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Oh Y, Oh JI. The RsfSR two-component system regulates SigF function by monitoring the state of the respiratory electron transport chain in Mycobacterium smegmatis. J Biol Chem 2024; 300:105764. [PMID: 38367670 PMCID: PMC10950880 DOI: 10.1016/j.jbc.2024.105764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024] Open
Abstract
In Mycobacterium smegmatis, the transcriptional activity of the alternative sigma factor SigF is posttranslationally regulated by the partner switching system consisting of SigF, the anti-SigF RsbW1, and three anti-SigF antagonists (RsfA, RsfB, and RsbW3). We previously demonstrated that expression of the SigF regulon is strongly induced in the Δaa3 mutant of M. smegmatis lacking the aa3 cytochrome c oxidase, the major terminal oxidase in the respiratory electron transport chain. Here, we identified and characterized the RsfSR two-component system involved in regulating the phosphorylation state of the major anti-SigF antagonist RsfB. RsfS (MSMEG_6130) is a histidine kinase with the cyclase/histidine kinase-associated sensing extracellular 3 domain at its N terminus, and RsfR (MSMEG_6131) is a receiver domain-containing protein phosphatase 2C-type phosphatase that can dephosphorylate phosphorylated RsfB. We demonstrated that phosphorylation of RsfR on Asp74 by RsfS reduces the phosphatase activity of RsfR toward phosphorylated RsfB and that the cellular abundance of the active unphosphorylated RsfB is increased in the Δaa3 mutant relative to the WT strain. We also demonstrated that the RsfSR two-component system is required for induction of the SigF regulon under respiration-inhibitory conditions such as inactivation of the cytochrome bcc1 complex and aa3 cytochrome c oxidase, as well as hypoxia, electron donor-limiting, high ionic strength, and low pH conditions. Collectively, our results reveal a key regulatory element involved in regulating the SigF signaling system by monitoring the state of the respiratory electron transport chain.
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Affiliation(s)
- Yuna Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea
| | - Jeong-Il Oh
- Department of Integrated Biological Science, Pusan National University, Busan, Korea; Microbiological Resource Research Institute, Pusan National University, Busan, Korea.
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2
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Luna-Bulbarela A, Romero-Gutiérrez MT, Tinoco-Valencia R, Ortiz E, Martínez-Romero ME, Galindo E, Serrano-Carreón L. Response of Bacillus velezensis 83 to interaction with Colletotrichum gloeosporioides resembles a Greek phalanx-style formation: A stress resistant phenotype with antibiosis capacity. Microbiol Res 2024; 280:127592. [PMID: 38199003 DOI: 10.1016/j.micres.2023.127592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Plant growth-promoting rhizobacteria, such as Bacillus spp., establish beneficial associations with plants and may inhibit the growth of phytopathogenic fungi. However, these bacteria are subject to multiple biotic stimuli from their competitors, causing stress and modifying their development. This work is a study of an in vitro interaction between two model microorganisms of socioeconomic relevance, using population dynamics and transcriptomic approaches. Co-cultures of Bacillus velezensis 83 with the phytopathogenic fungus Colletotrichum gloeosporioides 09 were performed to evaluate the metabolic response of the bacteria under conditions of non-nutritional limitation. The bacterial response was associated with the induction of a stress-resistant phenotype, characterized by a lower specific growth rate, but with antimicrobial production capacity. About 12% of co-cultured B. velezensis 83 coding sequences were differentially expressed, including the up-regulation of the general stress response (sigB regulon), and the down-regulation of alternative carbon sources catabolism (glucose preference). Defense strategies in B. velezensis are a determining factor in order to preserve the long-term viability of its population. Mostly, the presence of the fungus does not affect the expression of antibiosis genes, except for those corresponding to surfactin/bacillomycin D production. Indeed, the up-regulation of antibiosis genes expression is associated with bacterial growth, regardless of the presence of the fungus. This behavior in B. velezensis 83 resembles the strategy used by the classical Greek phalanx formation: by sacrificing growth rate and metabolic versatility, resources can be redistributed to defense (stress resistant phenotype) while maintaining the attack (antibiosis capacity). The presented results are the first characterization of the molecular phenotype at the transcriptome level of a biological control agent under biotic stress caused by a phytopathogen without nutrient limitation.
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Affiliation(s)
- Agustín Luna-Bulbarela
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico
| | - María Teresa Romero-Gutiérrez
- Technological Innovation Department, Tlajomulco University Center, University of Guadalajara, 45641 Tlajomulco de Zúñiga, Jalisco, Mexico; Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, 44430 Guadalajara, Jalisco, Mexico
| | - Raunel Tinoco-Valencia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - Ernesto Ortiz
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - María Esperanza Martínez-Romero
- Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - Enrique Galindo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico
| | - Leobardo Serrano-Carreón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico.
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3
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Bush SR, Sanders S, Frey N, Hamm CW, Toews M, Winburn S, Fayard EJ, Rodriguez A, Boyne NS, Osborne JS, Cabeen MT. Temporal σ B stress-response profiles impact Bacillus subtilis fitness. mSphere 2024; 9:e0071923. [PMID: 38236030 PMCID: PMC10900884 DOI: 10.1128/msphere.00719-23] [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: 11/20/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
The Gram-positive model organism Bacillus subtilis responds to environmental stressors by activating the alternative sigma factor σB. The sensing apparatus upstream of σB activation is thought to consist of cytoplasmic stressosomes-megadalton-sized protein complexes that include five paralogous proteins known as RsbRs. The RsbRs are presumed to be involved in stress sensing and the subsequent response. Perturbations to the RsbR complement in stressosomes by engineering cells that produce only one of the RsbR paralogs ("single-RsbR strains") lead to altered σB response dynamics with respect to timing and magnitude. Here, we asked whether such changes to σB response dynamics impact the relative fitness of a strain. We competed strain pairs with different RsbR complements under ethanol and sodium chloride stress and found not only differences in relative fitness among wild-type and single-RsbR strains but also different relative fitness values in the two different stressors. We found that the presence of RsbRA, which dominates the wild-type σB response, enhances fitness in ethanol but is detrimental to fitness in NaCl. Meanwhile, RsbRD-only cells were among the most fit in NaCl. Strains producing hybrid RsbR fusion proteins displayed different fitness values that depended on the RsbR proteins from which they were derived. Our results here suggest that σB response dynamics can impact fitness, highlighting the physiological importance of the unusual stressosome-based general stress response system of B. subtilis. IMPORTANCE The model bacterium Bacillus subtilis uses cytoplasmic multiprotein complexes, termed stressosomes, to activate the alternative sigma factor σB when facing environmental stresses. We have previously shown that genetically manipulating the complement of putative sensor proteins in stressosomes can alter the dynamics of the σB response in terms of its magnitude and timing. However, it is unknown whether these response dynamics impact the fitness of cells challenged by environmental stressors. Here, we examine the fitness of strains with different σB responses by competing strain pairs in exponential-phase co-cultures under environmental stress. We find that strains with different response dynamics show different competitive indices that differ by stressor. These results suggest that the dynamics of the σB response can affect the fitness of cells facing environmental stress, highlighting the relevance of different σB dynamics.
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Affiliation(s)
- Sidney R. Bush
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Shelby Sanders
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Nicholas Frey
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Christopher W. Hamm
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Madeline Toews
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Sarah Winburn
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Emily J. Fayard
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - AnaLisa Rodriguez
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Nicholas S. Boyne
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Jacob S. Osborne
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Matthew T. Cabeen
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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4
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Cutugno L, Mc Cafferty J, Pané-Farré J, O'Byrne C, Boyd A. The Vibrio vulnificus stressosome is dispensable in nutrient-rich media. Access Microbiol 2023; 5:acmi000523.v4. [PMID: 37601438 PMCID: PMC10436020 DOI: 10.1099/acmi.0.000523.v4] [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: 11/18/2022] [Accepted: 05/27/2023] [Indexed: 08/22/2023] Open
Abstract
The stressosome is a protein complex that senses environmental stresses and mediates the stress response in several Gram-positive bacteria through the activation of the alternative sigma factor SigB. The stressosome locus is found in 44 % of Gram-negative Vibrio vulnificus isolates. However, V. vulnificus does not possess SigB. Nonetheless, in nutrient-limited media, the stressosome modulates gene transcription and bacterial behaviour. In this work, the expression of the stressosome genes was proven during stationary phase in nutrient-rich media and co-transcription as one operonic unit of the stressosome locus and its putative downstream regulatory locus was demonstrated. The construction of a stressosome mutant lacking the genes encoding the four proteins constituting the stressosome complex (VvRsbR, VvRsbS, VvRsbT, VvRsbX) allowed us to examine the role of this complex in vivo. Extensive phenotypic characterization of the ΔRSTX mutant in nutrient-rich media showed that the stressosome does not contribute to growth of V. vulnificus . Moreover, the stressosome did not modulate the tolerance or survival response of V. vulnificus to the range of stresses tested, which included ethanol, hyperosmolarity, hypoxia, high temperature, acidity and oxidative stress. Furthermore, the stressosome was dispensable for motility and exoenzyme production of V. vulnificus in nutrient-rich media. Therefore, in conclusion, although stressosome gene transcription occurs in nutrient-rich media, the stressosome neither has an essential role in stress responses of V. vulnificus nor does it seem to modulate these activities in these conditions. We hypothesise that the stressosome is expressed in nutrient-rich conditions as a sensor complex, but that activation of the complex does not occur in this environment.
