Novel polynucleotides
AssigneesThe Kitasato Institute, National Institute of Technology and Evaluation
InventorsSatoshi Omura, Haruo Ikeda, Jun Ishikawa, Hiroshi Horikawa, Tadayoshi Shiba, Yoshiyuki Sakaki, Masahira Hattori
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Abstract
Novel polynucleotides derived from microorganisms belonging to actinomycetes and fragments thereof, polypeptides encoded by the polynucleotides and fragments thereof, polynucleotide arrays comprising the polynucleotides and fragments thereof, recording media in which the nucleotide sequences of the polynucleotide and fragments thereof have been recorded which are readable in a computer, and use of them.
Claims53
A method for at least one of the following:
- (A) identifying a mutation point of a gene derived from a mutant of an actinomycetes,
- (B) measuring an expression amount of a gene derived from an actinomycetes,
- (C) analyzing an expression profile of a gene derived from an actinomycetes,
- (D) analyzing expression patterns of genes derived from an actinomycetes, or
- (E) identifying a gene homologous to a gene derived from an actinomycetes,
- said method comprising:
- (a) producing a polynucleotide array by adhering to a solid support at least two polynucleotides selected from the group consisting of first polynucleotides comprising the nucleotide sequence represented by any one of SEQ ID NOs:1 to 7551, second polynucleotides which hybridize with the first polynucleotides under stringent conditions, and third polynucleotides comprising a sequence of 10 to 200 continuous bases of the first or second polynucleotides,
- (b) incubating the polynucleotide array with at least one of a labeled polynucleotide derived from an actinomycetes, a labeled polynucleotide derived from a mutant of the actinomycetes or a labeled polynucleotide to be examined, under hybridization conditions,
- (c) detecting any hybridization, and
- (d) analyzing the result of the hybridization.
A polynucleotide array, comprising:
- at least two polynucleotides selected from the group consisting of first polynucleotides comprising the nucleotide sequence represented by any one of SEQ ID NOs:1 to 7551, second polynucleotides which hybridize with the first polynucleotides under stringent conditions, and third polynucleotides comprising 10 to 200 continuous bases of the first or second polynucleotides, and
- a solid support adhered thereto.
A polynucleotide comprising the nucleotide sequence represented by SEQ ID NOs:1 to 7551 or a polynucleotide having a homology of at least 80% with the polynucleotide.
A polynucleotide comprising any one of the nucleotide sequences represented by SEQ ID NOs:2 to 7551, or a polynucleotide which hybridizes with the polynucleotide under stringent conditions.
A polynucleotide encoding a polypeptide having any one of the amino acid sequences represented by SEQ ID NOs:7552 to 15101, or a polynucleotide which hybridizes therewith under stringent conditions.
A polynucleotide which is present in the 5′ upstream or 3′ downstream of a polynucleotide encoding a protein in a polynucleotide comprising any one of the nucleotide sequence represented by SEQ ID NOs:2 to 3431, and has an activity of regulating an expression of the polynucleotide.
A polypeptide encoded by a polynucleotide comprising the nucleotide sequence selected from SEQ ID NOs:2 to 7551.
A polypeptide comprising the amino acid sequence selected from SEQ ID NOs:7552 to 15101.
A system based on a computer for identifying a target sequence or a target structure motif derived from an actinomycetes, comprising the following:
- (i) a user input device that inputs at least one nucleotide sequence information selected from SEQ ID NOs:1 to 7551, and target sequence or target structure motif information;
- (ii) a data storage device for at least temporarily storing the input information;
- (iii) a comparator that compares the at least one nucleotide sequence information selected from SEQ ID NOs:1 to 7551 with the target sequence or target structure motif information, recorded by the data storage device for screening and analyzing nucleotide sequence information which is coincident with or analogous to the target sequence or target structure motif information;
- and
- (iv) an output device that shows a screening or analyzing result obtained by the comparator.
