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El-Fakharany EM, Elsharkawy WB, El-Maradny YA, El-Gendi H. Moringa oleifera seed methanol extract with consolidated antimicrobial, antioxidant, anti-inflammatory, and anticancer activities. J Food Sci 2024; 89:5130-5149. [PMID: 38955793 DOI: 10.1111/1750-3841.17223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
The wide biological activity of the Moringa oleifera represents a potential opportunity for developing selective cancer treatment drugs. The bioactive phytochemicals in Moringa seed extract (MSE) indicated large numbers of phytochemicals (21 compounds) with dominant abundance for cycloisolongifolene, 8,9-dehydro-9-vinyl, and chamazulene accounting for 12.7% and 12.19% of the total detected compounds. The MSE showed a potent anticancer effect toward Caco-2, MDA, and HepG-2 cells with half-maximal inhibitory concentration (IC50) values of 9.15 ± 1.18, 4.85 ± 0.11, and 7.36 ± 0.22 µg/mL, respectively, with higher safety (≥31-folds) toward normal human cells (IC50 of 150.7 ± 11.11 µg/mL). It appears that MSE stimulates selective-dose-dependent cell shrinkage, and nuclear condensation in the tumor cells, which finally induces the apoptosis pathway to increase its anticancer action. Additionally, MSE showed a potent capability to stimulate cell cycle arrest in both main checkpoint phases (G0/G1 and G2/M) of cell population growth. The apoptotic death stimulation was confirmed through upregulation of tumor protein p53 (p53) and cyclin-dependent kinase inhibitor p21 (p21) expression by more than three- to sixfold and downregulation of B-cell lymphoma 2 expression (threefold) in MSE-treated cells compared to 5-fluorouracil (5-FU)-treated tumor cells. Furthermore, the MSE revealed strong anti-inflammatory activity with significant antioxidant activity by lowering nitric oxide levels and enhancing the superoxide dismutase activity. On the other hand, the MSE revealed broad-spectrum antibacterial activity in a dose-dependent manner against Staphylococcus aureus minimum inhibitory concentration (MIC of 1.25 mg/mL), followed by Salmonella typhimurium (MIC of 1.23 mg/mL), whereas Escherichia coli was the least sensitive to MSE activity (MIC of 22.5 mg/mL) with significant antibiofilm activity against sensitive pathogens.
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Affiliation(s)
- Esmail M El-Fakharany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria, Egypt
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria, Egypt
- Pharos University in Alexandria, Alexandria, Egypt
| | - Wafaa B Elsharkawy
- Physics Department, College of Science and Humanities Studies, Prince Sattam bin Abdulaziz University, AlKharj, Saudi Arabia
| | - Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Alexandria, Egypt
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El-Alamein, Egypt
| | - Hamada El-Gendi
- Bioprocess Development Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg El‑Arab City, Alexandria, Egypt
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2
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Li Z, Zhu Y, Zhang W, Mu W. Rcs signal transduction system in Escherichia coli: Composition, related functions, regulatory mechanism, and applications. Microbiol Res 2024; 285:127783. [PMID: 38795407 DOI: 10.1016/j.micres.2024.127783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/28/2024]
Abstract
The regulator of capsule synthesis (Rcs) system, an atypical two-component system prevalent in numerous gram-negative bacteria, serves as a sophisticated regulatory phosphorylation cascade mechanism. It plays a pivotal role in perceiving environmental stress and regulating the expression of downstream genes to ensure host survival. During the signaling transduction process, various proteins participate in phosphorylation to further modulate signal inputs and outputs. Although the structure of core proteins related to the Rcs system has been partially well-defined, and two models have been proposed to elucidate the intricate molecular mechanisms underlying signal sensing, a systematic characterization of the signal transduction process of the Rcs system remains challenging. Furthermore, exploring its corresponding regulator outputs is also unremitting. This review aimed to shed light on the regulation of bacterial virulence by the Rcs system. Moreover, with the assistance of the Rcs system, biosynthesis technology has developed high-value target production. Additionally, via this review, we propose designing chimeric Rcs biosensor systems to expand their application as synthesis tools. Finally, unsolved challenges are highlighted to provide the basic direction for future development of the Rcs system.
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Affiliation(s)
- Zeyu Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China.
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3
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Watanabe N, Savchenko A. Molecular insights into the initiation step of the Rcs signaling pathway. Structure 2024:S0969-2126(24)00221-1. [PMID: 38964336 DOI: 10.1016/j.str.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/05/2024] [Accepted: 06/07/2024] [Indexed: 07/06/2024]
Abstract
The Rcs pathway is repressed by the inner membrane protein IgaA under non-stressed conditions. This repression is hypothesized to be relieved by the binding of the outer membrane-anchored RcsF to IgaA. However, the precise mechanism by which RcsF binding triggers the signaling remains unclear. Here, we present the 1.8 Å resolution crystal structure capturing the interaction between IgaA and RcsF. Our comparative structural analysis, examining both the bound and unbound states of the periplasmic domain of IgaA (IgaAp), highlights rotational flexibility within IgaAp. Conversely, the conformation of RcsF remains unchanged upon binding. Our in vivo and in vitro studies do not support the model of a stable complex involving RcsF, IgaAp, and RcsDp. Instead, we demonstrate that the elements beyond IgaAp play a role in the interaction between IgaA and RcsD. These findings collectively allow us to propose a potential mechanism for the signaling across the inner membrane through IgaA.
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Affiliation(s)
- Nobuhiko Watanabe
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA
| | - Alexei Savchenko
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada; Center for Structural Biology for Infectious Diseases (CSBID) Chicago, IL, USA.
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4
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Méndez AAE, Argüello JM, Soncini FC, Checa SK. Scs system links copper and redox homeostasis in bacterial pathogens. J Biol Chem 2024; 300:105710. [PMID: 38309504 PMCID: PMC10907172 DOI: 10.1016/j.jbc.2024.105710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
The bacterial envelope is an essential compartment involved in metabolism and metabolites transport, virulence, and stress defense. Its roles become more evident when homeostasis is challenged during host-pathogen interactions. In particular, the presence of free radical groups and excess copper in the periplasm causes noxious reactions, such as sulfhydryl group oxidation leading to enzymatic inactivation and protein denaturation. In response to this, canonical and accessory oxidoreductase systems are induced, performing quality control of thiol groups, and therefore contributing to restoring homeostasis and preserving survival under these conditions. Here, we examine recent advances in the characterization of the Dsb-like, Salmonella-specific Scs system. This system includes the ScsC/ScsB pair of Cu+-binding proteins with thiol-oxidoreductase activity, an alternative ScsB-partner, the membrane-linked ScsD, and a likely associated protein, ScsA, with a role in peroxide resistance. We discuss the acquisition of the scsABCD locus and its integration into a global regulatory pathway directing envelope response to Cu stress during the evolution of pathogens that also harbor the canonical Dsb systems. The evidence suggests that the canonical Dsb systems cannot satisfy the extra demands that the host-pathogen interface imposes to preserve functional thiol groups. This resulted in the acquisition of the Scs system by Salmonella. We propose that the ScsABCD complex evolved to connect Cu and redox stress responses in this pathogen as well as in other bacterial pathogens.
