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Lamprecht O, Ratnikava M, Jacek P, Kaganovitch E, Buettner N, Fritz K, Biazruchka I, Köhler R, Pietsch J, Sourjik V. Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli. PLoS Genet 2023; 19:e1010750. [PMID: 37186613 DOI: 10.1371/journal.pgen.1010750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/25/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli gene expression also occurs in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by the second messenger c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of regulation by DgcE/PdeH and DgcM/PdeR pairs. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.
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Affiliation(s)
- Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Maryia Ratnikava
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Paulina Jacek
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Eugen Kaganovitch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Nina Buettner
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Kirstin Fritz
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ina Biazruchka
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Julian Pietsch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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Hartmann R, Jeckel H, Jelli E, Singh PK, Vaidya S, Bayer M, Rode DKH, Vidakovic L, Díaz-Pascual F, Fong JCN, Dragoš A, Lamprecht O, Thöming JG, Netter N, Häussler S, Nadell CD, Sourjik V, Kovács ÁT, Yildiz FH, Drescher K. Publisher Correction: Quantitative image analysis of microbial communities with BiofilmQ. Nat Microbiol 2021; 6:270. [PMID: 33420476 PMCID: PMC7840498 DOI: 10.1038/s41564-021-00863-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Eric Jelli
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sanika Vaidya
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Miriam Bayer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel K H Rode
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Jiunn C N Fong
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dubendorf, Switzerland
| | - Janne G Thöming
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Niklas Netter
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. .,Department of Physics, Philipps-Universität Marburg, Marburg, Germany. .,Zentrum für Synthetische Mikrobiologie, SYNMIKRO, Marburg, Germany.
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