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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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Guerreiro DN, Pucciarelli MG, Tiensuu T, Gudynaite D, Boyd A, Johansson J, García-del Portillo F, O’Byrne CP. Acid stress signals are integrated into the σB-dependent general stress response pathway via the stressosome in the food-borne pathogen Listeria monocytogenes. PLoS Pathog 2022; 18:e1010213. [PMID: 35275969 PMCID: PMC8942246 DOI: 10.1371/journal.ppat.1010213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/23/2022] [Accepted: 02/28/2022] [Indexed: 12/17/2022] Open
Abstract
The general stress response (GSR) in Listeria monocytogenes plays a critical role in the survival of this pathogen in the host gastrointestinal tract. The GSR is regulated by the alternative sigma factor B (σB), whose role in protection against acid stress is well established. Here, we investigated the involvement of the stressosome, a sensory hub, in transducing low pH signals to induce the GSR. Mild acid shock (15 min at pH 5.0) activated σB and conferred protection against a subsequent lethal pH challenge. A mutant strain where the stressosome subunit RsbR1 was solely present retained the ability to induce σB activity at pH 5.0. The role of stressosome phosphorylation in signal transduction was investigated by mutating the putative phosphorylation sites in the core stressosome proteins RsbR1 (rsbR1-T175A, -T209A, -T241A) and RsbS (rsbS-S56A), or the stressosome kinase RsbT (rsbT-N49A). The rsbS S56A and rsbT N49A mutations abolished the response to low pH. The rsbR1-T209A and rsbR1-T241A mutants displayed constitutive σB activity. Mild acid shock upregulates invasion genes inlAB and stimulates epithelial cell invasion, effects that were abolished in mutants with an inactive or overactive stressosome. Overall, the results show that the stressosome is required for acid-induced activation of σB in L. monocytogenes. Furthermore, they show that RsbR1 can function independently of its paralogues and signal transduction requires RsbT-mediated phosphorylation of RsbS on S56 and RsbR1 on T209 but not T175. These insights shed light on the mechanisms of signal transduction that activate the GSR in L. monocytogenes in response to acidic environments, and highlight the role this sensory process in the early stages of the infectious cycle. The stress sensing hub known as the stressosome, found in many bacterial and archaeal lineages, plays a crucial role in both stress tolerance and virulence in the food-borne pathogen Listeria monocytogenes. However, the mechanisms that lead to its activation and the subsequent activation of the general stress response have remained elusive. In this study, we examined the signal transduction mechanisms that operate in the stressosome in response to acid stress. We found that only one of the five putative sensory proteins present in L. monocytogenes, RsbR1, was required for effective transduction of acid tress signals. We further found that phosphorylation of RsbS and RsbR1, mediated by the RsbT kinase, is essential for signal transduction. Failure to phosphorylate RsbS on Serine 56 completely abolished acid sensing by the stressosome, which prevented the development of adaptive acid tolerance. The acid-induced activation of internalin gene expression was also abolished in mutants with defective stressosome signalling, suggesting a role for the stressosome in the invasion of host cells. Together the data provide new insights into the mechanisms that activate the stressosome in response to acid stress and highlight the role this sensory hub plays in virulence.
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Affiliation(s)
- Duarte N. Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
| | - M. Graciela Pucciarelli
- Laboratory of Intracellular Bacterial Pathogens, National Centre for Biotechnology (CNB)-CSIC, Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de Madrid, Centre of Molecular Biology ‘Severo Ochoa’ (CBMSO CSIC-UAM), Madrid, Spain
| | - Teresa Tiensuu
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre of Microbial Research, Umeå, Sweden
| | - Diana Gudynaite
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
| | - Aoife Boyd
- Pathogenic Mechanisms Research Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jörgen Johansson
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre of Microbial Research, Umeå, Sweden
| | | | - Conor P. O’Byrne
- Bacterial Stress Response Group, Microbiology, School of Biological and Chemical Sciences, National University of Ireland, Galway, Ireland
- * E-mail:
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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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Tran HT, Bonilla CY. SigB-regulated antioxidant functions in gram‐positive bacteria. World J Microbiol Biotechnol 2021; 37:38. [DOI: 10.1007/s11274-021-03004-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
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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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Guerreiro DN, Arcari T, O'Byrne CP. The σ B-Mediated General Stress Response of Listeria monocytogenes: Life and Death Decision Making in a Pathogen. Front Microbiol 2020; 11:1505. [PMID: 32733414 PMCID: PMC7358398 DOI: 10.3389/fmicb.2020.01505] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/10/2020] [Indexed: 12/17/2022] Open
Abstract
Sensing and responding to environmental cues is critical for the adaptability and success of the food-borne bacterial pathogen Listeria monocytogenes. A supramolecular multi-protein complex known as the stressosome, which acts as a stress sensing hub, is responsible for orchestrating the activation of a signal transduction pathway resulting in the activation of σB, the sigma factor that controls the general stress response (GSR). When σB is released from the anti-sigma factor RsbW, a rapid up-regulation of the large σB regulon, comprised of ≥ 300 genes, ensures that cells respond appropriately to the new environmental conditions. A diversity of stresses including low pH, high osmolarity, and blue light are known to be sensed by the stressosome, resulting in a generalized increase in stress resistance. Appropriate activation of the stressosome and deployment of σB are critical to fitness as there is a trade-off between growth and stress protection when the GSR is deployed. We review the recent developments in this field and describe an up-to-date model of how this sensory organelle might integrate environmental signals to produce an appropriate activation of the GSR. Some of the outstanding questions and challenges in this fascinating field are also discussed.
