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Jaiaue P, Srimongkol P, Thitiprasert S, Piluk J, Thammaket J, Assabumrungrat S, Cheirsilp B, Tanasupawat S, Thongchul N. Inactivation of guanylate kinase in Bacillus sp. TL7-3 cultivated under an optimized ratio of carbon and nitrogen sources influenced GTP regeneration capability and sporulation. Heliyon 2024; 10:e31956. [PMID: 38841476 PMCID: PMC11152743 DOI: 10.1016/j.heliyon.2024.e31956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
Bacillus sp. TL7-3 has potential as a dietary supplement to promote human and animal health. It produces spores that can survive in harsh environments. Thus, when supplemented with nutrients, these spores can withstand the acidic pH of the stomach and resume vegetative development in the gut when exposed to growth-promoting conditions. Spores are formed as a cellular defense mechanism when a culture experiences stress and process optimization to achieve high spore production in a typical batch process remains challenging. Existing literature on the manipulation of gene expression and enzyme activity during batch cultivation is limited. Studies on the growth patterns, morphological changes, and relevant gene expression have aided in enhancing spore production. The present study used the response surface methodology for medium optimization. The model suggested that yeast extract and NH4Cl were significant factors controlling spore production. A comparison between the high weight ratio of carbon and nitrogen (C:N) substrates (8.57:1) in the optimized and basal media (0.52:1) showed an 8.76-fold increase in the final spore concentration. The expression of major genes, including codY, spo0A, kinA, and spo0F, involved in the sporulation was compared when cultivating Bacillus sp. TL7-3 in media with varying C:N ratios. At high C:N ratios, spo0A, kinA, and spo0F were upregulated, whereas codY was downregulated. This led to decreased guanylate kinase activity, resulting in a low guanosine triphosphate concentration and inactivation of CodY, thereby reducing the repression of spo0A and CodY-repressed genes and stimulating sporulation.
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Affiliation(s)
- Phetcharat Jaiaue
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Piroonporn Srimongkol
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Sitanan Thitiprasert
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Jirabhorn Piluk
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Jesnipit Thammaket
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Suttichai Assabumrungrat
- Department of Chemical Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand
| | - Benjamas Cheirsilp
- Department of Industrial Biotechnology, Faculty of Agro-Industry, Prince of Songkla University, Songkla, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Nuttha Thongchul
- Center of Excellence in Bioconversion and Bioseparation for Platform Chemical Production, Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
- Institute of Biotechnology and Genetic Engineering, Chulalongkorn University, Bangkok, Thailand
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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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3
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Fu Y, Liu X, Su Z, Wang P, Guo Q, Ma P. Arabinose Plays an Important Role in Regulating the Growth and Sporulation of Bacillus subtilis NCD-2. Int J Mol Sci 2023; 24:17472. [PMID: 38139303 PMCID: PMC10744016 DOI: 10.3390/ijms242417472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/22/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
A microbial fungicide developed from Bacillus subtilis NCD-2 has been registered for suppressing verticillium wilt in crops in China. Spores are the main ingredient of this fungicide and play a crucial role in suppressing plant disease. Therefore, increasing the number of spores of strain NCD-2 during fermentation is important for reducing the cost of the fungicide. In this study, five kinds of carbon sources were found to promote the metabolism of strain NCD-2 revealed via Biolog Phenotype MicroArray (PM) technology. L-arabinose showed the strongest ability to promote the growth and sporulation of strain NCD-2. L-arabinose increased the bacterial concentration and the sporulation efficiency of strain NCD-2 by 2.04 times and 1.99 times compared with D-glucose, respectively. Moreover, L-arabinose significantly decreased the autolysis of strain NCD-2. Genes associated with arabinose metabolism, sporulation, spore resistance to heat, and spore coat formation were significantly up-regulated, and genes associated with sporulation-delaying protein were significantly down-regulated under L-arabinose treatment. The deletion of msmX, which is involved in arabinose transport in the Bacillus genus, decreased growth and sporulation by 53.71% and 86.46% compared with wild-type strain NCD-2, respectively. Complementing the mutant strain by importing an intact msmX gene restored the strain's growth and sporulation.