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Affiliation(s)
- Laura Cutugno
- School of Natural Sciences, University of Galway, Galway, Ireland
| | | | - Jan Pané-Farré
- Centre for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Conor O'Byrne
- School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Aoife Boyd
- School of Natural Sciences, University of Galway, Galway, Ireland
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5
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Tran BM, Linnik DS, Punter CM, Śmigiel WM, Mantovanelli L, Iyer A, O’Byrne C, Abee T, Johansson J, Poolman B. Super-resolving microscopy reveals the localizations and movement dynamics of stressosome proteins in Listeria monocytogenes. Commun Biol 2023; 6:51. [PMID: 36641529 PMCID: PMC9840623 DOI: 10.1038/s42003-023-04423-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
The human pathogen Listeria monocytogenes can cope with severe environmental challenges, for which the high molecular weight stressosome complex acts as the sensing hub in a complicated signal transduction pathway. Here, we show the dynamics and functional roles of the stressosome protein RsbR1 and its paralogue, the blue-light receptor RsbL, using photo-activated localization microscopy combined with single-particle tracking and single-molecule displacement mapping and supported by physiological studies. In live cells, RsbR1 is present in multiple states: in protomers with RsbS, large clusters of stressosome complexes, and in connection with the plasma membrane via Prli42. RsbL diffuses freely in the cytoplasm but forms clusters upon exposure to light. The clustering of RsbL is independent of the presence of Prli42. Our work provides a comprehensive view of the spatial organization and intracellular dynamics of the stressosome proteins in L. monocytogenes, which paves the way towards uncovering the stress-sensing mechanism of this signal transduction pathway.
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Affiliation(s)
- Buu Minh Tran
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Dmitrii Sergeevich Linnik
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Christiaan Michiel Punter
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Wojciech Mikołaj Śmigiel
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Luca Mantovanelli
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Aditya Iyer
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Conor O’Byrne
- Microbiology, School of Biological & Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Laboratory of Food Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Jörgen Johansson
- grid.12650.300000 0001 1034 3451Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Bert Poolman
- grid.4830.f0000 0004 0407 1981Department of Biochemistry, University of Groningen, Groningen, the Netherlands
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6
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Cutugno L, Tamayo BKS, Lens PN, O'Byrne C, Pané-Farré J, Boyd A. In vivo characterisation of the Vibrio vulnificus stressosome: A complex involved in reshaping glucose metabolism and motility regulation, in nutrient- and iron-limited growth conditions. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100186. [PMID: 36936406 PMCID: PMC10014275 DOI: 10.1016/j.crmicr.2023.100186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Stressosomes are signal-sensing and integration hubs identified in many bacteria. At present, the role of the stressosome has only been investigated in Gram-positive bacteria. This work represents the first in vivo characterisation of the stressosome in a Gram-negative bacterium, Vibrio vulnificus. Previous in vitro characterisation of the complex has led to the hypothesis of a complex involved in iron metabolism and control of c-di-GMP levels. We demonstrate that the stressosome is probably involved in reshaping the glucose metabolism in Fe- and nutrient-limited conditions and mutations of the locus affect the activation of the glyoxylate shunt. Moreover, we show that the stressosome is needed for the transcription of fleQ and to promote motility, consistent with the hypothesis that the stressosome is involved in regulating c-di-GMP. This report highlights the potential role of the stressosome in a Gram-negative bacterium, with implications for the metabolism and motility of this pathogen.
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Affiliation(s)
- Laura Cutugno
- School of Natural Sciences, University of Galway, Ireland
| | | | - Piet N.L. Lens
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Conor O'Byrne
- School of Biological and Chemical Sciences, University of Galway, Ireland
| | - Jan Pané-Farré
- Centre for synthetic Microbiology (SYNMIKRO) & Department of Chemistry, Philipps-University Marburg, Germany
| | - Aoife Boyd
- School of Natural Sciences, University of Galway, Ireland
- Corresponding author.
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7
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Bacillus subtilis Stressosome Sensor Protein Sequences Govern the Ability To Distinguish among Environmental Stressors and Elicit Different σ B Response Profiles. mBio 2022; 13:e0200122. [PMID: 36409125 PMCID: PMC9765535 DOI: 10.1128/mbio.02001-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteria use a variety of systems to sense stress and mount an appropriate response to ensure fitness and survival. Bacillus subtilis uses stressosomes-cytoplasmic multiprotein complexes-to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σB. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σB response profiles with respect to timing and intensity when facing an identical stressor. Here, we use a similar approach to address the question of whether the σB responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σB with characteristic transient response timing irrespective of stressor but show various response magnitudes. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative, and acid stress, implying that RsbR proteins can distinguish among stressors. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argue that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σB response timing. IMPORTANCE Bacterial survival depends on appropriate responses to diverse stressors. The general stress-response system in the environmental model bacterium Bacillus subtilis is constantly poised for an immediate response and uses unusual stress-sensing protein complexes called stressosomes. Stressosomes typically contain four different types of putative sensing protein. We asked whether each type of sensor has a distinct role in mediating response dynamics to different environmental stressors. We find that one sensor type always mediates a transient response, while the others show distinct response magnitude and timing to different stressors. We also find that a transient response is exceptional, as several engineered hybrid proteins did not show strong transient responses. Our work reveals functional distinctions among subunits of the stressosome complex and represents a step toward understanding how the general stress response of B. subtilis ensures its survival in natural environmental settings.
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Rangel K, Cabral FO, Lechuga GC, Villas-Bôas MHS, Midlej V, De-Simone SG. Effectiveness Evaluation of a UV-C-Photoinactivator against Selected ESKAPE-E Pathogens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:16559. [PMID: 36554438 PMCID: PMC9778679 DOI: 10.3390/ijerph192416559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Healthcare-associated infections (HAI) worldwide includes infections by ESKAPE-E pathogens. Environmental surfaces and fomites are important components in HAI transmission dynamics, and shoe soles are vectors of HAI. Ultraviolet (UV) disinfection is an effective method to inactivate pathogenic microorganisms. In this study, we investigated whether the SANITECH UV-C shoe sole decontaminator equipment that provides germicidal UV-C radiation could effectively reduce this risk of different pathogens. Six standard strains and four clinical MDR strains in liquid and solid medium were exposed to a UV-C System at specific concentrations at other times. Bacterial inactivation (growth and cultivability) was investigated using colony counts and resazurin as metabolic indicators. SEM was performed to assess the membrane damage. Statistically significant reduction in cell viability for all ATCCs strains occurred after 10 s of exposure to the UV-C system, except for S. enterica, which only occurred at 20 s. The cell viability of P. aeruginosa (90.9%), E. faecalis and A. baumannii (85.3%), S. enterica (82.9%), E. coli (79.2%) and S. aureus (71.9%) was reduced considerably at 20 s. In colony count, after 12 s of UV-C exposure, all ATCC strains showed a 100% reduction in CFU counts, except for A. baumannii, which reduced by 97.7%. A substantial reduction of colonies above 3 log10 was observed at 12 and 20 s in all bacterial strains tested, except for A. baumannii ATCC 19606 (12 s). The exposure of ATCCs bacterial strains to the UV-C system for only 2 s was able to reduce 100% in the colony forming units (CFU) count in all ATCCs strains, S. aureus, P. aeruginosa, E. coli, A. baumannii, E. faecalis, except the S. enterica strain which had a statistically significant reduction of 99.7%. In ATCC strains, there was a substantial decrease in colonies after 4 s (sec) of exposure to the UV-C system, with a reduction ranging from 3.78-4.15 log10 CFU/mL. This reduction was observed in MDR/ESKAPE-E strains within 10 s, showing that UV-C could eliminate above 3.84 log10 CFU/mL. SEM showed a reduction of pili-like appendages after UV-C treatment in all strains except for E. coli (ATCC 25922). The Sanitech UV-C shoe sole decontaminator equipment from Astech Serv. and Fabrication Ltd. (Petrópolis, Brazil), effectively killed in vitro a series of ATCCs and MDR/ESKAPE-E bacteria of sanitary interest, commonly found in the hospital environment.
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Affiliation(s)
- Karyne Rangel
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Epidemiology and Molecular Systematics (LESM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Fellipe O. Cabral
- Health Sciences Center, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-853, RJ, Brazil
| | - Guilherme C. Lechuga
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Epidemiology and Molecular Systematics (LESM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Maria H. S. Villas-Bôas
- Microbiology Department, National Institute for Quality Control in Health (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Victor Midlej
- Structural Biology Laboratory (LBE), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
| | - Salvatore G. De-Simone
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Laboratory of Epidemiology and Molecular Systematics (LESM), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Post-Graduation Program in Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University (UFF), Niterói 22040-036, RJ, Brazil
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9
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Molecular insights into intra-complex signal transmission during stressosome activation. Commun Biol 2022; 5:621. [PMID: 35760945 PMCID: PMC9237128 DOI: 10.1038/s42003-022-03549-9] [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: 05/28/2021] [Accepted: 05/31/2022] [Indexed: 11/24/2022] Open
Abstract
The stressosome is a pseudo-icosahedral megadalton bacterial stress-sensing protein complex consisting of several copies of two STAS-domain proteins, RsbR and RsbS, and the kinase RsbT. Upon perception of environmental stress multiple copies of RsbT are released from the surface of the stressosome. Free RsbT activates downstream proteins to elicit a global cellular response, such as the activation of the general stress response in Gram-positive bacteria. The molecular events triggering RsbT release from the stressosome surface remain poorly understood. Here we present the map of Listeria innocua RsbR1/RsbS complex at resolutions of 3.45 Å for the STAS domain core in icosahedral symmetry and of 3.87 Å for the STAS domain and N-terminal sensors in D2 symmetry, respectively. The structure reveals a conformational change in the STAS domain linked to phosphorylation in RsbR. Docking studies indicate that allosteric RsbT binding to the conformationally flexible N-terminal sensor domain of RsbR affects the affinity of RsbS towards RsbT. Our results bring to focus the molecular events within the stressosome complex and further our understanding of this ubiquitous signaling hub. Cryo-EM structures of the stress-sensing complex in Listeria innocua reveal conformational changes that initiate the signaling response to environmental stress.
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The Vibrio vulnificus stressosome is an oxygen-sensor involved in regulating iron metabolism. Commun Biol 2022; 5:622. [PMID: 35761021 PMCID: PMC9237108 DOI: 10.1038/s42003-022-03548-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 05/31/2022] [Indexed: 11/08/2022] Open
Abstract
Stressosomes are stress-sensing protein complexes widely conserved among bacteria. Although a role in the regulation of the general stress response is well documented in Gram-positive bacteria, the activating signals are still unclear, and little is known about the physiological function of stressosomes in the Gram-negative bacteria. Here we investigated the stressosome of the Gram-negative marine pathogen Vibrio vulnificus. We demonstrate that it senses oxygen and identified its role in modulating iron-metabolism. We determined a cryo-electron microscopy structure of the VvRsbR:VvRsbS stressosome complex, the first solved from a Gram-negative bacterium. The structure points to a variation in the VvRsbR and VvRsbS stoichiometry and a symmetry breach in the oxygen sensing domain of VvRsbR, suggesting how signal-sensing elicits a stress response. The findings provide a link between ligand-dependent signaling and an output – regulation of iron metabolism - for a stressosome complex. A cryo-electron microscopy reconstruction of a stressosome complex from a Gram-negative bacterium, Vibrio vulnificus, reveals variations in subunit composition and symmetry, which could serve to adjust the activation threshold in the response to low levels of oxygen and starvation.
