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Mardoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stülke J, Commichau FM. Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway. Microb Biotechnol 2024; 17:e14429. [PMID: 38483038 PMCID: PMC10938345 DOI: 10.1111/1751-7915.14429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, in the presence of arginine, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle.
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Affiliation(s)
| | - Johanna Rapp
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Katrin Gunka
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Jan Marienhagen
- Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyForschungszentrum JülichJülichGermany
- Institut of BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Fabian M. Commichau
- FG Molecular Microbiology, Institute for BiologyUniversity of HohenheimStuttgartGermany
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Meißner J, Königshof M, Wrede K, Warneke R, Mardoukhi MSY, Commichau FM, Stülke J. Control of asparagine homeostasis in Bacillus subtilis: identification of promiscuous amino acid importers and exporters. J Bacteriol 2024; 206:e0042023. [PMID: 38193659 PMCID: PMC10882977 DOI: 10.1128/jb.00420-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
The Gram-positive model bacterium B. subtilis is able to import all proteinogenic amino acids from the environment as well as to synthesize them. However, the players involved in the acquisition of asparagine have not yet been identified for this bacterium. In this work, we used d-asparagine as a toxic analog of l-asparagine to identify asparagine transporters. This revealed that d- but not l-asparagine is taken up by the malate/lactate antiporter MleN. Specific strains that are sensitive to the presence of l-asparagine due to the lack of the second messenger cyclic di-AMP or due to the intracellular accumulation of this amino acid were used to isolate and characterize suppressor mutants that were resistant to the presence of otherwise growth-inhibiting concentrations of l-asparagine. These screens identified the broad-spectrum amino acid importers AimA and BcaP as responsible for the acquisition of l-asparagine. The amino acid exporter AzlCD allows detoxification of l-asparagine in addition to 4-azaleucine and histidine. This work supports the idea that amino acids are often transported by promiscuous importers and exporters. However, our work also shows that even stereo-enantiomeric amino acids do not necessarily use the same transport systems.IMPORTANCETransport of amino acid is a poorly studied function in many bacteria, including the model organism Bacillus subtilis. The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for l-asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both in B. subtilis and in other bacteria.
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Affiliation(s)
- Janek Meißner
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Manuel Königshof
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Wrede
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Fabian M. Commichau
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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Benda M, Schulz LM, Stülke J, Rismondo J. Influence of the ABC Transporter YtrBCDEF of Bacillus subtilis on Competence, Biofilm Formation and Cell Wall Thickness. Front Microbiol 2021; 12:587035. [PMID: 33897624 PMCID: PMC8060467 DOI: 10.3389/fmicb.2021.587035] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis develops genetic competence for the uptake of foreign DNA when cells enter stationary phase and a high cell density is reached. These signals are integrated by the competence transcription factor ComK, which is subject to transcriptional, post-transcriptional and post-translational regulation. Many proteins are involved in the development of competence, both to control ComK activity and to mediate DNA uptake. However, for many proteins, the precise function they play in competence development is unknown. In this study, we assessed whether proteins required for genetic transformation play a role in the activation of ComK or rather act downstream of competence gene expression. While these possibilities could be distinguished for most of the tested factors, we assume that two proteins, PNPase and the transcription factor YtrA, are required both for full ComK activity and for the downstream processes of DNA uptake and integration. Further analyses of the role of the transcription factor YtrA for the competence development revealed that the overexpression of the YtrBCDEF ABC transporter in the ytrA mutant causes the loss of genetic competence. Moreover, overexpression of this ABC transporter also affects biofilm formation. Since the ytrGABCDEF operon is naturally induced by cell wall-targeting antibiotics, we tested the cell wall properties upon overexpression of the ABC transporter and observed an increased thickness of the cell wall. The composition and properties of the cell wall are important for competence development and biofilm formation, suggesting that the observed phenotypes are the result of the increased cell wall thickness as an outcome of YtrBCDEF overexpression.
