# US 2019/0270986 A1 · Compositions and methods for activating silent gene clusters

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- Number: US 2019/0270986 A1
- Document ID: US20190270986A1
- Status: Published application
- Kind: A1
- Application number: 16/415,528
- Filed: 2019-05-17
- Published: 2019-09-05
- Earliest claimed: 2015-05-29
- Assignees: Zymergen Inc.
- Applicants: Zymergen Inc.
- Inventors: Oliver Liu; Jeffrey Hoon Kim
- Web page: https://patentgrep.com/patent/US20190270986A1

## CPC

- C12N 15/1072: {Differential gene expression library synthesis, e.g. subtracted libraries, differential screening}
- C12N 7/00: Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof (preparing medicinal viral antigen or antibody compositions, e.g. virus vaccines, A61K39/00)
- C12N 15/63: Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N 15/76: for Actinomyces; for Streptomyces
- C12N 2795/10042: virus or viral particle as vehicle, e.g. encapsulating small organic molecule
- C12N 2795/10043: viral genome or elements thereof as genetic vector
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

The disclosure provides compositions and methods for producing natural products in microorganisms that are otherwise unexpressed, poorly expressed or poorly transcribed. In particular aspects, the disclosure provides compositions and methods for activating a silent gene or gene cluster with a bacteriophage and/or Streptomyces Antibiotic Regulatory Protein (SARP) transcription factor.

## Claims

### Claim 1

A method of identifying a product in a bacterial cell comprising:
(a) infecting a bacterial cell with a bacteriophage, wherein the bacteriophage comprises a nucleotide sequence that encodes one or more bacterial transcription factors,
(b) identifying products produced by the bacterial cell,
(c) comparing the products identified in step (b) to the products produced from a control bacterial cell that has not been infected with a bacteriophage that comprises a nucleotide sequence that encodes the one or more bacterial transcription factors, and
(d) identifying a product not produced by the control bacterial cell when there is a difference between the products identified in the bacterial cell and the control bacterial cell.

### Claim 2 (depends on 1)

The method of claim 1, wherein the products are identified through performing chromatography on bacterial cell pellets, bacterial cell lysis supernatants, or culture medium utilized in the growth of the bacteria.

### Claim 3 (depends on 2)

The method of claim 2, wherein the chromatography is selected from liquid chromatography, gas chromatography, column chromatography, flash chromatography, size-exclusion chromatography, hydrophilic interaction chromatography, ion exchange chromatography, and two-dimensional chromatography.

### Claim 4 (depends on 3)

The method of claim 3, wherein the liquid chromatography is UHPLC.

### Claim 5 (depends on 2)

The method of claim 2, wherein the chromatography is combined with mass spectrometry.

### Claim 6 (depends on 1)

The method of claim 1, wherein the one or more transcription factors are operably linked to one or more heterologous control sequences.

### Claim 7 (depends on 6)

The method of claim 6, wherein the bacterial cell is a member of phylum Actinobacteria.

### Claim 8 (depends on 6)

The method of claim 6, wherein the bacteriophage is selected from the group consisting of R4, ΦC31, ΦC62, ΦBT1, SV1 and ΦC43.