A method based on a computer for identifying a target sequence or a target structure motif derived from an actinomycetes, comprising the following:
- (i) inputting at least one nucleotide sequence information selected from SEQ ID NOs:1 to 7551, target sequence information or target structure motif information into a user input device;
- (ii) at least temporarily storing said information;
- (iii) comparing the at least one nucleotide sequence information selected from SEQ ID NOs:1 to 7551 with the target sequence or target structure motif information;
- and
- (iv) screening and analyzing nucleotide sequence information which is coincident with or analogous to the target sequence or target structure motif information.
A system based on a computer for identifying a target sequence or a target structure motif derived from an actinomycetes, comprising the following:
- (i) a user input device that inputs at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101, and target sequence or target structure motif information;
- (ii) a data storage device for at least temporarily storing the input information;
- (iii) a comparator that compares the at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101 with the target sequence or target structure motif information, recorded by the data storage device for screening and analyzing amino acid sequence information which is coincident with or analogous to the target sequence or target structure motif information;
- and
- (iv) an output device that shows a screening or analyzing result obtained by the comparator.
A method based on a computer for identifying a target sequence or a target structure motif derived from an actinomycetes, comprising the following:
- (i) inputting at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101, and target sequence information or target structure motif information into a user input device;
- (ii) at least temporarily storing said information;
- (iii) comparing the at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101 with the target sequence or target structure motif information;
- and
- (iv) screening and analyzing amino acid sequence information which is coincident with or analogous to the target sequence or target structure motif information.
A system based on a computer for determining a function of a polypeptide encoded by a polynucleotide having a target nucleotide sequence derived from an actinomycetes, comprising the following:
- (i) a user input device that inputs at least one nucleotide sequence information selected from SEQ ID NOs:2 to 7551, function information of a polypeptide encoded by the nucleotide sequence, and target nucleotide sequence information;
- (ii) a data storage device for at least temporarily storing the input information;
- (iii) a comparator that compares the at least one nucleotide sequence information selected from SEQ ID NOs:2 to 7551 with the target nucleotide sequence information for determining a function of a polypeptide encoded by a polynucleotide having the target nucleotide sequence which is coincident with or analogous to the polynucleotide having at least one nucleotide sequence selected from SEQ ID NOs:2 to 7551;
- and
- (iv) an output devices that shows a function obtained by the comparator.
A method based on a computer for determining a function of a polypeptide encoded by a polypeptide encoded by a polynucleotide having a target nucleotide sequence derived from an actinomycetes, comprising the following:
- (i) inputting at least one nucleotide sequence information selected from SEQ ID NOs:2 to 7551, function information of a polypeptide encoded by the nucleotide sequence, and target nucleotide sequence information;
- (ii) at least temporarily storing said information;
- (iii) comparing the at least one nucleotide sequence information selected from SEQ ID NOs:2 to 7551 with the target nucleotide sequence information;
- and
- (iv) determining a function of a polypeptide encoded by a polynucleotide having the target nucleotide sequence which is coincident with or analogous to the polynucleotide having at least one nucleotide sequence selected from SEQ ID NOs:2 to 7551.
A system based on a computer for determining a function of a polypeptide having a target amino acid sequence derived from an actinomycetes, comprising the following:
- (i) a user input device that inputs at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101, function information based on the amino acid sequence, and target amino acid sequence information;
- (ii) a data storing device for at least temporarily storing the input information;
- (iii) a comparator that compares the at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101 with the target amino acid sequence information for determining a function of a polypeptide having the target amino acid sequence which is coincident with or analogous to the polypeptide having at least one amino acid sequence selected from SEQ ID NOs:7552 to 15101;
- and
- (iv) an output device that shows a function obtained by the comparator.
A method based on a computer for determining a function of a polypeptide having a target amino acid sequence derived from an actinomycetes, comprising the following:
- (i) inputting at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101, function information based on the amino acid sequence, and target amino acid sequence information;
- (ii) at least temporarily storing said information;
- (iii) comparing the at least one amino acid sequence information selected from SEQ ID NOs:7552 to 15101 with the target amino acid sequence information;
- and
- (iv) determining a function of a polypeptide having the target amino acid sequence which is coincident with or analogous to the polypeptide having at least one amino acid sequence selected from SEQ ID NOs:7552 to 15101.