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Affiliation(s)
- Yifan Fu
- College of Plant Protection, Agricultural University of Hebei, Baoding 071000, China;
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
| | - Xiaomeng Liu
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
| | - Zhenhe Su
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
| | - Peipei Wang
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
| | - Qinggang Guo
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
| | - Ping Ma
- Key Laboratory of IPM on Crops in Northern Region of North China, Integrated Pest Management Innovation Centre of Hebei Province, Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Ministry of Agriculture and Rural Affairs of China, Baoding 071000, China; (X.L.); (Z.S.); (P.W.)
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Freire V, Del Río J, Gómara P, Salvador M, Condón S, Gayán E. Comparative study on the impact of equally stressful environmental sporulation conditions on thermal inactivation kinetics of B. subtilis spores. Int J Food Microbiol 2023; 405:110349. [PMID: 37591013 DOI: 10.1016/j.ijfoodmicro.2023.110349] [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: 03/08/2023] [Revised: 06/30/2023] [Accepted: 07/29/2023] [Indexed: 08/19/2023]
Abstract
Control of bacterial spores continues to be one of the main challenges for the food industry due to their wide dissemination and extremely high resistance to processing methods. Furthermore, the large variability in heat resistance in spores that contaminate foods makes it difficult to establish general processing conditions. Such heterogeneity not only derives from inherent differences among species and strains, but also from differences in sporulation environments that are generally ignored in spores encountered in foods. We evaluated heat inactivation kinetics and the thermodependency of resistance parameters in B. subtilis 168 spores sporulated at adverse temperatures, water activity (aw), and pH, applying an experimental approach that allowed us to quantitatively compare the impact of each condition. Reduction of incubation temperature from the optimal temperature dramatically reduced thermal resistance, and it was the most influential factor, especially at the highest treatment temperatures. These spores were also more sensitive to chemicals presumably acting in the inner membrane. Reducing sporulation aw increased heat resistance, although the magnitude of that effect depended on the solute and the treatment temperature. Thus, changes in sporulation environments varied 3D100°C values up to 10.4-fold and z values up to 1.7-fold, highlighting the relevance of taking such a source of variability into account when setting heat processing conditions. UV-C treatment and sodium hypochlorite efficiently inactivated all spore populations, including heat-resistant ones produced at low aw.
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Affiliation(s)
- Víctor Freire
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Javier Del Río
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Paula Gómara
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Maika Salvador
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Santiago Condón
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain
| | - Elisa Gayán
- Department of Animal Production and Food Science, AgriFood Institute of Aragon (IA2), University of Zaragoza-CITA, Faculty of Veterinary, Miguel Servet 177, 50013 Zaragoza, Spain.
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Bhowmick S, Shenouda ML, Tschowri N. Osmotic stress responses and the biology of the second messenger c-di-AMP in Streptomyces. MICROLIFE 2023; 4:uqad020. [PMID: 37223731 PMCID: PMC10117811 DOI: 10.1093/femsml/uqad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/25/2023]
Abstract
Streptomyces are prolific antibiotic producers that thrive in soil, where they encounter diverse environmental cues, including osmotic challenges caused by rainfall and drought. Despite their enormous value in the biotechnology sector, which often relies on ideal growth conditions, how Streptomyces react and adapt to osmotic stress is heavily understudied. This is likely due to their complex developmental biology and an exceptionally broad number of signal transduction systems. With this review, we provide an overview of Streptomyces' responses to osmotic stress signals and draw attention to open questions in this research area. We discuss putative osmolyte transport systems that are likely involved in ion balance control and osmoadaptation and the role of alternative sigma factors and two-component systems (TCS) in osmoregulation. Finally, we highlight the current view on the role of the second messenger c-di-AMP in cell differentiation and the osmotic stress responses with specific emphasis on the two models, S. coelicolor and S. venezuelae.
