Patent Application
20230030526
The present invention relates to a method for enzymatically producing maytansinol.
Maytansinol is an important intermediate used in the production of maytansines such as emtansine, which are used as a drug portion of antibody-drug conjugates, and is obtained by hydrolysis of the isobutyl ester of the 3-position of ansamitocin P3 (AP3) produced by microorganisms such as Actinosynnema pretiosum.
As the production methods of maytansinol, chemical conversion method and microbial conversion method are known. According to the chemical conversion method, maytansinol can be obtained from an ansamitocin compound obtained by fermentation or the like by reductive cleavage using lithium trimethoxyaluminum hydride (LATH) or another alkali metal (alkali) alkoxyaluminum hydride (Patent documents 1 to 3, and Non-patent document 1). As the microbial conversion method, there is known a method for producing maytansinol comprising contacting maytanacine, maytansinol propionate or ansamitocin antibiotic with culture of a microorganism belonging to the genus Streptomyces or a processed product thereof having an ability to convert the acyloxy group at the 8-position of the starting material to a hydroxyl group (Patent document 4).
The chemical conversion method mentioned above is not necessarily a satisfactory technique for industrialization, because LATH and its derivatives to be used are pyrophoric. In addition, as for the microbial conversion method mentioned above, the enzyme responsible for the reaction has not been identified, and it is not clear what kind of enzyme contributes to the reaction.
An object of the present invention is to provide a technique relating to a method for enzymatically producing maytansinol from an ansamitocin species such as AP3.
The present invention provides the followings.
[1] A method for producing maytansinol, which comprises enzymatically producing maytansinol from an ansamitocin species with any one of the proteins (A) to (F) and (AA) to (CC) mentioned below:
(A) a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(F) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(AA) a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(BB) a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(CC) a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[2] The production method according to 1, wherein the ansamitocin species is ansamitocin P2 (AP2), ansamitocin P3 (AP3), or ansamitocin P4 (AP4).
[3] The production method according to 1 or 2, wherein the ansamitocin species is AP3.
[4] A protein, which is any one of the proteins (D) to (F) and (AA) to (CC) mentioned below:
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(F) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(AA) a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(BB) a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(CC) a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[5] A polynucleotide encoding the protein according to 4.
[6] A polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 10 or 11.
[7] A bacterium transformed with a vector containing the polynucleotide according to 5 or 6.
[8] Use of any one of the proteins (A) to (F) and (AA) to (CC) mentioned below for the production of maytansinol:
(A) a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(F) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(AA) a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(BB) a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(CC) a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[9] A bacterium transformed with a vector containing any one of the polynucleotides (a) to (1) and (aa) to (cc) mentioned below:
(a) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(b) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(c) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(d) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(e) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(f) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(g) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 2;
(h) a polynucleotide consisting of a nucleotide sequence having an identity of at least 50% to the nucleotide sequence of SEQ ID NO: 1 or 2, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(i) a polynucleotide that hybridizes with the nucleotide sequence of SEQ ID NO: 1 or 2 under stringent conditions, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(j) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 10 or 11;
(k) a polynucleotide consisting of a nucleotide sequence having an identity of at least 50% to the nucleotide sequence of SEQ ID NO: 10 or 11, wherein base of nucleotide corresponding to the position 320 is G, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(l) a polynucleotide that hybridizes with the nucleotide sequence of SEQ ID NO: 10 or 11 under stringent conditions, wherein base of nucleotide corresponding to the position 320 is G, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(aa) a polynucleotide encoding a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(bb) a polynucleotide encoding a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(cc) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[10] The bacterium according to 9, wherein the polynucleotides are derived from Bacillus subtilis.
The present invention also provides the followings.
[1] A method for producing maytansinol, which comprises the step of enzymatically producing maytansinol from an ansamitocin species with any one of the following proteins (A) to (F):
(A) a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 9, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(F) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[2] The production method according to 1, wherein the ansamitocin species is ansamitocin P2 (AP2), ansamitocin P3 (AP3), or ansamitocin P4 (AP4).
[3] The production method according to 1, wherein the ansamitocin species is AP3.
[4] A protein, which is any one of the proteins (D) to (F) mentioned below:
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(F) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[5] A polynucleotide encoding the protein according to 4.