A method for breeding an actinomycetes using the nucleotide sequence information represented by SEQ ID NO:1, comprising the following:
- (i) comparing a nucleotide sequence of a genome or gene of a production strain derived an actinomycetes which has been subjected to mutation breeding so as to produce at least one compound selected from an amino acid, a nucleic acid, a vitamin, a saccharide, an organic acid, an antibiotic, and analogous thereof by a fermentation method, with a corresponding nucleotide sequence in SEQ ID NO:1;
- (ii) identifying a mutation point present in the production strain based on a result obtained by (i);
- (iii) introducing the mutation point into an actinomycetes which is free of the mutation point, or deleting the mutation point from an actinomycetes having the mutation point;
- and
- (iv) examining productivity by the fermentation method of the compound selected in (i) of the actinomycetes obtained in (iii).
A method for breading an actinomycetes using the nucleotide sequence information represented by SEQ ID NO:1, comprising:
- (i) comparing a nucleotide sequence of a genome or gene of a production strain derived an actinomycetes which has been subjected to mutation breeding so as to produce at least one compound selected from a biological active substance comprising an antibiotic and analogous thereof by a fermentation method, with a corresponding nucleotide sequence in SEQ ID NO:1;
- (ii) identifying a mutation point present in the production strain based on a result obtain by (i);
- (iii) deleting a mutation point from an actinomycetes having the mutation point;
- and
- (iv) examining productivity by the fermentation method of the compound selected in (i) of the actinomycetes obtained in (iii).
A method for breeding an actinomycetes using the nucleotide sequence information represented by SEQ ID NOs:2 to 7551, comprising the following:
- (i) identifying an isozyme relating to biosynthesis of at least one compound selected from an amino acid, a nucleic acid, a vitamin, a saccharide, an organic acid, an antibiotic, and analogous thereof, based on the nucleotide sequence information represented by SEQ ID NOs:2 to 7551;
- (ii) classifying the isozyme identified in (i) into an isozyme having the same activity;
- (iii) mutating all genes encoding the isozyme having the same activity simultaneously;
- and
- (iv) examining productivity by a fermentation method of the compound selected in (i) of the actinomycetes which have been transformed with the gene obtained in (iii).
A method for breeding an actinomycetes using the nucleotide sequence information represented by SEQ ID NOs:2 to 7551, comprising the following:
- (i) arranging a function information of an open reading frame (ORF) represented by SEQ ID NOs:2 to 7551;
- (ii) allowing the arranged ORF to correspond to an enzyme on a known biosynthesis or signal transmission pathway;
- (iii) explicating an unknown biosynthesis pathway or signal transmission pathway of an actinomycetes in combination with information relating known biosynthesis pathway or signal transmission pathway of an actinomycetes;
- (iv) comparing the pathway explicated in (iii) with a biosynthesis pathway of a target useful product;
- and
- (v) transgenetically varying an actinomycetes based on the nucleotide sequence information represented by SEQ ID NOs:2 to 7551 to either strengthen a pathway which is judged to be important in the biosynthesis of the target useful product in (iv) or weaken a pathway which is judged not to be important in the biosynthesis of the target useful product in (iv).
A method for identifying a protein relating to useful mutation based on proteome analysis, comprising the following:
- (i) preparing
- a protein derived from a bacterium of a production strain of an actinomycetes which has been subjected to mutation breeding by a fermentation process so as to produce at least one compound selected from an amino acid, a nucleic acid, a vitamin, a saccharide, an organic acid, an antibiotic, and analogues thereof, and
- a protein derived from a bacterium of a parent strain of the production strain;
- (ii) separating the proteins prepared in (i) by two dimensional electrophoresis;
- (iii) detecting the separated proteins, and comparing an expression amount of the protein derived from the production strain with that derived from the parent strain;
- (iv) treating the protein showing different expression amounts as a result of the comparison with a peptidase to extract peptide fragments;
- (v) analyzing amino acid sequences of the peptide fragments obtained in (iv);
- and
- (vi) comparing the amino acid sequences obtained in (v) with the amino acid sequence represented by SEQ ID NOs:7552 to 15101 to identifying the protein having the amino acid sequences.
Dependencies are inferred from the claim text.