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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 DOI: 10.1128/mmbr.00181-23] [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] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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2
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Pedraza-Reyes M, Abundiz-Yañez K, Rangel-Mendoza A, Martínez LE, Barajas-Ornelas RC, Cuéllar-Cruz M, Leyva-Sánchez HC, Ayala-García VM, Valenzuela-García LI, Robleto EA. Bacillus subtilis stress-associated mutagenesis and developmental DNA repair. Microbiol Mol Biol Rev 2024; 88:e0015823. [PMID: 38551349 DOI: 10.1128/mmbr.00158-23] [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] [Indexed: 04/04/2024] Open
Abstract
SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.
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Affiliation(s)
- Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Karen Abundiz-Yañez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Alejandra Rangel-Mendoza
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Lissett E Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Rocío C Barajas-Ornelas
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mayra Cuéllar-Cruz
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | | | | | - Luz I Valenzuela-García
- Department of Sustainable Engineering, Advanced Materials Research Center (CIMAV), Arroyo Seco, Durango, Mexico
| | - Eduardo A Robleto
- School of Life Sciences, University of Nevada, Las Vegas, Nevada, USA
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3
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Majou D. Endopeptidase activities of Clostridium botulinum toxins in the development of this bacterium. Res Microbiol 2024:104216. [PMID: 38897423 DOI: 10.1016/j.resmic.2024.104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
By-products like CO₂ and organic acids, produced during Clostridium botulinum growth, appear to inhibit its development and reduce ATP production. A decrease in ATP production creates an imbalance in the ATP/GTP ratio. GTP activates CodY, which regulates BoNT expression. This toxin is released into the extracellular medium. Its light chains act as a specific endopeptidase, targeting SNARE proteins. The specific amino acids released enter the cells and are metabolized by the Stickland reaction, resulting in the synthesis of ATP. This ATP might then be used by histidine kinases to activate Spo0A, the main regulator initiating sporulation, through phosphorylation.
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Affiliation(s)
- Didier Majou
- ACTIA, 149, Rue de Bercy, 75595 Paris Cedex 12, France.
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4
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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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5
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Liu Y, LaBonte S, Brake C, LaFayette C, Rosebrock AP, Caudy AA, Straight PD. MOB rules: Antibiotic Exposure Reprograms Metabolism to Mobilize Bacillus subtilis in Competitive Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585991. [PMID: 38562742 PMCID: PMC10983992 DOI: 10.1101/2024.03.20.585991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Antibiotics have dose-dependent effects on exposed bacteria. The medicinal use of antibiotics relies on their growth-inhibitory activities at sufficient concentrations. At subinhibitory concentrations, exposure effects vary widely among different antibiotics and bacteria. Bacillus subtilis responds to bacteriostatic translation inhibitors by mobilizing a population of cells (MOB-Mobilized Bacillus) to spread across a surface. How B. subtilis regulates the antibiotic-induced mobilization is not known. In this study, we used chloramphenicol to identify regulatory functions that B. subtilis requires to coordinate cell mobilization following subinhibitory exposure. We measured changes in gene expression and metabolism and mapped the results to a network of regulatory proteins that direct the mobile response. Our data reveal that several transcriptional regulators coordinately control the reprogramming of metabolism to support mobilization. The network regulates changes in glycolysis, nucleotide metabolism, and amino acid metabolism that are signature features of the mobilized population. Among the hundreds of genes with changing expression, we identified two, pdhA and pucA, where the magnitudes of their changes in expression, and in the abundance of associated metabolites, reveal hallmark metabolic features of the mobilized population. Using reporters of pdhA and pucA expression, we visualized the separation of major branches of metabolism in different regions of the mobilized population. Our results reveal a regulated response to chloramphenicol exposure that enables a population of bacteria in different metabolic states to mount a coordinated mobile response.
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Affiliation(s)
- Yongjin Liu
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
| | - Sandra LaBonte
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
| | - Courtney Brake
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | - Carol LaFayette
- Department of Visualization, Institute for Applied Creativity, Texas A&M University, College Station, Texas, USA
| | | | - Amy A. Caudy
- Maple Flavored Solutions, LLC, Indianapolis, Indiana, USA
| | - Paul D. Straight
- Biochemistry and Biophysics Department, Texas A&M University, AgriLife Research, College Station, Texas, USA
- Interdisciplinary Program in Genetics and Genomics,Texas A&M University, College Station, Texas, USA
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6
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Liu T, Zhang M, Fan Y, Zhao L, Huang D, Zhao L, Tan M, Ye BC, Xu JY. Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration. Proteomics 2024:e2300350. [PMID: 38491406 DOI: 10.1002/pmic.202300350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/18/2024]
Abstract
Lysine acylation has been extensively investigated due to its regulatory role in a diverse range of biological functions across prokaryotic and eukaryotic species. In-depth acylomic profiles have the potential to enhance comprehension of the biological implications of organisms. However, the extent of research on global acylation profiles in microorganisms is limited. Here, four lysine acylomes were conducted in Bacillus thuringiensis by using the LC-MS/MS based proteomics combined with antibody-enrichment strategies, and a total of 3438 acetylated sites, 5797 propionylated sites, 1705 succinylated sites, and 925 malonylated sites were identified. The motif analysis of these modified proteins revealed a high conservation of glutamate in acetylation and propionylation, whereas such conservation was not observed in succinylation and malonylation modifications. Besides, conservation analysis showed that homologous acylated proteins in Bacillus subtilis and Escherichia coli were connected with ribosome and aminoacyl-tRNA biosynthesis. Further biological experiments showed that lysine acylation lowered the RNA binding ability of CodY and impaired the in vivo protein activity of MetK. In conclusion, our study expanded the current understanding of the global acylation in Bacillus, and the comparative analysis demonstrated that shared acylation proteins could play important roles in regulating both metabolism and RNA transcription progression.
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Affiliation(s)
- Tianxian Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mingya Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yameng Fan
- School of Pharmacy, Henan University, Kaifeng, China
| | - Lei Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
| | - Dan Huang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Liuchang Zhao
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Henan University, Kaifeng, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jun-Yu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, China
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7
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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8
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Kang DY, Kim A, Kim JN. CcpA and CodY Regulate CRISPR-Cas System of Streptococcus mutans. Microbiol Spectr 2023; 11:e0182623. [PMID: 37367300 PMCID: PMC10434267 DOI: 10.1128/spectrum.01826-23] [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: 05/03/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are widely recognized as bacterial adaptive immune systems against invading viruses and bacteriophages. The oral pathogen Streptococcus mutans encodes two CRISPR-Cas loci (CRISPR1-Cas and CRISPR2-Cas), and their expression under environmental conditions is still under investigation. In this study, we investigated the transcriptional regulation of cas operons by CcpA and CodY, two global regulators that contribute to carbohydrate and (p)ppGpp metabolism. The possible promoter regions for cas operons and the binding sites for CcpA and CodY in the promoter regions of both CRISPR-Cas loci were predicted using computational algorithms. We found that CcpA could directly bind to the upstream region of both cas operons, and detected an allosteric interaction of CodY within the same region. The binding sequences of the two regulators were identified through footprinting analysis. Our results showed that the promoter activity of CRISPR1-Cas was enhanced under fructose-rich conditions, while deletion of the ccpA gene led to reduced activity of the CRISPR2-Cas promoter under the same conditions. Additionally, deletion of the CRISPR systems resulted in a significant decrease in fructose uptake ability compared to the parental strain. Interestingly, the accumulation of guanosine tetraphosphate (ppGpp) was reduced in the presence of mupirocin, which induces a stringent response, in the CRISPR1-Cas-deleted (ΔCR1cas) and both CRISPR-Cas-deleted (ΔCRDcas) mutant strains. Furthermore, the promoter activity of both CRISPRs was enhanced in response to oxidative or membrane stress, while the CRISPR1 promoter activity was reduced under low-pH conditions. Collectively, our findings demonstrate that the transcription of the CRISPR-Cas system is directly regulated by the binding of CcpA and CodY. These regulatory actions play a crucial role in modulating glycolytic processes and exerting effective CRISPR-mediated immunity in response to nutrient availability and environmental cues. IMPORTANCE An effective immune system has evolved not only in eukaryotic organisms but also in microorganisms, enabling them to rapidly detect and neutralize foreign invaders in the environment. Specifically, the CRISPR-Cas system in bacterial cells is established through a complex and sophisticated regulatory mechanism involving specific factors. In this study, we demonstrate that the expression of two CRISPR systems in S. mutans can be controlled by two global regulators, CcpA and CodY, which play critical roles in carbohydrate metabolism and amino acid biosynthesis. Importantly, our results show that the expression of the CRISPR-Cas system in S. mutans influences (p)ppGpp production during the stringent response, which is a gene expression regulatory response that aids in environmental stress adaptation. This transcriptional regulation by these regulators enables a CRISPR-mediated immune response in a host environment with limited availability of carbon sources or amino acids, while ensuring efficient carbon flux and energy expenditure to support multiple metabolic processes.