[6] A polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 10 or 11.
[7] A bacterium transformed with a vector containing the polynucleotide according to 5 or 6.
[8] Use of any one of the proteins (A) to (F) mentioned below for the production of maytansinol:
(A) a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 9, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(F) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[9] A bacterium transformed with a vector containing any one of the polynucleotides (a) to (1) mentioned below:
(a) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(b) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(c) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 9, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(d) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(e) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(f) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
(g) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 2;
(h) a polynucleotide consisting of a nucleotide sequence having an identity of at least 90% to the nucleotide sequence of SEQ ID NO: 1 or 2, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(i) a polynucleotide encoding a protein that hybridizes with the nucleotide sequence of SEQ ID NO: 1 or 2 under stringent conditions, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(j) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 10 or 11;
(k) a polynucleotide consisting of a nucleotide sequence having an identity of at least 90% to the nucleotide sequence of SEQ ID NO: 10 or 11, wherein base of nucleotide corresponding to the position 320 is G, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(l) a polynucleotide that hybridizes with the nucleotide sequence of SEQ ID NO: 10 or 11 under stringent conditions, wherein base of nucleotide corresponding to the position 320 is G, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
[10] The bacterium according to 9, wherein the polynucleotides are derived from Bacillus subtilis.
The present invention relates to a method for producing maytansinol, which comprises the step of enzymatically producing maytansinol from an ansamitocin species. The term ansamitocin species refers to compounds represented by the following formula having different ester substituents at the C3-position, wherein R is other than H (ansamitocin P0 wherein R is H is maytansinol).
The production method of the present invention is suitable for the production of ansamitocin C3-esters among the ansamitocin species, and it is particularly suitable for the production of ansamitocin P3 (AP3) among the ansamitocin C3-esters.
AP3 is a compound represented by the following formula.
The ansamitocin species can be microbiologically produced by conventional methods. They can also be synthesized from maytansinol by a method similar to the method of International Publication WO2014/052537 (Japanese Patent Unexamined Publication (Kohyo) No. 2016-500657, Japanese Patent No. 6517693). AP3 is commercially available as a reagent.
In this description, the present invention may be explained with reference to the production of maytansinol from AP3 among the ansamitocin species as an example, but those skilled in the art can understand the production of maytansinol from other ansamitocin species by appropriately applying the explanation to such a case.
The step of producing maytansinol from an ansamitocin species can be carried out by using any one of the following enzyme proteins (A) to (F).
(A) a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 9, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(F) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
The activity for catalyzing a reaction of producing maytansinol from an ansamitocin species is preferably an activity for catalyzing the reaction of producing maytansinol from AP3, and it more preferably refers to an activity for catalyzing the reaction of hydrolyzing AP3 to produce maytansinol. The presence or absence of such an activity can be confirmed by analyzing the presence or absence of maytansinol produced by the reaction or the amount thereof by HPLC or other methods.
Concerning the present invention, the expression that a certain protein has an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species means at least that the protein can produce 1.0 μg/mL or more (preferably 2.0 μg/mL or more, more preferably 3.0 μg/mL or more, further preferably 4.0 μg/mL or more) of maytansinol when the protein is allowed to act on 100 μg/mL ofAP3 under suitable conditions, unless especially stated. The suitable conditions are, for example, such conditions that the reaction is carried out at 20 to 30° C. and pH 3.0 to 8 for 48 hours or longer by using a sufficient amount of the enzyme.
In one embodiment of the invention, the enzyme protein to be used can be derived from a bacterium of the genus Bacillus, more specifically Bacillus subtilis, still more specifically Bacillus subtilis subsp. subtilis str168.
The nucleotide sequences of the enzymes identified by the inventors of the present invention and used in the examples described in this description are shown as SEQ ID NOS: 1 and 2, and the corresponding amino acid sequence is shown as SEQ ID NO: 9, in Sequence Listing. The sequence of SEQ ID NO: 1 is the nucleotide sequence for para-nitrobenzyl esterase (bspnbA) derived from Bacillus subtilis subsp. subtilis str168. The sequence of SEQ ID NO: 2 corresponds to the sequence of SEQ ID NO: 1 in which codons are optimized for expression in E. coli. The sequence identity between the sequences of SEQ ID NOS: 1 and 2 is 76%.