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Affiliation(s)
- Duarte N Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Talia Arcari
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Conor P O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
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Guerreiro DN, Wu J, Dessaux C, Oliveira AH, Tiensuu T, Gudynaite D, Marinho CM, Boyd A, García-Del Portillo F, Johansson J, O'Byrne CP. Mild Stress Conditions during Laboratory Culture Promote the Proliferation of Mutations That Negatively Affect Sigma B Activity in Listeria monocytogenes. J Bacteriol 2020; 202:e00751-19. [PMID: 32094160 PMCID: PMC7148139 DOI: 10.1128/jb.00751-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/01/2020] [Indexed: 12/18/2022] Open
Abstract
In Listeria monocytogenes, the full details of how stress signals are integrated into the σB regulatory pathway are not yet available. To help shed light on this question, we investigated a collection of transposon mutants that were predicted to have compromised activity of the alternative sigma factor B (σB). These mutants were tested for acid tolerance, a trait that is known to be under σB regulation, and they were found to display increased acid sensitivity, similar to a mutant lacking σB (ΔsigB). The transposon insertions were confirmed by whole-genome sequencing, but in each case, the strains were also found to carry a frameshift mutation in the sigB operon. The changes were predicted to result in premature stop codons, with negative consequences for σB activation, independently of the transposon location. Reduced σB activation in these mutants was confirmed. Growth measurements under conditions similar to those used during the construction of the transposon library revealed that the frameshifted sigB operon alleles conferred a growth advantage at higher temperatures, during late exponential phase. Mixed-culture experiments at 42°C demonstrated that the loss of σB activity allowed mutants to take over a population of parental bacteria. Together, our results suggest that mutations affecting σB activity can arise during laboratory culture because of the growth advantage conferred by these mutations under mild stress conditions. The data highlight the significant cost of stress protection in this foodborne pathogen and emphasize the need for whole-genome sequence analysis of newly constructed strains to confirm the expected genotype.IMPORTANCE In the present study, we investigated a collection of Listeria monocytogenes strains that all carried sigB operon mutations. The mutants all had reduced σB activity and were found to have a growth advantage under conditions of mild heat stress (42°C). In mixed cultures, these mutants outcompeted the wild type when mild heat stress was present but not at an optimal growth temperature. An analysis of 22,340 published L. monocytogenes genome sequences found a high rate of premature stop codons present in genes positively regulating σB activity. Together, these findings suggest that the occurrence of mutations that attenuate σB activity can be favored under conditions of mild stress, probably highlighting the burden on cellular resources that stems from deploying the general stress response.
