Systems and methods for identifying and expressing gene clusters

Patent metadata

Field	Value
Publication number	US-12456540-B2
Application number	US-202117158942-A
Country	US
Kind code	B2
Filing date	Jan 26, 2021
Priority date	Nov 16, 2016
Publication date	Oct 28, 2025
Grant date	Oct 28, 2025

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.

First claim

What is claimed is:

1. A method for producing a small molecule to screen for inhibition of a first target protein, the method comprising:
identifying a fungal protein based on its similarity to a first target protein, wherein the fungal protein has at least 60% sequence identity to the first target protein;
identifying a fungal gene cluster that is within 20,000 bases of a genomic region that encodes the fungal protein;
expressing the fungal gene cluster or a plurality of genes from the fungal gene cluster in a host cell to produce a compound;
isolating the compound produced by the fungal gene cluster or the plurality of genes from the fungal gene cluster; and
screening the isolated compound for inhibition of an activity of the first target protein;
wherein the first target protein is a mammalian protein.

2. The method of claim 1 , wherein the gene cluster includes a coding sequence for a protein that is an extracellular protein, a membrane tethered protein, a protein involved in a transport or secretion pathway, a protein homologous to a protein involved in a transport or secretion pathway, a protein with a peptide targeting signal, a protein with a terminal sequence with homology to a targeting signal, an enzyme that degrades small molecules, or a protein with homology to an enzyme that degrades small molecules.

3. The method of claim 1 , wherein the host cell is a yeast cell.

4. The method of claim 1 , wherein each expressed gene of the plurality of genes from the gene cluster is expressed under the control of a different promoter.

5. The method of claim 1 , wherein the protein that has at least 60% sequence identity to the first target protein has greater than 80% sequence identity to the first target protein.

6. The method of claim 1 , wherein the protein that has at least 60% sequence identity to the previously identified first target protein has greater than 90% sequence identity to the first target protein.

7. The method of claim 1 , wherein the first target protein is a human protein.

8. The method of claim 7 , wherein the fungal gene cluster is selected from the group consisting of (1) a cluster that comprises one or more polyketide synthases and (2) a cluster that comprises one or more non-ribosomal peptide synthetases, (3) a cluster that comprises one or more terpene synthases, (4) a cluster that comprises one or more UbiA-type terpene cyclases, and (5) a cluster that comprises one or more dimethylallyl transferases.

9. The method of claim 1 , wherein the host cell is a non-yeast fungus.

Assignees

• Univ Leland Stanford Junior

Inventors

• Naughton Brian Thomas
• Harvey Colin
• Schlecht Ulrich
• Hillenmeyer Maureen Elizabeth
• Horecka Joe

Classifications

• C12N15/79

  Vectors or expression systems specially adapted for eukaryotic hosts · CPC title

• G16B30/10

  Sequence alignment; Homology search · CPC title

• G16B5/00

  ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B10/00 Primary

  ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis · CPC title