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Affiliation(s)
- Andrea A E Méndez
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina.
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5
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George A, Patil AG, Mahalakshmi R. ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics. Protein Sci 2024; 33:e4896. [PMID: 38284489 PMCID: PMC10804688 DOI: 10.1002/pro.4896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/30/2024]
Abstract
Diderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across phyla and performing different regulatory roles. The ability of BAM complex to recognize and fold OM β-barrels of diverse sizes, and reproducibly execute their membrane insertion, is independent of electrochemical energy. Recent atomic structures, which captured BAM-substrate complexes, show the assembly function of BamA can be tailored, with different substrate types exhibiting different folding mechanisms. Here, we highlight common and unique features of its interactome. We discuss how this conserved protein complex has evolved the ability to effectively achieve the directed assembly of diverse OMPs of wide-ranging sizes (8-36 β-stranded monomers). Additionally, we discuss how darobactin-the first natural membrane protein inhibitor of Gram-negative bacteria identified in over five decades-selectively targets and specifically inhibits BamA. We conclude by deliberating how a detailed deduction of BAM complex-associated regulation of OMP biogenesis and OM remodeling will open avenues for the identification and development of effective next-generation therapeutics against Gram-negative pathogens.
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Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Akanksha Gajanan Patil
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
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6
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Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023; 24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.
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Affiliation(s)
- Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Elizaveta Semenova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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7
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TagElDein MA, Mohamed NG, Shahein YE, Ziko L, Hussein NA. Altering Escherichia coli envelope integrity by mimicking the lipoprotein RcsF. Arch Microbiol 2023; 206:12. [PMID: 38070002 PMCID: PMC10710380 DOI: 10.1007/s00203-023-03733-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/21/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
Escherichia coli cell envelope is crucial for stress sensing and signal transduction, mediated by numerous protein-protein interactions to enable adaptation and survival. Interfering with these interactions might affect envelope integrity leading to bacterial death. The outer membrane lipoprotein (RcsF) is the stress sensor of the regulator of capsule synthesis (Rcs) phosphorelay that senses envelope threats. RcsF interacts with two essential proteins, IgaA (repressing the Rcs system) and BamA (inserting β-barrel proteins in the outer membrane). Disturbing RcsF interactions may alter Rcs signaling and/or membrane integrity thus affecting bacterial survival. Here, we derived the sequence of a peptide mimicking RcsF (RcsFmim), based on the in silico docking of RcsF with IgaA. Expression of rcsFmim caused 3-to-4-fold activation of the Rcs system and perturbation of the outer membrane. Both effects result in decreased E. coli growth rate. We anticipate that RcsFmim present a candidate for future antibacterial peptide development.
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Affiliation(s)
- Moustafa A TagElDein
- Microbiology and Immunology Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Noha G Mohamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Sphinx University, Assiut, Egypt
| | - Yasser E Shahein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt
| | - Laila Ziko
- Department of Biochemistry, School of Life and Medical Sciences, University of Hertfordshire Hosted By the Global Academic Foundation, R5 New Garden City, New Administrative Capital, Cairo, Egypt
| | - Nahla A Hussein
- Molecular Biology Department, Biotechnology Research Institute, National Research Centre, Cairo, Egypt.
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Ramezanifard R, Golubeva YA, Palmer AD, Slauch JM. TamAB is regulated by PhoPQ and functions in outer membrane homeostasis during Salmonella pathogenesis. J Bacteriol 2023; 205:e0018323. [PMID: 37728604 PMCID: PMC10601761 DOI: 10.1128/jb.00183-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/12/2023] [Indexed: 09/21/2023] Open
Abstract
Salmonella survive and replicate in macrophages, which normally kill bacteria by exposing them to a variety of harsh conditions and antimicrobial effectors, many of which target the bacterial cell envelope. The PhoPQ two-component system responds to the phagosome environment and induces factors that protect the outer membrane, allowing adaptation and growth in the macrophage. We show that PhoPQ induces the transcription of the tamAB operon both in vitro and in macrophages. The TamA protein is structurally similar to BamA, an essential protein in the Bam complex that assembles β-barrel proteins in the outer membrane, while TamB is an AsmA-family protein implicated in lipid transport between the inner and outer membranes. We show that the Bam machinery is stressed in vitro under low Mg2+, low pH conditions that mimic the phagosome. Not surprisingly, mutations affecting Bam function confer significant virulence defects. Although loss of TamAB alone confers no virulence defect, a tamAB deletion confers a synthetic phenotype in bam mutant backgrounds in animals and macrophages, and in vitro upon treatment with vancomycin or sodium dodecyl sulfate. Mutations affecting YhdP, which functions in partial redundancy with TamB, also confer synthetic phenotypes with bam mutations in the animal, but this interaction is not evident in vitro. Thus, in the harsh phagocytic environment of the macrophage, the outer membrane Bam machinery is compromised, and the TamAB system, and perhaps other PhoPQ-regulated factors, is induced to compensate. It is most likely that TamAB and other systems assist the Bam complex indirectly by affecting outer membrane properties. IMPORTANCE The TamAB system has been implicated in both outer membrane protein localization and phospholipid transport between the inner and outer membranes. We show that the β-barrel protein assembly complex, Bam, is stressed under conditions thought to mimic the macrophage phagosome. TamAB expression is controlled by the PhoPQ two-component system and induced in macrophages. This system somehow compensates for the Bam complex as evidenced by the fact that mutations affecting the two systems confer synthetic phenotypes in animals, macrophages, and in vitro in the presence of vancomycin or SDS. This study has implications concerning the role of TamAB in outer membrane homeostasis. It also contributes to our understanding of the systems necessary for Salmonella to adapt and reproduce within the macrophage phagosome.
