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Warneke R, Herzberg C, Weiß M, Schramm T, Hertel D, Link H, Stülke J. DarA-the central processing unit for the integration of osmotic with potassium and amino acid homeostasis in Bacillus subtilis. J Bacteriol 2024:e0019024. [PMID: 38832794 DOI: 10.1128/jb.00190-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) is a second messenger involved in diverse metabolic processes including osmolyte uptake, cell wall homeostasis, as well as antibiotic and heat resistance. This study investigates the role of the c-di-AMP receptor protein DarA in the osmotic stress response in Bacillus subtilis. Through a series of experiments, we demonstrate that DarA plays a central role in the cellular response to osmotic fluctuations. Our findings show that DarA becomes essential under extreme potassium limitation as well as upon salt stress, highlighting its significance in mediating osmotic stress adaptation. Suppressor screens with darA mutants reveal compensatory mechanisms involving the accumulation of osmoprotectants, particularly potassium and citrulline. Mutations affecting various metabolic pathways, including the citric acid cycle as well as glutamate and arginine biosynthesis, indicate a complex interplay between the osmotic stress response and metabolic regulation. In addition, the growth defects of the darA mutant during potassium starvation and salt stress in a strain lacking the high-affinity potassium uptake systems KimA and KtrAB can be rescued by increased affinity of the remaining potassium channel KtrCD or by increased expression of ktrD, thus resulting in increased potassium uptake. Finally, the darA mutant can respond to salt stress by the increased expression of MleN , which can export sodium ions.IMPORTANCEEnvironmental bacteria are exposed to rapidly changing osmotic conditions making an effective adaptation to these changes crucial for the survival of the cells. In Gram-positive bacteria, the second messenger cyclic di-AMP plays a key role in this adaptation by controlling (i) the influx of physiologically compatible organic osmolytes and (ii) the biosynthesis of such osmolytes. In several bacteria, cyclic di-adenosine monophosphate (c-di-AMP) can bind to a signal transduction protein, called DarA, in Bacillus subtilis. So far, no function for DarA has been discovered in any organism. We have identified osmotically challenging conditions that make DarA essential and have identified suppressor mutations that help the bacteria to adapt to those conditions. Our results indicate that DarA is a central component in the integration of osmotic stress with the synthesis of compatible amino acid osmolytes and with the homeostasis of potassium, the first response to osmotic stress.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Martin Weiß
- Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Thorben Schramm
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Dietrich Hertel
- Department of Plant Ecology and Ecosystems Research, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - Jörg Stülke
- Interfaculty Institute for Microbiology and Infection Medicine, Eberhard Karls Universität Tübingen, Tübingen, Germany
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Schwedt I, Schöne K, Eckert M, Pizzinato M, Winkler L, Knotkova B, Richts B, Hau JL, Steuber J, Mireles R, Noda-Garcia L, Fritz G, Mittelstädt C, Hertel R, Commichau FM. The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates. Environ Microbiol 2023; 25:3604-3622. [PMID: 37822042 DOI: 10.1111/1462-2920.16518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023]
Abstract
Glyphosate (GS) inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase that is required for aromatic amino acid, folate and quinone biosynthesis in Bacillus subtilis and Escherichia coli. The inhibition of the EPSP synthase by GS depletes the cell of these metabolites, resulting in cell death. Here, we show that like the laboratory B. subtilis strains also environmental and undomesticated isolates adapt to GS by reducing herbicide uptake. Although B. subtilis possesses a GS-insensitive EPSP synthase, the enzyme is strongly inhibited by GS in the native environment. Moreover, the B. subtilis EPSP synthase mutant was only viable in rich medium containing menaquinone, indicating that the bacteria require a catalytically efficient EPSP synthase under nutrient-poor conditions. The dependency of B. subtilis on the EPSP synthase probably limits its evolvability. In contrast, E. coli rapidly acquires GS resistance by target modification. However, the evolution of a GS-resistant EPSP synthase under non-selective growth conditions indicates that GS resistance causes fitness costs. Therefore, in both model organisms, the proper function of the EPSP synthase is critical for the cellular viability. This study also revealed that the uptake systems for folate precursors, phenylalanine and tyrosine need to be identified and characterized in B. subtilis.
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Affiliation(s)
- Inge Schwedt
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Kerstin Schöne
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Maike Eckert
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Manon Pizzinato
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Laura Winkler
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Barbora Knotkova
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University of Göttingen, Göttingen, Germany
| | - Björn Richts
- Department of General Microbiology, Institute of Microbiology and Genetics, GZMB, Georg-August University of Göttingen, Göttingen, Germany
| | - Jann-Louis Hau
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Julia Steuber
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Raul Mireles
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
| | - Lianet Noda-Garcia
- Department of Plant Pathology and Microbiology, Hebrew University, Rehovot, Israel
| | - Günter Fritz
- FG Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Carolin Mittelstädt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
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Denise R, Babor J, Gerlt JA, de Crécy-Lagard V. Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes. Microb Genom 2023; 9:mgen000926. [PMID: 36729913 PMCID: PMC9997740 DOI: 10.1099/mgen.0.000926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis. Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.
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Affiliation(s)
- Rémi Denise
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Present address: APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jill Babor
- Department of Microbiology and Cell Sciences, Gainesville, USA
| | | | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, Gainesville, USA.,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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Tomanek I, Guet CC. Adaptation dynamics between copy-number and point mutations. eLife 2022; 11:82240. [PMID: 36546673 PMCID: PMC9833825 DOI: 10.7554/elife.82240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.
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Affiliation(s)
- Isabella Tomanek
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Călin C Guet
- Institute of Science and Technology AustriaKlosterneuburgAustria
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