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11
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Yadavalli SS, Yuan J. Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer. J Bacteriol 2022; 204:e0034421. [PMID: 34516282 PMCID: PMC8765417 DOI: 10.1128/jb.00344-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small membrane proteins represent a subset of recently discovered small proteins (≤100 amino acids), which are a ubiquitous class of emerging regulators underlying bacterial adaptation to environmental stressors. Until relatively recently, small open reading frames encoding these proteins were not designated genes in genome annotations. Therefore, our understanding of small protein biology was primarily limited to a few candidates associated with previously characterized larger partner proteins. Following the first systematic analyses of small proteins in Escherichia coli over a decade ago, numerous small proteins across different bacteria have been uncovered. An estimated one-third of these newly discovered proteins in E. coli are localized to the cell membrane, where they may interact with distinct groups of membrane proteins, such as signal receptors, transporters, and enzymes, and affect their activities. Recently, there has been considerable progress in functionally characterizing small membrane protein regulators aided by innovative tools adapted specifically to study small proteins. Our review covers prototypical proteins that modulate a broad range of cellular processes, such as transport, signal transduction, stress response, respiration, cell division, sporulation, and membrane stability. Thus, small membrane proteins represent a versatile group of physiology regulators at the membrane and the whole cell. Additionally, small membrane proteins have the potential for clinical applications, where some of the proteins may act as antibacterial agents themselves while others serve as alternative drug targets for the development of novel antimicrobials.
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Affiliation(s)
- Srujana S. Yadavalli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey, USA
- Department of Genetics, Rutgers University, Piscataway, New Jersey, USA
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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12
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Quereda JJ, Morón-García A, Palacios-Gorba C, Dessaux C, García-del Portillo F, Pucciarelli MG, Ortega AD. Pathogenicity and virulence of Listeria monocytogenes: A trip from environmental to medical microbiology. Virulence 2021; 12:2509-2545. [PMID: 34612177 PMCID: PMC8496543 DOI: 10.1080/21505594.2021.1975526] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
Listeria monocytogenes is a saprophytic gram-positive bacterium, and an opportunistic foodborne pathogen that can produce listeriosis in humans and animals. It has evolved an exceptional ability to adapt to stress conditions encountered in different environments, resulting in a ubiquitous distribution. Because some food preservation methods and disinfection protocols in food-processing environments cannot efficiently prevent contaminations, L. monocytogenes constitutes a threat to human health and a challenge to food safety. In the host, Listeria colonizes the gastrointestinal tract, crosses the intestinal barrier, and disseminates through the blood to target organs. In immunocompromised individuals, the elderly, and pregnant women, the pathogen can cross the blood-brain and placental barriers, leading to neurolisteriosis and materno-fetal listeriosis. Molecular and cell biology studies of infection have proven L. monocytogenes to be a versatile pathogen that deploys unique strategies to invade different cell types, survive and move inside the eukaryotic host cell, and spread from cell to cell. Here, we present the multifaceted Listeria life cycle from a comprehensive perspective. We discuss genetic features of pathogenic Listeria species, analyze factors involved in food contamination, and review bacterial strategies to tolerate stresses encountered both during food processing and along the host's gastrointestinal tract. Then we dissect host-pathogen interactions underlying listerial pathogenesis in mammals from a cell biology and systemic point of view. Finally, we summarize the epidemiology, pathophysiology, and clinical features of listeriosis in humans and animals. This work aims to gather information from different fields crucial for a comprehensive understanding of the pathogenesis of L. monocytogenes.
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Affiliation(s)
- Juan J. Quereda
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities. Valencia, Spain
| | - Alvaro Morón-García
- Departamento de Biología Celular. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid. Madrid, Spain
| | - Carla Palacios-Gorba
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad Cardenal Herrera-CEU, CEU Universities. Valencia, Spain
| | - Charlotte Dessaux
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
| | - Francisco García-del Portillo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
| | - M. Graciela Pucciarelli
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Biología Molecular ‘Severo Ochoa’. Departamento de Biología Molecular, Facultad de Ciencias, Universidad Autónoma de Madrid. Madrid, Spain
| | - Alvaro D. Ortega
- Departamento de Biología Celular. Facultad de Ciencias Biológicas, Universidad Complutense de Madrid. Madrid, Spain
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología (CNB)- Consejo Superior De Investigaciones Científicas (CSIC), Madrid, Spain
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13
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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14
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Listeria monocytogenes requires the RsbX protein to prevent SigB-activation under non-stressed conditions. J Bacteriol 2021; 204:e0048621. [PMID: 34694900 PMCID: PMC8765406 DOI: 10.1128/jb.00486-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The survival of microbial cells under changing environmental conditions requires an efficient reprogramming of transcription, often mediated by alternative sigma factors. The Gram-positive human pathogen Listeria monocytogenes senses and responds to environmental stress mainly through the alternative sigma factor σB (SigB), which controls expression of the general stress response regulon. SigB activation is achieved through a complex series of phosphorylation/dephosphorylation events culminating in the release of SigB from its anti-sigma factor RsbW. At the top of the signal transduction pathway lies a large multiprotein complex known as the stressosome that is believed to act as a sensory hub for stresses. Following signal detection, stressosome proteins become phosphorylated. Resetting of the stressosome is hypothesized to be exerted by a putative phosphatase, RsbX, which presumably removes phosphate groups from stressosome proteins poststress. We addressed the role of the RsbX protein in modulating the activity of the stressosome and consequently regulating SigB activity in L. monocytogenes. We show that RsbX is required to reduce SigB activation levels under nonstress conditions and that it is required for appropriate SigB-mediated stress adaptation. A strain lacking RsbX displayed impaired motility and biofilm formation and also an increased survival at low pH. Our results could suggest that absence of RsbX alters the multiprotein composition of the stressosome without dramatically affecting its phosphorylation status. Overall, the data show that RsbX plays a critical role in modulating the signal transduction pathway by blocking SigB activation under nonstressed conditions. IMPORTANCE Pathogenic bacteria need to sense and respond to stresses to survive harsh environments and also to turn off the response when no longer facing stress. Activity of the stress sigma factor SigB in the human pathogen Listeria monocytogenes is controlled by a hierarchic system having a large stress-sensing multiprotein complex known as the stressosome at the top. Following stress exposure, proteins in the stressosome become phosphorylated, leading to SigB activation. We have studied the role of a putative phosphatase, RsbX, which is hypothesized to dephosphorylate stressosome proteins. RsbX is critical not only to switch off the stress response poststress but also to keep the activity of SigB low at nonstressed conditions to prevent unnecessary gene expression and save energy.
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15
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Genetic Factors Affect the Survival and Behaviors of Selected Bacteria during Antimicrobial Blue Light Treatment. Int J Mol Sci 2021; 22:ijms221910452. [PMID: 34638788 PMCID: PMC8508746 DOI: 10.3390/ijms221910452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance is a global, mounting and dynamic issue that poses an immediate threat to human, animal, and environmental health. Among the alternative antimicrobial treatments proposed to reduce the external use of antibiotics is electromagnetic radiation, such as blue light. The prevailing mechanistic model is that blue light can be absorbed by endogenous porphyrins within the bacterial cell, inducing the production of reactive oxygen species, which subsequently inflict oxidative damages upon different cellular components. Nevertheless, it is unclear whether other mechanisms are involved, particularly those that can affect the efficacy of antimicrobial blue light treatments. In this review, we summarize evidence of inherent factors that may confer protection to a selected group of bacteria against blue light-induced oxidative damages or modulate the physiological characteristics of the treated bacteria, such as virulence and motility. These include descriptions of three major photoreceptors in bacteria, chemoreceptors, SOS-dependent DNA repair and non-SOS protective mechanisms. Future directions are also provided to assist with research efforts to increase the efficacy of antimicrobial blue light and to minimize the development of blue light-tolerant phenotypes.
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16
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Activation of the Listeria monocytogenes Stressosome in the Intracellular Eukaryotic Environment. Appl Environ Microbiol 2021; 87:e0039721. [PMID: 33811030 DOI: 10.1128/aem.00397-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous environmental bacterium and intracellular pathogen that responds to stress using predominantly the alternative sigma factor SigB. Stress is sensed by a multiprotein complex, the stressosome, extensively studied in bacteria grown in nutrient media. Following signal perception, the stressosome triggers a phosphorylation cascade that releases SigB from its anti-sigma factor. Whether the stressosome is activated during the intracellular infection is unknown. Here, we analyzed the subcellular distribution of stressosome proteins in L. monocytogenes located inside epithelial cells following their immunodetection in membrane and cytosolic fractions prepared from intracellular bacteria. Unlike bacteria in laboratory media, intracellular bacteria have a large proportion of the core stressosome protein RsbR1 associated with the membrane. However, another core protein, RsbS, is undetectable. Despite the absence of RsbS, a SigB-dependent reporter revealed that SigB activity increases gradually from early (1 h) to late (6 h) postinfection times. We also found that RsbR1 paralogues attenuate the intensity of the SigB response and that the miniprotein Prli42, reported to tether the stressosome to the membrane in response to oxidative stress, plays no role in associating RsbR1 to the membrane of intracellular bacteria. Altogether, these data indicate that, once inside host cells, the L. monocytogenes stressosome may adopt a unique configuration to sense stress and to activate SigB in the intracellular eukaryotic niche. IMPORTANCE The response to stress mediated by the alternative sigma factor SigB has been extensively characterized in Bacillus subtilis and Listeria monocytogenes. These bacteria sense stress using a supramacromolecular complex, the stressosome, which triggers a cascade that releases SigB from its anti-sigma factor. Despite the fact that many structural data on the complex are available and analyses have been performed in mutants lacking components of the stressosome or the signaling cascade, the integration of the stress signal and the dynamics of stressosome proteins following environmental changes remain poorly understood. Our study provides data at the protein level on essential stressosome components and SigB activity when L. monocytogenes, normally a saprophytic bacterium, adapts to an intracellular lifestyle. Our results support activation of the stressosome complex in intracellular bacteria. The apparent loss of the stressosome core protein RsbS in intracellular L. monocytogenes also challenges current models, favoring the idea of a unique stressosome architecture responding to intracellular host cues.
