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Wang K, Lu H, Zou M, Wang G, Zhao J, Huang X, Ren F, Hu H, Huang J, Min X. DegS protease regulates antioxidant capacity and adaptability to oxidative stress environment in Vibrio cholerae. Front Cell Infect Microbiol 2023; 13:1290508. [PMID: 38053530 PMCID: PMC10694293 DOI: 10.3389/fcimb.2023.1290508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/06/2023] [Indexed: 12/07/2023] Open
Abstract
Adaptation to oxidative stress is critical for survival of Vibrio cholerae in aquatic ecosystems and hosts. DegS activates the σE envelope stress response. We have previously revealed that DegS may be involved in regulating the oxidative stress response. In this study, we demonstrated that deletion of the degS gene attenuates the antioxidant capacity of V. cholerae. In addition, our results further revealed that the regulation of antioxidant capacity by DegS in V. cholerae could involve the cAMP-CRP complex, which regulates rpoS. XthA is an exonuclease that repairs oxidatively damaged cells and affects the bacterial antioxidant capacity. qRT-PCR showed that DegS, σE, cAMP, CRP, and RpoS positively regulate xthA gene transcription. XthA overexpression partially compensates for antioxidant deficiency in the degS mutant. These results suggest that DegS affects the antioxidant capacity of V.cholerae by regulating xthA expression via the cAMP-CRP-RpoS pathway. In a mouse intestinal colonization experiment, our data showed that V.cholerae degS, rpoE, and rpoS gene deletions were associated with significantly reduced resistance to oxidative stress and the ability to colonize the mouse intestine. In conclusion, these findings provide new insights into the regulation of antioxidant activity by V.cholerae DegS.
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Affiliation(s)
- Kaiying Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huifang Lu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Mei Zou
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangli Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiajun Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xiaoyu Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Fangyu Ren
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huaqin Hu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
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Maziero M, Lane D, Polard P, Bergé M. Fever-like temperature bursts promote competence development via an HtrA-dependent pathway in Streptococcus pneumoniae. PLoS Genet 2023; 19:e1010946. [PMID: 37699047 PMCID: PMC10516426 DOI: 10.1371/journal.pgen.1010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/22/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is well known for its ability to develop competence for natural DNA transformation. Competence development is regulated by an autocatalytic loop driven by variations in the basal level of transcription of the comCDE and comAB operons. These genes are part of the early gene regulon that controls expression of the late competence genes known to encode the apparatus of transformation. Several stressful conditions are known to promote competence development, although the induction pathways are remain poorly understood. Here we demonstrate that transient temperature elevation induces an immediate increase in the basal expression level of the comCDE operon and early genes that, in turn, stimulates its full induction, including that of the late competence regulon. This thermal regulation depends on the HtrA chaperone/protease and its proteolytic activity. We find that other competence induction stimulus, like norfloxacin, is not conveyed by the HtrA-dependent pathway. This finding strongly suggests that competence can be induced by at least two independent pathways and thus reinforces the view that competence is a general stress response system in the pneumococcus.
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Affiliation(s)
- Mickaël Maziero
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - David Lane
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Patrice Polard
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
| | - Mathieu Bergé
- Laboratoire de Microbiologie et Génétique Moléculaires (LMGM), UMR5100, Centre de Biologie Intégrative (CBI), Centre Nationale de la Recherche Scientifique (CNRS), Toulouse, France
- Université Paul Sabatier (Toulouse III), Toulouse, France
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3
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Gupta AK, Singh K, Patidar Y, Sharma R, Sardesai AA, Reddy G, Gopal B. Allosteric Determinants in High Temperature Requirement A Enzymes Are Conserved and Regulate the Population of Active Conformations. ACS Chem Biol 2023; 18:1487-1499. [PMID: 37319329 DOI: 10.1021/acschembio.2c00921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
High temperature requirement A (HtrA) are allosterically regulated enzymes wherein effector binding to the PDZ domain triggers proteolytic activity. Yet, it remains unclear if the inter-residue network governing allostery is conserved across HtrA enzymes. Here, we investigated and identified the inter-residue interaction networks by molecular dynamics simulations on representative HtrA proteases, Escherichia coli DegS and Mycobacterium tuberculosis PepD, in effector-bound and free forms. This information was used to engineer mutations that could potentially perturb allostery and conformational sampling in a different homologue, M. tuberculosis HtrA. Mutations in HtrA perturbed allosteric regulation─a finding consistent with the hypothesis that the inter-residue interaction network is conserved across HtrA enzymes. Electron density from data collected on cryo-protected HtrA crystals revealed that mutations altered the topology of the active site. Ensemble models fitted into electron density calculated from room-temperature diffraction data showed that only a fraction of these models had a catalytically competent active site conformation alongside a functional oxyanion hole thus providing experimental evidence that these mutations influenced conformational sampling. Mutations at analogous positions in the catalytic domain of DegS perturbed the coupling between effector binding and proteolytic activity, thus confirming the role of these residues in the allosteric response. The finding that a perturbation in the conserved inter-residue network alters conformational sampling and the allosteric response suggests that an ensemble allosteric model best describes regulated proteolysis in HtrA enzymes.