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Affiliation(s)
- Rouhallah Ramezanifard
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Yekaterina A. Golubeva
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - Alexander D. Palmer
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
| | - James M. Slauch
- Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, Illinois, USA
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Rodríguez L, Peñalver M, Casino P, García-del Portillo F. Evolutionary analysis and structure modelling of the Rcs-repressor IgaA unveil a functional role of two cytoplasmic small β-barrel (SBB) domains. Heliyon 2023; 9:e16661. [PMID: 37303533 PMCID: PMC10248123 DOI: 10.1016/j.heliyon.2023.e16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
The Rcs sensor system, comprising the RcsB/RcsC/RcsD and RcsF proteins, is used by bacteria of the order Enterobacterales to withstand envelope damage. In non-stress conditions, Rcs is repressed by IgaA, a membrane protein with three cytoplasmic regions (cyt-1, cyt-2 and cyt-3). How the Rcs-IgaA axis evolved within Enterobacterales has not been yet explored. Here, we report phylogenetic data supporting co-evolution of IgaA with RcsC/RcsD. Functional exchange assays showed that IgaA from Shigella and Dickeya, but not from Yersinia or the endosymbionts Photorhabdus and Sodalis, repress the Rcs system of Salmonella. IgaA from Dickeya, however, repress only partially the Rcs system despite being produced at high levels in the complementation assay. The modelled structures of these IgaA variants uncovered one periplasmic and two cytoplasmic conserved β-rich architectures forming partially closed small β-barrel (SBB) domains. Conserved residues map in a connector linking cytoplasmic SSB-1 and SBB-2 domains (E180-R265); a region of cyt-1 facing cyt-2 (R188-E194-D309 and T191-H326); and between cyt-2 and cyt-3 (H293-E328-R686). These structures validated early in vivo studies in Salmonella that assigned a role in function to R188, T191 and G262, and in addition revealed a previously unnoticed "hybrid" SBB-2 domain to which cyt-1 and cyt-2 contribute. IgaA variants not functional or partially functional in Salmonella lack H192-P249 and R255-D313 interactions. Among these variants, only IgaA from Dickeya conserves the helix α6 in SSB-1 that is present in IgaA from Salmonella and Shigella. RcsF and RcsD, which interact directly with IgaA, failed to show structural features linked to specific IgaA variants. Altogether, our data provide new insights into IgaA by mapping residues selected differently during evolution and involved in function. Our data also infer contrasting lifestyles of Enterobacterales bacteria as source of variability in the IgaA-RcsD/IgaA-RcsF interactions.
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Affiliation(s)
- Leticia Rodríguez
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Patricia Casino
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario de Biotecnología y Biomedicina BIOTECMED, Universitat de València, Burjassot, Spain
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Francisco García-del Portillo
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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10
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Cho THS, Wang J, Raivio TL. NlpE Is an OmpA-Associated Outer Membrane Sensor of the Cpx Envelope Stress Response. J Bacteriol 2023; 205:e0040722. [PMID: 37022159 PMCID: PMC10127795 DOI: 10.1128/jb.00407-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023] Open
Abstract
Gram-negative bacteria utilize several envelope stress responses (ESRs) to sense and respond to diverse signals within a multilayered cell envelope. The CpxRA ESR responds to multiple stresses that perturb envelope protein homeostasis. Signaling in the Cpx response is regulated by auxiliary factors, such as the outer membrane (OM) lipoprotein NlpE, an activator of the response. NlpE communicates surface adhesion to the Cpx response; however, the mechanism by which NlpE accomplishes this remains unknown. In this study, we report a novel interaction between NlpE and the major OM protein OmpA. Both NlpE and OmpA are required to activate the Cpx response in surface-adhered cells. Furthermore, NlpE senses OmpA overexpression and the NlpE C-terminal domain transduces this signal to the Cpx response, revealing a novel signaling function for this domain. Mutation of OmpA peptidoglycan-binding residues abrogates signaling during OmpA overexpression, suggesting that NlpE signaling from the OM through the cell wall is coordinated via OmpA. Overall, these findings reveal NlpE to be a versatile envelope sensor that takes advantage of its structure, localization, and cooperation with other envelope proteins to initiate adaptation to diverse signals. IMPORTANCE The envelope is not only a barrier that protects bacteria from the environment but also a crucial site for the transduction of signals critical for colonization and pathogenesis. The discovery of novel complexes between NlpE and OmpA contributes to an emerging understanding of the key contribution of OM β-barrel protein and lipoprotein complexes to envelope stress signaling. Overall, our findings provide mechanistic insight into how the Cpx response senses signals relevant to surface adhesion and biofilm growth to facilitate bacterial adaptation.
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Affiliation(s)
- Timothy H. S. Cho
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Junshu Wang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tracy L. Raivio
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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11
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Guo XP, Yan HQ, Yang W, Yin Z, Vadyvaloo V, Zhou D, Sun YC. A frameshift in Yersinia pestis rcsD alters canonical Rcs signalling to preserve flea-mammal plague transmission cycles. eLife 2023; 12:e83946. [PMID: 37010269 PMCID: PMC10191623 DOI: 10.7554/elife.83946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/02/2023] [Indexed: 04/04/2023] Open
Abstract
Multiple genetic changes in the enteric pathogen Yersinia pseudotuberculosis have driven the emergence of Yesinia pestis, the arthropod-borne, etiological agent of plague. These include developing the capacity for biofilm-dependent blockage of the flea foregut to enable transmission by flea bite. Previously, we showed that pseudogenization of rcsA, encoding a component of the Rcs signalling pathway, is an important evolutionary step facilitating Y. pestis flea-borne transmission. Additionally, rcsD, another important gene in the Rcs system, harbours a frameshift mutation. Here, we demonstrated that this rcsD mutation resulted in production of a small protein composing the C-terminal RcsD histidine-phosphotransferase domain (designated RcsD-Hpt) and full-length RcsD. Genetic analysis revealed that the rcsD frameshift mutation followed the emergence of rcsA pseudogenization. It further altered the canonical Rcs phosphorylation signal cascade, fine-tuning biofilm production to be conducive with retention of the pgm locus in modern lineages of Y. pestis. Taken together, our findings suggest that a frameshift mutation in rcsD is an important evolutionary step that fine-tuned biofilm production to ensure perpetuation of flea-mammal plague transmission cycles.