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Affiliation(s)
- Da-Young Kang
- Department of Integrated Biological Science, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Andy Kim
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Jeong Nam Kim
- Department of Integrated Biological Science, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
- Department of Microbiology, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
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9
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Hainzl T, Bonde M, Almqvist F, Johansson J, Sauer-Eriksson A. Structural insights into CodY activation and DNA recognition. Nucleic Acids Res 2023; 51:7631-7648. [PMID: 37326020 PMCID: PMC10415144 DOI: 10.1093/nar/gkad512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/18/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023] Open
Abstract
Virulence factors enable pathogenic bacteria to infect host cells, establish infection, and contribute to disease progressions. In Gram-positive pathogens such as Staphylococcus aureus (Sa) and Enterococcus faecalis (Ef), the pleiotropic transcription factor CodY plays a key role in integrating metabolism and virulence factor expression. However, to date, the structural mechanisms of CodY activation and DNA recognition are not understood. Here, we report the crystal structures of CodY from Sa and Ef in their ligand-free form and their ligand-bound form complexed with DNA. Binding of the ligands-branched chain amino acids and GTP-induces conformational changes in the form of helical shifts that propagate to the homodimer interface and reorient the linker helices and DNA binding domains. DNA binding is mediated by a non-canonical recognition mechanism dictated by DNA shape readout. Furthermore, two CodY dimers bind to two overlapping binding sites in a highly cooperative manner facilitated by cross-dimer interactions and minor groove deformation. Our structural and biochemical data explain how CodY can bind a wide range of substrates, a hallmark of many pleiotropic transcription factors. These data contribute to a better understanding of the mechanisms underlying virulence activation in important human pathogens.
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Affiliation(s)
- Tobias Hainzl
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå Centre of Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Mari Bonde
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- QureTech Bio, Umeå, Sweden
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå Centre of Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Umeå Centre of Microbial Research (UCMR), Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Molecular Infection Medicine, Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
| | - A Elisabeth Sauer-Eriksson
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Umeå Centre of Microbial Research (UCMR), Umeå University, Umeå, Sweden
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10
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Norris MH, Bluhm AP, Metrailer MC, Jiranantasak T, Kirpich A, Hadfield T, Ponciano JM, Blackburn JK. Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans. Sci Rep 2023; 13:5060. [PMID: 36977718 PMCID: PMC10050317 DOI: 10.1038/s41598-023-32162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
The Bacillus anthracis exosporium nap is the outermost portion of spore that interacts with the environment and host systems. Changes to this layer have the potential to impact wide-ranging physiological and immunological processes. The unique sugar, anthrose, normally coats the exosporium nap at its most distal points. We previously identified additional mechanisms rendering B. anthracis anthrose negative. In this work, several new ant - B. anthracis strains are identified and the impact of anthrose negativity on spore physiology is investigated. We demonstrate that live-attenuated Sterne vaccines as well as culture filtrate anthrax vaccines generate antibodies targeting non-protein components of the spore. The role of anthrose as a vegetative B. anthracis Sterne signaling molecule is implicated by luminescent expression strain assays, RNA-seq experiments, and toxin secretion analysis by western blot. Pure anthrose and the sporulation-inducing nucleoside analogue decoyinine had similar effects on toxin expression. Co-culture experiments demonstrated gene expression changes in B. anthracis depend on intracellular anthrose status (cis) in addition to anthrose status of extracellular interactions (trans). These findings provide a mechanism for how a unique spore-specific sugar residue affects physiology, expression and genetics of vegetative B. anthracis with impacts on the ecology, pathogenesis, and vaccinology of anthrax.
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Affiliation(s)
- Michael H Norris
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Andrew P Bluhm
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Morgan C Metrailer
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Treenate Jiranantasak
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Alexander Kirpich
- Department of Population Health Sciences, School of Public Health, Georgia State University, Atlanta, GA, USA
| | - Ted Hadfield
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | | | - Jason K Blackburn
- Spatial Epidemiology and Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
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11
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Carrilero L, Urwin L, Ward E, Choudhury NR, Monk IR, Turner CE, Stinear TP, Corrigan RM. Stringent Response-Mediated Control of GTP Homeostasis Is Required for Long-Term Viability of Staphylococcus aureus. Microbiol Spectr 2023; 11:e0044723. [PMID: 36877013 PMCID: PMC10101089 DOI: 10.1128/spectrum.00447-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 03/07/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterial pathogen that often results in difficult-to-treat infections. One mechanism used by S. aureus to enhance survival during infection is the stringent response. This is a stress survival pathway that utilizes the nucleotides (p)ppGpp to reallocate bacterial resources, shutting down growth until conditions improve. Small colony variants (SCVs) of S. aureus are frequently associated with chronic infections, and this phenotype has previously been linked to a hyperactive stringent response. Here, we examine the role of (p)ppGpp in the long-term survival of S. aureus under nutrient-restricted conditions. When starved, a (p)ppGpp-null S. aureus mutant strain ((p)ppGpp0) initially had decreased viability. However, after 3 days we observed the presence and dominance of a population of small colonies. Similar to SCVs, these small colony isolates (p0-SCIs) had reduced growth but remained hemolytic and sensitive to gentamicin, phenotypes that have been tied to SCVs previously. Genomic analysis of the p0-SCIs revealed mutations arising within gmk, encoding an enzyme in the GTP synthesis pathway. We show that a (p)ppGpp0 strain has elevated levels of GTP, and that the mutations in the p0-SCIs all lower Gmk enzyme activity and consequently cellular GTP levels. We further show that in the absence of (p)ppGpp, cell viability can be rescued using the GuaA inhibitor decoyinine, which artificially lowers the intracellular GTP concentration. Our study highlights the role of (p)ppGpp in GTP homeostasis and underscores the importance of nucleotide signaling for long-term survival of S. aureus in nutrient-limiting conditions, such as those encountered during infections. IMPORTANCE Staphylococcus aureus is a human pathogen that upon invasion of a host encounters stresses, such as nutritional restriction. The bacteria respond by switching on a signaling cascade controlled by the nucleotides (p)ppGpp. These nucleotides function to shut down bacterial growth until conditions improve. Therefore, (p)ppGpp are important for bacterial survival and have been implicated in promoting chronic infections. Here, we investigate the importance of (p)ppGpp for long-term survival of bacteria in nutrient-limiting conditions similar to those in a human host. We discovered that in the absence of (p)ppGpp, bacterial viability decreases due to dysregulation of GTP homeostasis. However, the (p)ppGpp-null bacteria were able to compensate by introducing mutations in the GTP synthesis pathway that led to a reduction in GTP build-up and a rescue of viability. This study therefore highlights the importance of (p)ppGpp for the regulation of GTP levels and for long-term survival of S. aureus in restricted environments.
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Affiliation(s)
- Laura Carrilero
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy Urwin
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ezra Ward
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Naznin R. Choudhury
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Ian R. Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca M. Corrigan
- The Florey Institute, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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12
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Yang S, Wang Y, Liu Y, Jia K, Zhang Z, Dong Q. Cereulide and Emetic Bacillus cereus: Characterizations, Impacts and Public Precautions. Foods 2023; 12:foods12040833. [PMID: 36832907 PMCID: PMC9956921 DOI: 10.3390/foods12040833] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Cereulide, which can be produced by Bacillus cereus, is strongly associated with emetic-type food poisoning outbreaks. It is an extremely stable emetic toxin, which is unlikely to be inactivated by food processing. Considering the high toxicity of cereulide, its related hazards raise public concerns. A better understanding of the impact of B. cereus and cereulide is urgently needed to prevent contamination and toxin production, thereby protecting public health. Over the last decade, a wide range of research has been conducted regarding B. cereus and cereulide. Despite this, summarized information highlighting precautions at the public level involving the food industry, consumers and regulators is lacking. Therefore, the aim of the current review is to summarize the available data describing the characterizations and impacts of emetic B. cereus and cereulide; based on this information, precautions at the public level are proposed.
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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase. PLoS Genet 2023; 19:e1010618. [PMID: 36735730 PMCID: PMC9931155 DOI: 10.1371/journal.pgen.1010618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 01/14/2023] [Indexed: 02/04/2023] Open
Abstract
Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb_rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase.
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14
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Tolibia SEM, Pacheco AD, Balbuena SYG, Rocha J, López Y López VE. Engineering of global transcription factors in Bacillus, a genetic tool for increasing product yields: a bioprocess overview. World J Microbiol Biotechnol 2022; 39:12. [PMID: 36372802 DOI: 10.1007/s11274-022-03460-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
Abstract
Transcriptional factors are well studied in bacteria for their global interactions and the effects they produce at the phenotypic level. Particularly, Bacillus subtilis has been widely employed as a model Gram-positive microorganism used to characterize these network interactions. Bacillus species are currently used as efficient commercial microbial platforms to produce diverse metabolites such as extracellular enzymes, antibiotics, surfactants, industrial chemicals, heterologous proteins, among others. However, the pleiotropic effects caused by the genetic modification of specific genes that codify for global regulators (transcription factors) have not been implicated commonly from a bioprocess point of view. Recently, these strategies have attracted the attention in Bacillus species because they can have an application to increase production efficiency of certain commercial interest metabolites. In this review, we update the recent advances that involve this trend in the use of genetic engineering (mutations, deletion, or overexpression) performed to global regulators such as Spo0A, CcpA, CodY and AbrB, which can provide an advantage for the development or improvement of bioprocesses that involve Bacillus species as production platforms. Genetic networks, regulation pathways and their relationship to the development of growth stages are also discussed to correlate the interactions that occur between these regulators, which are important to consider for application in the improvement of commercial-interest metabolites. Reported yields from these products currently produced mostly under laboratory conditions and, in a lesser extent at bioreactor level, are also discussed to give valuable perspectives about their potential use and developmental level directed to process optimization at large-scale.
