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Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development

Julian Haist, Sara Alina Neumann, Mahmoud M Al-Bassam, Sandra Lindenberg, Marie A Elliot, View ORCID ProfileNatalia Tschowri
doi: https://doi.org/10.1101/2020.04.24.060822
Julian Haist
1Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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Sara Alina Neumann
1Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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Mahmoud M Al-Bassam
2Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, USA
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Sandra Lindenberg
1Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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Marie A Elliot
3Department of Biology, McMaster University, Hamilton, Canada
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Natalia Tschowri
1Department of Biology / Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
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  • ORCID record for Natalia Tschowri
  • For correspondence: natalia.tschowri@hu-berlin.de
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Abstract

Levels of the second messenger bis-3’-5’-cyclic di-guanosinemonophosphate (c-di-GMP) determine when Streptomyces initiate sporulation to survive under adverse conditions. c-di-GMP signals are integrated into the genetic differentiation network by the regulator BldD and the sigma factor σWhiG. However, functions of the development-specific c-di-GMP diguanylate cyclases (DGCs) CdgB and CdgC, and the phosphodiesterases (PDEs) RmdA and RmdB, are poorly understood. Here, we provide biochemical evidence that the GGDEF-EAL domain protein RmdB from S. venezuelae is a monofunctional PDE that hydrolyzes c-di-GMP to 5’pGpG. Despite having an equivalent GGDEF-EAL domain arrangement, RmdA cleaves c-di-GMP to GMP and exhibits residual DGC activity. We show that an intact EAL motif is crucial for the in vivo function of both enzymes since strains expressing protein variants with an AAA motif instead of EAL are delayed in development, similar to null mutants. Global transcriptome analysis of ΔcdgB, ΔcdgC, ΔrmdA and ΔrmdB strains revealed that the c-di-GMP specified by these enzymes has a global regulatory role, with about 20 % of all S. venezuelae genes being differentially expressed in the cdgC mutant. Our data suggest that the major c-di-GMP-controlled targets determining the timing and mode of sporulation are genes involved cell division and the production of the hydrophobic sheath that covers Streptomyces aerial hyphae and spores. Altogether, this study provides a global view of the c-di-GMP-dependent genes that contribute to the hyphae-to-spores transition and sheds light on the shared and specific functions of the key enzymes involved in c-di-GMP metabolism in S. venezuelae.

Importance Streptomyces are important producers of clinical antibiotics. The ability to synthesize these natural products is connected to their developmental biology, which includes a transition from filamentous cells to spores. The widespread bacterial second messenger c-di-GMP controls this complex switch and is a promising tool to improve antibiotic production. Here, we analyzed the enzymes that make and break c-di-GMP in S. venezuelae by studying the genome-wide transcriptional effects of the DGCs CdgB and CdgC and the PDEs RmdA and RmdB. We found that the c-di-GMP specified by these enzymes has a global regulatory role. However, despite shared enzymatic activities, the four c-di-GMP enzymes have specialized inputs into differentiation. Altogether, we demonstrate that altering c-di-GMP levels through the action of selected enzymes yields characteristically distinct transcriptional profiles; this can be an important consideration when modulating c-di-GMP for the purposes of natural product synthesis in Streptomyces.

Competing Interest Statement

The authors have declared no competing interest.

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Posted April 25, 2020.
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Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development
Julian Haist, Sara Alina Neumann, Mahmoud M Al-Bassam, Sandra Lindenberg, Marie A Elliot, Natalia Tschowri
bioRxiv 2020.04.24.060822; doi: https://doi.org/10.1101/2020.04.24.060822
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Specialized and shared functions of diguanylate cyclases and phosphodiesterases in Streptomyces development
Julian Haist, Sara Alina Neumann, Mahmoud M Al-Bassam, Sandra Lindenberg, Marie A Elliot, Natalia Tschowri
bioRxiv 2020.04.24.060822; doi: https://doi.org/10.1101/2020.04.24.060822

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