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Affiliation(s)
- Xiao-Peng Guo
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Hai-Qin Yan
- Department of Basic Medical Sciences, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical CollegeBengbuChina
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Wenhui Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Viveka Vadyvaloo
- Paul G. Allen School for Global Health, Washington State UniversityPullmanUnited States
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Yi-Cheng Sun
- NHC key laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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12
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Liang Y, Zhao Y, Kwan J, Wang Y, Qiao Y. Escherichia coli has robust regulatory mechanisms against elevated peptidoglycan cleavage by lytic transglycosylases. J Biol Chem 2023; 299:104615. [PMID: 36931392 PMCID: PMC10139938 DOI: 10.1016/j.jbc.2023.104615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/25/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Peptidoglycan (PG) is an essential and conserved exoskeletal component in all bacteria that protects cells from lysis. Gram-negative bacteria such as Escherichia coli encode multiple redundant lytic transglycosylases (LTs) that engage in PG cleavage, a potentially lethal activity requiring proper regulation to prevent autolysis. To elucidate the potential effects and cellular regulatory mechanisms of elevated LT activity, we individually cloned the periplasmic domains of two membrane-bound LTs, MltA and MltB under the control of the arabinose-inducible system for overexpression in the periplasmic space in E. coli. Interestingly, upon induction, the culture undergoes an initial period of cell lysis followed by robust growth restoration. The LT-overexpressing E. coli exhibits altered morphology with larger spherical cells, which is in line with the weakening of the PG layer due to aberrant LT activity. On the other hand, the restored cells display a similar rod shape and peptidoglycan profile that is indistinguishable from the uninduced control. Quantitative proteomics analysis of the restored cells identified significant protein enrichment in the regulator of capsule synthesis (Rcs) regulon, a two-component stress response known to be specifically activated by PG damage. We showed that LT-overexpressing E. coli with an inactivated Rcs system partially impairs the growth restoration process, supporting the involvement of the Rcs system in countering aberrant PG cleavage. Furthermore, we demonstrated that the elevated LT activity specifically potentiates β-lactam antibiotics against E. coli with a defective Rcs regulon, suggesting the dual effects of augmented PG cleavage and blocked PG synthesis as a potential antimicrobial strategy.
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Affiliation(s)
- Yaquan Liang
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - Yilin Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - JericMunChung Kwan
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371
| | - Yue Wang
- A*STAR Infectious Disease Labs, Singapore 138648
| | - Yuan Qiao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technical University, Singapore 637371.
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13
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Cho SH, Dekoninck K, Collet JF. Envelope-Stress Sensing Mechanism of Rcs and Cpx Signaling Pathways in Gram-Negative Bacteria. J Microbiol 2023; 61:317-329. [PMID: 36892778 DOI: 10.1007/s12275-023-00030-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
The global public health burden of bacterial antimicrobial resistance (AMR) is intensified by Gram-negative bacteria, which have an additional membrane, the outer membrane (OM), outside of the peptidoglycan (PG) cell wall. Bacterial two-component systems (TCSs) aid in maintaining envelope integrity through a phosphorylation cascade by controlling gene expression through sensor kinases and response regulators. In Escherichia coli, the major TCSs defending cells from envelope stress and adaptation are Rcs and Cpx, which are aided by OM lipoproteins RcsF and NlpE as sensors, respectively. In this review, we focus on these two OM sensors. β-Barrel assembly machinery (BAM) inserts transmembrane OM proteins (OMPs) into the OM. BAM co-assembles RcsF, the Rcs sensor, with OMPs, forming the RcsF-OMP complex. Researchers have presented two models for stress sensing in the Rcs pathway. The first model suggests that LPS perturbation stress disassembles the RcsF-OMP complex, freeing RcsF to activate Rcs. The second model proposes that BAM cannot assemble RcsF into OMPs when the OM or PG is under specific stresses, and thus, the unassembled RcsF activates Rcs. These two models may not be mutually exclusive. Here, we evaluate these two models critically in order to elucidate the stress sensing mechanism. NlpE, the Cpx sensor, has an N-terminal (NTD) and a C-terminal domain (CTD). A defect in lipoprotein trafficking results in NlpE retention in the inner membrane, provoking the Cpx response. Signaling requires the NlpE NTD, but not the NlpE CTD; however, OM-anchored NlpE senses adherence to a hydrophobic surface, with the NlpE CTD playing a key role in this function.
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Affiliation(s)
- Seung-Hyun Cho
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium. .,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.
| | - Kilian Dekoninck
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium.,University of California, Berkeley, CA, 94720, USA
| | - Jean-Francois Collet
- WELBIO-Walloon Excellence in Life Sciences and Biotechnology, 1200, Brussels, Belgium.,de Duve Institute, Université Catholique de Louvain, 1200, Brussels, Belgium
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14
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Lach SR, Kumar S, Kim S, Im W, Konovalova A. Conformational rearrangements in the sensory RcsF/OMP complex mediate signal transduction across the bacterial cell envelope. PLoS Genet 2023; 19:e1010601. [PMID: 36706155 PMCID: PMC9907809 DOI: 10.1371/journal.pgen.1010601] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/08/2023] [Accepted: 01/06/2023] [Indexed: 01/28/2023] Open
Abstract
Timely detection and repair of envelope damage are paramount for bacterial survival. The Regulator of Capsule Synthesis (Rcs) stress response can transduce the stress signals across the multilayered gram-negative cell envelope to regulate gene expression in the cytoplasm. Previous studies defined the overall pathway, which begins with the sensory lipoprotein RcsF interacting with several outer membrane proteins (OMPs). RcsF can also interact with the periplasmic domain of the negative regulator IgaA, derepressing the downstream RcsCDB phosphorelay. However, how the RcsF/IgaA interaction is regulated at the molecular level to activate the signaling in response to stress remains poorly understood. In this study, we used a site-saturated mutant library of rcsF to carry out several independent genetic screens to interrogate the mechanism of signal transduction from RcsF to IgaA. We analyzed several distinct classes of rcsF signaling mutants, and determined the region of RcsF that is critically important for signal transduction. This region is bifunctional as it is important for RcsF interaction with both IgaA and OMPs. The mutant analysis provides strong evidence for conformational changes in the RcsF/OMP complex mediating signal transduction to IgaA, and the first direct evidence that OMPs play an important regulatory role in Rcs signaling.