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Affiliation(s)
- Sukanya Bhowmick
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Mary L Shenouda
- Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany
| | - Natalia Tschowri
- Corresponding author. Institute of Microbiology, Leibniz Universität Hannover, 30419 Hannover, Germany. E-mail:
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Salihoglu R, Srivastava M, Liang C, Schilling K, Szalay A, Bencurova E, Dandekar T. PRO-Simat: Protein network simulation and design tool. Comput Struct Biotechnol J 2023; 21:2767-2779. [PMID: 37181657 PMCID: PMC10172639 DOI: 10.1016/j.csbj.2023.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023] Open
Abstract
PRO-Simat is a simulation tool for analysing protein interaction networks, their dynamic change and pathway engineering. It provides GO enrichment, KEGG pathway analyses, and network visualisation from an integrated database of more than 8 million protein-protein interactions across 32 model organisms and the human proteome. We integrated dynamical network simulation using the Jimena framework, which quickly and efficiently simulates Boolean genetic regulatory networks. It enables simulation outputs with in-depth analysis of the type, strength, duration and pathway of the protein interactions on the website. Furthermore, the user can efficiently edit and analyse the effect of network modifications and engineering experiments. In case studies, applications of PRO-Simat are demonstrated: (i) understanding mutually exclusive differentiation pathways in Bacillus subtilis, (ii) making Vaccinia virus oncolytic by switching on its viral replication mainly in cancer cells and triggering cancer cell apoptosis and (iii) optogenetic control of nucleotide processing protein networks to operate DNA storage. Multilevel communication between components is critical for efficient network switching, as demonstrated by a general census on prokaryotic and eukaryotic networks and comparing design with synthetic networks using PRO-Simat. The tool is available at https://prosimat.heinzelab.de/ as a web-based query server.
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Affiliation(s)
- Rana Salihoglu
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Mugdha Srivastava
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Core Unit Systems Medicine, University of Würzburg, 97080 Würzburg, Germany
| | - Chunguang Liang
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Klaus Schilling
- Informatics VII, Robotics and Telematics, Department of Mathematics and Informatics, Am Hubland, University of Würzburg, D-97074 Würzburg, Germany
| | - Aladar Szalay
- Dept. of Biochemistry, Biocenter, Am Hubland, University of Würzburg, D-97074 Würzburg, Germany
- Department of Radiation Medicine and Applied Sciences, Rebecca & John Moores Comprehensive Cancer Center, University of California, San Diego, CA, USA
- Dept. of Pathology, Center of Immune technologies, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Corresponding author.
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- Corresponding author at: Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.
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7
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Stecker D, Hoffmann T, Link H, Commichau FM, Bremer E. L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism. Front Microbiol 2022; 13:908304. [PMID: 35783388 PMCID: PMC9245794 DOI: 10.3389/fmicb.2022.908304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
The accumulation of the compatible solute L-proline by Bacillus subtilis via synthesis is a cornerstone in the cell’s defense against high salinity as the genetic disruption of this biosynthetic process causes osmotic sensitivity. To understand how B. subtilis could potentially cope with high osmolarity surroundings without the functioning of its natural osmostress adaptive L-proline biosynthetic route (ProJ-ProA-ProH), we isolated suppressor strains of proA mutants under high-salinity growth conditions. These osmostress-tolerant strains carried mutations affecting either the AhrC transcriptional regulator or its operator positioned in front of the argCJBD-carAB-argF L-ornithine/L-citrulline/L-arginine biosynthetic operon. Osmostress protection assays, molecular analysis and targeted metabolomics showed that these mutations, in conjunction with regulatory mutations affecting rocR-rocDEF expression, connect and re-purpose three different physiological processes: (i) the biosynthetic pathway for L-arginine, (ii) the RocD-dependent degradation route for L-ornithine, and (iii) the last step in L-proline biosynthesis. Hence, osmostress adaptation without a functional ProJ-ProA-ProH route is made possible through a naturally existing, but inefficient, metabolic shunt that allows to substitute the enzyme activity of ProA by feeding the RocD-formed metabolite γ-glutamate-semialdehyde/Δ1-pyrroline-5-carboxylate into the biosynthetic route for the compatible solute L-proline. Notably, in one class of mutants, not only substantial L-proline pools but also large pools of L-citrulline were accumulated, a rather uncommon compatible solute in microorganisms. Collectively, our data provide an example of the considerable genetic plasticity and metabolic resourcefulness of B. subtilis to cope with everchanging environmental conditions.