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Affiliation(s)
- Shirlley Elizabeth Martínez Tolibia
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico
| | - Adrián Díaz Pacheco
- Unidad Profesional Interdisciplinaria de Ingeniería Campus Tlaxcala del Instituto Politécnico Nacional, CP 90000, Guillermo Valle, Tlaxcala, Mexico
| | - Sulem Yali Granados Balbuena
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico
| | - Jorge Rocha
- CONACyT - Unidad Regional Hidalgo, Centro de Investigación en Alimentación y Desarrollo, A.C. Blvd. Santa Catarina, SN, C.P. 42163, San Agustín Tlaxiaca, Hidalgo, Mexico
| | - Víctor Eric López Y López
- Centro de Investigación en Biotecnología Aplicada del Instituto Politécnico Nacional, Carretera Estatal Santa Inés Tecuexcomac-Tepetitla, Km 1.5, C.P. 90700, Tepetitla de Lardizábal, Tlaxcala, Mexico.
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15
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He H, Li Y, Zhang L, Ding Z, Shi G. Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective. J Adv Res 2022:S2090-1232(22)00205-3. [PMID: 36103961 DOI: 10.1016/j.jare.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022] Open
Abstract
BACKGROUND Nitrogen sources play an essential role in maintaining the physiological and biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism metabolism, makes bacteria able to autonomously respond to different external nitrogen environments by exercising complex internal regulatory networks to help them stay in an ideal state. Although various studies have been put forth to better understand this regulation in Bacillus, and many valuable viewpoints have been obtained, these views need to be presented systematically and their possible applications need to be specified. AIM OF REVIEW The intention is to provide a deep and comprehensive understanding of nitrogen metabolism in Bacillus, an important industrial microorganism, and thereby apply this regulatory logic to synthetic biology to improve biosynthesis competitiveness. In addition, the potential researches in the future are also discussed. KEY SCIENTIFIC CONCEPT OF REVIEW Understanding the meticulous regulation process of nitrogen metabolism in Bacillus not only could facilitate research on metabolic engineering but also could provide constructive insights and inspiration for studies of other microorganisms.
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Affiliation(s)
- Hehe He
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
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16
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Abstract
Since Jacques Monod's foundational work in the 1940s, investigators studying bacterial physiology have largely (but not exclusively) focused on the exponential phase of bacterial cultures, which is characterized by rapid growth and high biosynthesis activity in the presence of excess nutrients. However, this is not the predominant state of bacterial life. In nature, most bacteria experience nutrient limitation most of the time. In fact, investigators even prior to Monod had identified other aspects of bacterial growth, including what is now known as the stationary phase, when nutrients become limiting. This review will discuss how bacteria transition to growth arrest in response to nutrient limitation through changes in transcription, translation, and metabolism. We will then examine how these changes facilitate survival during potentially extended periods of nutrient limitation, with particular attention to the metabolic strategies that underpin bacterial longevity in this state.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA;
| | - Caroline S Harwood
- Department of Microbiology, University of Washington, Seattle, Washington, USA;
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17
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Yang J, Barra JT, Fung DK, Wang JD. Bacillus subtilis produces (p)ppGpp in response to the bacteriostatic antibiotic chloramphenicol to prevent its potential bactericidal effect. MLIFE 2022; 1:101-113. [PMID: 38817674 PMCID: PMC10989873 DOI: 10.1002/mlf2.12031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/24/2022] [Indexed: 06/01/2024]
Abstract
Antibiotics combat bacteria through their bacteriostatic (by growth inhibition) or bactericidal (by killing bacteria) action. Mechanistically, it has been proposed that bactericidal antibiotics trigger cellular damage, while bacteriostatic antibiotics suppress cellular metabolism. Here, we demonstrate how the difference between bacteriostatic and bactericidal activities of the antibiotic chloramphenicol can be attributed to an antibiotic-induced bacterial protective response: the stringent response. Chloramphenicol targets the ribosome to inhibit the growth of the Gram-positive bacterium Bacillus subtilis. Intriguingly, we found that chloramphenicol becomes bactericidal in B. subtilis mutants unable to produce (p)ppGpp. We observed a similar (p)ppGpp-dependent bactericidal effect of chloramphenicol in the Gram-positive pathogen Enterococcus faecalis. In B. subtilis, chloramphenicol treatment induces (p)ppGpp accumulation through the action of the (p)ppGpp synthetase RelA. (p)ppGpp subsequently depletes the intracellular concentration of GTP and antagonizes GTP action. This GTP regulation is critical for preventing chloramphenicol from killing B. subtilis, as bypassing (p)ppGpp-dependent GTP regulation potentiates chloramphenicol killing, while reducing GTP synthesis increases survival. Finally, chloramphenicol treatment protects cells from the classical bactericidal antibiotic vancomycin, reminiscent of the clinical phenomenon of antibiotic antagonism. Taken together, our findings suggest a role of (p)ppGpp in the control of the bacteriostatic and bactericidal activity of antibiotics in Gram-positive bacteria, which can be exploited to potentiate the efficacy of existing antibiotics.
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Affiliation(s)
- Jin Yang
- Department of BacteriologyUniversity of WisconsinMadisonUSA
| | | | - Danny K. Fung
- Department of BacteriologyUniversity of WisconsinMadisonUSA
| | - Jue D. Wang
- Department of BacteriologyUniversity of WisconsinMadisonUSA
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18
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Development of a Dual-Fluorescent-Reporter System in Clostridioides difficile Reveals a Division of Labor between Virulence and Transmission Gene Expression. mSphere 2022; 7:e0013222. [PMID: 35638354 PMCID: PMC9241537 DOI: 10.1128/msphere.00132-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The bacterial pathogen Clostridioides difficile causes gastroenteritis by producing toxins and transmits disease by making resistant spores. Toxin and spore production are energy-expensive processes that are regulated by multiple transcription factors in response to many environmental inputs. While toxin and sporulation genes are both induced in only a subset of C. difficile cells, the relationship between these two subpopulations remains unclear. To address whether C. difficile coordinates the generation of these subpopulations, we developed a dual-transcriptional-reporter system that allows toxin and sporulation gene expression to be simultaneously visualized at the single-cell level using chromosomally encoded mScarlet and mNeonGreen fluorescent transcriptional reporters. We then adapted an automated image analysis pipeline to quantify toxin and sporulation gene expression in thousands of individual cells under different medium conditions and in different genetic backgrounds. These analyses revealed that toxin and sporulation gene expression rarely overlap during growth on agar plates, whereas broth culture increases this overlap. Our results suggest that certain growth conditions promote a “division of labor” between transmission and virulence gene expression, highlighting how environmental inputs influence these subpopulations. Our data further suggest that the RstA transcriptional regulator skews the population to activate sporulation genes rather than toxin genes. Given that recent work has revealed population-wide heterogeneity for numerous cellular processes in C. difficile, we anticipate that our dual-reporter system will be broadly useful for determining the overlap between these subpopulations. IMPORTANCEClostridioides difficile is an important nosocomial pathogen that causes severe diarrhea by producing toxins and transmits disease by producing spores. While both processes are crucial for C. difficile disease, only a subset of cells express toxins and/or undergo sporulation. Whether C. difficile coordinates the subset of cells inducing these energy-expensive processes remains unknown. To address this question, we developed a dual-fluorescent-reporter system coupled with an automated image analysis pipeline to rapidly compare the expression of two genes of interest across thousands of cells. Using this system, we discovered that certain growth conditions, particularly growth on agar plates, induce a “division of labor” between toxin and sporulation gene expression. Since C. difficile exhibits phenotypic heterogeneity for numerous vital cellular processes, this novel dual-reporter system will enable future studies aimed at understanding how C. difficile coordinates various subpopulations throughout its infectious disease cycle.