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Affiliation(s)
- Martin Benda
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Lisa Maria Schulz
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
| | - Jeanine Rismondo
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
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Coutte F, Niehren J, Dhali D, John M, Versari C, Jacques P. Modeling leucine's metabolic pathway and knockout prediction improving the production of surfactin, a biosurfactant from
Bacillus subtilis. Biotechnol J 2015. [DOI: 10.1002/biot.201400541] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- François Coutte
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
| | - Joachim Niehren
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
- Inria Lille, Villeneuve d'Ascq, France
| | - Debarun Dhali
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
| | - Mathias John
- University of Lille, Villeneuve d'Ascq, France
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
| | - Cristian Versari
- University of Lille, Villeneuve d'Ascq, France
- BioComputing team, CRIStAL Lab (CNRS UMR9189), University of Lille, Villeneuve d'Ascq, France
| | - Philippe Jacques
- ProBioGEM team, Research Institute for Food and Biotechnology ‐ Charles Viollette (EA7394), University of Lille, Villeneuve d'Ascq, France
- University of Lille, Villeneuve d'Ascq, France
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Shiyan A, Thompson M, Köcher S, Tausendschön M, Santos H, Hänelt I, Müller V. Glutamine synthetase 2 is not essential for biosynthesis of compatible solutes in Halobacillus halophilus. Front Microbiol 2014; 5:168. [PMID: 24782854 PMCID: PMC3995056 DOI: 10.3389/fmicb.2014.00168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/27/2014] [Indexed: 11/13/2022] Open
Abstract
Halobacillus halophilus, a moderately halophilic bacterium isolated from salt marshes, produces various compatible solutes to cope with osmotic stress. Glutamate and glutamine are dominant compatible solutes at mild salinities. Glutamine synthetase activity in cell suspensions of Halobacillus halophilus wild type was shown to be salt dependent and chloride modulated. A possible candidate to catalyze glutamine synthesis is glutamine synthetase A2, whose transcription is stimulated by chloride. To address the role of GlnA2 in the biosynthesis of the osmolytes glutamate and glutamine, a deletion mutant (ΔglnA2) was generated and characterized in detail. We compared the pool of compatible solutes and performed transcriptional analyses of the principal genes controlling the solute production in the wild type strain and the deletion mutant. These measurements did not confirm the hypothesized role of GlnA2 in the osmolyte production. Most likely the presence of another, yet to be identified enzyme has the main contribution in the measured activity in crude extracts and probably determines the total chloride-modulated profile. The role of GlnA2 remains to be elucidated.
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Affiliation(s)
- Anna Shiyan
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Melanie Thompson
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Saskia Köcher
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Michaela Tausendschön
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
| | - Inga Hänelt
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University of Frankfurt am Main Frankfurt am Main, Germany
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Michna RH, Commichau FM, Tödter D, Zschiedrich CP, Stülke J. SubtiWiki-a database for the model organism Bacillus subtilis that links pathway, interaction and expression information. Nucleic Acids Res 2013; 42:D692-8. [PMID: 24178028 PMCID: PMC3965029 DOI: 10.1093/nar/gkt1002] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Genome annotation and access to information from large-scale experimental approaches at the genome level are essential to improve our understanding of living cells and organisms. This is even more the case for model organisms that are the basis to study pathogens and technologically important species. We have generated SubtiWiki, a database for the Gram-positive model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). In addition to the established companion modules of SubtiWiki, SubtiPathways and SubtInteract, we have now created SubtiExpress, a third module, to visualize genome scale transcription data that are of unprecedented quality and density. Today, SubtiWiki is one of the most complete collections of knowledge on a living organism in one single resource.
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Affiliation(s)
- Raphael H Michna
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstrasse 8, D-37077 Göttingen, Germany
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Zaprasis A, Hoffmann T, Wünsche G, Flórez LA, Stülke J, Bremer E. Mutational activation of the RocR activator and of a crypticrocDEFpromoter bypass loss of the initial steps of proline biosynthesis inBacillus subtilis. Environ Microbiol 2013; 16:701-17. [DOI: 10.1111/1462-2920.12193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/07/2013] [Accepted: 06/11/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Adrienne Zaprasis
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Guido Wünsche
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
| | - Lope A. Flórez
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Jörg Stülke
- Department of General Microbiology; Institute of Microbiology and Genetics; Georg-August University Göttingen; Grisebachstr. 8 Göttingen D-37077 Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology; Philipps-University Marburg; Karl-von-Frisch Str. 8 Marburg D-35032 Germany
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Gunka K, Stannek L, Care RA, Commichau FM. Selection-driven accumulation of suppressor mutants in bacillus subtilis: the apparent high mutation frequency of the cryptic gudB gene and the rapid clonal expansion of gudB(+) suppressors are due to growth under selection. PLoS One 2013; 8:e66120. [PMID: 23785476 PMCID: PMC3681913 DOI: 10.1371/journal.pone.0066120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/01/2013] [Indexed: 11/25/2022] Open
Abstract
Soil bacteria like Bacillus subtilis can cope with many growth conditions by adjusting gene expression and metabolic pathways. Alternatively, bacteria can spontaneously accumulate beneficial mutations or shape their genomes in response to stress. Recently, it has been observed that a B. subtilis mutant lacking the catabolically active glutamate dehydrogenase (GDH), RocG, mutates the cryptic gudBCR gene at a high frequency. The suppressor mutants express the active GDH GudB, which can fully replace the function of RocG. Interestingly, the cryptic gudBCR allele is stably inherited as long as the bacteria synthesize the functional GDH RocG. Competition experiments revealed that the presence of the cryptic gudBCR allele provides the bacteria with a selective growth advantage when glutamate is scarce. Moreover, the lack of exogenous glutamate is the driving force for the selection of mutants that have inactivated the active gudB gene. In contrast, two functional GDHs are beneficial for the cells when glutamate was available. Thus, the amount of GDH activity strongly affects fitness of the bacteria depending on the availability of exogenous glutamate. At a first glance the high mutation frequency of the cryptic gudBCR allele might be attributed to stress-induced adaptive mutagenesis. However, other loci on the chromosome that could be potentially mutated during growth under the selective pressure that is exerted on a GDH-deficient mutant remained unaffected. Moreover, we show that a GDH-proficient B. subtilis strain has a strong selective growth advantage in a glutamate-dependent manner. Thus, the emergence and rapid clonal expansion of the active gudB allele can be in fact explained by spontaneous mutation and growth under selection without an increase of the mutation rate. Moreover, this study shows that the selective pressure that is exerted on a maladapted bacterium strongly affects the apparent mutation frequency of mutational hot spots.