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17
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Intracellular localization of the mycobacterial stressosome complex. Sci Rep 2021; 11:10060. [PMID: 33980893 PMCID: PMC8115616 DOI: 10.1038/s41598-021-89069-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/19/2021] [Indexed: 11/09/2022] Open
Abstract
Microorganisms survive stresses by alternating the expression of genes suitable for surviving the immediate and present danger and eventually adapt to new conditions. Many bacteria have evolved a multiprotein "molecular machinery" designated the "Stressosome" that integrates different stress signals and activates alternative sigma factors for appropriate downstream responses. We and others have identified orthologs of some of the Bacillus subtilis stressosome components, RsbR, RsbS, RsbT and RsbUVW in several mycobacteria and we have previously reported mutual interactions among the stressosome components RsbR, RsbS, RsbT and RsbUVW from Mycobacterium marinum. Here we provide evidence that "STAS" domains of both RsbR and RsbS are important for establishing the interaction and thus critical for stressosome assembly. Fluorescence microscopy further suggested co-localization of RsbR and RsbS in multiprotein complexes visible as co-localized fluorescent foci distributed at scattered locations in the M. marinum cytoplasm; the number, intensity and distribution of such foci changed in cells under stressed conditions. Finally, we provide bioinformatics data that 17 (of 244) mycobacteria, which lack the RsbRST genes, carry homologs of Bacillus cereus genes rsbK and rsbM indicating the existence of alternative σF activation pathways among mycobacteria.
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18
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Goekoop R, de Kleijn R. How higher goals are constructed and collapse under stress: A hierarchical Bayesian control systems perspective. Neurosci Biobehav Rev 2021; 123:257-285. [PMID: 33497783 DOI: 10.1016/j.neubiorev.2020.12.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 11/19/2020] [Accepted: 12/19/2020] [Indexed: 01/26/2023]
Abstract
In this paper, we show that organisms can be modeled as hierarchical Bayesian control systems with small world and information bottleneck (bow-tie) network structure. Such systems combine hierarchical perception with hierarchical goal setting and hierarchical action control. We argue that hierarchical Bayesian control systems produce deep hierarchies of goal states, from which it follows that organisms must have some form of 'highest goals'. For all organisms, these involve internal (self) models, external (social) models and overarching (normative) models. We show that goal hierarchies tend to decompose in a top-down manner under severe and prolonged levels of stress. This produces behavior that favors short-term and self-referential goals over long term, social and/or normative goals. The collapse of goal hierarchies is universally accompanied by an increase in entropy (disorder) in control systems that can serve as an early warning sign for tipping points (disease or death of the organism). In humans, learning goal hierarchies corresponds to personality development (maturation). The failure of goal hierarchies to mature properly corresponds to personality deficits. A top-down collapse of such hierarchies under stress is identified as a common factor in all forms of episodic mental disorders (psychopathology). The paper concludes by discussing ways of testing these hypotheses empirically.
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Affiliation(s)
- Rutger Goekoop
- Parnassia Group, PsyQ, Department of Anxiety Disorders, Early Detection and Intervention Team (EDIT), Netherlands.
| | - Roy de Kleijn
- Cognitive Psychology Unit, Leiden University, Netherlands
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19
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Pessione E. The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions. Front Microbiol 2021; 11:571417. [PMID: 33584557 PMCID: PMC7873842 DOI: 10.3389/fmicb.2020.571417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms' symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.
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Affiliation(s)
- Enrica Pessione
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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20
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Choi S, Nakasone Y, Hellingwerf KJ, Terazima M. Photoreaction Dynamics of a Full-Length Protein YtvA and Intermolecular Interaction with RsbRA. Biochemistry 2020; 59:4703-4710. [PMID: 33287544 DOI: 10.1021/acs.biochem.0c00888] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
YtvA from Bacillus subtilis is a sensor protein that responds to blue light stress and regulates the activity of transcription factor σB. It is composed of the N-terminal LOV (light-oxygen-voltage) domain, the C-terminal STAS (sulfate transporter and anti-sigma factor antagonist) domain, and a linker region connecting them. In this study, the photoreaction and kinetics of full-length YtvA and the intermolecular interaction with a downstream protein, RsbRA, were revealed by the transient grating method. Although N-YLOV-linker, which is composed of the LOV domain of YtvA with helices A'α and Jα, exhibits a diffusion change due to the rotational motion of the helices, the YtvA dimer does not show the diffusion change. This result suggests that the STAS domain inhibits the rotational movement of helices A'α and Jα. We found that the YtvA dimer formed a heterotetramer with the RsbRA dimer probably via the interaction between the STAS domains, and we showed the diffusion change upon blue light illumination with a time constant faster than 70 μs. This result suggests a conformational change of the STAS domains; i.e., the interface between the STAS domains of the proteins changes to enhance the friction with water by the rotation structural change of helices A'α and Jα of YtvA.
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Affiliation(s)
- Seokwoo Choi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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21
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Dessaux C, Guerreiro DN, Pucciarelli MG, O'Byrne CP, García-Del Portillo F. Impact of osmotic stress on the phosphorylation and subcellular location of Listeria monocytogenes stressosome proteins. Sci Rep 2020; 10:20837. [PMID: 33257749 PMCID: PMC7705745 DOI: 10.1038/s41598-020-77738-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Listeria monocytogenes responds to environmental stress using a supra-macromolecular complex, the stressosome, to activate the stress sigma factor SigB. The stressosome structure, inferred from in vitro-assembled complexes, consists of the core proteins RsbR (here renamed RsbR1) and RsbS and, the kinase RsbT. The active complex is proposed to be tethered to the membrane and to support RsbR1/RsbS phosphorylation by RsbT and the subsequent release of RsbT following signal perception. Here, we show in actively-growing cells that L. monocytogenes RsbR1 and RsbS localize mostly in the cytosol in a fully phosphorylated state regardless of osmotic stress. RsbT however distributes between cytosolic and membrane-associated pools. The kinase activity of RsbT on RsbR1/RsbS and its requirement for maximal SigB activation in response to osmotic stress were demonstrated in vivo. Cytosolic RsbR1 interacts with RsbT, while this interaction diminishes at the membrane when RsbR1 paralogues (RsbR2, RsbR3 and RsbL) are present. Altogether, the data support a model in which phosphorylated RsbR1/RsbS may sustain basal SigB activity in unstressed cells, probably assuring a rapid increase in such activity in response to stress. Our findings also suggest that in vivo the active RsbR1-RsbS-RsbT complex forms only transiently and that membrane-associated RsbR1 paralogues could modulate its assembly.
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Affiliation(s)
- Charlotte Dessaux
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin 3, 28049, Madrid, Spain
| | - Duarte N Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - M Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin 3, 28049, Madrid, Spain.,Department of Molecular Biology, Centre of Molecular Biology 'Severo Ochoa' (CBMSO)-CSIC, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Conor P O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, H91 TK33, Ireland
| | - Francisco García-Del Portillo
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Darwin 3, 28049, Madrid, Spain.
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22
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Rodriguez Ayala F, Bartolini M, Grau R. The Stress-Responsive Alternative Sigma Factor SigB of Bacillus subtilis and Its Relatives: An Old Friend With New Functions. Front Microbiol 2020; 11:1761. [PMID: 33042030 PMCID: PMC7522486 DOI: 10.3389/fmicb.2020.01761] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/06/2020] [Indexed: 12/13/2022] Open
Abstract
Alternative sigma factors have led the core RNA polymerase (RNAP) to recognize different sets of promoters to those recognized by the housekeeping sigma A-directed RNAP. This change in RNAP promoter selectivity allows a rapid and flexible reformulation of the genetic program to face environmental and metabolic stimuli that could compromise bacterial fitness. The model bacterium Bacillus subtilis constitutes a matchless living system in the study of the role of alternative sigma factors in gene regulation and physiology. SigB from B. subtilis was the first alternative sigma factor described in bacteria. Studies of SigB during the last 40 years have shown that it controls a genetic universe of more than 150 genes playing crucial roles in stress response, adaption, and survival. Activation of SigB relies on three separate pathways that specifically respond to energy, environmental, and low temperature stresses. SigB homologs, present in other Gram-positive bacteria, also play important roles in virulence against mammals. Interestingly, during recent years, other unexpected B. subtilis responses were found to be controlled by SigB. In particular, SigB controls the efficiencies of spore and biofilm formation, two important features that play critical roles in adaptation and survival in planktonic and sessile B. subtilis communities. In B. subtilis, SigB induces the expression of the Spo0E aspartyl-phosphatase, which is responsible for the blockage of sporulation initiation. The upregulated activity of Spo0E connects the two predominant adaptive pathways (i.e., sporulation and stress response) present in B. subtilis. In addition, the RsbP serine-phosphatase, belonging to the energy stress arm of the SigB regulatory cascade, controls the expression of the key transcription factor SinR to decide whether cells residing in the biofilm remain in and maintain biofilm growth or scape to colonize new niches through biofilm dispersal. SigB also intervenes in the recognition of and response to surrounding microorganisms, a new SigB role that could have an agronomic impact. SigB is induced when B. subtilis is confronted with phytopathogenic fungi (e.g., Fusarium verticillioides) and halts fungal growth to the benefit of plant growth. In this article, we update and review literature on the different regulatory networks that control the activation of SigB and the new roles that have been described the recent years.