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Regulatory Networks Controlling Neurotoxin Synthesis in Clostridium botulinum and Clostridium tetani. Toxins (Basel) 2022; 14:toxins14060364. [PMID: 35737025 PMCID: PMC9229411 DOI: 10.3390/toxins14060364] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/16/2022] [Accepted: 05/21/2022] [Indexed: 12/30/2022] Open
Abstract
Clostridium botulinum and Clostridium tetani are Gram-positive, spore-forming, and anaerobic bacteria that produce the most potent neurotoxins, botulinum toxin (BoNT) and tetanus toxin (TeNT), responsible for flaccid and spastic paralysis, respectively. The main habitat of these toxigenic bacteria is the environment (soil, sediments, cadavers, decayed plants, intestinal content of healthy carrier animals). C. botulinum can grow and produce BoNT in food, leading to food-borne botulism, and in some circumstances, C. botulinum can colonize the intestinal tract and induce infant botulism or adult intestinal toxemia botulism. More rarely, C. botulinum colonizes wounds, whereas tetanus is always a result of wound contamination by C. tetani. The synthesis of neurotoxins is strictly regulated by complex regulatory networks. The highest levels of neurotoxins are produced at the end of the exponential growth and in the early stationary growth phase. Both microorganisms, except C. botulinum E, share an alternative sigma factor, BotR and TetR, respectively, the genes of which are located upstream of the neurotoxin genes. These factors are essential for neurotoxin gene expression. C. botulinum and C. tetani share also a two-component system (TCS) that negatively regulates neurotoxin synthesis, but each microorganism uses additional distinct sets of TCSs. Neurotoxin synthesis is interlocked with the general metabolism, and CodY, a master regulator of metabolism in Gram-positive bacteria, is involved in both clostridial species. The environmental and nutritional factors controlling neurotoxin synthesis are still poorly understood. The transition from amino acid to peptide metabolism seems to be an important factor. Moreover, a small non-coding RNA in C. tetani, and quorum-sensing systems in C. botulinum and possibly in C. tetani, also control toxin synthesis. However, both species use also distinct regulatory pathways; this reflects the adaptation of C. botulinum and C. tetani to different ecological niches.
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20
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Pellegrini A, Lentini G, Famà A, Bonacorsi A, Scoffone VC, Buroni S, Trespidi G, Postiglione U, Sassera D, Manai F, Pietrocola G, Firon A, Biondo C, Teti G, Beninati C, Barbieri G. CodY Is a Global Transcriptional Regulator Required for Virulence in Group B Streptococcus. Front Microbiol 2022; 13:881549. [PMID: 35572655 PMCID: PMC9096947 DOI: 10.3389/fmicb.2022.881549] [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: 02/22/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Group B Streptococcus (GBS) is a Gram-positive bacterium able to switch from a harmless commensal of healthy adults to a pathogen responsible for invasive infections in neonates. The signals and regulatory mechanisms governing this transition are still largely unknown. CodY is a highly conserved global transcriptional regulator that links nutrient availability to the regulation of major metabolic and virulence pathways in low-G+C Gram-positive bacteria. In this work, we investigated the role of CodY in BM110, a GBS strain representative of a hypervirulent lineage associated with the majority of neonatal meningitis. Deletion of codY resulted in a reduced ability of the mutant strain to cause infections in neonatal and adult animal models. The observed decreased in vivo lethality was associated with an impaired ability of the mutant to persist in the blood, spread to distant organs, and cross the blood-brain barrier. Notably, the codY null mutant showed reduced adhesion to monolayers of human epithelial cells in vitro and an increased ability to form biofilms, a phenotype associated with strains able to asymptomatically colonize the host. RNA-seq analysis showed that CodY controls about 13% of the genome of GBS, acting mainly as a repressor of genes involved in amino acid transport and metabolism and encoding surface anchored proteins, including the virulence factor Srr2. CodY activity was shown to be dependent on the availability of branched-chain amino acids, which are the universal cofactors of this regulator. These results highlight a key role for CodY in the control of GBS virulence.
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Affiliation(s)
- Angelica Pellegrini
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Germana Lentini
- Department of Human Pathology and Medicine, University of Messina, Messina, Italy
| | - Agata Famà
- Department of Human Pathology and Medicine, University of Messina, Messina, Italy
| | - Andrea Bonacorsi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Viola Camilla Scoffone
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Gabriele Trespidi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Umberto Postiglione
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | - Federico Manai
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
| | | | - Arnaud Firon
- Institut Pasteur, Université de Paris, CNRS UMR 6047, Unité Biologie des Bactéries Pathogènes à Gram-positif, Paris, France
| | - Carmelo Biondo
- Department of Human Pathology and Medicine, University of Messina, Messina, Italy
| | | | - Concetta Beninati
- Department of Human Pathology and Medicine, University of Messina, Messina, Italy
| | - Giulia Barbieri
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, Pavia, Italy
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21
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Influence of the Phagemid PfNC7401 on Cereulide-Producing Bacillus cereus NC7401. Microorganisms 2022; 10:microorganisms10050953. [PMID: 35630395 PMCID: PMC9143728 DOI: 10.3390/microorganisms10050953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
A phagemid-cured strain, NC7401-∆Pf, was constructed to survey the biological function of the plasmidal prophage PfNC7401 in cereulide-producing Bacillus cereus NC7401. The transcriptome analysis between the mutant and the wild strains revealed a series of differentially expressed genes mainly involved in different function classifications, including the two-component signal transduction system, bacterial structure, transporters, related antibiotic response, purine biosynthesis, non-ribosomal peptide synthetases (NRPS) and related secondary metabolites, and aromatic or other amino acid synthesis. BIOLOG and phenotypic experiment analyses confirmed that PfNC7401 may affect phage immunity and the metabolism of several amino acids, including L-Alanine, which was suggested to be related to one precursor (D-Alanine) of cereulide synthesis. However, neither the transcription levels of the cereulide production-related genes (e.g., ilvB, cesA, cesB, and cesH) nor the cereulide production nor cell cytotoxicity were affected by the presence or absence of PfNC7401, corresponding with the transcriptome data, in which only four genes unrelated to cereulide synthesis on the plasmid-carrying ces gene cluster were affected by the curing of PfNC7401.
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22
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Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int J Mol Sci 2022; 23:ijms23063405. [PMID: 35328823 PMCID: PMC8953710 DOI: 10.3390/ijms23063405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.
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23
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Harrison MA, Kaur H, Wren BW, Dawson LF. Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage. Front Cell Infect Microbiol 2021; 11:757599. [PMID: 34778108 PMCID: PMC8588808 DOI: 10.3389/fcimb.2021.757599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of C. difficile is the distinctive production of high levels of the antimicrobial compound para-cresol. p-Cresol production provides C. difficile with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. p-Cresol is produced by the conversion of para-hydroxyphenylacetic acid (p-HPA) via the actions of HpdBCA decarboxylase coded by the hpdBCA operon. Host cells and certain bacterial species produce p-HPA; however, the effects of p-HPA on the viability of C. difficile and other gut microbiota are unknown. Here we show that representative strains from all five C. difficile clades are able to produce p-cresol by two distinct mechanisms: (i) via fermentation of p-tyrosine and (ii) via uptake and turnover of exogenous p-HPA. We observed strain-specific differences in p-cresol production, resulting from differential efficiency of p-tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of p-cresol via tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of p-cresol. All five lineages share at least 97.3% homology across the hpdBCA operon, responsible for decarboxylation of p-HPA to p-cresol, suggesting that the limiting step in p-cresol production may result from tyrosine to p-HPA conversion. We identified that elevated intracellular p-HPA, modulated indirectly via CodY, controls p-cresol production via inducing the expression of HpdBCA decarboxylase ubiquitously in C. difficile populations. Efficient turnover of p-HPA is advantageous to C. difficile as p-HPA has a deleterious effect on the growth of C. difficile and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in C. difficile pathogenesis, both in terms of p-cresol production and detoxification of p-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of p-cresol production across C. difficile species.
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Affiliation(s)
- Mark A. Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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24
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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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25
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The Food Poisoning Toxins of Bacillus cereus. Toxins (Basel) 2021; 13:toxins13020098. [PMID: 33525722 PMCID: PMC7911051 DOI: 10.3390/toxins13020098] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
Bacillus cereus is a ubiquitous soil bacterium responsible for two types of food-associated gastrointestinal diseases. While the emetic type, a food intoxication, manifests in nausea and vomiting, food infections with enteropathogenic strains cause diarrhea and abdominal pain. Causative toxins are the cyclic dodecadepsipeptide cereulide, and the proteinaceous enterotoxins hemolysin BL (Hbl), nonhemolytic enterotoxin (Nhe) and cytotoxin K (CytK), respectively. This review covers the current knowledge on distribution and genetic organization of the toxin genes, as well as mechanisms of enterotoxin gene regulation and toxin secretion. In this context, the exceptionally high variability of toxin production between single strains is highlighted. In addition, the mode of action of the pore-forming enterotoxins and their effect on target cells is described in detail. The main focus of this review are the two tripartite enterotoxin complexes Hbl and Nhe, but the latest findings on cereulide and CytK are also presented, as well as methods for toxin detection, and the contribution of further putative virulence factors to the diarrheal disease.