The protein consisting of the amino acid sequence of SEQ ID NO: 9 encoded by the nucleotide sequence of SEQ ID NO: 1 is the para-nitrobenzyl esterase (bspnbA) derived from Bacillus subtilis subsp. subtilis str168. The ability of this enzyme to convert an ansamitocin species to maytansinol was not known so far. There is not any report about finding of any specific enzyme that converts an ansamitocin species to maytansinol, and there is not any structural information based on cocrystals with similar structures, either. Thus, it is very difficult to predict the activity of bspnbA for converting an ansamitocin species to maytansinol even based on the amino acid sequence and three-dimensional structural information thereof.
According to the study of the inventors of the present invention, it was found that bspnbA used in the examples belongs to the carboxylesterase family, and has an a/P hydrolase fold. If a sequence is shown, motif analysis thereof can be appropriately performed by those skilled in the art by using software publicly opened on websites, such as Pfam in GenomeNet (http://www.genome.jp/), and whether or not a protein has an activity for catalyzing a reaction of producing maytansinol using an ansamitocin species as a substrate can be appropriately assessed by those skilled in the art with reference to descriptions of this description.
According to the study of the inventors of the present invention, it is important that, in the enzyme having the amino acid sequence of SEQ ID NO: 9, amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP for maintaining the activity. Therefore, if the amino acid sequence of the rest of the sequence has an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, the protein has a necessary degree of the enzymatic activity, and can produce maytansinol from an ansamitocin species. As examples of such an enzyme, the inventors of the present invention obtained a variety of mutant enzymes listed in Table 2 mentioned in the section of Examples of this description. The identity percentages of the mutant enzymes to the sequence of SEQ ID NO: 9 are also shown in the same table. Among the mutant enzymes, the amino acid sequences of A3N3, AN4, FC15A2, AN1, and 3rdD_EPLA7lib_anc13 are shown as SEQ ID NOS: 18 to 22, respectively.
Therefore, the step of producing maytansinol from an ansamitocin species can be carried out by using any one of the enzyme proteins (B) to (F) and (AA) to (CC) mentioned below:
(B) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(C) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(F) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(AA) a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(BB) a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(CC) a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
As for the activity of a mutant enzyme of the enzyme having the amino acid sequence of SEQ ID NO: 9, it is determined that the enzyme sufficiently has the activity (e.g., A) when a maytansinol area value equivalent to 0.3 μg/mL or more is detected in HPLC analysis conducted under the conditions described in Example 3 of this description after the conversion reaction performed at an AP3 concentration of 100 μg/mL, and such a case can be determined by distinguishing it from other cases (e.g., B).
The enzymes used in the method for producing maytansinol of the present invention can be produced from a bacterium having a polynucleotide encoding any of the enzyme proteins so that the bacterium can express the protein. Such a bacterium may be obtained by transformation as described later.
The conditions for producing maytansinol from an ansamitocin species using such an enzyme can be appropriately designed by those skilled in the art.
[Mutant bspnbA and Use of the Same]
In one embodiment of the present invention, a mutant bspnbA is used. An example of such a mutant bspnbA is the protein consisting of the amino acid sequence of SEQ ID NO: 12 used in the examples described in this description. The amino acid sequence of the mutant bspnbA of SEQ ID NO: 12 differs from the amino acid sequence of bspnbA of SEQ ID NO: 9 (wild type, WT) by one amino acid (in 489 amino acids).
Such a mutant bspnbA is novel as a protein. Therefore, the present invention also provides a protein that is any one of the proteins (D) to (F) mentioned below:
(D) a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein amino acid corresponding to the position 107 is G, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(F) a protein consisting of an amino acid sequence having an identity of at least 90% to the amino acid sequence of SEQ ID NO: 12, wherein amino acid corresponding to the position 107 is G, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
The present invention also provides an enzyme protein that is any one of the proteins (E) to (F) and (AA) to (CC) mentioned below:
(E) a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(F) a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(AA) a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(BB) a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(CC) a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
In the present invention, the expression that an amino acid corresponding to the position Y is a specific amino acid used for an amino acid sequence (subject amino acid sequence) having an identity to the amino acid sequence of SEQ ID NO: X means that the amino acid in the subject amino acid sequence corresponding to the amino acid at the position Y in the amino acid sequence of SEQ ID NO: X is the specific amino acid. The amino acid corresponding to the position Y refers to the amino acid in the subject amino acid sequence that corresponds to the amino acid at the position Y of the amino acid sequence of SEQ ID NO: X, when the amino acid sequence of SEQ ID NO: X and the subject amino acid sequence are aligned so that there are the largest number of positions at which the amino acids of both sequences are identical.