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Affiliation(s)
- Arvind Kumar Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Yogesh Patidar
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Ravish Sharma
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | | | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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Zhang Y, Huang Y, Ding H, Ma J, Tong X, Zhang Y, Tao Z, Wang Q. A σE-mediated temperature gauge orchestrates type VI secretion system, biofilm formation and cell invasion in pathogen Pseudomonas plecoglossicida. Microbiol Res 2023; 266:127220. [DOI: 10.1016/j.micres.2022.127220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022]
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Zou M, Wang K, Zhao J, Lu H, Yang H, Huang M, Wang L, Wang G, Huang J, Min X. DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae. Front Microbiol 2023; 14:1159986. [PMID: 37089576 PMCID: PMC10113495 DOI: 10.3389/fmicb.2023.1159986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
In bacteria, DegS protease functions as an activating factor of the σE envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σE to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.
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Affiliation(s)
- Mei Zou
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kaiying Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiajun Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huifang Lu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hui Yang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meirong Huang
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Lu Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangli Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
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Wang H, Yang Z, Swingle B, Kvitko BH. AlgU, a Conserved Sigma Factor Regulating Abiotic Stress Tolerance and Promoting Virulence in Pseudomonas syringae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:326-336. [PMID: 33264045 DOI: 10.1094/mpmi-09-20-0254-cr] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pseudomonas syringae can rapidly deploy specialized functions to deal with abiotic and biotic stresses. Host niches pose specific sets of environmental challenges driven, in part, by immune defenses. Bacteria use a "just-in-time" strategy of gene regulation, meaning that they only produce the functions necessary for survival as needed. Extracytoplasmic function (ECF) sigma factors transduce a specific set of environmental signals and change gene expression patterns by altering RNA polymerase promoter specificity, to adjust bacterial physiology, structure, or behavior, singly or in combination, to improve chances of survival. The broadly conserved ECF sigma factor AlgU affects virulence in both animal and plant pathogens. Pseudomonas syringae AlgU controls expression of more than 800 genes, some of which contribute to suppression of plant immunity and bacterial fitness in plants. This review discusses AlgU activation mechanisms, functions controlled by AlgU, and how these functions contribute to P. syringae survival in plants.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. 2021.
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Affiliation(s)
- Haibi Wang
- Department of Plant Pathology, University of Georgia, 120 Carlton St., Athens, GA 30602, U.S.A
| | - Zichu Yang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Bldg., Ithaca, NY 14853, U.S.A
| | - Bryan Swingle
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Bldg., Ithaca, NY 14853, U.S.A
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853, U.S.A
| | - Brian H Kvitko
- Department of Plant Pathology, University of Georgia, 120 Carlton St., Athens, GA 30602, U.S.A
- The Plant Center, University of Georgia, Athens, GA 30602, U.S.A
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Heywood A, Lamont IL. Cell envelope proteases and peptidases of Pseudomonas aeruginosa: multiple roles, multiple mechanisms. FEMS Microbiol Rev 2020; 44:857-873. [PMID: 32804218 DOI: 10.1093/femsre/fuaa036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is commonly isolated from damp environments. It is also a major opportunistic pathogen, causing a wide range of problematic infections. The cell envelope of P. aeruginosa, comprising the cytoplasmic membrane, periplasmic space, peptidoglycan layer and outer membrane, is critical to the bacteria's ability to adapt and thrive in a wide range of environments. Over 40 proteases and peptidases are located in the P. aeruginosa cell envelope. These enzymes play many crucial roles. They are required for protein secretion out of the cytoplasm to the periplasm, outer membrane, cell surface or the environment; for protein quality control and removal of misfolded proteins; for controlling gene expression, allowing adaptation to environmental changes; for modification and remodelling of peptidoglycan; and for metabolism of small molecules. The key roles of cell envelope proteases in ensuring normal cell functioning have prompted the development of inhibitors targeting some of these enzymes as potential new anti-Pseudomonas therapies. In this review, we summarise the current state of knowledge across the breadth of P. aeruginosa cell envelope proteases and peptidases, with an emphasis on recent findings, and highlight likely future directions in their study.