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Affiliation(s)
- Sarah R. Lach
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
| | - Santosh Kumar
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Seonghoon Kim
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, United States of America
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Wonpil Im
- Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, Pennsylvania, United States of America
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas, United States of America
- * E-mail:
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15
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Quintero-Yanes A, Mayard A, Hallez R. The two-component system ChvGI maintains cell envelope homeostasis in Caulobacter crescentus. PLoS Genet 2022; 18:e1010465. [PMID: 36480504 PMCID: PMC9731502 DOI: 10.1371/journal.pgen.1010465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 10/09/2022] [Indexed: 12/13/2022] Open
Abstract
Two-component systems (TCS) are often used by bacteria to rapidly assess and respond to environmental changes. The ChvG/ChvI (ChvGI) TCS conserved in α-proteobacteria is known for regulating expression of genes related to exopolysaccharide production, virulence and growth. The sensor kinase ChvG autophosphorylates upon yet unknown signals and phosphorylates the response regulator ChvI to regulate transcription. Recent studies in Caulobacter crescentus showed that chv mutants are sensitive to vancomycin treatment and fail to grow in synthetic minimal media. In this work, we identified the osmotic imbalance as the main cause of growth impairment in synthetic minimal media. We also determined the ChvI regulon and found that ChvI regulates cell envelope architecture by controlling outer membrane, peptidoglycan assembly/recycling and inner membrane proteins. In addition, we found that ChvI phosphorylation is also activated upon antibiotic treatment with vancomycin. We also challenged chv mutants with other cell envelope related stress and found that treatment with antibiotics targeting transpeptidation of peptidoglycan during cell elongation impairs growth of the mutant. Finally, we observed that the sensor kinase ChvG relocates from a patchy-spotty distribution to distinctive foci after transition from complex to synthetic minimal media. Interestingly, this pattern of (re)location has been described for proteins involved in cell growth control and peptidoglycan synthesis upon osmotic shock. Overall, our data support that the ChvGI TCS is mainly used to monitor and respond to osmotic imbalances and damages in the peptidoglycan layer to maintain cell envelope homeostasis.
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Affiliation(s)
- Alex Quintero-Yanes
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Aurélie Mayard
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
| | - Régis Hallez
- Bacterial Cell cycle & Development (BCcD), Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Science (NARILIS), University of Namur, Namur, Belgium
- WELBIO, University of Namur, Namur, Belgium
- * E-mail:
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16
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Bian Z, Liu W, Jin J, Hao Y, Jiang L, Xie Y, Zhang H. Rcs phosphorelay affects the sensitivity of Escherichia coli to plantaricin BM-1 by regulating biofilm formation. Front Microbiol 2022; 13:1071351. [PMID: 36504793 PMCID: PMC9729257 DOI: 10.3389/fmicb.2022.1071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction: Plantaricin BM-1 is a class IIa bacteriocin produced by Lactobacillus plantarum BM-1 that exerts significant antibacterial activity against many foodborne bacteria. Studies have shown that class IIa bacteriocins inhibit Gram-positive bacteria via the mannose phosphotransferase system; however, their mechanism of action against Gram-negative bacteria remains unknown. In this study, we explored the mechanism through which the Rcs phosphorelay affects the sensitivity of Escherichia coli K12 cells to plantaricin BM-1. Methods and Results: The minimum inhibitory concentrations of plantaricin BM-1 against E. coli K12, E. coli JW5917 (rcsC mutant), E. coli JW2204 (rcsD mutant), and E. coli JW2205 (rcsB mutant) were 1.25, 0.59, 1.31, and 1.22 mg/ml, respectively. Growth curves showed that E. coli JW5917 sensitivity to plantaricin BM-1 increased to the same level as that of E. coli K12 after complementation. Meanwhile, scanning electron microscopy and transmission electron microscopy revealed that, under the action of plantaricin BM-1, the appearance of E. coli JW5917 cells did not significantly differ from that of E. coli K12 cells; however, cell contents were significantly reduced and plasmolysis and shrinkage were observed at both ends. Crystal violet staining and laser scanning confocal microscopy showed that biofilm formation was significantly reduced after rcsC mutation, while proteomic analysis identified 382 upregulated and 260 downregulated proteins in E. coli JW5917. In particular, rcsC mutation was found to affect the expression of proteins related to biofilm formation, with growth curve assays showing that the deletion of these proteins increased E. coli sensitivity to plantaricin BM-1. Discussion: Consequently, we speculated that the Rcs phosphorelay may regulate the sensitivity of E. coli to plantaricin BM-1 by affecting biofilm formation. This finding of class IIa bacteriocin against Gram-negative bacteria mechanism provides new insights.
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Affiliation(s)
- Zheng Bian
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Wenbo Liu
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Junhua Jin
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China
| | - Yanling Hao
- Department of Nutrition and Health, Key Laboratory of Functional Dairy, Co-constructed by Ministry of Education and Beijing Government, China Agricultural University, Beijing, China
| | - Linshu Jiang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Yuanhong Xie
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China,*Correspondence: Yuanhong Xie, ; Hongxing Zhang,
| | - Hongxing Zhang
- Beijing Laboratory of Food Quality and Safety, Beijing Key Laboratory of Agricultural Product Detection and Control of Spoilage Organisms and Pesticide Residue, Beijing Engineering Technology Research Center of Food Safety Immune Rapid Detection, College of Food Science and Engineering, Beijing University of Agriculture, Beijing, China,*Correspondence: Yuanhong Xie, ; Hongxing Zhang,
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17
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Wade N, Wesseling CMJ, Innocenti P, Slingerland CJ, Koningstein GM, Luirink J, Martin NI. Synthesis and Structure-Activity Studies of β-Barrel Assembly Machine Complex Inhibitor MRL-494. ACS Infect Dis 2022; 8:2242-2252. [PMID: 36318734 PMCID: PMC9673140 DOI: 10.1021/acsinfecdis.2c00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In the hunt for new antibiotics with activity against Gram-negative pathogens, the outer membrane β-barrel assembly machine (BAM) complex has become an increasingly interesting target. The recently reported BAM complex inhibitor, MRL-494, was discovered via a screening campaign for molecules that target the outer membrane. Notably, MRL-494 was reported to be an unintended byproduct generated during the synthesis of an unrelated compound, and as such no synthesis of the compound was disclosed. We here present a convenient and reliable route for the synthesis of MRL-494 that scales well. The antibacterial activity measured for synthesized MRL-494 matches that reported in the literature. Furthermore, MRL-494 was found to exhibit potent synergistic activity with rifampicin against Gram-negative bacteria, including E. coli, K. pneumoniae, A. baumannii, and P. aeruginosa. MRL-494 was also found to cause outer membrane disruption and induction of the Rcs stress response pathway. In addition, we undertook a focused structure-activity study specifically aimed at elucidating the roles played by the two guanidine moieties contained within the structure of MRL-494.