The present invention also provides polynucleotides encoding the proteins mentioned above, polynucleotides (SEQ ID NOS: 10 and 11) encoding the mutant bspnbA (SEQ ID NO: 12), a vector containing any of those polynucleotides, and a bacterium transformed with the vector.
The enzyme used in the method for producing maytansinol from an ansamitocin species of the present invention can be produced from a bacterium having a polynucleotide encoding that enzyme protein so that the bacterium can express the protein. As such a bacterium, the present invention also provides a genetically modified bacterium that produces the enzyme.
Such a genetically modified bacterium is a bacterium transformed with a vector containing any one of the polynucleotides (a) to (1) mentioned below:
(a) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 9;
(b) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 9 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(c) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 9, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(d) a polynucleotide encoding a protein consisting of the amino acid sequence of SEQ ID NO: 12;
(e) a polynucleotide encoding a protein consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 12 by substitution, deletion, insertion, and/or addition of one or more amino acids, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(f) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 50% to the amino acid sequence of SEQ ID NO: 12, wherein:
amino acids corresponding to the positions 66 to 68 are DLL or AGA, amino acids corresponding to the positions 139 to 141 are GPF, amino acids corresponding to the positions 146 to 148 are LSS or LSP, amino acids corresponding to the positions 247 to 249 are LHT, amino acids corresponding to the position 323 are HSX or ASX (where X is Q, K, E, or M), amino acids corresponding to the positions 374 to 376 are QSX (where X is H, R, D, or Q), and amino acids corresponding to the positions 443 to 445 are GNP, and
having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(g) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 2;
(h) a polynucleotide consisting of a nucleotide sequence having an identity of at least 50% to the nucleotide sequence of SEQ ID NO: 1 or 2, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(i) a polynucleotide that hybridizes with the nucleotide sequence of SEQ ID NO: 1 or 2 under stringent conditions, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(j) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 10 or 11;
(k) a polynucleotide consisting of a nucleotide sequence having an identity of at least 50% to the nucleotide sequence of SEQ ID NO: 10 or 11, wherein base of nucleotide corresponding to the position 320 is G, and encoding a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(l) a polynucleotide that hybridizes with the nucleotide sequence of SEQ ID NO: 10 or 11 under stringent conditions, wherein base of nucleotide corresponding to the position 320 is G, and encodes a protein having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species;
(aa) a polynucleotide encoding a protein consisting of any one of the amino acid sequences of SEQ ID NOS: 18 to 21;
(bb) a polynucleotide encoding a protein consisting of an amino acid sequence derived from any one of the amino acid sequences of SEQ ID NOS: 18 to 21 by substitution, deletion, insertion, and/or addition of one or more amino acids, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species; and
(cc) a polynucleotide encoding a protein consisting of an amino acid sequence having an identity of at least 80% to any one of the amino acid sequences of SEQ ID NOS: 18 to 21, and having an activity for catalyzing a reaction of producing maytansinol from an ansamitocin species.
One group of the preferred examples of the polynucleotides mentioned above consists of those derived from Bacillus subtilis.
As a bacterium to be transformed (host), any microorganism that can incorporate a target DNA and produce a target enzyme protein can be used without any particular restriction. Examples of the bacterium to be transformed include bacteria belonging to the phylum Proteobacteria (also referred to simply as Proteobacteria). Proteobacteria include bacteria belonging to the class Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, Zetaproteobacteria, or Oligoflexus. Among these, one example of such a bacterium to be preferably used for the present invention is a bacterium belonging to the class Gammaproteobacteria (also referred to simply as Gammaproteobacteria), more specifically Escherichia coli. Various strains belonging to Escherichia coli can be used for the present invention. Preferred examples of such strains include E. coli BL21 (DE3), and so forth.