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Affiliation(s)
- Astra Heywood
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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Wettstadt S, Llamas MA. Role of Regulated Proteolysis in the Communication of Bacteria With the Environment. Front Mol Biosci 2020; 7:586497. [PMID: 33195433 PMCID: PMC7593790 DOI: 10.3389/fmolb.2020.586497] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/22/2020] [Indexed: 12/29/2022] Open
Abstract
For bacteria to flourish in different niches, they need to sense signals from the environment and translate these into appropriate responses. Most bacterial signal transduction systems involve proteins that trigger the required response through the modification of gene transcription. These proteins are often produced in an inactive state that prevents their interaction with the RNA polymerase and/or the DNA in the absence of the inducing signal. Among other mechanisms, regulated proteolysis is becoming increasingly recognized as a key process in the modulation of the activity of these signal response proteins. Regulated proteolysis can either produce complete degradation or specific cleavage of the target protein, thus modifying its function. Because proteolysis is a fast process, the modulation of signaling proteins activity by this process allows for an immediate response to a given signal, which facilitates adaptation to the surrounding environment and bacterial survival. Moreover, regulated proteolysis is a fundamental process for the transmission of extracellular signals to the cytosol through the bacterial membranes. By a proteolytic mechanism known as regulated intramembrane proteolysis (RIP) transmembrane proteins are cleaved within the plane of the membrane to liberate a cytosolic domain or protein able to modify gene transcription. This allows the transmission of a signal present on one side of a membrane to the other side where the response is elicited. In this work, we review the role of regulated proteolysis in the bacterial communication with the environment through the modulation of the main bacterial signal transduction systems, namely one- and two-component systems, and alternative σ factors.
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Affiliation(s)
- Sarah Wettstadt
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín-Consejo Superior de Investigaciones Científicas, Granada, Spain
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Huang J, Chen Y, Chen J, Liu C, Zhang T, Luo S, Huang M, Min X. Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing. PeerJ 2019; 7:e7959. [PMID: 31660280 PMCID: PMC6815195 DOI: 10.7717/peerj.7959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/29/2019] [Indexed: 01/25/2023] Open
Abstract
Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.
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Affiliation(s)
- Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuxi Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jie Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Changjin Liu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Tao Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shilu Luo
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Meirong Huang
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Hart EM, O'Connell A, Tang K, Wzorek JS, Grabowicz M, Kahne D, Silhavy TJ. Fine-Tuning of σ E Activation Suppresses Multiple Assembly-Defective Mutations in Escherichia coli. J Bacteriol 2019; 201:e00745-18. [PMID: 30858299 PMCID: PMC6509652 DOI: 10.1128/jb.00745-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/25/2019] [Indexed: 12/19/2022] Open
Abstract
The Gram-negative outer membrane (OM) is a selectively permeable asymmetric bilayer that allows vital nutrients to diffuse into the cell but prevents toxins and hydrophobic molecules from entering. Functionally and structurally diverse β-barrel outer membrane proteins (OMPs) build and maintain the permeability barrier, making the assembly of OMPs crucial for cell viability. In this work, we characterize an assembly-defective mutant of the maltoporin LamB, LamBG439D We show that the folding defect of LamBG439D results in an accumulation of unfolded substrate that is toxic to the cell when the periplasmic protease DegP is removed. Selection for suppressors of this toxicity identified the novel mutant degSA323E allele. The mutant DegSA323E protein contains an amino acid substitution at the PDZ/protease domain interface that results in a partially activated conformation of this protein. This activation increases basal levels of downstream σE stress response signaling. Furthermore, the enhanced σE activity of DegSA323E suppresses a number of other assembly-defective conditions without exhibiting the toxicity associated with high levels of σE activity. We propose that the increased basal levels of σE signaling primes the cell to respond to envelope stress before OMP assembly defects threaten cell viability. This finding addresses the importance of envelope stress responses in monitoring the OMP assembly process and underpins the critical balance between envelope defects and stress response activation.IMPORTANCE Gram-negative bacteria, such as Escherichia coli, inhabit a natural environment that is prone to flux. In order to cope with shifting growth conditions and the changing availability of nutrients, cells must be capable of quickly responding to stress. Stress response pathways allow cells to rapidly shift gene expression profiles to ensure survival in this unpredictable environment. Here we describe a mutant that partially activates the σE stress response pathway. The elevated basal level of this stress response allows the cell to quickly respond to overwhelming stress to ensure cell survival.