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Affiliation(s)
- Nicola Wade
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Charlotte M. J. Wesseling
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Paolo Innocenti
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Cornelis J. Slingerland
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Gregory M. Koningstein
- Department
of Molecular Microbiology, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Joen Luirink
- Department
of Molecular Microbiology, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Nathaniel I. Martin
- Biological
Chemistry Group, Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands,
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18
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The Roles of the Two-Component System, MtrAB, in Response to Diverse Cell Envelope Stresses in Dietzia sp. DQ12-45-1b. Appl Environ Microbiol 2022; 88:e0133722. [PMID: 36190258 PMCID: PMC9599347 DOI: 10.1128/aem.01337-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Two-component systems (TCSs) act as common regulatory systems allowing bacteria to detect and respond to multiple environmental stimuli, including cell envelope stress. The MtrAB TCS of Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance, and thus is found to be highly conserved across this phylum. However, how precisely the MtrAB TCS regulates cellular homeostasis in response to environmental stress remains unclear. Here, we show that the MtrAB TCS plays an important role in the tolerance to different types of cell envelope stresses, including environmental stresses (i.e., oxidative stress, lysozyme, SDS, osmotic pressure, and alkaline pH stresses) and envelope-targeting antibiotics (i.e., isoniazid, ethambutol, glycopeptide, and β-lactam antibiotics) in Dietzia sp. DQ12-45-1b. An mtrAB mutant strain exhibited slower growth compared to the wild-type strain and was characterized by abnormal cell shapes when exposed to various environmental stresses. Moreover, deletion of mtrAB resulted in decreased resistance to isoniazid, ethambutol, and β-lactam antibiotics. Further, Cleavage under targets and tagmentation sequencing (CUT&Tag-seq) and electrophoretic mobility shift assays (EMSAs) revealed that MtrA binds the promoters of genes involved in peptidoglycan biosynthesis (ldtB, ldtA, murJ), hydrolysis (GJR88_03483, GJR88_4713), and cell division (ftsE). Together, our findings demonstrated that the MtrAB TCS is essential for the survival of Dietzia sp. DQ12-45-1b under various cell envelope stresses, primarily by controlling multiple downstream cellular pathways. Our work suggests that TCSs act as global sensors and regulators in maintaining cellular homeostasis, such as during episodes of various environmental stresses. The present study should shed light on the understanding of mechanisms for bacterial adaptivity to extreme environments. IMPORTANCE The multilayered cell envelope is the first line of bacterial defense against various extreme environments. Bacteria utilize a large number of sensing and regulatory systems to maintain cell envelope homeostasis under multiple stress conditions. The two-component system (TCS) is the main sensing and responding apparatus for environmental adaptation. The MtrAB TCS highly conserved in Actinobacteria is critical for cell wall homeostasis, cell proliferation, osmoprotection, and antibiotic resistance. However, how MtrAB works with regard to signals impacting changes to the cell envelope is not fully understood. Here, we found that in the Actinobacterium Dietzia sp. DQ12-45-1b, a TCS named MtrAB is pivotal for ensuring normal cell growth as well as maintaining proper cell morphology in response to various cell envelope stresses, namely, by regulating the expression of cell envelope-related genes. Our findings should greatly advance our understanding of the adaptive mechanisms responsible for maintaining cell integrity in times of sustained environmental shocks.
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19
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A Defect in Lipoprotein Modification by Lgt Leads to Abnormal Morphology and Cell Death in Escherichia coli That Is Independent of Major Lipoprotein Lpp. J Bacteriol 2022; 204:e0016422. [PMID: 35938851 PMCID: PMC9487459 DOI: 10.1128/jb.00164-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Lgt is an essential enzyme in proteobacteria and therefore a potential target for novel antibiotics. The effect of Lgt depletion on growth, morphology, and viability was studied in Escherichia coli to assess whether absence of Lgt leads to cell death. Two Lgt depletion strains were used in which lgt was under the control of an arabinose-inducible promoter that allowed regulation of Lgt protein levels. Reduced levels of Lgt led to severe growth and morphological defects that could be restored by expressing lgt in trans, demonstrating that only Lgt is responsible for the distorted phenotypes. In the absence of major lipoprotein Lpp, growth defects were partially restored when low levels of Lgt were still present; however, lgt could not be deleted in the absence of Lpp. Our results demonstrate that Lpp is not the main cause of cell death under conditions of Lgt depletion and that other lipoproteins are important in cell envelope biogenesis and cell viability. Specific inhibitors of Lgt are thus promising for the development of novel antibiotics. IMPORTANCE Incomplete maturation and envelope mislocalization of lipoproteins, through inhibition or mutations in lipoprotein modification enzymes or transport to the outer membrane, are lethal in proteobacteria. Resistance to small-molecule inhibition or the appearance of suppressor mutations is often directly correlated with the presence of abundant outer membrane lipoprotein Lpp. Our results show that Lgt, the first enzyme of the lipoprotein modification pathway, is still required for growth and viability in the absence of Lpp and thus is necessary for the function of other essential lipoproteins in the cell envelope. This adds credence to the hypothesis that Lgt is essential in proteobacteria and an attractive target for the development of novel antibiotics.
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20
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Lin L, Capozzoli R, Ferrand A, Plum M, Vettiger A, Basler M. Subcellular localization of Type VI secretion system assembly in response to cell–cell contact. EMBO J 2022; 41:e108595. [PMID: 35634969 PMCID: PMC9251886 DOI: 10.15252/embj.2021108595] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 04/18/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Bacteria require a number of systems, including the type VI secretion system (T6SS), for interbacterial competition and pathogenesis. The T6SS is a large nanomachine that can deliver toxins directly across membranes of proximal target cells. Since major reassembly of T6SS is necessary after each secretion event, accurate timing and localization of T6SS assembly can lower the cost of protein translocation. Although critically important, mechanisms underlying spatiotemporal regulation of T6SS assembly remain poorly understood. Here, we used super‐resolution live‐cell imaging to show that while Acinetobacter and Burkholderia thailandensis can assemble T6SS at any site, a significant subset of T6SS assemblies localizes precisely to the site of contact between neighboring bacteria. We identified a class of diverse, previously uncharacterized, periplasmic proteins required for this dynamic localization of T6SS to cell–cell contact (TslA). This precise localization is also dependent on the outer membrane porin OmpA. Our analysis links transmembrane communication to accurate timing and localization of T6SS assembly as well as uncovers a pathway allowing bacterial cells to respond to cell–cell contact during interbacterial competition.
