided in a glass container, which is dissolved into 5 mL of toluene (Sigma-Aldrich, catalog No. 245511), to thereby obtain a catalyst solution. After that, the catalyst solution is taken out from the glove box and added to the monomer solution, which is then subjected to polymerization at 50° C. for 120 minutes.
After the polymerization, 1 mL of an isopropanol solution containing, by 5 mass %, 2,2′-methylene-bis(4-ethyl-6-t-butylphenol) (NS-5), is added to stop the reaction. Then, a large amount of methanol is further added to isolate the polymer, and the polymer is vacuum dried at 70° C. to obtain a polymer.
Example 6: Production of Rubber Compound
The rubber compositions formulated as shown in Table 28 are prepared, which are vulcanized at 145° C. for 35 minutes.









TABLE 28







Parts by mass



















Polyisoprene
100



Stearic Acid
2



Carbon Black (HAF class)
50



Antioxidant (*1)
1



Zinc Oxide
3



Cure Accelerator (*2)
0.5



Sulfur
1.5







(*1) N-(1,3-dimethylbutyl)-N′-p-phenylenediamine



(*2) N-cyclohexyl-2-benzothiazolesulfenamide






Where a numerical limit or range is stated herein, the endpoints are included. Also, all values and subranges within a numerical limit or range are specifically included as if explicitly written out.
As used herein the words “a” and “an” and the like carry the meaning of “one or more.”
Obviously, numerous modifications and variations of the present invention are possible in light of the above teachings. It is therefore to be understood that, within the scope of the appended claims, the invention may be practiced otherwise than as specifically described herein.
All patents and other references mentioned above are incorporated in full herein by this reference, the same as if set forth at length.

## Claims

1. A modified isoprene synthase, having an amino acid sequence at least 90 identical to the amino acid sequence of SEQ ID NO: 4,
wherein the modified isoprene synthase has at least one mutation of an amino acid residue corresponding to at least one amino acid residue in SEQ ID NO: 4 selected from the group consisting of: C286, E321, C370, A390, E471, C480, I518, and C521, and
the modified isoprene synthase has an isoprene synthetic activity.

2. The modified isoprene synthase of claim 1, wherein the at least one mutation in the modified isoprene synthase corresponds to at least one mutation in SEQ ID NO: 4 selected from the group consisting of: C286V, E321D, C370E, A390C, E471C, C480N, I518C, C521V, and C521I.

3. The modified isoprene synthase of claim 1, wherein the modified isoprene synthase further comprises a signal sequence at the N-terminus.

4. A modified isoprene synthase, having an amino acid sequence at least 90% identical to the amino acid sequence of SEQ ID NO: 2,
wherein the modified isoprene synthase has at least one mutation of an amino acid residue corresponding to at least one amino acid residue in SEQ ID NO: 2 selected from the group consisting of: C329, E364, C413, A433, E514, C523, I561, and C564, and
the modified isoprene synthase has an isoprene synthetic activity.

5. The modified isoprene synthase of claim 4, wherein the at least one mutation in the modified isoprene synthase corresponds to at least one mutation in SEQ ID NO: 2 selected from the group consisting of: C329V, E364D, A433C, E514C, C523N, I561C, C564V, and C564I.

6. The modified isoprene synthase of claim 1, wherein the amino acid sequence of the modified isoprene synthase has 95% or more identity to the amino acid sequence of SEQ ID NO: 4.

7. The modified isoprene synthase of claim 1, wherein the at least one mutation in the modified isoprene synthase corresponds to at least one mutation in SEQ ID NO: 4 selected from the group consisting of: C286I, C286V, E321D, C370K, A390C, E471C, C480N, I518C, C521V, and C521I.

8. The modified isoprene synthase of claim 1, wherein the at least one mutation in the modified isoprene synthase corresponds to at least two mutations in SEQ ID NO: 4 selected from the group consisting of: C286I, C286V, E321D, C370K, A390C, E471C, C480N, I518C, C521V, and C521I.

9. The modified isoprene synthase of claim 2, wherein the modified isoprene synthase further comprises a signal sequence at the N-terminus.