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Affiliation(s)
- Daniela Stecker
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Hannes Link
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Fabian M. Commichau
- Insitute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
- Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, Germany
| | - Erhard Bremer
- Faculty of Biology, Philipps-University Marburg, Marburg, Germany
- SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
- *Correspondence: Erhard Bremer,
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Wang M, Wamp S, Gibhardt J, Holland G, Schwedt I, Schmidtke KU, Scheibner K, Halbedel S, Commichau FM. Adaptation of Listeria monocytogenes to perturbation of c-di-AMP metabolism underpins its role in osmoadaptation and identifies a fosfomycin uptake system. Environ Microbiol 2022; 24:4466-4488. [PMID: 35688634 DOI: 10.1111/1462-2920.16084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
The human pathogen Listeria monocytogenes synthesizes and degrades c-di-AMP using the diadenylate cyclase CdaA and the phosphodiesterases PdeA and PgpH respectively. c-di-AMP is essential because it prevents the uncontrolled uptake of osmolytes. Here, we studied the phenotypes of cdaA, pdeA, pgpH and pdeA pgpH mutants with defects in c-di-AMP metabolism and characterized suppressor mutants restoring their growth defects. The characterization of the pdeA pgpH mutant revealed that the bacteria show growth defects in defined medium, a phenotype that is invariably suppressed by mutations in cdaA. The previously reported growth defect of the cdaA mutant in rich medium is suppressed by mutations that osmotically stabilize the c-di-AMP-free strain. We also found that the cdaA mutant has an increased sensitivity against isoleucine. The isoleucine-dependent growth inhibition of the cdaA mutant is suppressed by codY mutations that likely reduce the DNA-binding activity of encoded CodY variants. Moreover, the characterization of the cdaA suppressor mutants revealed that the Opp oligopeptide transport system is involved in the uptake of the antibiotic fosfomycin. In conclusion, the suppressor analysis corroborates a key function of c-di-AMP in controlling osmolyte homeostasis in L. monocytogenes.
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Affiliation(s)
- Mengyi Wang
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Sabrina Wamp
- Division of Enteropathogenic Bacteria and Legionella, Robert-Koch-Institute, 38855, Wernigerode, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,Research Complex NanoBio, Peter the Great Saint Petersburg Polytechnic University, Politekhnicheskaya ulitsa 29A, Saint Petersburg, 195251, Russia
| | - Gudrun Holland
- ZBS4 - Advanced Light and Electron Microscopy, Robert-Koch-Institute, Seestraße 10, 13353, Berlin, Germany
| | - Inge Schwedt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
| | - Kai-Uwe Schmidtke
- FG Enzyme Technology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Katrin Scheibner
- FG Enzyme Technology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Sven Halbedel
- Division of Enteropathogenic Bacteria and Legionella, Robert-Koch-Institute, 38855, Wernigerode, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.,FG Molecular Microbiology, Institute of Biology, University of Hohenheim, 70599, Stuttgart, Germany
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Andryukov BG, Karpenko AA, Lyapun IN. Learning from Nature: Bacterial Spores as a Target for Current Technologies in Medicine (Review). Sovrem Tekhnologii Med 2021; 12:105-122. [PMID: 34795986 PMCID: PMC8596247 DOI: 10.17691/stm2020.12.3.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 01/05/2023] Open
Abstract
The capability of some representatives of Clostridium spp. and Bacillus spp. genera to form spores in extreme external conditions long ago became a subject of medico-biological investigations. Bacterial spores represent dormant cellular forms of gram-positive bacteria possessing a high potential of stability and the capability to endure extreme conditions of their habitat. Owing to these properties, bacterial spores are recognized as the most stable systems on the planet, and spore-forming microorganisms became widely spread in various ecosystems. Spore-forming bacteria have been attracted increased interest for years due to their epidemiological danger. Bacterial spores may be in the quiescent state for dozens or hundreds of years but after they appear in the favorable conditions of a human or animal organism, they turn into vegetative forms causing an infectious process. The greatest threat among the pathogenic spore-forming bacteria is posed by the causative agents of anthrax (B. anthracis), food toxicoinfection (B. cereus), pseudomembranous colitis (C. difficile), botulism (C. botulinum), gas gangrene (C. perfringens). For the effective prevention of severe infectious diseases first of all it is necessary to study the molecular structure of bacterial spores and the biochemical mechanisms of sporulation and to develop innovative methods of detection and disinfection of dormant cells. There is another side of the problem: the necessity to investigate exo- and endospores from the standpoint of obtaining similar artificially synthesized models in order to use them in the latest medical technologies for the development of thermostable vaccines, delivery of biologically active substances to the tissues and intracellular structures. In recent years, bacterial spores have become an interesting object for the exploration from the point of view of a new paradigm of unicellular microbiology in order to study microbial heterogeneity by means of the modern analytical tools.