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Affiliation(s)
- Facundo Rodriguez Ayala
- Departamento de Micro y Nanotecnología, Instituto de Nanociencia y Nanotecnología - Comisión Nacional de Energía Atómica (CNEA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marco Bartolini
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Roberto Grau
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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23
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Kolich LR, Chang YT, Coudray N, Giacometti SI, MacRae MR, Isom GL, Teran EM, Bhabha G, Ekiert DC. Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation. eLife 2020; 9:e60030. [PMID: 32602838 PMCID: PMC7367683 DOI: 10.7554/elife.60030] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
ABC transporters facilitate the movement of diverse molecules across cellular membranes, but how their activity is regulated post-translationally is not well understood. Here we report the crystal structure of MlaFB from E. coli, the cytoplasmic portion of the larger MlaFEDB ABC transporter complex, which drives phospholipid trafficking across the bacterial envelope to maintain outer membrane integrity. MlaB, a STAS domain protein, binds the ABC nucleotide binding domain, MlaF, and is required for its stability. Our structure also implicates a unique C-terminal tail of MlaF in self-dimerization. Both the C-terminal tail of MlaF and the interaction with MlaB are required for the proper assembly of the MlaFEDB complex and its function in cells. This work leads to a new model for how an important bacterial lipid transporter may be regulated by small proteins, and raises the possibility that similar regulatory mechanisms may exist more broadly across the ABC transporter family.
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Affiliation(s)
- Ljuvica R Kolich
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Ya-Ting Chang
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolas Coudray
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
- Applied Bioinformatics Laboratory, New York University School of MedicineNew YorkUnited States
| | - Sabrina I Giacometti
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Mark R MacRae
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Georgia L Isom
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Evelyn M Teran
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Gira Bhabha
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
- Department of Microbiology, New York University School of MedicineNew YorkUnited States
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24
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Steinberg N, Keren-Paz A, Hou Q, Doron S, Yanuka-Golub K, Olender T, Hadar R, Rosenberg G, Jain R, Cámara-Almirón J, Romero D, van Teeffelen S, Kolodkin-Gal I. The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms. Sci Signal 2020; 13:13/632/eaaw8905. [PMID: 32430292 DOI: 10.1126/scisignal.aaw8905] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In nature, bacteria form biofilms-differentiated multicellular communities attached to surfaces. Within these generally sessile biofilms, a subset of cells continues to express motility genes. We found that this subpopulation enabled Bacillus subtilis biofilms to expand on high-friction surfaces. The extracellular matrix (ECM) protein TasA was required for the expression of flagellar genes. In addition to its structural role as an adhesive fiber for cell attachment, TasA acted as a developmental signal stimulating a subset of biofilm cells to revert to a motile phenotype. Transcriptomic analysis revealed that TasA stimulated the expression of a specific subset of genes whose products promote motility and repress ECM production. Spontaneous suppressor mutations that restored motility in the absence of TasA revealed that activation of the biofilm-motility switch by the two-component system CssR/CssS antagonized the TasA-mediated reversion to motility in biofilm cells. Our results suggest that although mostly sessile, biofilms retain a degree of motility by actively maintaining a motile subpopulation.
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Affiliation(s)
- Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Department of Microbiology, Institute Pasteur, Paris, France
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Yanuka-Golub
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Hadar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rakeshkumar Jain
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jesus Cámara-Almirón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | | | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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25
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Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms. Nat Commun 2020; 11:950. [PMID: 32075967 PMCID: PMC7031267 DOI: 10.1038/s41467-020-14431-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/17/2019] [Indexed: 12/27/2022] Open
Abstract
Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σB in individual cells during biofilm development. Both σB and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σB represses sporulation. As predicted by a simple mathematical model, increasing σB expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development. Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.
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26
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He K, Xin YP, Shan Y, Zhang X, Song HH, Fang WH. Phosphorylation residue T175 in RsbR protein is required for efficient induction of sigma B factor and survival of Listeria monocytogenes under acidic stress. J Zhejiang Univ Sci B 2020; 20:660-669. [PMID: 31273963 DOI: 10.1631/jzus.b1800551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Listeria monocytogenes is an important zoonotic foodborne pathogen that can tolerate a number of environmental stresses. RsbR, an upstream regulator of the sigma B (SigB) factor, is thought to sense environmental challenges and trigger the SigB pathway. In Bacillus subtilis, two phosphorylation sites in RsbR are involved in activating the SigB pathway and a feedback mechanism, respectively. In this study, the role of RsbR in L. monocytogenes under mild and severe stresses was investigated. Strains with genetic deletion (ΔrsbR), complementation (C-ΔrsbR), and phosphorylation site mutations in the rsbR (RsbR-T175A, RsbR-T209A, and RsbR-T175A-T209A) were constructed to evaluate the roles of these RsbR sequences in listerial growth and survival. SigB was examined at the transcriptional and translational levels. Deletion of rsbR reduced listerial growxth and survival in response to acidic stress. Substitution of the phosphorylation residue RsbR-T175A disabled RsbR complementation, while RsbR-T209A significantly upregulated SigB expression and listerial survival. Our results provide clear evidence that two phosphorylation sites of RsbR are functional in L. monocytogenes under acidic conditions, similar to the situation in B. subtilis.
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Affiliation(s)
- Ke He
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an 311300, China.,Zhejiang University Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Yong-Ping Xin
- Zhejiang University Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Ying Shan
- Zhejiang University Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
| | - Xian Zhang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an 311300, China
| | - Hou-Hui Song
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an 311300, China
| | - Wei-Huan Fang
- College of Animal Science and Technology, Zhejiang A&F University, Lin'an 311300, China.,Zhejiang University Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
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27
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Dyer SW, Needoba JA. Use of High-Resolution Pressure Nephelometry To Measure Gas Vesicle Collapse as a Means of Determining Growth and Turgor Changes in Planktonic Cyanobacteria. Appl Environ Microbiol 2020; 86:e01790-19. [PMID: 31676479 PMCID: PMC6952233 DOI: 10.1128/aem.01790-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/27/2019] [Indexed: 01/10/2023] Open
Abstract
Previous work has demonstrated that the physical properties of intracellular bacterial gas vesicles (GVs) can be analyzed in vivo using pressure nephelometry. In analyzing the buoyant state of GV-containing cyanobacteria, hydrostatic pressure within a sample cell is increased in a stepwise manner, where the concomitant collapse of GVs due to pressure and the resultant decrease in suspended cells are detected by changes in nephelometric scattering. As the relative pressure at which GVs collapse is a function of turgor pressure and cellular osmotic gradients, pressure nephelometry is a powerful tool for assaying changes in metabolism that affect turgor, such as photosynthetic and osmoregulatory processes. We have developed an updated and automated pressure nephelometer that utilizes visible-infrared (Vis-IR) spectra to accurately quantify GV critical collapse pressure, critical collapse pressure distribution, and cell turgor pressure. Here, using the updated pressure nephelometer and axenic cultures of Microcystis aeruginosa PCC7806, we demonstrate that GV critical collapse pressure is stable during mid-exponential growth phase, introduce pressure-sensitive turbidity as a robust metric for the abundance of gas-vacuolate cyanobacteria, and demonstrate that pressure-sensitive turbidity is a more accurate proxy for abundance and growth than photopigment fluorescence. As cyanobacterium-dominated harmful algal bloom (cyanoHAB) formation is dependent on the constituent cells possessing gas vesicles, characterization of environmental cyanobacteria populations via pressure nephelometry is identified as an underutilized monitoring method. Applications of this instrument focus on physiological and ecological studies of cyanobacteria, for example, cyanoHAB dynamics and the drivers associated with cyanotoxin production in aquatic ecosystems.IMPORTANCE The increased prevalence of bloom-forming cyanobacteria and associated risk of exposure to cyanobacterial toxins through drinking water utilities and recreational waterways are growing public health concerns. Cost-effective, early-detection methodologies specific to cyanobacteria are crucial for mitigating these risks, with a gas vesicle-specific signal offering a number of benefits over photopigment fluorescence, including improved detection limits and discrimination against non-gas-vacuolate phototrophs. Here, we present a multiplexed instrument capable of quantifying the relative abundance of cyanobacteria based on the signal generated from the presence of intracellular gas vesicles specific to bloom-forming cyanobacteria. Additionally, as cell turgor can be measured in vivo via pressure nephelometry, the measurement furnishes information about the internal osmotic pressure of gas-vacuolate cyanobacteria, which relates to the metabolic state of the cell. Together these advances may improve routine waterway monitoring and the mitigation of human health threats due to cyanobacterial blooms.
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Affiliation(s)
- Stuart W Dyer
- Oregon Health and Science University, Institute of Environmental Health, Portland, Oregon, USA
- Oregon Health and Science University-Portland State University, School of Public Health, Portland, Oregon, USA
| | - Joseph A Needoba
- Oregon Health and Science University, Institute of Environmental Health, Portland, Oregon, USA
- Oregon Health and Science University-Portland State University, School of Public Health, Portland, Oregon, USA
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28
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Dorey AL, Lee BH, Rotter B, O'Byrne CP. Blue Light Sensing in Listeria monocytogenes Is Temperature-Dependent and the Transcriptional Response to It Is Predominantly SigB-Dependent. Front Microbiol 2019; 10:2497. [PMID: 31798538 PMCID: PMC6874125 DOI: 10.3389/fmicb.2019.02497] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/16/2019] [Indexed: 11/17/2022] Open
Abstract
Listeria monocytogenes is an important food-borne pathogen that is tolerant to many of the stresses commonly used during food preservation. Outside the host, the bacterium has a saprophytic lifestyle that includes periodic exposure to solar irradiance. The blue component of this light is known to influence the activity of the stress-inducible sigma factor Sigma B (σB). In this study, the influence of temperature and growth phase on the response of L. monocytogenes to blue light was investigated and the global transcriptional response to blue light was elucidated using an RNAseq-based approach. Stationary phase cells were found to be significantly more resistant to killing by blue light (470 nm) than exponential phase cells. Temperature also had a marked effect on blue light resistance with cells cultured at 37°C being much more sensitive than cells grown at 30°C. The role of σB in light tolerance was confirmed but this effect was observed only at 30°C. σB activation by blue light was assessed by measuring the transcriptional response of known σB-dependent genes (sigB, lmo2230, and opuCA) to light. The transcripts were induced by blue light only at 30°C suggesting that blue light fails to activate σB at 37°C. The light-induced transcription at 30°C was dependent on a functional blue light sensor, Lmo0799 (which we rename herein as RsbL). A transcriptomic analysis of the response to sub-lethal levels of blue light found that the changes in transcription were almost entirely σB-dependent. A mutant where the light sensing mechanism of RsbL was inactivated through an amino acid substitution (Cys56Ala) was found to have an attenuated response to blue light, but residual activation of σB-dependent genes suggested that alternative routes for activation of σB by light are likely to exist. Overall, the study highlights the central role of σB in the response of this pathogen to visible light and further shows that light sensing is absent at temperatures that exist within the mammalian host.