Means for incorporating a foreign polynucleotide into a host and making the host express it are not particularly limited, and such operation can be performed by using, for example, the methods described in Molecular Cloning: A Laboratory Manual, 2nd ed., Current Protocols in Molecular Biology (edited by Frederick M., Ausubel et al., 1987). The host and plasmid vector system is not particularly limited as long as it is such a system that the target polynucleotide can be stably retained and expressed in the host. The plasmid may also contain an autonomous replication sequence, promoter sequence, terminator sequence, drug resistance gene, and so forth in addition to the target polynucleotide, and as for the type of the plasmid, the plasmid may be not only an autonomously replicable plasmid, but also an integrative plasmid having a sequence homologous to a certain region of the genome of the host to be used. The site for incorporation of the target polynucleotide may be either on the plasmid or on the genome of the host microorganism.
In the case of using E. coli as the host, examples of the autonomously replicable vector include pUC19, pRSFDuet-1, etc., examples of the promoter sequence include lac, T7, etc., examples of the terminator sequence include lacZ terminator, T7 terminator, etc., and examples of the drug resistance gene include ampicillin resistance gene, kanamycin resistance gene, etc.
The conditions for the production of the enzyme by the transformed bacterium can be appropriately designed by those skilled in the art according to the type of the bacterium to be used. When E. coli is used as the host, the bacterial cells can be grown by inoculating an appropriate amount of the microorganism into a commonly used medium containing an antibiotic as a selection marker, and performing culture at 20 to 40° C. for 6 to 72 hours, preferably 9 to 60 hours, more preferably 12 to 48 hours, if necessary, with stirring or shaking at 100 to 400 rpm. The target substance can be obtained in the culture medium by, if necessary, supplying an appropriate inducer (e.g., isopropylthio-β-galactoside (IPTG)), further performing culture at 20 to 40° C. for 3 to 72 hours, preferably 4 to 60 hours, more preferably 6 to 48 hours, if necessary, with stirring or shaking the culture medium at 100 to 400 rpm. The endpoint of the culture can be appropriately determined by those skilled in the art, taking into account the production amount of the target substance, and so forth.
According to a preferred embodiment of the present invention, a transformed E. coli is provided. A preferred example of the transformed E. coli is one having an ability to produce 1 sg or more of maytansinol per 1 mL of culture medium.
Concerning the expression that a polynucleotide “hybridizes under stringent conditions” used in connection with the present invention, the hybridization conditions can be appropriately selected depending on the polynucleotide to be obtained for any polynucleotide according to the descriptions of Molecular Cloning: A Laboratory Manual, 4th ed. (Sambrook et al., Cold Spring Harbor Laboratory Press) and Hybridization of Nucleic Acid Immobilization on Solid Supports (ANALYTICAL BIOCHEMISTRY, 138, 267-284 (1984)), unless especially noted. For example, when a DNA having an identity of 50% or higher is to be obtained, hybridization can be performed at 40° C. in SSC solution at 6-fold concentration (SSC solution at 1-fold concentration contains 150 mM sodium chloride and 15 mM sodium citrate solution) in the presence of 5% formamide, and then the filter can be washed at 49° C. with SSC solution at 4-fold concentration. When a DNA having an identity of 85% or higher is to be obtained, hybridization can be performed at 40° C. in SSC solution at 2-fold concentration in the presence of 50% formamide, and then the filter can be washed at 57° C. with SSC solution at 0.1-fold concentration. When a DNA having an identity of 90% or higher is to be obtained, hybridization can be performed at 45° C. in SSC solution at 2-fold concentration in the presence of 50% formamide, and then the filter can be washed at 62° C. with SSC solution at 0.1-fold concentration.
As for the expression of “an amino acid sequence derived by substitution, deletion, insertion, and/or addition of one or more amino acids” used for a protein or amino acid sequence in the present invention, the number of amino acids substituted or the like is not limited for any protein, unless especially stated, so long as the protein having the amino acid sequence has a desired function, but it may be about 1 to 250, 1 to 200, 1 to 150, 1 to 100, 1 to 50, 1 to 40, 1 to 30, 1 to 20, 1 to 15, 1 to 9, or 1 to 4, or in the case of substitution of amino acids of similar properties, a further larger number of amino acids may be substituted or the like. Means for preparing polynucleotides for such amino acid sequences and such proteins are well known to those skilled in the art.
