Compositions and methods for activating silent gene clusters
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.
1. A method of identifying native products in a population of bacterial cells comprising:
(a) infecting the population of bacterial cells with a plurality of recombinant bacteriophages, wherein the plurality of recombinant bacteriophages comprises a nucleotide sequence that encodes one or more bacterial transcription factors,
(b) identifying the native products produced by the population of bacterial cells,
(c) comparing the native products identified in step (b) to the native products produced from a control population of bacterial cells that has not been infected with a plurality of bacteriophages that comprises nucleotide sequence that encodes the one or more bacterial transcription factors, and
(d) identifying the native products not produced by the control population of bacterial cells when there is a difference between the native products identified in the population of bacterial cells and the control population of bacterial cells.
2. The method of claim 1 , wherein the native products are identified through performing chromatography on bacterial cell pellets, bacterial cell lysis supernatants, or culture medium utilized in the growth of the bacteria.
3. The method of claim 2 , wherein the chromatography is selected from liquid chromatography, gas chromatography, column chromatography, flash chromatography, size-exclusion chromatography, hydrophi lie interaction chromatography, ion exchange chromatography, and two-dimensional chromatography.
4. The method of claim 3 , wherein the liquid chromatography is UHPLC.
5. The method of claim 2 , wherein the chromatography is combined with mass spectrometry.
6. The method of claim 1 , wherein the one or more transcription factors are operably linked to one or more heterologous control sequences.
7. The method of claim 6 , wherein the population of bacterial cells is a member of phylum Actinobacteria.
8. The method of claim 6 , wherein the plurality of recombinant bacteriophages is selected from the group consisting of R4, ϕC31, ϕC62 , ϕBTI, SVI and ϕC43.