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Affiliation(s)
- Duarte N Guerreiro
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Jialun Wu
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Charlotte Dessaux
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology (CNB)-CSIC, Madrid, Spain
| | - Ana H Oliveira
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Teresa Tiensuu
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Diana Gudynaite
- Molecular Microbiology Department, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catarina M Marinho
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Université Bourgogne Franche-Conté, Dijon, France
- Institut National de la Recherche Agronomique, UMR Agroécologie, Dijon, France
| | - Aoife Boyd
- Pathogenic Mechanisms Research Group, National University of Ireland, Galway, Ireland
| | | | - Jörgen Johansson
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Center of Microbial Research, Umeå, Sweden
| | - Conor P O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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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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Fan K, Yuan S, Chen J, Chen Y, Li Z, Lin W, Zhang Y, Liu J, Lin W. Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays. PLANTA 2019; 250:1521-1538. [PMID: 31346803 DOI: 10.1007/s00425-019-03243-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/16/2019] [Indexed: 05/19/2023]
Abstract
97 ZmPP2Cs were clustered into 10 subfamilies with biased subfamily evolution and lineage-specific expansion. Segmental duplication after the divergence of maize and sorghum might have led to primary expansion of ZmPP2Cs. The protein phosphatase 2C (PP2C) enzymes control many stress responses and developmental processes in plants. In Zea mays, a comprehensive understanding of the evolution and expansion of the PP2C family is still lacking. In the current study, 97 ZmPP2Cs were identified and clustered into 10 subfamilies. Through the analysis of the PP2C family in monocots, the ZmPP2C subfamilies displayed biased subfamily molecular evolution and lineage-specific expansion, as evidenced by their differing numbers of member genes, expansion and evolutionary rates, conserved subdomains, chromosomal distributions, expression levels, responsive-regulatory elements and regulatory networks. Moreover, while segmental duplication events have caused the primary expansion of the ZmPP2Cs, the majority of their diversification occurred following the additional whole-genome duplication that took place after the divergence of maize and sorghum (Sorghum bicolor). After this event, the PP2C subfamilies showed asymmetric evolutionary rates, with the D, F2 and H subfamily likely the most closely to resemble its ancestral subfamily's genes. These findings could provide novel insights into the molecular evolution and expansion of the PP2C family in maize, and lay the foundation for the functional analysis of these enzymes in maize and related monocots.
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Affiliation(s)
- Kai Fan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Shuna Yuan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences/Danzhou Investigation and Experiment Station of Tropical Crops, Ministry of Agriculture, Danzhou, 571737, China
| | - Jie Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yunrui Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Zhaowei Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Weiwei Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Yongqiang Zhang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Jianping Liu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China
| | - Wenxiong Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Key Laboratory of Crop Ecology and Molecular Physiology (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, 35002, China.
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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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11
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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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12
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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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13
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Khitun A, Ness TJ, Slavoff SA. Small open reading frames and cellular stress responses. Mol Omics 2019; 15:108-116. [PMID: 30810554 DOI: 10.1039/c8mo00283e] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small open reading frames (smORFs) encoding polypeptides of less than 100 amino acids in eukaryotes (50 amino acids in prokaryotes) were historically excluded from genome annotation. However, recent advances in genomics, ribosome footprinting, and proteomics have revealed thousands of translated smORFs in genomes spanning evolutionary space. These smORFs can encode functional polypeptides, or act as cis-translational regulators. Herein we review evidence that some smORF-encoded polypeptides (SEPs) participate in stress responses in both prokaryotes and eukaryotes, and that some upstream ORFs (uORFs) regulate stress-responsive translation of downstream cistrons in eukaryotic cells. These studies provide insight into a regulated subclass of smORFs and suggest that at least some SEPs may participate in maintenance of cellular homeostasis under stress.
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Affiliation(s)
- Alexandra Khitun
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Travis J Ness
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Sarah A Slavoff
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA. and Department of Chemistry, Yale University, New Haven, CT 06520, USA and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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14
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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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15
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Ding Y, Lv J, Shi Y, Gao J, Hua J, Song C, Gong Z, Yang S. EGR2 phosphatase regulates OST1 kinase activity and freezing tolerance in Arabidopsis. EMBO J 2018; 38:embj.201899819. [PMID: 30429206 DOI: 10.15252/embj.201899819] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 10/04/2018] [Accepted: 10/19/2018] [Indexed: 01/08/2023] Open
Abstract