In the explanations of the present invention, as for amino acids or amino acid residues, A stands for alanine, C for cysteine, D for aspartic acid, E for glutamic acid, F for phenylalanine, G for glycine, H for histidine, I for isoleucine, K for lysine, L for leucine, M for methionine, N for asparagine, P for proline, Q for glutamine, R for arginine, S for serine, T for threonine, U for selenocysteine(3), V for valine, W for tryptophan, and Y for tyrosine.
Concerning the present invention, the term “identity” used for nucleotide sequences (also referred to as base sequence) or amino acid sequence means percentage of the number of identical nucleotides or amino acids of two sequences determined by aligning the two sequences in an optimal manner for any nucleotide sequence or amino acid sequence, unless especially stated. It can be calculated in accordance with the equation: Identity=(Number of matching positions/Total number of positions)×100, and can be calculated by using a commercially available algorithm. Such an algorithm is also incorporated into the NBLAST and XBLAST programs described in Altschul et al., J. Mol. Biol., 215 (1990) 403-410. In more detail, the search and analysis for nucleotide or amino acid sequence identity can be performed with algorithms or programs well known to those skilled in the art (e.g., BLASTN, BLASTP, BLASTX, ClustalW, etc.). When such a program is used, parameters for it can be appropriately set by those skilled in the art, or default parameters of each program can be used. The specific procedures for these analysis methods are also well known to those skilled in the art. Genetic information processing software GENETYX (registered trademark, Genetyx Corporation) may be used for calculating the identity. If the sequence for which the % identity is to be calculated has an additional sequence that does not exist in the sequence to be compared, such as a tag sequence, such an additional sequence is not included in the calculation of the % identity.
Concerning the present invention, identity for a nucleotide sequence or an amino acid sequence is sequence identity of at least 50%, for example, 60% or higher, 70% or higher, preferably 80% or higher, more preferably 85% or higher, further preferably 90% or higher, further preferably 95% or higher, further preferably 97.5% or higher, further preferably 99% or higher, for any case, unless especially stated.
The polynucleotides or genes, and proteins or enzymes used in the present invention can be prepared by those skilled in the art using conventional techniques.
Hereafter, the present invention will be specifically explained with reference to examples, but is not limited by them.
By referring to databases, a nucleotide sequence of para-nitrobenzyl esterase (bspnbA) derived from Bacillus subtilis subsp. subtilis str168 (SEQ ID NO: 1) was artificially synthesized (GenScript Inc.) as a sequence in which codons were optimized for expression in E. coli (SEQ ID NO: 2). The sequence was amplified by PCR using primers FCapA-BspnbA and RCapA-BspnbA (SEQ ID NOS: 3 and 4). Similarly, the pCDF-capA vector (
The E. coli JM109 (TAKARA) was transformed with the resulting In-Fusion solution, and incubated overnight. By performing colony PCR for the resulting colonies, plasmid containing the insert was searched for to prepare a plasmid. The obtained plasmid was designated as pCDF-capA-bspnbA.
E. coli BL21 (DE3) (Nippon Gene Co., Ltd.) was transformed with pRSF-bspnbA (obtained by cloning the sequence of SEQ ID NO: 2 into the multi-cloning site of pRSFDuet-1), and pCDF-capA-bspnbA, and the resulting colonies were each inoculated into the M9 seed liquid medium (0.68% Na2HPO4, 0.3% KH2PO4, 0.1% NH4Cl, 0.05% NaCl, 1.0% casamino acid, 0.002% thymine, 0.1 mM CaCl2), 0.4% D-glucose, 1.0 mM MgCl2) containing kanamycin sulfate (25 μg/mL) and streptomycin sulfate (10 μg/mL), and cultured at 28° C. for 20 hours with shaking at 220 rpm.
The culture medium was added to the M9 main medium (0.68% Na2HPO4, 0.3% KH2PO4, 0.1% NH4Cl, 0.05% NaCl, 1.0% casamino acid, 0.002% thymine, 0.1 mM CaCl2) containing kanamycin sulfate (25 μg/mL) and Overnight Express AutoInduction Systems (Merck), and culture was performed at 28° C. for 6 hours with shaking at 220 rpm. Then, IPTG was added at a final concentration of 1 mM, and culture was performed at 28° C. for about 16 hours with shaking at 220 rpm. The cells were collected by centrifugation of 0.5 mL of the resulting culture medium, the supernatant was discarded, then 10 mM Tris-HCl and 100 μg/mL of AP3 (dissolved in acetonitrile) were added as final concentrations, and the conversion reaction was allowed at 30° C. and 220 rpm. After 24 to 96 hours, an equal volume of acetone was added, the mixture was stirred for 10 minute, and then centrifuged, and the supernatant was subjected to HPLC analysis.