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Affiliation(s)
- B G Andryukov
- Leading Researcher, Laboratory of Molecular Microbiology; G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia; Professor, Department of Fundamental Sciences; Far Eastern Federal University, 10 Village Ayaks, Island Russkiy, Vladivostok, 690922, Russia
| | - A A Karpenko
- Senior Researcher, Laboratory of Cell Biophysics; A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 17 Palchevskogo St., Vladivostok, 690041, Russia
| | - I N Lyapun
- Researcher, Laboratory of Molecular Microbiology G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia
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10
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Sun J, Liu Y, Lin F, Lu Z, Lu Y. CodY, ComA, DegU and Spo0A controlling lipopeptides biosynthesis in Bacillus amyloliquefaciens fmbJ. J Appl Microbiol 2021; 131:1289-1304. [PMID: 33460520 DOI: 10.1111/jam.15007] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 01/09/2023]
Abstract
AIM In the study, we investigated the regulatory effects of these genes (codY, comA, degU and spo0A) on the biosynthesis of three lipopeptides (bacillomycin D, fengycin and surfactin) in Bacillus amyloliquefaciens. METHODS AND RESULTS The codY, comA, degU and spo0A genes in B. amyloliquefaciens fmbJ were knocked out. The results showed that the productions of bacillomycin D were significantly reduced compared with that of fmbJ. Their deletion induced great changes in the levels of transcripts specifying metabolic pathways, quorum sensing system and substance transport system in fmbJ. Moreover, overexpression of these genes improved the productions of bacillomycin D. In particular, the overexpression of spo0A enhanced bacillomycin D yield up to 648·9 ± 60·9 mg l-1 from 277·3 ± 30·5 mg l-1 . In addition, the yields of surfactin in fmbJΔcodY and fmbJΔdegU were significantly improved, and the regulatory factor CodY had no significant effect on the synthesis of fengycin. CONCLUSIONS These genes positively regulated the expression of bacillomycin D and fengycin synthase genes in strain fmbJ. However, codY and degU negatively regulated surfactin biosynthesis. Moreover, it was found that CodY had a concentration dependence on bacillomycin D synthesis. Spo0A might play a direct regulatory role in the synthesis and secretion of bacillomycin D. SIGNIFICANCE AND IMPACT OF THE STUDY This study indicated that genetic engineering of regulatory genes was an effective strategy to improve the yields of antimicrobial lipopeptides and provided promising strains for industrial production of lipopeptides.