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Affiliation(s)
- Amber L Dorey
- Microbiology, School of Natural Sciences, Bacterial Stress Response Group, National University of Ireland Galway, Galway, Ireland
| | | | | | - Conor P O'Byrne
- Microbiology, School of Natural Sciences, Bacterial Stress Response Group, National University of Ireland Galway, Galway, Ireland
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29
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Kwon E, Pathak D, Kim HU, Dahal P, Ha SC, Lee SS, Jeong H, Jeoung D, Chang HW, Jung HS, Kim DY. Structural insights into stressosome assembly. IUCRJ 2019; 6:938-947. [PMID: 31576226 PMCID: PMC6760441 DOI: 10.1107/s205225251900945x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/02/2019] [Indexed: 05/05/2023]
Abstract
The stressosome transduces environmental stress signals to SigB to upregulate SigB-dependent transcription, which is required for bacterial viability. The stressosome core is composed of RsbS and at least one of the RsbR paralogs. A previous cryo-electron microscopy (cryo-EM) structure of the RsbRA-RsbS complex determined under a D2 symmetry restraint showed that the stressosome core forms a pseudo-icosahedron consisting of 60 STAS domains of RsbRA and RsbS. However, it is still unclear how RsbS and one of the RsbR paralogs assemble into the stressosome. Here, an assembly model of the stressosome is presented based on the crystal structure of the RsbS icosahedron and cryo-EM structures of the RsbRA-RsbS complex determined under diverse symmetry restraints (nonsymmetric C1, dihedral D2 and icosahedral I envelopes). 60 monomers of the crystal structure of RsbS fitted well into the I-restrained cryo-EM structure determined at 4.1 Å resolution, even though the STAS domains in the I envelope were averaged. This indicates that RsbS and RsbRA share a highly conserved STAS fold. 22 protrusions observed in the C1 envelope, corresponding to dimers of the RsbRA N-domain, allowed the STAS domains of RsbRA and RsbS to be distinguished in the stressosome core. Based on these, the model of the stressosome core was reconstructed. The mutation of RsbRA residues at the binding interface in the model (R189A/Q191A) significantly reduced the interaction between RsbRA and RsbS. These results suggest that nonconserved residues in the conserved STAS folds between RsbS and RsbR paralogs determine stressosome assembly.
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Affiliation(s)
- Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Deepak Pathak
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Han-ul Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Pawan Dahal
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyeongseop Jeong
- Center for Electron Microscopy Research, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Hyeun Wook Chang
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
- Correspondence e-mail: ,
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
- Correspondence e-mail: ,
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30
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Hayashi K, Hirayama J, Goldsmith CE, Coulter WA, Millar BC, Dooley JSG, Loughrey A, Rooney PJ, Matsuda M, Moore JE. Exposure to clinical X-ray radiation does not alter antibiotic susceptibility or genotype profile in Gram-negative and Gram-positive clinical pathogens. Br J Biomed Sci 2019. [DOI: 10.1080/09674845.2012.12069137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K. Hayashi
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Japan
| | - J. Hirayama
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Japan
| | - C. E. Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
| | - W. A. Coulter
- School of Dentistry, The Queen's University of Belfast, Royal Group of Hospitals, Belfast
| | - B. C. Millar
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
| | - J. S. G. Dooley
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK
| | - A. Loughrey
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
| | - P. J. Rooney
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
| | - M. Matsuda
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Japan
| | - J. E. Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK
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31
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Tiensuu T, Guerreiro DN, Oliveira AH, O’Byrne C, Johansson J. Flick of a switch: regulatory mechanisms allowing Listeria monocytogenes to transition from a saprophyte to a killer. Microbiology (Reading) 2019; 165:819-833. [DOI: 10.1099/mic.0.000808] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Teresa Tiensuu
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS); Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Duarte N. Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Ana H. Oliveira
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS); Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Conor O’Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway H91 TK33, Ireland
| | - Jörgen Johansson
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS); Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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32
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Williams AH, Redzej A, Rolhion N, Costa TRD, Rifflet A, Waksman G, Cossart P. The cryo-electron microscopy supramolecular structure of the bacterial stressosome unveils its mechanism of activation. Nat Commun 2019; 10:3005. [PMID: 31285450 PMCID: PMC6614362 DOI: 10.1038/s41467-019-10782-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/22/2019] [Indexed: 01/18/2023] Open
Abstract
How the stressosome, the epicenter of the stress response in bacteria, transmits stress signals from the environment has remained elusive. The stressosome consists of multiple copies of three proteins RsbR, RsbS and RsbT, a kinase that is important for its activation. Using cryo-electron microscopy, we determined the atomic organization of the Listeria monocytogenes stressosome at 3.38 Å resolution. RsbR and RsbS are organized in a 60-protomers truncated icosahedron. A key phosphorylation site on RsbR (T209) is partially hidden by an RsbR flexible loop, whose "open" or "closed" position could modulate stressosome activity. Interaction between three glutamic acids in the N-terminal domain of RsbR and the membrane-bound mini-protein Prli42 is essential for Listeria survival to stress. Together, our data provide the atomic model of the stressosome core and highlight a loop important for stressosome activation, paving the way towards elucidating the mechanism of signal transduction by the stressosome in bacteria.
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Affiliation(s)
- Allison H Williams
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur, Groupe Avenir, INSERM, 75015, Paris, France.
| | - Adam Redzej
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK
| | - Nathalie Rolhion
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015, Paris, France.,Inserm, U604, 75015, Paris, France.,INRA, Unité sous-contrat 2020, 75015, Paris, France
| | - Tiago R D Costa
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK
| | - Aline Rifflet
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur, Groupe Avenir, INSERM, 75015, Paris, France
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck, London, WC1E 7HX, UK.
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, 75015, Paris, France. .,Inserm, U604, 75015, Paris, France. .,INRA, Unité sous-contrat 2020, 75015, Paris, France.
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33
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Tran V, Geraci K, Midili G, Satterwhite W, Wright R, Bonilla CY. Resilience to oxidative and nitrosative stress is mediated by the stressosome, RsbP and SigB in Bacillus subtilis. J Basic Microbiol 2019; 59:834-845. [PMID: 31210376 DOI: 10.1002/jobm.201900076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/10/2019] [Accepted: 05/11/2019] [Indexed: 01/19/2023]
Abstract
A bacterium's ability to thrive in the presence of multiple environmental stressors simultaneously determines its resilience. We showed that activation of the SigB-controlled general stress response by mild environmental or energy stress provided significant cross-protection to subsequent lethal oxidative, disulfide and nitrosative stress in Bacillus subtilis. SigB activation is mediated via the stressosome and RsbP, the main conduits of environmental and energy stress, respectively. Cells exposed to mild environmental stress while lacking the major stressosome components RsbT or RsbRA were highly sensitive to subsequent oxidative stress, whereas rsbRB, rsbRC, rsbRD, and ytvA null mutants showed a spectrum of sensitivity, confirming their redundant roles and suggesting they could modulate the signals generated by environmental or oxidative stress. By contrast, cells encountering stationary phase stress required RsbP but not RsbT to survive subsequent oxidative stress. Interestingly, optimum cross-protection against nitrosative stress caused by sodium nitropruside required SigB but not the known regulators, RsbT and RsbP, suggesting an additional and as yet uncharacterized route of SigB activation independent of the known regulators. Together, these results provide mechanistic information on how B. subtilis promotes enhanced resistance against lethal oxidative stress during mild environmental and energy stress conditions.
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Affiliation(s)
- Vina Tran
- Biology Department, Gonzaga University, Spokane, Washington
| | - Kara Geraci
- Biology Department, Gonzaga University, Spokane, Washington
| | | | | | - Rachel Wright
- Biology Department, Gonzaga University, Spokane, Washington
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34
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The σBsignalling activation pathway in the enteropathogenClostridioides difficile. Environ Microbiol 2019; 21:2852-2870. [DOI: 10.1111/1462-2920.14642] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 01/05/2023]
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35
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Tuning the Mycobacterium tuberculosis Alternative Sigma Factor SigF through the Multidomain Regulator Rv1364c and Osmosensory Kinase Protein Kinase D. J Bacteriol 2019; 201:JB.00725-18. [PMID: 30642988 DOI: 10.1128/jb.00725-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 01/02/2019] [Indexed: 12/20/2022] Open
Abstract
Bacterial alternative sigma factors are mostly regulated by a partner-switching mechanism. Regulation of the virulence-associated alternative sigma factor SigF of Mycobacterium tuberculosis has been an area of intrigue, with SigF having more predicted regulators than other sigma factors in this organism. Rv1364c is one such predicted regulator, the mechanism of which is confounded by the presence of both anti-sigma factor and anti-sigma factor antagonist functions in a single polypeptide. Using protein binding and phosphorylation assays, we demonstrate that the anti-sigma factor domain of Rv1364c mediates autophosphorylation of its antagonist domain and binds efficiently to SigF. Furthermore, we identified a direct role for the osmosensor serine/threonine kinase PknD in regulating the SigF-Rv1364c interaction, adding to the current understanding about the intersection of these discrete signaling networks. Phosphorylation of SigF also showed functional implications in its DNA binding ability, which may help in activation of the regulon. In M. tuberculosis, osmotic stress-dependent induction of espA, a SigF target involved in maintaining cell wall integrity, is curtailed upon overexpression of Rv1364c, showing its role as an anti-SigF factor. Overexpression of Rv1364c led to induction of another target, pks6, involved in lipid metabolism. This induction was, however, curtailed in the presence of osmotic stress conditions, suggesting modulation of SigF target gene expression via Rv1364c. These data provide evidence that Rv1364c acts an independent SigF regulator that is sensitive to the osmosensory signal, mediating the cross talk of PknD with the SigF regulon.IMPORTANCE Mycobacterium tuberculosis, capable of latently infecting the host and causing aggressive tissue damage during active tuberculosis, is endowed with a complex regulatory capacity built of several sigma factors, protein kinases, and phosphatases. These proteins regulate expression of genes that allow the bacteria to adapt to various host-derived stresses, like nutrient starvation, acidic pH, and hypoxia. The cross talk between these systems is not well understood. SigF is one such regulator of gene expression that helps M. tuberculosis to adapt to stresses and imparts virulence. This work provides evidence for its inhibition by the multidomain regulator Rv1364c and activation by the kinase PknD. The coexistence of negative and positive regulators of SigF in pathogenic bacteria reveals an underlying requirement for tight control of virulence factor expression.