The analysis conditions are described below.
Analytical instrument: SHIMADZU Nexera XR
Column used: Imtakt Unison UK-C8 (50×3 mm)
Separation conditions: 0 to 9 minutes (3 to 90% of B), 9 to 9.50 minutes (90% of B),
9.51 to 12 minutes (3% of B), 12.01 minutes (stop)
Flow rate: 0.7 mL/minute
Injection volume: 10 μL
Column temperature: 40° C.
HPLC and LC/MS charts are shown in
There is not any report about finding of any specific enzyme that converts AP3 to maytansinol, and there is not any structural information based on cocrystals with similar structures, either. Thus, it is extremely difficult to predict the activity of this enzyme even based on the amino acid sequence and three-dimensional structural information thereof.
According to the study of the inventors of the present invention, a peak of maytansinol could be similarly detected by HPLC when AP2 was used instead of AP3. In addition, it can be easily analogized that the pnb esterase also acts on AP4 (isobutyl ester) in the same way as that for AP2 (ethyl ester) and AP3 (isopropyl ester). Therefore, the pnb esterase is an enzyme that catalyzes the reaction that converts various ansamitocin species to maytansinol.
Although the enzyme was not purified in the activity evaluations of Examples 2 and 3, and standardization was not performed for protein concentration or bacterial growth rate, either, it was assumed that the activity of this enzyme for AP3 could be further enhanced, therefore saturation mutation was site-specifically introduced into the active center of bspnbA, and a highly active enzyme was screened for. The mutation site is shown in
Mutant enzyme library fragments were amplified by inverse PCR using primers FpnbA_A107X and RpnbA_A107X (SEQ ID NOS: 7 and 8) and pCDF-capA-bspnbA as the template, cyclized by using T4 kinase (Toyobo) and Ligation high (Toyobo), and used to transform E. coli JM109 (TAKARA), and the bacteria were incubated overnight at 37° C. All the obtained colonies were suspended in the LB liquid medium and collected, and the plasmids were extracted from them to construct a mutant enzyme library. It was introduced into E. coli BL21(DE3) according to the method of Example 2, and 93 clones were inoculated into the M9 seed liquid medium containing streptomycin sulfate (10 μg/mL) contained in wells of a 96-deep well plate, and cultured at 30° C. for 20 hours with shaking at 800 rpm. The culture medium was added to the M9 main medium (0.68% Na2HPO4, 0.3% KH2PO4, 0.1% NH4Cl, 0.05% NaCl, 1.0% casamino acid, 0.002% thymine, 0.1 mM CaCl2) containing streptomycin sulfate (10 μg/mL) and Overnight Express AutoInduction Systems (Merck), and culture was performed at 30° C. for 6 hours with shaking at 800 rpm. Then, IPTG was added at a final concentration of 10 mM, and culture was performed at 30° C. for 24 hours with shaking at 800 rpm. The cells were collected by centrifugation of the resulting culture medium, the supernatant was discarded, then 10 mM Tris-HCl and 100 μg/mL AP3 (dissolved in acetonitrile) were added as final concentrations, and the conversion reaction was allowed at 37° C. and 800 rpm. After 24 hours, an equal volume of acetone was added, the mixture was stirred for 10 minute, and then centrifuged, and the supernatant was subjected to HPLC analysis.
As for the analytical conditions, see Example 3. As a result of this test, A107G mutant enzyme of which AP3 conversion activity was increased by about 5 times compared with that of the wild-type esterase was obtained (
In the same manner as that of Example 1, a designed enzyme A3N3 gene was artificially synthesized in a sequence in which codons were optimized for expression in E. coli (GENEWIZ), and amplified by PCR using primers A3N3_Fw and A3N3_Rv (SEQ ID NOS: 13 and 14). Similarly, pRSFDuet-1 vector (SEQ ID NO: 15) was amplified by PCR using primers pRSF_Fw and pRSF_Rv (SEQ ID NOS: 16 and 17). The resulting two fragments were cloned by using In-Fusion kit of TAKARA. Genes for the other mutant enzymes were prepared in the same manner.
