Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Emma J. Gehrke; Xiafei Zhang; Sheila M. Pimentel-Elardo; Andrew R. Johnson; Christiaan A. Rees; Stephanie E. Jones; Hindra; Sebastian S. Gehrke; Sonya Turvey; Suzanne Boursalie; Jane E. Hill; Erin E. Carlson; Justin R. Nodwell; Marie A. Elliot

doi:10.7554/eLife.47691

Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Emma J. Gehrke, Xiafei Zhang, Sheila M. Pimentel-Elardo, Andrew R. Johnson, Christiaan A. Rees, Stephanie E. Jones, Hindra, Sebastian S. Gehrke, Sonya Turvey, Suzanne Boursalie, Jane E. Hill, Erin E. Carlson, Justin R. Nodwell, Marie A. Elliot

Chemistry (Twin Cities)

Research output: Contribution to journal › Article › peer-review

47 Scopus citations

Abstract

Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.

Original language	English (US)
Article number	e47691
Journal	eLife
Volume	8
DOIs	https://doi.org/10.7554/eLife.47691
State	Published - 2019

Bibliographical note

Funding Information:
We wish to thank Michael Hewak, Talha Qureshi, Dan Seale, Lilian Raphael, and Christine Pham for technical assistance, Stephen Miller for computational/data mining expertise, and Gerry Wright for access to his library of wild Streptomyces species. We are also grateful to Mervyn Bibb, Mark Buttner and Govind Chandra (John Innes Centre), Ben Evans (McMaster University), and Will Navarre and Jun Liu (University of Toronto) for helpful discussions. This work was supported by Cystic Fibrosis Canada (to JN and MAE), the Canadian Institutes of Health Research (to MAE) and the Boris Family Foundation (to MAE). EJG was supported by a Department of Foreign Affairs and International Trade fellowship, and the Drug Safety and Efficacy Cross-disciplinary Training program from the Canadian Institutes of Health Research.

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© Gehrke et al.

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Gehrke, E. J., Zhang, X., Pimentel-Elardo, S. M., Johnson, A. R., Rees, C. A., Jones, S. E., Hindra, Gehrke, S. S., Turvey, S., Boursalie, S., Hill, J. E., Carlson, E. E., Nodwell, J. R., & Elliot, M. A. (2019). Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2. eLife, 8, Article e47691. https://doi.org/10.7554/eLife.47691

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title = "Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2",

abstract = "Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces{\textquoteright} arsenal of signaling and antagonistic compounds.",

author = "Gehrke, {Emma J.} and Xiafei Zhang and Pimentel-Elardo, {Sheila M.} and Johnson, {Andrew R.} and Rees, {Christiaan A.} and Jones, {Stephanie E.} and Hindra and Gehrke, {Sebastian S.} and Sonya Turvey and Suzanne Boursalie and Hill, {Jane E.} and Carlson, {Erin E.} and Nodwell, {Justin R.} and Elliot, {Marie A.}",

note = "Funding Information: We wish to thank Michael Hewak, Talha Qureshi, Dan Seale, Lilian Raphael, and Christine Pham for technical assistance, Stephen Miller for computational/data mining expertise, and Gerry Wright for access to his library of wild Streptomyces species. We are also grateful to Mervyn Bibb, Mark Buttner and Govind Chandra (John Innes Centre), Ben Evans (McMaster University), and Will Navarre and Jun Liu (University of Toronto) for helpful discussions. This work was supported by Cystic Fibrosis Canada (to JN and MAE), the Canadian Institutes of Health Research (to MAE) and the Boris Family Foundation (to MAE). EJG was supported by a Department of Foreign Affairs and International Trade fellowship, and the Drug Safety and Efficacy Cross-disciplinary Training program from the Canadian Institutes of Health Research. Publisher Copyright: {\textcopyright} Gehrke et al.",

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AU - Gehrke, Emma J.

AU - Zhang, Xiafei

AU - Pimentel-Elardo, Sheila M.

AU - Johnson, Andrew R.

AU - Rees, Christiaan A.

AU - Jones, Stephanie E.

AU - Hindra,

AU - Gehrke, Sebastian S.

AU - Turvey, Sonya

AU - Boursalie, Suzanne

AU - Hill, Jane E.

AU - Carlson, Erin E.

AU - Nodwell, Justin R.

AU - Elliot, Marie A.

N1 - Funding Information: We wish to thank Michael Hewak, Talha Qureshi, Dan Seale, Lilian Raphael, and Christine Pham for technical assistance, Stephen Miller for computational/data mining expertise, and Gerry Wright for access to his library of wild Streptomyces species. We are also grateful to Mervyn Bibb, Mark Buttner and Govind Chandra (John Innes Centre), Ben Evans (McMaster University), and Will Navarre and Jun Liu (University of Toronto) for helpful discussions. This work was supported by Cystic Fibrosis Canada (to JN and MAE), the Canadian Institutes of Health Research (to MAE) and the Boris Family Foundation (to MAE). EJG was supported by a Department of Foreign Affairs and International Trade fellowship, and the Drug Safety and Efficacy Cross-disciplinary Training program from the Canadian Institutes of Health Research. Publisher Copyright: © Gehrke et al.

PY - 2019

Y1 - 2019

N2 - Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.

AB - Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces’ arsenal of signaling and antagonistic compounds.

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Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Abstract

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