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36
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de Ruiter MV, Klem R, Luque D, Cornelissen JJLM, Castón JR. Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis. NANOSCALE 2019; 11:4130-4146. [PMID: 30793729 DOI: 10.1039/c8nr09204d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.
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Affiliation(s)
- Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
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37
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Role and regulation of the stress activated sigma factor sigma B (σ B) in the saprophytic and host-associated life stages of Listeria monocytogenes. ADVANCES IN APPLIED MICROBIOLOGY 2019; 106:1-48. [PMID: 30798801 DOI: 10.1016/bs.aambs.2018.11.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The stress activated sigma factor sigma B (σB) plays a pivotal role in allowing the food-borne bacterial pathogen Listeria monocytogenes to modulate its transcriptional landscape in order to survive in a variety of harsh environments both outside and within the host. While we have a comparatively good understanding of the systems under the control of this sigma factor much less is known about how the activity of σB is controlled. In this review, we present a current model describing how this sigma factor is thought to be controlled including an overview of what is known about stress sensing and the early signal transduction events that trigger its activation. We discuss the known regulatory overlaps between σB and other protein and RNA regulators in the cell. Finally, we describe the role of σB in surviving both saprophytic and host-associated stresses. The complexity of the regulation of this sigma factor reflects the significant role that it plays in the persistence of this important pathogen in the natural environment, the food chain as well as within the host during the early stages of an infection. Understanding its regulation will be a critical step in helping to develop rational strategies to prevent its growth and survival in the food destined for human consumption and in the prevention of listeriosis.
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38
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Bouillet S, Arabet D, Jourlin-Castelli C, Méjean V, Iobbi-Nivol C. Regulation of σ factors by conserved partner switches controlled by divergent signalling systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:127-139. [PMID: 29393573 DOI: 10.1111/1758-2229.12620] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
Partner-Switching Systems (PSS) are widespread regulatory systems, each comprising a kinase-anti-σ, a phosphorylatable anti-σ antagonist and a phosphatase module. The anti-σ domain quickly sequesters or delivers the target σ factor according to the phosphorylation state of the anti-σ antagonist induced by environmental signals. The PSS components are proteins alone or merged to other domains probably to adapt to the input signals. PSS are involved in major cellular processes including stress response, sporulation, biofilm formation and pathogenesis. Surprisingly, the target σ factors are often unknown and the sensing modules acting upstream from the PSS diverge according to the bacterial species. Indeed, they belong to either two-component systems or complex pathways as the stressosome or Chemosensory Systems (CS). Based on a phylogenetic analysis, we propose that the sensing module in Gram-negative bacteria is often a CS.
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Affiliation(s)
- Sophie Bouillet
- Aix-Marseille University, CNRS, BIP UMR7281, 13402 Marseille, France
| | - Dallel Arabet
- Université des Frères Mentouri Constantine 1, Constantine, Algeria
| | | | - Vincent Méjean
- Aix-Marseille University, CNRS, BIP UMR7281, 13402 Marseille, France
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39
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Radoshevich L, Cossart P. Listeria monocytogenes: towards a complete picture of its physiology and pathogenesis. Nat Rev Microbiol 2018; 16:32-46. [PMID: 29176582 DOI: 10.1038/nrmicro.2017.126] [Citation(s) in RCA: 456] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Listeria monocytogenes is a food-borne pathogen responsible for a disease called listeriosis, which is potentially lethal in immunocompromised individuals. This bacterium, first used as a model to study cell-mediated immunity, has emerged over the past 20 years as a paradigm in infection biology, cell biology and fundamental microbiology. In this Review, we highlight recent advances in the understanding of human listeriosis and L. monocytogenes biology. We describe unsuspected modes of hijacking host cell biology, ranging from changes in organelle morphology to direct effects on host transcription via a new class of bacterial effectors called nucleomodulins. We then discuss advances in understanding infection in vivo, including the discovery of tissue-specific virulence factors and the 'arms race' among bacteria competing for a niche in the microbiota. Finally, we describe the complexity of bacterial regulation and physiology, incorporating new insights into the mechanisms of action of a series of riboregulators that are critical for efficient metabolic regulation, antibiotic resistance and interspecies competition.
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Affiliation(s)
- Lilliana Radoshevich
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, F-75015 Paris, France
- Inserm, U604, F-75015 Paris, France
- French National Institute for Agricultural Research (INRA), Unité sous-contrat 2020, F-75015 Paris, France
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
| | - Pascale Cossart
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, F-75015 Paris, France
- Inserm, U604, F-75015 Paris, France
- French National Institute for Agricultural Research (INRA), Unité sous-contrat 2020, F-75015 Paris, France
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40
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D'Imprima E, Salzer R, Bhaskara RM, Sánchez R, Rose I, Kirchner L, Hummer G, Kühlbrandt W, Vonck J, Averhoff B. Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus. eLife 2017; 6. [PMID: 29280731 PMCID: PMC5745081 DOI: 10.7554/elife.30483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/13/2017] [Indexed: 11/13/2022] Open
Abstract
Secretins form multimeric channels across the outer membrane of Gram-negative bacteria that mediate the import or export of substrates and/or extrusion of type IV pili. The secretin complex of Thermus thermophilus is an oligomer of the 757-residue PilQ protein, essential for DNA uptake and pilus extrusion. Here, we present the cryo-EM structure of this bifunctional complex at a resolution of ~7 Å using a new reconstruction protocol. Thirteen protomers form a large periplasmic domain of six stacked rings and a secretin domain in the outer membrane. A homology model of the PilQ protein was fitted into the cryo-EM map. A crown-like structure outside the outer membrane capping the secretin was found not to be part of PilQ. Mutations in the secretin domain disrupted the crown and abolished DNA uptake, suggesting a central role of the crown in natural transformation.
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Affiliation(s)
- Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ralf Salzer
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ricardo Sánchez
- Sofja Kovalevskaja Group, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Ilona Rose
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Lennart Kirchner
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt, Germany.,Institute of Biophysics, Goethe University Frankfurt, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Janet Vonck
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
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41
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Duval M, Cossart P. Small bacterial and phagic proteins: an updated view on a rapidly moving field. Curr Opin Microbiol 2017; 39:81-88. [PMID: 29111488 DOI: 10.1016/j.mib.2017.09.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/17/2017] [Indexed: 01/21/2023]
Abstract
Small proteins, that is, polypeptides of 50 amino acids (aa) or less, are increasingly recognized as important regulators in bacteria. Secreted or not, their small size make them versatile proteins, involved in a wide range of processes. They may allow bacteria to sense and to respond to stresses, to send signals and communicate, and to modulate infections. Bacteriophages also produce small proteins to influence lysogeny/lysis decisions. In this review, we update the present view on small proteins functions, and discuss their possible applications.
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Affiliation(s)
- Mélodie Duval
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris F-75015, France; Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France; Institut National de la Recherche Agronomique, Unité Sous Contrat 2020, Paris F-75015, France.
| | - Pascale Cossart
- Unité des Interactions Bactéries-Cellules, Institut Pasteur, Paris F-75015, France; Institut National de la Santé et de la Recherche Médicale, U604, Paris F-75015, France; Institut National de la Recherche Agronomique, Unité Sous Contrat 2020, Paris F-75015, France.
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42
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Chen JC, Chang CF, Hsu DW, Shu JC, Chen HY, Chen CY, Lu CY, Chen CC. Temporal regulation of σ B by partner-switching mechanism at a distinct growth stage in Bacillus cereus. Int J Med Microbiol 2017; 307:521-532. [PMID: 28919098 DOI: 10.1016/j.ijmm.2017.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/15/2017] [Accepted: 09/04/2017] [Indexed: 12/01/2022] Open
Abstract
The alternative transcription factor σB in Bacillus cereus governs the transcription of a number of genes that confer protection against general stress. This transcription factor is regulated by protein-protein interactions among RsbV, RsbW, σB, RsbY, RsbM and RsbK, all encoded in the sigB cluster. Among these regulatory proteins, RsbV, RsbW and σB comprise a partner-switching mechanism. Under normal conditions, σB remains inactive by associating with anti-sigma factor RsbW, which prevents σB from binding to the core RNA polymerase. During environmental stress, RsbK activates RsbY to hydrolyze phosphorylated RsbV, and the dephosphorylated RsbV then sequesters RsbW to liberate σB from RsbW. Although the σB partner-switching module is thought to be the core mechanism for σB regulation, the actual protein-protein interactions among these three proteins in the cell remain to be investigated. In the current study, we show that RsbW and RsbV form a long-lived complex under transient stress treatment, resulting in high persistent expression of RsbV, RsbW and σB from mid-log phase to stationary phase. Full sequestration of RsbW by excess RsbV and increased RsbW:RsbV complex stability afforded by cellular ADP contribute to the prolonged activation of σB. Interestingly, the high expression levels of RsbV, RsbW and σB were dramatically decreased beginning from the transition stage to the stationary phase. Thus, protein interactions among σB partner-switching components are required for the continued induction of σB during environmental stress in the log phase and significant down-regulation of σB is observed in the stationary phase. Our data show that σB is temporally regulated in B. cereus.