The obtained In-Fusion solution was used for introduction into E. coli BL21(DE3) according to the method of Example 2, the obtained clones were inoculated into 2 mL of the M9 seed medium (14-mL test tubes) and pre-cultured overnight at 28° C. and 220 rpm. The culture medium was added to 10 mL of the M9 main medium (0.68% Na2HPO4, 0.3% KH2PO4, 0.1% NH4Cl, 0.05% NaCl, 1.0% casamino acid, 0.002% thymine, 0.1 mM CaCl2) containing kanamycin sulfate (25 μg/mL) and Overnight Express Autoinduction System 1 (Merck), and culture was performed at 28° C. for 6 hours with shaking at 220 rpm. Then, IPTG was added at a final concentration of 100 μM, and culture was performed at 28° C. for 12 hours with shaking at 220 rpm. The cells were collected by centrifugation of 1 mL of the resulting culture medium, the supernatant was discarded, then 250 μL of 50 mM Tris-HCl containing 100 mg/L of AP3 as the substrate was added, the cells were suspended on a vortex mixer, and the conversion reaction was allowed at 37° C. and 220 rpm. After 24 hours, an equal volume of acetone was added, the mixture was stirred for 10 minute, and then centrifuged, and the supernatant was subjected to HPLC analysis.
The conversion reaction was carried out at an AP3 concentration of 100 μg/mL, and HPLC analysis was performed under the conditions described in Example 3. When a maytansinol area corresponding to 0.3 μg/mL or more was detected, the result was represented as A (there was sufficient activity), and the other results were represented as B. The parts considered to relate to the activity (positions corresponding to positions of the SEQ ID NO: 9, secondary structure) and the results of this test are summarized in the tables mentioned below, together with the % identities to the sequence of the SEQ ID NO: 9. The secondary structure is based on the information of BspnbA (PDB:1QE3) (https://www.rcsb.org/sequence/1QE3).
A3N3, AN4, FC15A2, AN1, and 3rdD_EPLA7lib_anc13 had particularly high activity.
SEQ ID NO: 1, Nucleotide sequence of pnbA derived from Bacillus subtilis subsp. subtilis str168
SEQ ID NO: 2, Nucleotide sequence of pnbA E. coli
SEQ ID NO: 3, PCR primer, FCapA-BspnbA
SEQ ID NO: 4, PCR primer, RCapA-BspnbA
SEQ ID NO: 5, PCR primer, FCapApCDFXhoI
SEQ ID NO: 6, PCR primer, RCapApCDFNdeI
SEQ ID NO: 7, PCR primer, FpnbA_A107X
SEQ ID NO: 8, PCR primer, RpnbA_A107X
SEQ ID NO: 9, Amino acid sequence of pnbA
SEQ ID NO: 10, Nucleotide sequence for A107G mutant enzyme
SEQ ID NO: 11, Nucleotide sequence for A107G mutant enzyme (E. coli type)
SEQ ID NO: 12, Amino acid sequence of A107G mutant enzyme
SEQ ID NO: 13, PCR primer, A3N3_Fw
SEQ ID NO: 14, PCR primer, A3N3_Rv
SEQ ID NO: 15, Vector, pRSFDuet-1
SEQ ID NO: 16, PCR primer, pRSF_Fw
SEQ ID NO: 17, PCR primer, pRSF_Rv
SEQ ID NO: 18, Amino acid sequence of mutant enzyme A3N3
SEQ ID NO: 19, Amino acid sequence of mutant enzyme AN4
SEQ ID NO: 20, Amino acid sequence of mutant enzyme FC15A2
SEQ ID NO: 21, Amino acid sequence of mutant enzyme AN1
SEQ ID NO: 22, Amino acid sequence of mutant enzyme 3rdD_EPLA7lib_anc13
| Number | Date | Country | Kind |
|---|---|---|---|
| 2019-217460 | Nov 2019 | JP | national |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/JP2020/044347 | 11/27/2020 | WO |