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Affiliation(s)
- J Sun
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, People's Republic of China.,College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Y Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - F Lin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Z Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Y Lu
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, People's Republic of China
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11
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Thüring M, Ganapathy S, Schlüter MAC, Lechner M, Hartmann RK. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol 2020; 18:79-92. [PMID: 32862759 DOI: 10.1080/15476286.2020.1795408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Bacterial 6S RNA regulates transcription via binding to the active site of RNA polymerase holoenzymes. 6S RNA has been identified in the majority of bacteria, in most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two 6S RNA paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that the regulatory role of 6S RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed 6S RNA deletion mutants of the undomesticated B. subtilis wild-type strain NCIB 3610. We observed a strong phenotype for the ∆6S-2 RNA strain that showed increased biofilm formation on solid media and the ability to form surface-attached biofilms in liquid culture. This phenotype remained undetected in derived laboratory strains (168, PY79) that are defective in biofilm formation. Quantitative RT-PCR data revealed transcriptional upregulation of biofilm marker genes such as tasA, epsA and bslA in the ∆6S-2 RNA strain, particularly during transition from exponential to stationary growth phase. Salt stress, which blocks sporulation at a very early stage, was found to override the derepressed biofilm phenotype of the ∆6S-2 RNA strain. Furthermore, the ∆6S-2 RNA strain showed retarded swarming activity and earlier spore formation. Finally, the ∆6S-1&2 RNA double deletion strain showed a prolonged lag phase of growth under oxidative, high salt and alkaline stress conditions, suggesting that the interplay of both 6S RNAs in B. subtilis optimizes and fine-tunes transcriptomic adaptations, thereby contributing to the fitness of B. subtilis under the unsteady and temporarily harsh conditions encountered in natural habitats.
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Affiliation(s)
- Marietta Thüring
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Sweetha Ganapathy
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - M Amri C Schlüter
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Bioinformatics Core Facility , Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
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12
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Rath H, Sappa PK, Hoffmann T, Gesell Salazar M, Reder A, Steil L, Hecker M, Bremer E, Mäder U, Völker U. Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis. Environ Microbiol 2020; 22:3266-3286. [PMID: 32419322 DOI: 10.1111/1462-2920.15087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 12/15/2022]
Abstract
The Gram-positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole-transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one-fourth of the protein-coding genes and of numerous non-coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm formation under high-salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high-salinity, but also under standard growth conditions.
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Affiliation(s)
- Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Praveen K Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Reder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Michael Hecker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
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13
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Salt Tolerance Mechanism and Species Identification of the Plant Rhizosphere Bacterium JYZ-SD2. Curr Microbiol 2019; 77:388-395. [DOI: 10.1007/s00284-019-01835-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022]
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14
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Wang Y, Shi Y, Hu L, Du G, Chen J, Kang Z. Engineering strong and stress-responsive promoters in Bacillus subtilis by interlocking sigma factor binding motifs. Synth Syst Biotechnol 2019; 4:197-203. [PMID: 31750410 PMCID: PMC6849360 DOI: 10.1016/j.synbio.2019.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/11/2019] [Accepted: 10/29/2019] [Indexed: 01/24/2023] Open
Abstract
Prokaryotic gene expression is largely regulated on transcriptional levels with the involvement of promoters, RNA polymerase and sigma factors. Developing new promoters to customize gene transcriptional regulation becomes increasingly demanded in synthetic biology and biotechnology. In this study, we designed synthetic promoters in the Gram-positive model bacterium Bacillus subtilis by interlocking the binding motifs of σA for house-keeping gene expression and that of two alternative sigma factors σH and σB which are involved in responding post-exponential growth and general stress, respectively. The developed promoters are recognized by multiple sigma factors and hence generate strong transcriptional strength when host cells grow under normal or stressed conditions. With green fluorescent protein as the reporter, a set of strong promoters were identified, in which the transcription activities of PHA-1, PHAB-4, PHAB-7 were 18.6, 4.1, 3.3 fold of that of the commonly used promoter P43, respectively. Moreover, some of the promoters such as PHA-1, PHAB-4, PHAB-7, PBA-2 displayed increased transcriptional activities in response to high salinity or low pH. The promoters developed in this study should enrich the biotechnological toolboxes of B. subtilis.
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Affiliation(s)
- Yang Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yanan Shi
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Litao Hu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Zhen Kang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
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15
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Zeaiter Z, Marasco R, Booth JM, Prosdocimi EM, Mapelli F, Callegari M, Fusi M, Michoud G, Molinari F, Daffonchio D, Borin S, Crotti E. Phenomics and Genomics Reveal Adaptation of Virgibacillus dokdonensis Strain 21D to Its Origin of Isolation, the Seawater-Brine Interface of the Mediterranean Sea Deep Hypersaline Anoxic Basin Discovery. Front Microbiol 2019; 10:1304. [PMID: 31244812 PMCID: PMC6581673 DOI: 10.3389/fmicb.2019.01304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/27/2019] [Indexed: 12/03/2022] Open
Abstract
The adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5 M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.