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Affiliation(s)
- Katrin Gunka
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Lorena Stannek
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Rachel A. Care
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Fabian M. Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
- * E-mail:
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John M, Nebut M, Niehren J. Knockout Prediction for Reaction Networks with Partial Kinetic Information. LECTURE NOTES IN COMPUTER SCIENCE 2013. [DOI: 10.1007/978-3-642-35873-9_22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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10
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Gunka K, Commichau FM. Control of glutamate homeostasis in Bacillus subtilis: a complex interplay between ammonium assimilation, glutamate biosynthesis and degradation. Mol Microbiol 2012; 85:213-24. [DOI: 10.1111/j.1365-2958.2012.08105.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Chatsurachai S, Furusawa C, Shimizu H. An in silico platform for the design of heterologous pathways in nonnative metabolite production. BMC Bioinformatics 2012; 13:93. [PMID: 22578364 PMCID: PMC3506926 DOI: 10.1186/1471-2105-13-93] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/24/2012] [Indexed: 02/04/2023] Open
Abstract
Background Microorganisms are used as cell factories to produce valuable compounds in pharmaceuticals, biofuels, and other industrial processes. Incorporating heterologous metabolic pathways into well-characterized hosts is a major strategy for obtaining these target metabolites and improving productivity. However, selecting appropriate heterologous metabolic pathways for a host microorganism remains difficult owing to the complexity of metabolic networks. Hence, metabolic network design could benefit greatly from the availability of an in silico platform for heterologous pathway searching. Results We developed an algorithm for finding feasible heterologous pathways by which nonnative target metabolites are produced by host microorganisms, using Escherichia coli, Corynebacterium glutamicum, and Saccharomyces cerevisiae as templates. Using this algorithm, we screened heterologous pathways for the production of all possible nonnative target metabolites contained within databases. We then assessed the feasibility of the target productions using flux balance analysis, by which we could identify target metabolites associated with maximum cellular growth rate. Conclusions This in silico platform, designed for targeted searching of heterologous metabolic reactions, provides essential information for cell factory improvement.
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Affiliation(s)
- Sunisa Chatsurachai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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A high-frequency mutation in Bacillus subtilis: requirements for the decryptification of the gudB glutamate dehydrogenase gene. J Bacteriol 2011; 194:1036-44. [PMID: 22178973 DOI: 10.1128/jb.06470-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Common laboratory strains of Bacillus subtilis encode two glutamate dehydrogenases: the enzymatically active protein RocG and the cryptic enzyme GudB that is inactive due to a duplication of three amino acids in its active center. The inactivation of the rocG gene results in poor growth of the bacteria on complex media due to the accumulation of toxic intermediates. Therefore, rocG mutants readily acquire suppressor mutations that decryptify the gudB gene. This decryptification occurs by a precise deletion of one part of the 9-bp direct repeat that causes the amino acid duplication. This mutation occurs at the extremely high frequency of 10(-4). Mutations affecting the integrity of the direct repeat result in a strong reduction of the mutation frequency; however, the actual sequence of the repeat is not essential. The mutation frequency of gudB was not affected by the position of the gene on the chromosome. When the direct repeat was placed in the completely different context of an artificial promoter, the precise deletion of one part of the repeat was also observed, but the mutation frequency was reduced by 3 orders of magnitude. Thus, transcription of the gudB gene seems to be essential for the high frequency of the appearance of the gudB1 mutation. This idea is supported by the finding that the transcription-repair coupling factor Mfd is required for the decryptification of gudB. The Mfd-mediated coupling of transcription to mutagenesis might be a built-in precaution that facilitates the accumulation of mutations preferentially in transcribed genes.
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