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26
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Takada H, Roghanian M, Caballero-Montes J, Van Nerom K, Jimmy S, Kudrin P, Trebini F, Murayama R, Akanuma G, Garcia-Pino A, Hauryliuk V. Ribosome association primes the stringent factor Rel for tRNA-dependent locking in the A-site and activation of (p)ppGpp synthesis. Nucleic Acids Res 2021; 49:444-457. [PMID: 33330919 PMCID: PMC7797070 DOI: 10.1093/nar/gkaa1187] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
In the Gram-positive Firmicute bacterium Bacillus subtilis, amino acid starvation induces synthesis of the alarmone (p)ppGpp by the RelA/SpoT Homolog factor Rel. This bifunctional enzyme is capable of both synthesizing and hydrolysing (p)ppGpp. To detect amino acid deficiency, Rel monitors the aminoacylation status of the ribosomal A-site tRNA by directly inspecting the tRNA’s CCA end. Here we dissect the molecular mechanism of B. subtilis Rel. Off the ribosome, Rel predominantly assumes a ‘closed’ conformation with dominant (p)ppGpp hydrolysis activity. This state does not specifically select deacylated tRNA since the interaction is only moderately affected by tRNA aminoacylation. Once bound to the vacant ribosomal A-site, Rel assumes an ‘open’ conformation, which primes its TGS and Helical domains for specific recognition and stabilization of cognate deacylated tRNA on the ribosome. The tRNA locks Rel on the ribosome in a hyperactivated state that processively synthesises (p)ppGpp while the hydrolysis is suppressed. In stark contrast to non-specific tRNA interactions off the ribosome, tRNA-dependent Rel locking on the ribosome and activation of (p)ppGpp synthesis are highly specific and completely abrogated by tRNA aminoacylation. Binding pppGpp to a dedicated allosteric site located in the N-terminal catalytic domain region of the enzyme further enhances its synthetase activity.
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Affiliation(s)
- Hiraku Takada
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Mohammad Roghanian
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Julien Caballero-Montes
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Katleen Van Nerom
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Steffi Jimmy
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Pavel Kudrin
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Fabio Trebini
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden
| | - Rikinori Murayama
- Akita Prefectural Research Center for Public Health and Environment, 6-6 Senshu-Kubotamachi, Akita, 010-0874, Japan
| | - Genki Akanuma
- Department of Life Science, Graduate School of Science, Gakushuin University, Tokyo, Japan
| | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles (ULB), Building BC, Room 1C4 203, Boulevard du Triomphe, 1050 Brussels, Belgium.,WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden.,University of Tartu, Institute of Technology, 50411 Tartu, Estonia
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27
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Transcriptional Regulators in Bacillus anthracis: A Potent Biothreat Agent. RECENT DEVELOPMENTS IN MICROBIAL TECHNOLOGIES 2021. [DOI: 10.1007/978-981-15-4439-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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28
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Xu C, Weston BR, Tyson JJ, Cao Y. Cell cycle control and environmental response by second messengers in Caulobacter crescentus. BMC Bioinformatics 2020; 21:408. [PMID: 32998723 PMCID: PMC7526171 DOI: 10.1186/s12859-020-03687-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, virulence, quorum sensing, and proliferation. While c-di-GMP and (p)ppGpp are both synthesized from GTP molecules, they play antagonistic roles in regulating the cell cycle. In C. crescentus, c-di-GMP works as a major regulator of pole morphogenesis and cell development. It inhibits cell motility and promotes S-phase entry by inhibiting the activity of the master regulator, CtrA. Intracellular (p)ppGpp accumulates under starvation, which helps bacteria to survive under stressful conditions through regulating nucleotide levels and halting proliferation. (p)ppGpp responds to nitrogen levels through RelA-SpoT homolog enzymes, detecting glutamine concentration using a nitrogen phosphotransferase system (PTS Ntr). This work relates the guanine nucleotide-based second messenger regulatory network with the bacterial PTS Ntr system and investigates how bacteria respond to nutrient availability. Results We propose a mathematical model for the dynamics of c-di-GMP and (p)ppGpp in C. crescentus and analyze how the guanine nucleotide-based second messenger system responds to certain environmental changes communicated through the PTS Ntr system. Our mathematical model consists of seven ODEs describing the dynamics of nucleotides and PTS Ntr enzymes. Our simulations are consistent with experimental observations and suggest, among other predictions, that SpoT can effectively decrease c-di-GMP levels in response to nitrogen starvation just as well as it increases (p)ppGpp levels. Thus, the activity of SpoT (or its homologues in other bacterial species) can likely influence the cell cycle by influencing both c-di-GMP and (p)ppGpp. Conclusions In this work, we integrate current knowledge and experimental observations from the literature to formulate a novel mathematical model. We analyze the model and demonstrate how the PTS Ntr system influences (p)ppGpp, c-di-GMP, GMP and GTP concentrations. While this model does not consider all aspects of PTS Ntr signaling, such as cross-talk with the carbon PTS system, here we present our first effort to develop a model of nutrient signaling in C. crescentus.
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Affiliation(s)
- Chunrui Xu
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, 24061, VA, USA
| | - Bronson R Weston
- Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, 24061, VA, USA
| | - John J Tyson
- Department of Biological Sciences, Virginia Tech, Blacksburg, 24061, VA, USA
| | - Yang Cao
- Department of Computer Science, Virginia Tech, Blacksburg, 24061, VA, USA.
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29
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Wang B, Grant RA, Laub MT. ppGpp Coordinates Nucleotide and Amino-Acid Synthesis in E. coli During Starvation. Mol Cell 2020; 80:29-42.e10. [PMID: 32857952 DOI: 10.1016/j.molcel.2020.08.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/10/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022]
Abstract
(p)ppGpp is a nucleotide messenger universally produced in bacteria following nutrient starvation. In E. coli, ppGpp inhibits purine nucleotide synthesis by targeting several different enzymes, but the physiological significance of their inhibition is unknown. Here, we report the structural basis of inhibition for one target, Gsk, the inosine-guanosine kinase. Gsk creates an unprecedented, allosteric binding pocket for ppGpp by restructuring terminal sequences, which restrains conformational dynamics necessary for catalysis. Guided by this structure, we generated a chromosomal mutation that abolishes Gsk regulation by ppGpp. This mutant strain accumulates abnormally high levels of purine nucleotides following amino-acid starvation, compromising cellular fitness. We demonstrate that this unrestricted increase in purine nucleotides is detrimental because it severely depletes pRpp and essential, pRpp-derived metabolites, including UTP, histidine, and tryptophan. Thus, our results reveal the significance of ppGpp's regulation of purine nucleotide synthesis and a critical mechanism by which E. coli coordinates biosynthetic processes during starvation.
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Affiliation(s)
- Boyuan Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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30
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Xiang M, Kang Q, Zhang D. Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell. Synth Syst Biotechnol 2020; 5:245-251. [PMID: 32775709 PMCID: PMC7394859 DOI: 10.1016/j.synbio.2020.07.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis, has been broadly applied in various fields because of its low pathogenicity and strong protein secretion ability, as well as its well-developed fermentation technology. B. subtilis is considered as an attractive host in the field of metabolic engineering, in particular for protein expression and secretion, so it has been well studied and applied in genetic engineering. In this review, we discussed why B. subtilis is a good chassis cell for metabolic engineering. We also summarized the latest research progress in systematic biology, synthetic biology and evolution-based engineering of B. subtilis, and showed systemic metabolic engineering expedite the harnessing B. subtilis for bioproduction.
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Affiliation(s)
- Mengjie Xiang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qian Kang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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31
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Rudra P, Boyd JM. Metabolic control of virulence factor production in Staphylococcus aureus. Curr Opin Microbiol 2020; 55:81-87. [PMID: 32388086 DOI: 10.1016/j.mib.2020.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/27/2022]
Abstract
As investigators decipher the underlining mechanisms of Staphylococcus aureus pathogenesis, it is becoming apparent that perturbations in central metabolism alter virulence factor production and infection outcomes. It is also evident that S. aureus has the ability to metabolically adapt to improve colonization and overcome challenges imparted by the immune system. Altered metabolite pools modify virulence factor production suggesting that proper functioning of a core metabolic network is necessary for successful niche colonization and pathogenesis. Herein we discuss four examples of transcriptional regulators that monitor metabolic status. These regulatory systems sense perturbations in the metabolic network and respond by altering the transcription of genes utilized for central metabolism, energy generation and pathogenesis.
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Affiliation(s)
- Paulami Rudra
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA.