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Affiliation(s)
- Elizabeth M Hart
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Aileen O'Connell
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, New York, USA
| | - Kimberly Tang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Joseph S Wzorek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Novartis Institute for BioMedical Research, Inc., Cambridge, Massachusetts, USA
| | - Marcin Grabowicz
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
- Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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11
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Ichikawa DM, Corbi-Verge C, Shen MJ, Snider J, Wong V, Stagljar I, Kim PM, Noyes MB. A Multireporter Bacterial 2-Hybrid Assay for the High-Throughput and Dynamic Assay of PDZ Domain-Peptide Interactions. ACS Synth Biol 2019; 8:918-928. [PMID: 30969105 DOI: 10.1021/acssynbio.8b00499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The accurate determination of protein-protein interactions has been an important focus of molecular biology toward which much progress has been made due to the continuous development of existing and new technologies. However, current methods can have limitations, including scale and restriction to high affinity interactions, limiting our understanding of a large subset of these interactions. Here, we describe a modified bacterial-hybrid assay that employs combined selectable and scalable reporters that enable the sensitive screening of large peptide libraries followed by the sorting of positive interactions by the level of reporter output. We have applied this tool to characterize a set of human and E. coli PDZ domains. Our results are consistent with prior characterization of these proteins, and the improved sensitivity increases our ability to predict known and novel in vivo binding partners. This approach allows for the recovery of a wide range of affinities with a high throughput method that does not sacrifice the scale of the screen.
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Affiliation(s)
- David M. Ichikawa
- Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, New York 10016, United States
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Michael J. Shen
- Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, New York 10016, United States
| | - Jamie Snider
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Victoria Wong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Igor Stagljar
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Philip M. Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Marcus B. Noyes
- Department of Biochemistry Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, New York 10016, United States
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12
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Cabrera AC, Melo E, Roth D, Topp A, Delobel F, Stucki C, Chen CY, Jakob P, Banfai B, Dunkley T, Schilling O, Huber S, Iacone R, Petrone P. HtrA1 activation is driven by an allosteric mechanism of inter-monomer communication. Sci Rep 2017; 7:14804. [PMID: 29093542 PMCID: PMC5666011 DOI: 10.1038/s41598-017-14208-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/04/2017] [Indexed: 11/26/2022] Open
Abstract
The human protease family HtrA is responsible for preventing protein misfolding and mislocalization, and a key player in several cellular processes. Among these, HtrA1 is implicated in several cancers, cerebrovascular disease and age-related macular degeneration. Currently, HtrA1 activation is not fully characterized and relevant for drug-targeting this protease. Our work provides a mechanistic step-by-step description of HtrA1 activation and regulation. We report that the HtrA1 trimer is regulated by an allosteric mechanism by which monomers relay the activation signal to each other, in a PDZ-domain independent fashion. Notably, we show that inhibitor binding is precluded if HtrA1 monomers cannot communicate with each other. Our study establishes how HtrA1 trimerization plays a fundamental role in proteolytic activity. Moreover, it offers a structural explanation for HtrA1-defective pathologies as well as mechanistic insights into the degradation of complex extracellular fibrils such as tubulin, amyloid beta and tau that belong to the repertoire of HtrA1.
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Affiliation(s)
- Alvaro Cortes Cabrera
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Esther Melo
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Doris Roth
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Andreas Topp
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Frederic Delobel
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Corinne Stucki
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Chia-Yi Chen
- Institute of Molecular Medicine and Cell Research, University of Freiburg, 79104, Freiburg, Germany
| | - Peter Jakob
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Balazs Banfai
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
- Soladis GmbH, 4052, Basel, Switzerland
| | - Tom Dunkley
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104, Freiburg, Germany
| | - Sylwia Huber
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Roberto Iacone
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland
| | - Paula Petrone
- Pharma Research & Early Development (pRED). Roche Innovation Center Basel, Basel, Switzerland.
- Barcelonabeta Brain Research Center, Fundacion Pascual Maragall. Carrer de Wellington, 30, 08005, Barcelona, Spain.
