Compositions, methods and systems for discovery of lipopeptides
AssigneeEcopia BioSciences, Inc.
InventorsChris M. Farnet, Alfredo Staffa, Emmanuel Zazopoulos
Life of this patent
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Abstract
The invention relates to isolated polypeptides involved in lipopeptide biosynthesis and polynucleotides encoding such polypeptides. In particular, the isolated polypeptide may be an acyl-specific C-domain, an adenylating enzyme, or an acyl carrier. The invention also relates to methods for detecting a polypeptide involved in lipopeptide biosynthesis or a polynucleotide encoding such a polypeptide, as well as relevant useful computer readable medium and computer systems.
Claims26
An isolated polynucleotide encoding an acyl-specific C-domain, wherein said isolated polynucleotide encodes a polypeptide which comprises at least 45% sequence identity to at least one sequence selected from SEQ ID NOS:
- 1 and 2.
An isolated polynucleotide comprising a sequence selected from the group consisting of:
- (a) a sequence selected from the group consisting of SEQ ID NOS:
- 5, 7, 9, 11, 13, 15, 17 and 19;
- (b) a sequence that is complementary to (a);
- (c) a sequence which hybridizes to said sequence of (a) or (b) under conditions of high stringency;
- and
- (d) a sequence which has at least 70% or higher homology to said sequence of (a), (b), or (c).
An isolated polynucleotide comprising a sequence selected from the group consisting of:
- (a) a sequence selected from the group consisting of SEQ ID NOs. 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45 and 47;
- (b) a sequence that is complementary to (a);
- (c) a sequence which hybridizes to said sequence of (a) or (b) under conditions of high stringency, and
- (d) a sequence which has at least 70% or higher homology to said sequence of (a), (b), or (c).
An isolated acyl-specific C-domain, encoded by a polynucleotide which comprises a sequence selected from the group consisting of:
- (a) a sequence selected from the group consisting of SEQ ID NOs. 5, 7, 9, 11, 13, 15, 17, 19;
- and
- (b) a sequence that is complementary to (a);
- (c) a sequence which hybridizes to said sequence of (a) or (b) under conditions of high stringency;
- and
- (d) a sequence which has at least 70% or higher homology to said sequence of (a), (b), or (c).
An isolated acyl-specific C-domain comprising at least 45% sequence homology to at least one sequence selected from SEQ ID NO. 1 and SEQ ID NO. 2.
An isolated acyl-specific C-domain comprising a polypeptide sequence selected from the group consisting of:
- (a) a sequence selected from the group consisting of SEQ ID NOs. 6, 8, 10, 12, 14, 16, 18, 20 and 22;
- and
- (b) a sequence which has at least 70% or higher homology to said sequence of (a).
An isolated polypeptide comprising a polypeptide selected from the group consisting of:
- (a) SEQ ID NOs. 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46 and 48;
- and
- (b) a sequence which has at least 70% or higher homology to said sequence of (a).
An N-acyl-capping cassette comprising at least one acyl-specific C-domain polypeptide and another polypeptide selected from the group consisting of an adenylating protein and an acyl-carrier protein.
A computer readable medium, comprising:
- (a) a computer program stored on said media containing instructions sufficient to implement a process for effecting the identification, analysis, or modeling of a representation of a polynucleotide or polypeptide sequence;
- (b) data stored on said media representing a sequence of a polynucleotide selected from the group consisting of:
- i) a polynucleotide encoding an acyl-specific C-domain, said polynucleotide encoding a polypeptide having at least 45% sequence identity with either SEQ ID NO:
- 1 or SEQ ID NO:
- 2;
- ii) a polynucleotide encoding a polypeptide having at least 55% sequence identity with SEQ ID NO:
- 3;
- and
- iii) a polynucleotide encoding a polypeptide having at least 50% sequence identity with SEQ ID NO:
- 4;
- and
- (c) a data structure reflecting the underlying organization and structure of said data to facilitate said computer program access to data elements corresponding to logical sub-components of the sequence, said data structure being inherent in said program and in the way in which said computer program organizes and accesses said data.
A computer readable medium, comprising:
- (a) a computer program stored on said media containing instructions sufficient to implement a process for effecting the identification, analysis, or modeling of a representation of a polypeptide sequence;
- (b) data stored on said media representing a sequence of a polypeptide selected from the group consisting of:
- i) polypeptide representing an acyl-specific C-domain and having at least 45% sequence identity with either SEQ ID NO:
- 1 or SEQ ID NO:
- 2;
- ii) a polypeptide having at least 55% sequence identity with SEQ ID NO:
- 3;
- and
- iii) a polypeptide having at least 50% sequence identity with SEQ ID NO:
- 4 and
- (c) a data structure reflecting the underlying organization and structure of said data to facilitate said computer program access to data elements corresponding to logical sub-components of the sequence, said data structure being inherent in said program and in the way in which said computer program organizes and accesses said data.
A memory for storing data that can be accessed by a computer programmed to implement a process for effecting the identification, analysis, or modeling of a sequence of a polynucleotide or a polypeptide, said memory comprising data representing a polynucleotide selected from the group consisting of:
- (a) a polynucleotide encoding an acyl-specific C-domain, said polynucleotide encoding a polypeptide having at least 45% sequence identity with either SEQ ID NO:
- 1 or SEQ ID NO:
- 2;
- (b) a polynucleotide encoding a polypeptide having at least 55% sequence identity with SEQ ID NO:
- 3;
- and
- (c) a polynucleotide encoding a polypeptide having at least 50% sequence identity with SEQ ID NO:
- 4.
A memory for storing data that can be accessed by a computer programmed to implement a process for effecting the identification, analysis, or modeling of a sequence of a polypeptide, said memory comprising data representing a polypeptide selected from the group consisting of:
- (a) a polypeptide having at least 45% sequence identity with either SEQ ID NO:
- 1 or SEQ ID NO:
- 2;
- (b) a polypeptide having at least 55% sequence identity with SEQ ID NO:
- 3;
- and
- (c) a polypeptide having at least 50% sequence identity with SEQ ID NO:
- 4.
A method for detecting a polypeptide involved in lipopeptide biosynthesis or a polynucleotide encoding such a polypeptide comprising the step of identifying:
- (a) a polypeptide having at least 45% sequence identity to SEQ ID NO:1 or SEQ ID NO:2, or
- (b) a polynucleotide encoding a polypeptide having at least 45% sequence identity to SEQ ID NO:1 or SEQ ID NO:2, and
- wherein said at least 45% sequence identity indicates a polypeptide involved in lipopeptide biosynthesis.
A computer system comprising:
- (a) a database of reference sequences, wherein the reference sequences encode proteins involved in lipid biosynthesis, and wherein the reference sequences include one or more of:
- (i) a polypeptide sequence representing an acyl-specific C-domain or a polynucleotide encoding an acyl-specific C-domain;
- and
- (b) a user interface capable of:
- (i) receiving a test sequence for comparing against each of the reference sequences in the database;
- and
- (ii) displaying the results of the comparison.
Dependencies are inferred from the claim text.