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Affiliation(s)
- Lin Lin
- Biozentrum University of Basel Basel Switzerland
| | | | - Alexia Ferrand
- Biozentrum Imaging Core Facility University of Basel Basel Switzerland
| | - Miro Plum
- Biozentrum University of Basel Basel Switzerland
| | | | - Marek Basler
- Biozentrum University of Basel Basel Switzerland
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21
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Sun J, Rutherford ST, Silhavy TJ, Huang KC. Physical properties of the bacterial outer membrane. Nat Rev Microbiol 2022; 20:236-248. [PMID: 34732874 PMCID: PMC8934262 DOI: 10.1038/s41579-021-00638-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
It has long been appreciated that the Gram-negative outer membrane acts as a permeability barrier, but recent studies have uncovered a more expansive and versatile role for the outer membrane in cellular physiology and viability. Owing to recent developments in microfluidics and microscopy, the structural, rheological and mechanical properties of the outer membrane are becoming apparent across multiple scales. In this Review, we discuss experimental and computational studies that have revealed key molecular factors and interactions that give rise to the spatial organization, limited diffusivity and stress-bearing capacity of the outer membrane. These physical properties suggest broad connections between cellular structure and physiology, and we explore future prospects for further elucidation of the implications of outer membrane construction for cellular fitness and survival.
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Affiliation(s)
- Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Steven T. Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA 94080, USA,To whom correspondence should be addressed: , ,
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA,To whom correspondence should be addressed: , ,
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA. .,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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22
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Hermansen S, Linke D, Leo JC. Transmembrane β-barrel proteins of bacteria: From structure to function. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:113-161. [PMID: 35034717 DOI: 10.1016/bs.apcsb.2021.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The outer membrane of Gram-negative bacteria is a specialized organelle conferring protection to the cell against various environmental stresses and resistance to many harmful compounds. The outer membrane has a number of unique features, including an asymmetric lipid bilayer, the presence of lipopolysaccharides and an individual proteome. The vast majority of the integral transmembrane proteins in the outer membrane belongs to the family of β-barrel proteins. These evolutionarily related proteins share a cylindrical, anti-parallel β-sheet core fold spanning the outer membrane. The loops and accessory domains attached to the β-barrel allow for a remarkable versatility in function for these proteins, ranging from diffusion pores and transporters to enzymes and adhesins. We summarize the current knowledge on β-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets.
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Affiliation(s)
- Simen Hermansen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C Leo
- Antimicrobial resistance, Omics and Microbiota Group, Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom.
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23
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Csoma N, Colau D, Collet JF. Detecting Lipoproteins Sneaking Out of the Lipopolysaccharide Leaflet. Methods Mol Biol 2022; 2548:169-178. [PMID: 36151498 DOI: 10.1007/978-1-0716-2581-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The envelope of Gram-negative bacteria is an essential compartment which is in direct contact with the environment; the envelope maintains cellular integrity and functions as a permeability barrier protecting the cell from toxic compounds. The outer layer of the envelope is an asymmetric membrane whose external leaflet is mainly composed of lipopolysaccharide molecules. Recently, there has been growing evidence that lipoproteins (i.e., soluble proteins anchored to a membrane by a lipid moiety) decorate the lipopolysaccharide leaflet in the model bacterium Escherichia coli, challenging the current paradigm that lipoproteins remain in the periplasm in this organism. However, assessing the surface exposure of lipoproteins is challenging. Here, we describe an optimized and reproducible dotblot protocol to assess the presence of lipoproteins at the surface of E. coli and other bacterial models. We added all necessary controls to reduce the possibility of artifacts giving rise to false-positive results. We selected the stress sensor RcsF as a model lipoprotein to illustrate the method, which can be used for any other lipoprotein.
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Affiliation(s)
- Naemi Csoma
- de Duve Institute, Université catholique de Louvain and WELBIO, Brussels, Belgium
| | - Didier Colau
- de Duve Institute, Université catholique de Louvain and WELBIO, Brussels, Belgium
| | - Jean-François Collet
- de Duve Institute, Université catholique de Louvain and WELBIO, Brussels, Belgium.
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24
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Adler BA, Kazakov AE, Zhong C, Liu H, Kutter E, Lui LM, Nielsen TN, Carion H, Deutschbauer AM, Mutalik VK, Arkin AP. The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34910616 PMCID: PMC8744999 DOI: 10.1099/mic.0.001126] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance and host-range is sparse. Here, we employed genome-wide screens in Salmonella enterica serovar Typhimurium to discover host determinants involved in resistance to eleven diverse lytic phages including four new phages isolated from a therapeutic phage cocktail. We uncovered 301 diverse host factors essential in phage infection, many of which are shared between multiple phages demonstrating potential cross-resistance mechanisms. We validate many of these novel findings and uncover the intricate interplay between RpoS, the virulence-associated general stress response sigma factor and RpoN, the nitrogen starvation sigma factor in phage cross-resistance. Finally, the infectivity pattern of eleven phages across a panel of 23 genome sequenced Salmonella strains indicates that additional constraints and interactions beyond the host factors uncovered here define the phage host range.
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Affiliation(s)
- Benjamin A Adler
- The UC Berkeley-UCSF Graduate Program in Bioengineering, Berkeley, California, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexey E Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Crystal Zhong
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Lauren M Lui
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Torben N Nielsen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Heloise Carion
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Vivek K Mutalik
- Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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25
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Increased Production of Colanic Acid by an Engineered Escherichia coli Strain, Mediated by Genetic and Environmental Perturbations. Appl Biochem Biotechnol 2021; 193:4083-4096. [PMID: 34542821 DOI: 10.1007/s12010-021-03671-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Colanic acid (CA) is a major exopolysaccharide synthesized by Escherichia coli that serves as a constituent of biofilm matrices. CA demonstrates potential applications in the food, cosmetics, and pharmaceutical industry. Moreover, L-fucose, a monomeric constituent of CA, exhibits various physiological activities, such as antitumor, anti-inflammatory, and skin-whitening. Here, the effects of genetic and environmental perturbations were investigated for improving CA production by E. coli. When rcsF, a positive regulator gene of CA synthesis, was expressed in E. coli ΔwaaF, a CA-producing strain constructed previously, the CA titer increased to 3051.2 mg/L as compared to 2052.8 mg/L observed with E. coli ΔwaaF. Among the environmental factors tested, namely, osmotic and oxidative stresses and pH, pH was a primary factor that significantly improved CA production. When the pH of the culture medium of E. coli ΔwaaF + rcsF was maintained at 7, the CA titer significantly increased to 4351.6 mg/L. The CA yield obtained with E. coli ΔwaaF + rcsF grown at pH 7 was 5180.4 mg CA/g dry cell weight, which is the highest yield of CA reported so far. This engineered E. coli system with optimization of environmental conditions can be employed for fast and economically-feasible production of CA.