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Affiliation(s)
- Jung-Chi Chen
- Department of Biotechnology, National Kaohsiung Normal University, 62 Shenjhong Road, Yanchao District, Kaohsiung 82444, Taiwan
| | - Chuan-Fu Chang
- Department of Biotechnology, National Kaohsiung Normal University, 62 Shenjhong Road, Yanchao District, Kaohsiung 82444, Taiwan
| | - Duen-Wei Hsu
- Department of Biotechnology, National Kaohsiung Normal University, 62 Shenjhong Road, Yanchao District, Kaohsiung 82444, Taiwan
| | - Jwu-Ching Shu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan County 333, Taiwan
| | - Hong-Yi Chen
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Wen-Hwa 1st Road, Kwei-Shan, Tao-Yuan County 333, Taiwan
| | - Chien-Yen Chen
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi 62102, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, 62 Shenjhong Road, Yanchao District, Kaohsiung 82444, Taiwan.
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Abstract
BrisSynBio is the Bristol-based Biotechnology and Biological Sciences Research Council (BBSRC)/Engineering and Physical Sciences Research Council (EPSRC)-funded Synthetic Biology Research Centre. It is one of six such Centres in the U.K. BrisSynBio's emphasis is on rational and predictive bimolecular modelling, design and engineering in the context of synthetic biology. It trains the next generation of synthetic biologists in these approaches, to facilitate translation of fundamental synthetic biology research to industry and the clinic, and to do this within an innovative and responsible research framework.
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44
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Abstract
The discovery of the globin-coupled sensor (GCS) family of haem proteins has provided new insights into signalling proteins and pathways by which organisms sense and respond to changing oxygen levels. GCS proteins consist of a sensor globin domain linked to a variety of output domains, suggesting roles in controlling numerous cellular pathways, and behaviours in response to changing oxygen concentration. Members of this family of proteins have been identified in the genomes of numerous organisms and characterization of GCS with output domains, including methyl accepting chemotaxis proteins, kinases, and diguanylate cyclases, have yielded an understanding of the mechanism by which oxygen controls activity of GCS protein output domains, as well as downstream proteins and pathways regulated by GCS signalling. Future studies will expand our understanding of these proteins both in vitro and in vivo, likely demonstrating broad roles for GCS in controlling oxygen-dependent microbial physiology and phenotypes.
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45
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Cabeen MT, Russell JR, Paulsson J, Losick R. Use of a microfluidic platform to uncover basic features of energy and environmental stress responses in individual cells of Bacillus subtilis. PLoS Genet 2017; 13:e1006901. [PMID: 28727759 PMCID: PMC5542698 DOI: 10.1371/journal.pgen.1006901] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/03/2017] [Accepted: 06/29/2017] [Indexed: 11/19/2022] Open
Abstract
Bacteria use a variety of stress-sensing systems to sense and respond to diverse stressors and to ensure their survival under adverse conditions. The gram-positive bacterium Bacillus subtilis responds to energy stress (ATP depletion) and to environmental stressors using two distinct stress-sensing pathways that converge on the alternative sigma factor σB to provoke a general stress response. Past efforts to study the σB stress response in bulk culture and on agarose pads were unable to visualize the responses of individual cells under tightly controlled conditions for extended periods of time. Here we use a microfluidics-based strategy to discern the basic features of σB activation in single cells in response to energy and environmental stress, both immediately upon stressor exposure and for tens of generations thereafter. Upon energy stress at various levels of stressor, cells exhibited fast, transient, and amplitude-modulated responses but not frequency modulation as previously reported. Upon environmental stress, which is mediated by the stressosome complex, wild-type cells primarily exhibited a transient and amplitude-modulated response. However, mutant cells producing only one of the four paralogous RsbR stressosome proteins showed striking and previously unseen differences. Whereas RsbRA-only cells mimicked the wild type, RsbRC-only cells displayed a slower but sustained overall response composed of repeated activation events in single cells.
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Affiliation(s)
- Matthew T. Cabeen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jonathan R. Russell
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
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46
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A Mutation in the Bacillus subtilis rsbU Gene That Limits RNA Synthesis during Sporulation. J Bacteriol 2017; 199:JB.00212-17. [PMID: 28461450 DOI: 10.1128/jb.00212-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
Abstract
Mutants of Bacillis subtilis that are temperature sensitive for RNA synthesis during sporulation were isolated after selection with a 32P suicide agent. Whole-genome sequencing revealed that two of the mutants carried an identical lesion in the rsbU gene, which encodes a phosphatase that indirectly activates SigB, the stress-responsive RNA polymerase sigma factor. The mutation appeared to cause RsbU to be hyperactive, because the mutants were more resistant than the parent strain to ethanol stress. In support of this hypothesis, pseudorevertants that regained wild-type levels of sporulation at high temperature had secondary mutations that prevented expression of the mutant rsbU gene. The properties of these RsbU mutants support the idea that activation of SigB diminishes the bacterium's ability to sporulate.IMPORTANCE Most bacterial species encode multiple RNA polymerase promoter recognition subunits (sigma factors). Each sigma factor directs RNA polymerase to different sets of genes; each gene set typically encodes proteins important for responses to specific environmental conditions, such as changes in temperature, salt concentration, and nutrient availability. A selection for mutants of Bacillus subtilis that are temperature sensitive for RNA synthesis during sporulation unexpectedly yielded strains with a point mutation in rsbU, a gene that encodes a protein that normally activates sigma factor B (SigB) under conditions of salt stress. The mutation appears to cause RsbU, and therefore SigB, to be active inappropriately, thereby inhibiting, directly or indirectly, the ability of the cells to transcribe sporulation genes.
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47
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Su H, Lin J, Wang Y, Chen Q, Wang G, Tan F. Engineering Brevibacterium flavum
for the production of renewable bioenergy: C4-C5 advanced alcohols. Biotechnol Bioeng 2017; 114:1946-1958. [DOI: 10.1002/bit.26324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 12/30/2022]
Affiliation(s)
- HaiFeng Su
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - JiaFu Lin
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province; Sichuan Industrial Institute of Antibiotics, Chengdu University; Chengdu P. R. China
| | - YuanHong Wang
- Center of Analysis and Testing; School of Public Health; Institute of Analytical Chemistry for Life Science; Nantong University; Nantong P. R. China
| | - Qiao Chen
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - GuangWei Wang
- Chongqing Institute of Green and Interligent Technology; Chinese Academy of Science; 266, Fangzheng Avenue, Shuitu High-Tech Park, Beibei Chongqing 400714 P. R. China
| | - FuRong Tan
- Biogas Institute of Ministry of Agriculture; Chengdu 610041 Sichuan P. R. China
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48
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Bremer E. Clostridium difficile: A bad bug goes into defensive mode. Environ Microbiol 2017; 19:2523-2528. [PMID: 28447375 DOI: 10.1111/1462-2920.13776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von Frisch Str. 8, Marburg, D-35043, Germany.,LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str. 6, Marburg, D-35043, Germany
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49
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Impens F, Rolhion N, Radoshevich L, Bécavin C, Duval M, Mellin J, García Del Portillo F, Pucciarelli MG, Williams AH, Cossart P. N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes. Nat Microbiol 2017; 2:17005. [PMID: 28191904 DOI: 10.1038/nmicrobiol.2017.5] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/04/2017] [Indexed: 12/25/2022]
Abstract
To adapt to changing environments, bacteria have evolved numerous pathways that activate stress response genes. In Gram-positive bacteria, the stressosome, a cytoplasmic complex, relays external cues and activates the sigma B regulon. The stressosome is structurally well-characterized in Bacillus, but how it senses stress remains elusive. Here, we report a genome-wide N-terminomic approach in Listeria that strikingly led to the discovery of 19 internal translation initiation sites and 6 miniproteins, among which one, Prli42, is conserved in Firmicutes. Prli42 is membrane-anchored and interacts with orthologues of Bacillus stressosome components. We reconstituted the Listeria stressosome in vitro and visualized its supramolecular structure by electron microscopy. Analysis of a series of Prli42 mutants demonstrated that Prli42 is important for sigma B activation, bacterial growth following oxidative stress and for survival in macrophages. Taken together, our N-terminonic approach unveiled Prli42 as a long-sought link between stress and the stressosome.
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Affiliation(s)
- Francis Impens
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | - Nathalie Rolhion
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | - Lilliana Radoshevich
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | - Christophe Bécavin
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France.,Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Mélodie Duval
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | - Jeffrey Mellin
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
| | | | - M Graciela Pucciarelli
- Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.,Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC), Madrid, Spain
| | - Allison H Williams
- Département de Microbiologie, Institut Pasteur, Unité des Biologie et génétique de la paroi bactérienne, F-75015 Paris, France.,INSERM, Groupe Avenir, F-75015 Paris, France
| | - Pascale Cossart
- Département de Biologie Cellulaire et Infection, Institut Pasteur, Unité des Interactions Bactéries-Cellules, F-75015 Paris, France.,Inserm, U604, F-75015 Paris, France.,INRA, Unité sous-contrat 2020, F-75015 Paris, France
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50
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Abstract
The stressosome is a multi-protein signal integration and transduction hub found in a wide range of bacterial species. The role that the stressosome plays in regulating the transcription of genes involved in the general stress response has been studied most extensively in the Gram-positive model organism Bacillus subtilis. The stressosome receives and relays the signal(s) that initiate a complex phosphorylation-dependent partner switching cascade, resulting in the activation of the alternative sigma factor σB. This sigma factor controls transcription of more than 150 genes involved in the general stress response. X-ray crystal structures of individual components of the stressosome and single-particle cryo-EM reconstructions of stressosome complexes, coupled with biochemical and single cell analyses, have permitted a detailed understanding of the dynamic signalling behaviour that arises from this multi-protein complex. Furthermore, bioinformatics analyses indicate that genetic modules encoding key stressosome proteins are found in a wide range of bacterial species, indicating an evolutionary advantage afforded by stressosome complexes. Interestingly, the genetic modules are associated with a variety of signalling modules encoding secondary messenger regulation systems, as well as classical two-component signal transduction systems, suggesting a diversification in function. In this chapter we review the current research into stressosome systems and discuss the functional implications of the unique structure of these signalling complexes.
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