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13
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Zurawa-Janicka D, Wenta T, Jarzab M, Skorko-Glonek J, Glaza P, Gieldon A, Ciarkowski J, Lipinska B. Structural insights into the activation mechanisms of human HtrA serine proteases. Arch Biochem Biophys 2017; 621:6-23. [PMID: 28396256 DOI: 10.1016/j.abb.2017.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022]
Abstract
Human HtrA1-4 proteins belong to the HtrA family of evolutionarily conserved serine proteases and function as important modulators of many physiological processes, including maintenance of mitochondrial homeostasis, cell signaling and apoptosis. Disturbances in their action are linked to severe diseases, including oncogenesis and neurodegeneration. The HtrA1-4 proteins share structural and functional features of other members of the HtrA protein family, however there are several significant differences in structural architecture and mechanisms of action which makes each of them unique. Our goal is to present recent studies regarding human HtrAs. We focus on their physiological functions, structure and regulation, and describe current models of activation mechanisms. Knowledge of molecular basis of the human HtrAs' action is a subject of great interest; it is crucial for understanding their relevance in cellular physiology and pathogenesis as well as for using them as targets in future therapies of diseases such as neurodegenerative disorders and cancer.
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Affiliation(s)
- Dorota Zurawa-Janicka
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Tomasz Wenta
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Miroslaw Jarzab
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Przemyslaw Glaza
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Artur Gieldon
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Jerzy Ciarkowski
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Barbara Lipinska
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
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14
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Jarzab M, Wenta T, Zurawa-Janicka D, Polit A, Gieldon AJ, Wysocka M, Glaza P, Skorko-Glonek J, Ciarkowski J, Lesner A, Lipinska B. Intra- and intersubunit changes accompanying thermal activation of the HtrA2(Omi) protease homotrimer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:283-296. [PMID: 26702898 DOI: 10.1016/j.bbapap.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/26/2015] [Accepted: 12/14/2015] [Indexed: 01/16/2023]
Abstract
HtrA2(Omi) protease is involved in the maintenance of mitochondrial homeostasis and stimulation of apoptosis as well as in development of cancer and neurodegenerative disorders. The protein is a homotrimer whose subunits comprise serine protease domain (PD) and PDZ regulatory domain. In the basal, inactive state, a tight interdomain interface limits access both to the PDZ peptide (carboxylate) binding site and to the PD catalytic center. The molecular mechanism of activation is not well understood. To further the knowledge of HtrA2 thermal activation we monitored the dynamics of the PDZ-PD interactions during temperature increase using tryptophan-induced quenching (TrIQ) method. The TrIQ results suggested that during activation the PDZ domain changed its position versus PD inside a subunit, including a prominent change affecting the L3 regulatory loop of PD, and also changed its interactions with the PD of the adjacent subunit (PD*), specifically with its L1* regulatory loop containing the active site serine. The α5 helix of PDZ was involved in both, the intra- and intersubunit changes of interactions and thus seems to play an important role in HtrA2 activation. The amino acid substitutions designed to decrease the PDZ interactions with the PD or PD* promoted protease activity at a wide range of temperatures, which supports the conclusions based on the TrIQ analysis. The model presented in this work describes PDZ movement in relation to PD and PD*, resulting in an increased access to the peptide binding and active sites, and conformational changes of the L3 and L1* loops.
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Affiliation(s)
- Miroslaw Jarzab
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Tomasz Wenta
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Dorota Zurawa-Janicka
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Agnieszka Polit
- Department of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Artur J Gieldon
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Magdalena Wysocka
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Przemyslaw Glaza
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Joanna Skorko-Glonek
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Jerzy Ciarkowski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-952 Gdansk, Poland
| | - Barbara Lipinska
- Department of Biochemistry, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
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15
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Two stress sensor proteins for the expression of sigmaE regulon: DegS and RseB. J Microbiol 2015; 53:306-10. [PMID: 25935301 DOI: 10.1007/s12275-015-5112-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/17/2022]
Abstract
In E. coli, sigmaE-dependent transcription is controlled by regulated-proteolysis of RseA. RseA, which holds sigmaE as an anti-sigma factor, is sequentially digested by DegS, RseP and cytoplasmic proteases to liberate sigmaE in response to dysfunction in outer-membrane biogenesis. Additionally, the sequential proteolysis is regulated by RseB binding to RseA (Fig. 1A). Direct interaction between RseA and RseB inhibits RseA-cleavage by DegS. Both proteolytic activation of DegS and binding disruption of RseB are thus required to initiate sigmaE-stress response. For the induction of sigmaEstress response, DegS and RseB recognize the states of OMP and LPS for outer-membrane biogenesis. DegS is activated by binding of unfolded OMPs and RseB binding to RseA is antagonized by LPS accumulated in periplasm. In this regard, DegS and RseB are proposed to be stress sensor proteins for sigmaE signal transduction. Interestingly, biogenesis of OMP and LPS appears to cross-talk with each other, indicating that dysfunction of either OMP or LPS can initiate RseA proteolysis. This review aims to briefly introduce two stress sensor proteins, DegS and RseB, which regulate sigmaEdependent transcription.
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