OST1 (open stomata 1) protein kinase plays a central role in regulating freezing tolerance in Arabidopsis; however, the mechanism underlying cold activation of OST1 remains unknown. Here, we report that a plasma membrane-localized clade-E growth-regulating 2 (EGR2) phosphatase interacts with OST1 and inhibits OST1 activity under normal conditions. EGR2 is N-myristoylated by N-myristoyltransferase NMT1 at 22°C, which is important for its interaction with OST1. Moreover, myristoylation of EGR2 is required for its function in plant freezing tolerance. Under cold stress, the interaction of EGR2 and NMT1 is attenuated, leading to the suppression of EGR2 myristoylation in plants. Plant newly synthesized unmyristoylated EGR2 has decreased binding ability to OST1 and also interferes with the EGR2-OST1 interaction under cold stress. Consequently, the EGR2-mediated inhibition of OST1 activity is released. Consistently, mutations of EGRs cause plant tolerance to freezing, whereas overexpression of EGR2 exhibits decreased freezing tolerance. This study thus unravels a molecular mechanism underlying cold activation of OST1 by membrane-localized EGR2 and suggests that a myristoyl switch on EGR2 helps plants to adapt to cold stress.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Lv
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yiting Shi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Junping Gao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jian Hua
- Department of Plant Biology, Cornell University, Ithaca, NY, USA
| | - Chunpeng Song
- Institute of Plant Stress Biology, Collaborative Innovation Center of Crop Stress Biology, Henan University, Kaifeng, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
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16
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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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17
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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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18
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Yu W, Chen Z, Shen L, Wang Y, Li Q, Yan S, Zhong CJ, He N. Proteomic profiling ofBacillus licheniformisreveals a stress response mechanism in the synthesis of extracellular polymeric flocculants. Biotechnol Bioeng 2015; 113:797-806. [DOI: 10.1002/bit.25838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Wencheng Yu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Zhen Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Yuanpeng Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Qingbiao Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
| | - Shan Yan
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
| | - Chuan-Jian Zhong
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering; Xiamen University; Xiamen PR China
- Department of Chemistry; State University of New York at Binghamton; Binghamton 13902 New York
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19
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van der Steen JB, Hellingwerf KJ. Activation of the General Stress Response of Bacillus subtilis by Visible Light. Photochem Photobiol 2015; 91:1032-45. [PMID: 26189730 DOI: 10.1111/php.12499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/25/2015] [Indexed: 12/20/2022]
Abstract
A key challenge for microbiology is to understand how evolution has shaped the wiring of regulatory networks. This is amplified by the paucity of information of power-spectra of physicochemical stimuli to which microorganisms are exposed. Future studies of genome evolution, driven by altered stimulus regimes, will therefore require a versatile signal transduction system that allows accurate signal dosing. Here, we review the general stress response of Bacillus subtilis, and its upstream signal transduction network, as a candidate system. It can be activated by red and blue light, and by many additional stimuli. Signal integration therefore is an intricate function of this system. The blue-light response is elicited via the photoreceptor YtvA, which forms an integral part of stressosomes, to activate expression of the stress regulon of B. subtilis. Signal transfer through this network can be assayed with reporter enzymes, while intermediate steps can be studied with live-cell imaging of fluorescently tagged proteins. Different parts of this system have been studied in vitro, such that its computational modeling has made significant progress. One can directly relate the microscopic characteristics of YtvA with activation of the general stress regulon, making this system a very well-suited system for network evolution studies.
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Affiliation(s)
- Jeroen B van der Steen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Fluoro-phenyl-styrene-sulfonamide, a novel inhibitor of σB activity, prevents the activation of σB by environmental and energy stresses in Bacillus subtilis. J Bacteriol 2013; 195:2509-17. [PMID: 23524614 DOI: 10.1128/jb.00107-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Sigma B (σ(B)) is an alternative sigma factor that regulates the general stress response in Bacillus subtilis and in many other Gram-positive organisms. σ(B) activity in B. subtilis is tightly regulated via at least three distinct pathways within a complex signal transduction cascade in response to a variety of stresses, including environmental stress, energy stress, and growth at high or low temperatures. We probed the ability of fluoro-phenyl-styrene-sulfonamide (FPSS), a small-molecule inhibitor of σ(B) activity in Listeria monocytogenes, to inhibit σ(B) activity in B. subtilis through perturbation of signal transduction cascades under various stress conditions. FPSS inhibited the activation of σ(B) in response to multiple categories of stress known to induce σ(B) activity in B. subtilis. Specifically, FPSS prevented the induction of σ(B) activity in response to energy stress, including entry into stationary phase, phosphate limitation, and azide stress. FPSS also inhibited chill induction of σ(B) activity in a ΔrsbV strain, suggesting that FPSS does not exclusively target the RsbU and RsbP phosphatases or the anti-anti-sigma factor RsbV, all of which contribute to posttranslational regulation of σ(B) activity. Genetic and biochemical experiments, including artificial induction of σ(B), analysis of the phosphorylation state of the anti-anti-sigma factor RsbV, and in vitro transcription assays, indicate that while FPSS does not bind directly to σ(B) to inhibit activity, it appears to prevent the release of B. subtilis σ(B) from its anti-sigma factor RsbW.
