Systems and Methods for Identifying and Expressing Gene Clusters
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsBrian Thomas Naughton, Colin Harvey, Ulrich Schlecht, Maureen Elizabeth Hillenmeyer, Joe Horecka
Life of this patent
Estimating the term…
Abstract
Methods for identifying biosynthetic gene clusters that include genes for producing compounds that interact with specific target proteins are disclosed. Some methods relate to bioinformatics methods for identifying and/or prioritizing biosynthetic gene clusters. Related systems, components, and tools for the identification and expression of such gene clusters are also disclosed.
Claims18
A method for producing a small molecule for modulating a first target protein, the method comprising:
- selecting, from a database comprising a list of biosynthetic gene clusters, one or more gene clusters that include or are positioned proximal to a region that encodes a protein that is identical with or homologous to the first target protein,
- expressing the gene cluster or a plurality of genes from the gene cluster in a host cell;
- and
- isolating a compound produced by the gene cluster.
A system for identifying biosynthetic gene clusters for introduction into a host organism to produce one or more compounds that modulate a specific target protein, the system comprising:
- a processor;
- a memory containing a gene cluster identification application;
- wherein the gene cluster identification application directs the processor to:
- load data describing at least one target protein into the memory;
- load data describing a plurality of biosynthetic gene clusters into the memory;
- score each of the plurality of biosynthetic gene clusters based upon:
- performing a homolog search for each biosynthetic gene cluster to determine a presence of at least one homolog of a target protein within or adjacent the biosynthetic gene cluster;
- output a report identifying biosynthetic gene clusters that are most likely to produce a compound that modulates the at least one target protein.
A method for producing a compound that binds a protein of interest, the method comprising:
- obtaining sequence information for a plurality of contiguous sequences, wherein each contiguous sequence includes a biosynthetic gene cluster and flanking genomic sequences;
- analyzing the contiguous sequences for the presence of a gene that encodes a protein with homology to the protein of interest, and
- selecting a biosynthetic gene cluster which includes, or is proximal to, a gene that encodes a protein that is homologous to the protein of interest,
- expressing the biosynthetic gene cluster or a plurality of genes from the biosynthetic gene cluster in a host cell;
- and
- isolating a compound produced by the biosynthetic gene cluster.
Dependencies are inferred from the claim text.