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32
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Ahn SJ, Kim HM, Desai S, Deep K, Rice KC. Regulation of cid and lrg expression by CodY in Streptococcus mutans. Microbiologyopen 2020; 9:e1040. [PMID: 32282137 PMCID: PMC7349109 DOI: 10.1002/mbo3.1040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/21/2020] [Accepted: 03/21/2020] [Indexed: 12/14/2022] Open
Abstract
The ability of Streptococcus mutans to persist in a variety of adverse environments and to emerge as a numerically dominant member of stable oral biofilm communities are essential elements for its cariogenicity. The S. mutans Cid/Lrg system has been studied as a key player in the integration of complex environmental signals into regulatory networks that modulate virulence and cell homeostasis. Cid/Lrg has also been shown to be closely associated with metabolic pathways of this organism, due to distinct patterns of cid and lrg expression in response to growth phase and glucose/oxygen levels. In this study, a comparison of cid and lrg promoter regions with conserved CodY (a regulator which responds to starvation stress)-binding motifs revealed the presence of a potential CodY-binding site, which is arranged similarly in both cid and lrg promoters. Electrophoretic mobility shift assays (EMSAs) and promoter reporter assays demonstrated that expression of the cid and lrg operons is directly mediated by the global transcriptional regulator CodY. DNase I footprinting analyses confirmed the predicted binding sequences for CodY in both the cid and the lrg promoter regions. Overexpression of CodY had no obvious effect on lrgAB expression, but deficiency of CodY still affected lrgAB expression in a lytST-overexpressing strain, suggesting that CodY is required for the full regulation of lrgAB by LytST. We also demonstrated that both CodY and CcpA are involved in regulating pyruvate flux and utilization. Collectively, these data show that CodY directly regulates cid and lrg expression, and together with CcpA (previously shown to directly regulate cid and lrg promoters) contributes to coordinating pyruvate uptake and utilization in response to both the external environment and the cellular metabolic status.
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Affiliation(s)
- Sang-Joon Ahn
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hey-Min Kim
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Shailja Desai
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Kamal Deep
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
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33
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Schäfer H, Beckert B, Frese CK, Steinchen W, Nuss AM, Beckstette M, Hantke I, Driller K, Sudzinová P, Krásný L, Kaever V, Dersch P, Bange G, Wilson DN, Turgay K. The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PLoS Genet 2020; 16:e1008275. [PMID: 32176689 PMCID: PMC7098656 DOI: 10.1371/journal.pgen.1008275] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 03/26/2020] [Accepted: 02/26/2020] [Indexed: 11/24/2022] Open
Abstract
Bacillus subtilis cells are well suited to study how bacteria sense and adapt to proteotoxic stress such as heat, since temperature fluctuations are a major challenge to soil-dwelling bacteria. Here, we show that the alarmones (p)ppGpp, well known second messengers of nutrient starvation, are also involved in the heat stress response as well as the development of thermo-resistance. Upon heat-shock, intracellular levels of (p)ppGpp rise in a rapid but transient manner. The heat-induced (p)ppGpp is primarily produced by the ribosome-associated alarmone synthetase Rel, while the small alarmone synthetases RelP and RelQ seem not to be involved. Furthermore, our study shows that the generated (p)ppGpp pulse primarily acts at the level of translation, and only specific genes are regulated at the transcriptional level. These include the down-regulation of some translation-related genes and the up-regulation of hpf, encoding the ribosome-protecting hibernation-promoting factor. In addition, the alarmones appear to interact with the activity of the stress transcription factor Spx during heat stress. Taken together, our study suggests that (p)ppGpp modulates the translational capacity at elevated temperatures and thereby allows B. subtilis cells to respond to proteotoxic stress, not only by raising the cellular repair capacity, but also by decreasing translation to concurrently reduce the protein load on the cellular protein quality control system.
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Affiliation(s)
- Heinrich Schäfer
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Wieland Steinchen
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Aaron M. Nuss
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Beckstette
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ingo Hantke
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | | | - Petra Sudzinová
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Volkhard Kaever
- Hannover Medical School, Research Core Unit Metabolomics, Hannover, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, University of Münster, Münster, Germany
| | - Gert Bange
- Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Marburg, Germany
| | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
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34
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Osaka N, Kanesaki Y, Watanabe M, Watanabe S, Chibazakura T, Takada H, Yoshikawa H, Asai K. Novel (p)ppGpp 0 suppressor mutations reveal an unexpected link between methionine catabolism and GTP synthesis in Bacillus subtilis. Mol Microbiol 2020; 113:1155-1169. [PMID: 32052499 DOI: 10.1111/mmi.14484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 11/29/2022]
Abstract
In bacteria, guanosine (penta)tetra-phosphate ([p]ppGpp) is essential for controlling intracellular metabolism that is needed to adapt to environmental changes, such as amino acid starvation. The (p)ppGpp0 strain of Bacillus subtilis, which lacks (p)ppGpp synthetase, is unable to form colonies on minimal medium. Here, we found suppressor mutations in the (p)ppGpp0 strain, in the purine nucleotide biosynthesis genes, prs, purF and rpoB/C, which encode RNA polymerase core enzymes. In comparing our work with prior studies of ppGpp0 suppressors, we discovered that methionine addition masks the suppression on minimal medium, especially of rpoB/C mutations. Furthermore, methionine addition increases intracellular GTP in rpoB suppressor and this effect is decreased by inhibiting GTP biosynthesis, indicating that methionine addition activated GTP biosynthesis and inhibited growth under amino acid starvation conditions in (p)ppGpp0 backgrounds. Furthermore, we propose that the increase in intracellular GTP levels induced by methionine is due to methionine derivatives that increase the activity of the de novo GTP biosynthesis enzyme, GuaB. Our study sheds light on the potential relationship between GTP homeostasis and methionine metabolism, which may be the key to adapting to environmental changes.
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Affiliation(s)
- Natsuki Osaka
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Megumi Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Taku Chibazakura
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiraku Takada
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | | | - Kei Asai
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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The oligopeptide ABC-importers are essential communication channels in Gram-positive bacteria. Res Microbiol 2019; 170:338-344. [PMID: 31376485 DOI: 10.1016/j.resmic.2019.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/12/2019] [Indexed: 12/27/2022]
Abstract
The transport of peptides in microorganisms plays an important role in their physiology and behavior, both as a nutrient source and as a proxy to sense their environment. This latter function is evidenced in Gram-positive bacteria where cell-cell communication is mediated by small peptides. Here, we highlight the importance of the oligopeptide permease (Opp) systems in the various major processes controlled by signaling peptides, such as sporulation, virulence and conjugation. We underline that the functioning of these communication systems is tightly linked to the developmental status of the bacteria via the regulation of opp gene expression by transition phase regulators.
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Rouzeau-Szynalski K, Stollewerk K, Messelhäusser U, Ehling-Schulz M. Why be serious about emetic Bacillus cereus: Cereulide production and industrial challenges. Food Microbiol 2019; 85:103279. [PMID: 31500702 DOI: 10.1016/j.fm.2019.103279] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 01/06/2023]
Abstract
Cereulide, a potent toxin produced by Bacillus cereus, is a small, highly heat- and acid-resistant depsipeptide toxin, which confronts food industry with several challenges. Due to the ubiquitous presence of B. cereus in the environment, this opportunistic pathogen can enter food production and processing at almost any stage. Although the bacteria itself might be removed during food processing, the cereulide toxin will most likely not be destroyed or inactivated by these processes. Because of the high toxicity of cereulide and the high incidence rates often observed in connection with foodborne outbreaks, the understanding of the mechanisms of toxin production as well as accurate data on contamination sources and factors promoting toxin formation are urgently needed to prevent contamination and toxin production in food production processes. Over the last decade, considerable progress had been made on the understanding of cereulide toxin biosynthesis in emetic B. cereus, but an overview of current knowledge on this toxin with regards to food industry perspective is lacking. Thus, we aim in this work to summarize data available on extrinsic parameters acting on cereulide toxin synthesis in emetic B. cereus and to discuss the food industry specific challenges related to this toxin. Furthermore, we emphasize how identification of the cardinals in food production processes can lead to novel effective strategies for prevention of toxin formation in the food processing chain and could contribute to the improvement of existing HACCP studies.
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Affiliation(s)
| | - Katharina Stollewerk
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria
| | - Ute Messelhäusser
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764, Oberschleissheim, Germany
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine Vienna, Austria.
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Dubois T, Lemy C, Perchat S, Lereclus D. The signaling peptide NprX controlling sporulation and necrotrophism is imported into Bacillus thuringiensis by two oligopeptide permease systems. Mol Microbiol 2019; 112:219-232. [PMID: 31017318 DOI: 10.1111/mmi.14264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2019] [Indexed: 11/30/2022]
Abstract
The infectious cycle of Bacillus thuringiensis in the insect host is regulated by quorum sensors of the RNPP family. The activity of these regulators is modulated by their cognate signaling peptides translocated into the bacterial cells by oligopeptide permeases (Opp systems). In B. thuringiensis, the quorum sensor NprR is a bi-functional regulator that connects sporulation to necrotrophism. The binding of the signaling peptide NprX switches NprR from a dimeric inhibitor of sporulation to a tetrameric transcriptional activator involved in the necrotrophic lifestyle of B. thuringiensis. Here, we report that NprX is imported into the bacterial cells by two different oligopeptide permease systems. The first one is Opp, the system known to be involved in the import of the signaling peptide PapR in B. thuringiensis and Bacillus cereus. The second, designated as Npp (NprX peptide permease), was not previously described. We show that at least two substrate binding proteins (SBPs) are able to translocate NprX through OppBCDF. In contrast, we demonstrate that a unique SBP (NppA) can translocate NprX through NppDFBC. We identified the promoter of the npp operon, and we showed that transcription starts at the onset of stationary phase and is repressed by the nutritional regulator CodY during the exponential growth phase.