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Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O. Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT. BMC SYSTEMS BIOLOGY 2013; 7:3. [PMID: 23320651 PMCID: PMC3556497 DOI: 10.1186/1752-0509-7-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/07/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND The stressosome is a bacterial signalling complex that responds to environmental changes by initiating a protein partner switching cascade, which leads to the release of the alternative sigma factor, σB. Stress perception increases the phosphorylation of the stressosome sensor protein, RsbR, and the scaffold protein, RsbS, by the protein kinase, RsbT. Subsequent dissociation of RsbT from the stressosome activates the σB cascade. However, the sequence of physical events that occur in the stressosome during signal transduction is insufficiently understood. RESULTS Here, we use computational modelling to correlate the structure of the stressosome with the efficiency of the phosphorylation reactions that occur upon activation by stress. In our model, the phosphorylation of any stressosome protein is dependent upon its nearest neighbours and their phosphorylation status. We compare different hypotheses about stressosome activation and find that only the model representing the allosteric activation of the kinase RsbT, by phosphorylated RsbR, qualitatively reproduces the experimental data. CONCLUSIONS Our simulations and the associated analysis of published data support the following hypotheses: (i) a simple Boolean model is capable of reproducing stressosome dynamics, (ii) different stressors induce identical stressosome activation patterns, and we also confirm that (i) phosphorylated RsbR activates RsbT, and (ii) the main purpose of RsbX is to dephosphorylate RsbS-P.
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Affiliation(s)
- Ulf W Liebal
- Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, 18051, Rostock, Germany
| | - Thomas Millat
- Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, 18051, Rostock, Germany
| | - Jon Marles-Wright
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Institute of Structural and Molecular Biology, School of Biological Sciences, Edinburgh University, Edinburgh, EH9 3JR, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, 18051, Rostock, Germany
- Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, 7600, South Africa
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23
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Differentiation of function among the RsbR paralogs in the general stress response of Bacillus subtilis with regard to light perception. J Bacteriol 2012; 194:1708-16. [PMID: 22287516 DOI: 10.1128/jb.06705-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The general stress response of Bacillus subtilis can be activated by a wide range of signals, including low intensities of visible light. It is regulated by a dedicated σ factor via a complex signal transduction pathway that makes use of stressosomes: hetero-oligomeric complexes that include one or more of the RsbR proteins (RsbRA, RsbRB, RsbRC, and RsbRD). The response to blue light is mediated by the photoreceptor YtvA. We show here which of the four RsbR proteins are necessary for the activation of the σ(B) response by blue light. Experiments performed with single-, double-, and triple-deletion strains in the rsbR genes show that RsbRB and RsbRA function antagonistically, with the former being a negative regulator and the latter a positive regulator of the YtvA-dependent light activation of the stress response. A strain with RsbRB as the only RsbR protein is unable to respond to light-activation of σ(B). Furthermore, RsbRC and RsbRD can replace RsbRA's function only in the absence of RsbRB. This differentiation of function is confined to light stress, since strains with RsbRA or RsbRB as the only RsbR protein behave similarly in our experimental conditions in response to physicochemical stresses. Interestingly, RsbRB's absence is sufficient to result in light activation of the general stress response at wild-type expression levels of ytvA, while it was previously reported that YtvA could only activate σ(B) when overproduced, or when cells are supplemented with an additional environmental stress.
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Misra SK, Milohanic E, Aké F, Mijakovic I, Deutscher J, Monnet V, Henry C. Analysis of the serine/threonine/tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes reveals phosphorylated proteins related to virulence. Proteomics 2011; 11:4155-65. [PMID: 21956863 DOI: 10.1002/pmic.201100259] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/19/2011] [Accepted: 08/04/2011] [Indexed: 11/05/2022]
Abstract
Phosphorylation is the most common and widely studied post-translational protein modification in bacteria. It plays an important role in all kinds of cellular processes and controls key regulatory mechanisms, including virulence in certain pathogens. To gain insight into the role of protein phosphorylation in the pathogen Listeria monocytogenes, the serine (Ser), threonine (Thr) and tyrosine (Tyr) phosphoproteome of this bacterium was determined. We used the "gel free" proteomic approach with high accuracy mass spectrometry after enrichment of phosphopeptides. A total of 143 sites of phosphorylation were clearly identified, on 155 unique peptides of 112 phosphoproteins. The Ser/Thr/Tyr phosphorylation site distribution was 93:43:7. All identified phosphopeptides are monophosphorylated, except one and many identified phosphoproteins are related to virulence, translation, phosphoenolpyruvate:sugar phosphotransferase system, glycolysis and stress response. A description of these phosphoproteins is provided together with a comparison of the phosphosites in the L. monocytogenes proteins and in their homologues of other bacteria for which the phosphoproteome has been determined. Compared with the previous studies, we noticed a more extended conservation of the phosphorylation sites in glycolytic enzymes as well as ribosomal proteins.
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