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Affiliation(s)
- Zahraa Zeaiter
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Ramona Marasco
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jenny M. Booth
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Erica M. Prosdocimi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Francesca Mapelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Matteo Callegari
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Marco Fusi
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Francesco Molinari
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
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16
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Wicke D, Schulz LM, Lentes S, Scholz P, Poehlein A, Gibhardt J, Daniel R, Ischebeck T, Commichau FM. Identification of the first glyphosate transporter by genomic adaptation. Environ Microbiol 2019; 21:1287-1305. [PMID: 30666812 DOI: 10.1111/1462-2920.14534] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/12/2023]
Abstract
The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.
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Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Lisa M Schulz
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Till Ischebeck
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
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17
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Bressuire-Isoard C, Broussolle V, Carlin F. Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms. FEMS Microbiol Rev 2018; 42:614-626. [DOI: 10.1093/femsre/fuy021] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
Affiliation(s)
- Christelle Bressuire-Isoard
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
| | - Véronique Broussolle
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
| | - Frédéric Carlin
- UMR408 SQPOV “Sécurité et Qualité des Produits d'Origine Végétale”, INRA–Avignon Université, Centre de Recherche PACA, CS40509, Site Agroparc, 84914 Avignon Cedex 9, France
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18
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Reuß DR, Rath H, Thürmer A, Benda M, Daniel R, Völker U, Mäder U, Commichau FM, Stülke J. Changes of DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis mutant lacking carbon catabolite repression. Metab Eng 2017; 45:171-179. [PMID: 29242163 DOI: 10.1016/j.ymben.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Bacteria are able to prioritize preferred carbon sources from complex mixtures. This is achieved by the regulatory phenomenon of carbon catabolite repression. To allow the simultaneous utilization of multiple carbon sources and to prevent the time-consuming adaptation to each individual nutrient in biotechnological applications, mutants lacking carbon catabolite repression can be used. However, such mutants often exhibit pleiotropic growth defects. We have isolated and characterized mutations that overcome the growth defect of Bacillus subtilis ccpA mutants lacking the major regulator of catabolite repression, in particular their glutamate auxotrophy. Here we show, that distinct mutations affecting the essential DNA topoisomerase I (TopA) cause glutamate prototrophy of the ccpA mutant. These suppressing variants of the TopA enzyme exhibit increased activity resulting in enhanced relaxation of the DNA. Reduced DNA supercoiling results in enhanced expression of the gltAB operon encoding the biosynthetic glutamate synthase. This is achieved by a significant re-organization of the global transcription network accompanied by re-routing of metabolism, which results in inactivation of the glutamate dehydrogenase. Our results provide a link between DNA topology, the global transcriptional network, and glutamate metabolism and suggest that specific topA mutants may be well suited for biotechnological purposes.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Benda
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany.