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Affiliation(s)
- Thomas Dubois
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Christelle Lemy
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Stéphane Perchat
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
| | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, France
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Hesketh A, Oliver SG. High-energy guanine nucleotides as a signal capable of linking growth to cellular energy status via the control of gene transcription. Curr Genet 2019; 65:893-897. [PMID: 30937517 PMCID: PMC6620469 DOI: 10.1007/s00294-019-00963-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022]
Abstract
This mini-review considers the idea that guanylate nucleotide energy charge acts as an integrative signal for the regulation of gene expression in eukaryotic cells and discusses possible routes for that signal's transduction. Gene expression is intimately linked with cell nutrition and diverse signaling systems serve to coordinate the synthesis of proteins required for growth and proliferation with the prevailing cellular nutritional status. Using short pathways for the inducible and futile consumption of ATP or GTP in engineered cells of Saccharomyces cerevisiae, we have recently shown that GTP levels can also play a role in determining how genes act to respond to changes in cellular energy supply. This review aims to interpret the importance of GTP as an integrative signal in the context of an increasing body of evidence indicating the spatio-temporal complexity of cellular de novo purine nucleotide biosynthesis.
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Affiliation(s)
- Andy Hesketh
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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Schäfer H, Turgay K. Spx, a versatile regulator of the Bacillus subtilis stress response. Curr Genet 2019; 65:871-876. [DOI: 10.1007/s00294-019-00950-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 02/26/2019] [Accepted: 02/28/2019] [Indexed: 01/16/2023]
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Daou N, Wang Y, Levdikov VM, Nandakumar M, Livny J, Bouillaut L, Blagova E, Zhang K, Belitsky BR, Rhee K, Wilkinson AJ, Sun X, Sonenshein AL. Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027. PLoS One 2019; 14:e0206896. [PMID: 30699117 PMCID: PMC6353076 DOI: 10.1371/journal.pone.0206896] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/25/2018] [Indexed: 12/16/2022] Open
Abstract
Toxin synthesis and endospore formation are two of the most critical factors that determine the outcome of infection by Clostridioides difficile. The two major toxins, TcdA and TcdB, are the principal factors causing damage to the host. Spores are the infectious form of C. difficile, permit survival of the bacterium during antibiotic treatment and are the predominant cell form that leads to recurrent infection. Toxin production and sporulation have their own specific mechanisms of regulation, but they share negative regulation by the global regulatory protein CodY. Determining the extent of such regulation and its detailed mechanism is important for understanding the linkage between two apparently independent biological phenomena and raises the possibility of creating new ways of limiting infection. The work described here shows that a codY null mutant of a hypervirulent (ribotype 027) strain is even more virulent than its parent in a mouse model of infection and that the mutant expresses most sporulation genes prematurely during exponential growth phase. Moreover, examining the expression patterns of mutants producing CodY proteins with different levels of residual activity revealed that expression of the toxin genes is dependent on total CodY inactivation, whereas most sporulation genes are turned on when CodY activity is only partially diminished. These results suggest that, in wild-type cells undergoing nutrient limitation, sporulation genes can be turned on before the toxin genes.
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Affiliation(s)
- Nadine Daou
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Yuanguo Wang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Vladimir M. Levdikov
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Madhumitha Nandakumar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Laurent Bouillaut
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Elena Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Keshan Zhang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Boris R. Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Kyu Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America
| | - Abraham L. Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
- * E-mail:
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Leiser OP, Blackburn JK, Hadfield TL, Kreuzer HW, Wunschel DS, Bruckner-Lea CJ. Laboratory strains of Bacillus anthracis exhibit pervasive alteration in expression of proteins related to sporulation under laboratory conditions relative to genetically related wild strains. PLoS One 2018; 13:e0209120. [PMID: 30557394 PMCID: PMC6296524 DOI: 10.1371/journal.pone.0209120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently taken up by another host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis. Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature, providing a basis for the type of response by public health officials and investigators.
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Affiliation(s)
- Owen P. Leiser
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason K. Blackburn
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Ted L. Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David S. Wunschel
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Cindy J. Bruckner-Lea
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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42
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Leonard A, Lalk M. Infection and metabolism – Streptococcus pneumoniae metabolism facing the host environment. Cytokine 2018; 112:75-86. [DOI: 10.1016/j.cyto.2018.07.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/15/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022]
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Ransom EM, Kaus GM, Tran PM, Ellermeier CD, Weiss DS. Multiple factors contribute to bimodal toxin gene expression in Clostridioides (Clostridium) difficile. Mol Microbiol 2018; 110:533-549. [PMID: 30125399 PMCID: PMC6446242 DOI: 10.1111/mmi.14107] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/10/2018] [Accepted: 08/11/2018] [Indexed: 12/14/2022]
Abstract
Clostridioides (formerly Clostridium) difficile produces two major toxins, TcdA and TcdB, upon entry into stationary phase. Transcription of tcdA and tcdB requires the specialized sigma factor, σTcdR , which also directs RNA Polymerase to transcribe tcdR itself. We fused a gene for a red fluorescent protein to the tcdA promoter to study toxin gene expression at the level of individual C. difficile cells. Surprisingly, only a subset of cells became red fluorescent upon entry into stationary phase. Breaking the positive feedback loop that controls σTcdR production by engineering cells to express tcdR from a tetracycline-inducible promoter resulted in uniform fluorescence across the population. Experiments with two regulators of tcdR expression, σD and CodY, revealed neither is required for bimodal toxin gene expression. However, σD biased cells toward the Toxin-ON state, while CodY biased cells toward the Toxin-OFF state. Finally, toxin gene expression was observed in sporulating cells. We conclude that (i) toxin production is regulated by a bistable switch governed by σTcdR , which only accumulates to high enough levels to trigger toxin gene expression in a subset of cells, and (ii) toxin production and sporulation are not mutually exclusive developmental programs.
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Affiliation(s)
- Eric M. Ransom
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Gabriela M. Kaus
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Phuong M. Tran
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Craig D. Ellermeier
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242
| | - David S. Weiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242
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Redirection of Metabolism in Response to Fatty Acid Kinase in Staphylococcus aureus. J Bacteriol 2018; 200:JB.00345-18. [PMID: 30012726 DOI: 10.1128/jb.00345-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/06/2018] [Indexed: 12/23/2022] Open
Abstract
Staphylococcus aureus is capable of phosphorylating exogenous fatty acids for incorporation into the bacterium's membrane via the fatty acid kinase, FakA. Additionally, FakA plays a significant role in virulence factor regulation and skin infections. We previously showed that a fakA mutant displays altered growth kinetics in vitro, observed during the late-exponential phase of growth. Here, we demonstrate that the absence of FakA leads to key metabolic changes. First, the fakA mutant has an altered acetate metabolism, with acetate being consumed at an increased rate than in the wild-type strain. Moreover, the growth benefit was diminished with inactivation of the acetate-generating enzyme AckA. Using a mass spectrometry-based approach, we identified altered concentrations of tricarboxylic acid (TCA) cycle intermediates and both intracellular and extracellular amino acids. Together, these data demonstrate a change in carbohydrate carbon utilization and altered amino acid metabolism in the fakA mutant. Energy status analysis revealed the mutant had a similar ADP/ATP ratio to that of the wild type, but a reduced adenylate energy charge. The inactivation of fakA changed the NAD+/NADH and NADP+/NADPH ratios, indicating a more oxidized cellular environment. Evidence points to the global metabolic regulatory proteins CcpA and CodY being important contributors to the altered growth in a fakA mutant. Indeed, it was found that directing amino acids from the urea cycle into the TCA cycle via glutamate dehydrogenase was an essential component of S. aureus growth after glucose depletion. Together, these data identify a previously unidentified role of FakA in the global physiology of S. aureus, linking external fatty acid utilization and central metabolism.IMPORTANCE The fatty acid kinase, FakA, of Staphylococcus aureus plays several important roles in the cell. FakA is important for the activation of the SaeRS two-component system and secreted virulence factors like α-hemolysin. However, the contribution of FakA to cellular metabolism has not been explored. Here, we highlight the metabolic consequence of removal of FakA from the cell. The absence of FakA leads to altered acetate metabolism and altered redox balance, as well as a change in intracellular amino acids. Additionally, the use of environmental amino acid sources is affected by FakA. Together, these results demonstrate for the first time that FakA provides a link between the pathways for exogenous fatty acid use, virulence factor regulation, and other metabolic processes.
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Branching Out: Alterations in Bacterial Physiology and Virulence Due to Branched-Chain Amino Acid Deprivation. mBio 2018; 9:mBio.01188-18. [PMID: 30181248 PMCID: PMC6123439 DOI: 10.1128/mbio.01188-18] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The branched-chain amino acids (BCAAs [Ile, Leu, and Val]) represent important nutrients in bacterial physiology, with roles that range from supporting protein synthesis to signaling and fine-tuning the adaptation to amino acid starvation. In some pathogenic bacteria, the adaptation to amino acid starvation includes induction of virulence gene expression: thus, BCAAs support not only proliferation during infection, but also the evasion of host defenses. The branched-chain amino acids (BCAAs [Ile, Leu, and Val]) represent important nutrients in bacterial physiology, with roles that range from supporting protein synthesis to signaling and fine-tuning the adaptation to amino acid starvation. In some pathogenic bacteria, the adaptation to amino acid starvation includes induction of virulence gene expression: thus, BCAAs support not only proliferation during infection, but also the evasion of host defenses. A body of research has accumulated over the years to describe the multifaceted physiological roles of BCAAs and the mechanisms bacteria use to maintain their intracellular levels. More recent studies have focused on understanding how fluctuations in their intracellular levels impact global regulatory pathways that coordinate the adaptation to nutrient limitation, especially in pathogenic bacteria. In this minireview, we discuss how these studies have refined the individual roles of BCAAs, shed light on how BCAA auxotrophy might promote higher sensitivity to exogenous BCAA levels, and revealed pathogen-specific responses to BCAA deprivation. These advancements improve our understanding of how bacteria meet their nutritional requirements for growth while simultaneously remaining responsive to changes in environmental nutrient availability to promote their survival in a range of environments.
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Cao H, Villatoro-Hernandez J, Weme RDO, Frenzel E, Kuipers OP. Boosting heterologous protein production yield by adjusting global nitrogen and carbon metabolic regulatory networks in Bacillus subtilis. Metab Eng 2018; 49:143-152. [DOI: 10.1016/j.ymben.2018.08.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/23/2018] [Accepted: 08/06/2018] [Indexed: 01/19/2023]
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MsaB and CodY Interact To Regulate Staphylococcus aureus Capsule in a Nutrient-Dependent Manner. J Bacteriol 2018; 200:JB.00294-18. [PMID: 29941424 DOI: 10.1128/jb.00294-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus has a complex regulatory network for controlling the production of capsule polysaccharide. In S. aureus, capsule production is controlled by several regulators in response to various environmental stimuli. Previously, we described MsaB as a new regulator that specifically binds to the cap promoter in a growth phase- or nutrient-dependent manner. In addition to MsaB, several other regulators have also been shown to bind the same region. In this study, we examined the interactions between MsaB and other nutrient-sensing regulators (CodY and CcpE) with respect to binding to the cap promoter in a nutrient-dependent manner. We observed that msaABCR and ccpE interact in a complex fashion to regulate capsule production. However, we confirmed that ccpE does not bind cap directly. We also defined the regulatory relationship between msaABCR and CodY. When nutrients (branched-chain amino acids) are abundant, CodY binds to the promoter region of the cap operon and represses its transcription. However, when nutrient concentrations decrease, MsaB, rather than CodY, binds to the cap promoter. Binding of MsaB to the cap promoter activates transcription of the cap operon. We hypothesize that this same mechanism may be used by S. aureus to regulate other virulence factors.IMPORTANCE Findings from this study define the mechanism of regulation of capsule production in Staphylococcus aureus Specifically, we show that two key regulators, MsaB and CodY, coordinate their functions to control the expression of capsule in response to nutrients. S. aureus fine-tunes the production of capsule by coordinating the activity of several regulators and by sensing nutrient levels. This study demonstrates the importance of incorporating multiple inputs prior to the expression of costly virulence factors, such as capsule.
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48
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Giaretta S, Treu L, Vendramin V, da Silva Duarte V, Tarrah A, Campanaro S, Corich V, Giacomini A. Comparative Transcriptomic Analysis of Streptococcus thermophilus TH1436 and TH1477 Showing Different Capability in the Use of Galactose. Front Microbiol 2018; 9:1765. [PMID: 30131781 PMCID: PMC6090898 DOI: 10.3389/fmicb.2018.01765] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/16/2018] [Indexed: 12/03/2022] Open
Abstract
Streptococcus thermophilus is a species widely used in the dairy industry for its capability to rapidly ferment lactose and lower the pH. The capability to use galactose produced from lactose hydrolysis is strain dependent and most of commercial S. thermophilus strains are galactose-negative (Gal−), although galactose-positive (Gal+) would be more technologically advantageous because this feature could provide additional metabolic products and prevent galactose accumulation in foods. In this study, a next generation sequencing transcriptome approach was used to compare for the first time a Gal+ and a Gal− strain to characterize their whole metabolism and shed light on their different properties, metabolic performance and gene regulation. Transcriptome analysis revealed that all genes of the gal operon were expressed very differently in Gal+ and in the Gal− strains. The expression of several genes involved in mixed acid fermentation, PTS sugars transporter and stress response were found enhanced in Gal+. Conversely, genes related to amino acids, proteins metabolism and CRISPR associated proteins were under-expressed. In addition, the strains showed a diverse series of predicted genes controlled by the transcriptional factor catabolite control protein A (CcpA). Overall, transcriptomic analysis suggests that the Gal+ strain underwent a metabolic remodeling to cope with the changed environmental conditions.
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Affiliation(s)
- Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | - Laura Treu
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy.,Department of Environmental Engineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Veronica Vendramin
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | | | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | | | - Viviana Corich
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
| | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animal and Environment, University of Padova, Padova, Italy
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Cui W, Suo F, Cheng J, Han L, Hao W, Guo J, Zhou Z. Stepwise modifications of genetic parts reinforce the secretory production of nattokinase in Bacillus subtilis. Microb Biotechnol 2018; 11:930-942. [PMID: 29984489 PMCID: PMC6116739 DOI: 10.1111/1751-7915.13298] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 12/27/2022] Open
Abstract
Nattokinase (NK) is an important serine‐protease with direct fibrinolytic activity involving the prevention of cardiovascular disease as an antithrombotic agent. Dozens of studies have focused on the characterization of intrinsic novel promoters and signal peptides to the secretory production of recombinant proteins in Bacillus subtilis. However, intrinsic genetic elements have several drawbacks, which cannot mediate the production of NK to the desired level. In this study, the genetic elements, which were used to overproduce the recombinant secretory NK, were rationally modified in B. subtilis in a stepwise manner. The first step was to select a suitable signal peptide for the highly efficient secretion of NK. By comparison of the secretory levels mediated by two different signal peptides, which were encoded by the genes of a minor extracellular protease epr (SPepr) and cell‐wall associated protease wapA (SPwapA), respectively, SPwapA was verified as the superior secretory element. Second, P04, which was a synthetic promoter screened from an array of mutants based on the promoter cloned from the operon of a quorum‐sensing associated gene srfA (PsrfA), was paired to SPwapA. The secretory level of NK was obviously augmented by the combination of these two genetic elements. Third, the cis‐acting element CodY‐binding sequence positioned at the 5′UTR was deleted (yielding P08), and thus the secretory level was significantly elevated. The activity of NK, which was defined as fibrinolytic units (FU), reached to a level of 270 FU ml−1. Finally, the superior genetic element composed of P08 and SPwapA was utilized to overproduce NK in the host B. subtilis WB800, which was able to produce the secretory NK at 292 FU ml−1. The strategy established in this study can not only be used to overproduce NK in B. subtilis but also might be a promising pipeline to modify the genetic element for the synthetic secretory system.
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Affiliation(s)
- Wenjing Cui
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Feiya Suo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Jintao Cheng
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Laichuang Han
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Wenliang Hao
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Junling Guo
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Key Laboratory of Industrial Biotechnology (Ministry of Education), Jiangnan University, Wuxi, Jiangsu, 214122, China
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Prusa J, Zhu DX, Stallings CL. The stringent response and Mycobacterium tuberculosis pathogenesis. Pathog Dis 2018; 76:5035815. [PMID: 29947752 PMCID: PMC7191866 DOI: 10.1093/femspd/fty054] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/08/2018] [Indexed: 12/23/2022] Open
Abstract
During infection, the host restrains Mycobacterium tuberculosis (Mtb) from proliferating by imposing an arsenal of stresses. Despite this onslaught of attacks, Mtb is able to persist for the lifetime of the host, indicating that this pathogen has substantial molecular mechanisms to resist host-inflicted damage. The stringent response is a conserved global stress response in bacteria that involves the production of the hyperphosphorylated guanine nucleotides ppGpp and pppGpp (collectively called (p)ppGpp). (p)ppGpp then regulates a number of cellular processes to adjust the physiology of the bacteria to promote survival in different environments. Survival in the presence of host-generated stresses is an essential quality of successful pathogens, and the stringent response is critical for the intracellular survival of a number of pathogenic bacteria. In addition, the stringent response has been linked to virulence gene expression, persistence, latency and drug tolerance. In Mtb, (p)ppGpp synthesis is required for survival in low nutrient conditions, long term culture and during chronic infection in animal models, all indicative of a strict requirement for (p)ppGpp during exposure to stresses associated with infection. In this review we discuss (p)ppGpp metabolism and how this functions as a critical regulator of Mtb virulence.
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Affiliation(s)
- Jerome Prusa
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Dennis X Zhu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Christina L Stallings
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA
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