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19
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Rosenberg J, Yeak KC, Commichau FM. A two-step evolutionary process establishes a non-native vitamin B6 pathway in Bacillus subtilis. Environ Microbiol 2017; 20:156-168. [PMID: 29027347 DOI: 10.1111/1462-2920.13950] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022]
Abstract
Pyridoxal 5'-phosphate (PLP), the most important form of vitamin B6 serves as a cofactor for many proteins. Two alternative pathways for de novo PLP biosynthesis are known: the short deoxy-xylulose-5-phosphate (DXP)-independent pathway, which is present in the Gram-positive model bacterium Bacillus subtilis and the longer DXP-dependent pathway, which has been intensively studied in the Gram-negative model bacterium Escherichia coli. Previous studies revealed that bacteria contain many promiscuous enzymes causing a so-called 'underground metabolism', which can be important for the evolution of novel pathways. Here, we evaluated the potential of B. subtilis to use a truncated non-native DXP-dependent PLP pathway from E. coli for PLP synthesis. Adaptive laboratory evolution experiments revealed that two non-native enzymes catalysing the last steps of the DXP-dependent PLP pathway and two genomic alterations are sufficient to allow growth of vitamin B6 auxotrophic bacteria as rapid as the wild type. Thus, the existence of an underground metabolism in B. subtilis facilitates the generation of a pathway for synthesis of PLP using parts of a non-native vitamin B6 pathway. The introduction of non-native enzymes into a metabolic network and rewiring of native metabolism could be helpful to generate pathways that might be optimized for producing valuable substances.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - KahYen C Yeak
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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20
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Hoffmann T, Bremer E. Guardians in a stressful world: the Opu family of compatible solute transporters from Bacillus subtilis. Biol Chem 2017; 398:193-214. [PMID: 27935846 DOI: 10.1515/hsz-2016-0265] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 01/09/2023]
Abstract
The development of a semi-permeable cytoplasmic membrane was a key event in the evolution of microbial proto-cells. As a result, changes in the external osmolarity will inevitably trigger water fluxes along the osmotic gradient. The ensuing osmotic stress has consequences for the magnitude of turgor and will negatively impact cell growth and integrity. No microorganism can actively pump water across the cytoplasmic membrane; hence, microorganisms have to actively adjust the osmotic potential of their cytoplasm to scale and direct water fluxes in order to prevent dehydration or rupture. They will accumulate ions and physiologically compliant organic osmolytes, the compatible solutes, when they face hyperosmotic conditions to retain cell water, and they rapidly expel these compounds through the transient opening of mechanosensitive channels to curb water efflux when exposed to hypo-osmotic circumstances. Here, we provide an overview on the salient features of the osmostress response systems of the ubiquitously distributed bacterium Bacillus subtilis with a special emphasis on the transport systems and channels mediating regulation of cellular hydration and turgor under fluctuating osmotic conditions. The uptake of osmostress protectants via the Opu family of transporters, systems of central importance for the management of osmotic stress by B. subtilis, will be particularly highlighted.
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21
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Nagler K, Krawczyk AO, De Jong A, Madela K, Hoffmann T, Laue M, Kuipers OP, Bremer E, Moeller R. Identification of Differentially Expressed Genes during Bacillus subtilis Spore Outgrowth in High-Salinity Environments Using RNA Sequencing. Front Microbiol 2016; 7:1564. [PMID: 27766092 PMCID: PMC5052260 DOI: 10.3389/fmicb.2016.01564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 09/20/2016] [Indexed: 12/02/2022] Open
Abstract
In its natural habitat, the soil bacterium Bacillus subtilis often has to cope with fluctuating osmolality and nutrient availability. Upon nutrient depletion it can form dormant spores, which can revive to form vegetative cells when nutrients become available again. While the effects of salt stress on spore germination have been analyzed previously, detailed knowledge on the salt stress response during the subsequent outgrowth phase is lacking. In this study, we investigated the changes in gene expression during B. subtilis outgrowth in the presence of 1.2 M NaCl using RNA sequencing. In total, 402 different genes were upregulated and 632 genes were downregulated during 90 min of outgrowth in the presence of salt. The salt stress response of outgrowing spores largely resembled the osmospecific response of vegetative cells exposed to sustained high salinity and included strong upregulation of genes involved in osmoprotectant uptake and compatible solute synthesis. The σB-dependent general stress response typically triggered by salt shocks was not induced, whereas the σW regulon appears to play an important role for osmoadaptation of outgrowing spores. Furthermore, high salinity induced many changes in the membrane protein and transporter transcriptome. Overall, salt stress seemed to slow down the complex molecular reorganization processes (“ripening”) of outgrowing spores by exerting detrimental effects on vegetative functions such as amino acid metabolism.
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Affiliation(s)
- Katja Nagler
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
| | - Antonina O Krawczyk
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Anne De Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Kazimierz Madela
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Tamara Hoffmann
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Michael Laue
- Advanced Light and Electron Microscopy, Center for Biological Threats and Special Pathogens, Robert Koch Institute Berlin, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Erhard Bremer
- Laboratory of Microbiology, Department of Biology, Philipps-University Marburg Marburg, Germany
| | - Ralf Moeller
- Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center Cologne, Germany
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