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26
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Steenhuis M, Corona F, ten Hagen-Jongman CM, Vollmer W, Lambin D, Selhorst P, Klaassen H, Versele M, Chaltin P, Luirink J. Combining Cell Envelope Stress Reporter Assays in a Screening Approach to Identify BAM Complex Inhibitors. ACS Infect Dis 2021; 7:2250-2263. [PMID: 34125508 PMCID: PMC8369490 DOI: 10.1021/acsinfecdis.0c00728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Indexed: 12/11/2022]
Abstract
The development of new antibiotics is particularly problematic in Gram-negative bacteria due to the presence of the outer membrane (OM), which serves as a permeability barrier. Recently, the β-barrel assembly machine (BAM), located in the OM and responsible for β-barrel type OM protein (OMP) assembly, has been validated as a novel target for antibiotics. Here, we identified potential BAM complex inhibitors using a screening approach that reports on cell envelope σE and Rcs stress in Escherichia coli. Screening a library consisting of 316 953 compounds yielded five compounds that induced σE and Rcs stress responses, while not inducing the intracellular heat-shock response. Two of the five compounds (compounds 2 and 14) showed the characteristics of known BAM complex inhibitors: synergy with OMP biogenesis mutants, decrease in the abundance of various OMPs, and loss of OM integrity. Importantly, compound 2 also inhibited BAM-dependent OMP folding in an in vitro refolding assay using purified BAM complex reconstituted in proteoliposomes.
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Affiliation(s)
- Maurice Steenhuis
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Federico Corona
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, United
Kingdom
| | - Corinne M. ten Hagen-Jongman
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, United
Kingdom
| | - Dominique Lambin
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Philippe Selhorst
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Hugo Klaassen
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Matthias Versele
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Patrick Chaltin
- Center
for Drug Design and Development (CD3), KU
Leuven R&D, Waaistraat 6, B-3000 Leuven, Belgium
| | - Joen Luirink
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
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27
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High-throughput suppressor screen demonstrates that RcsF monitors outer membrane integrity and not Bam complex function. Proc Natl Acad Sci U S A 2021; 118:2100369118. [PMID: 34349021 DOI: 10.1073/pnas.2100369118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The regulator of capsule synthesis (Rcs) is a complex signaling cascade that monitors gram-negative cell envelope integrity. The outer membrane (OM) lipoprotein RcsF is the sensory component, but how RcsF functions remains elusive. RcsF interacts with the β-barrel assembly machinery (Bam) complex, which assembles RcsF in complex with OM proteins (OMPs), resulting in RcsF's partial cell surface exposure. Elucidating whether RcsF/Bam or RcsF/OMP interactions are important for its sensing function is challenging because the Bam complex is essential, and partial loss-of-function mutations broadly compromise the OM biogenesis. Our recent discovery that, in the absence of nonessential component BamE, RcsF inhibits function of the central component BamA provided a genetic tool to select mutations that specifically prevent RcsF/BamA interactions. We employed a high-throughput suppressor screen to isolate a collection of such rcsF and bamA mutants and characterized their impact on RcsF/OMP assembly and Rcs signaling. Using these mutants and BamA inhibitors MRL-494L and darobactin, we provide multiple lines of evidence against the model in which RcsF senses Bam complex function. We show that Rcs activation in bam mutants results from secondary OM and lipopolysaccharide defects and that RcsF/OMP assembly is required for this activation, supporting an active role of RcsF/OMP complexes in sensing OM stress.
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28
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Disorder is a critical component of lipoprotein sorting in Gram-negative bacteria. Nat Chem Biol 2021; 17:1093-1100. [PMID: 34326538 DOI: 10.1038/s41589-021-00845-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/29/2021] [Indexed: 01/01/2023]
Abstract
Gram-negative bacteria express structurally diverse lipoproteins in their cell envelope. Here, we find that approximately half of lipoproteins destined to the Escherichia coli outer membrane display an intrinsically disordered linker at their N terminus. Intrinsically disordered regions are common in proteins, but establishing their importance in vivo has remained challenging. As we sought to unravel how lipoproteins mature, we discovered that unstructured linkers are required for optimal trafficking by the Lol lipoprotein sorting system, whereby linker deletion re-routes three unrelated lipoproteins to the inner membrane. Focusing on the stress sensor RcsF, we found that replacing the linker with an artificial peptide restored normal outer-membrane targeting only when the peptide was of similar length and disordered. Overall, this study reveals the role played by intrinsic disorder in lipoprotein sorting, providing mechanistic insight into the biogenesis of these proteins and suggesting that evolution can select for intrinsic disorder that supports protein function.
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29
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Abstract
Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.
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Affiliation(s)
| | - Urs Jenal
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland; ,
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30
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Abstract
By evolving strains of E. coli that hyper-resist sedimentation, we discovered an uncharacterized mechanism that bacteria can use to remain in suspension indefinitely without expending energy. This unusual phenotype was traced to the anchoring of long colanic acid polymers (CAP) that project from the cell surface. Although each characterized mutant activated this same mechanism, the genes responsible and the strengths of the phenotypes varied. Mutations in rcsC, lpp, igaA, or the yjbEFGH operon were sufficient to stimulate sedimentation resistance, while mutations altering the cps promoter, cdgI, or yjbF provided phenotypic enhancements. The sedimentation resistances changed in response to temperature, growth phase, and carbon source and each mutant exhibited significantly reduced biofilm formation. We discovered that the degree of colony mucoidy exhibited by these mutants was not related to the degree of Rcs pathways activation or to the amount of CAP that was produced; rather, it was related to the fraction of CAP that was shed as a true exopolysaccharide. Therefore, these and other mutations that activate this phenotype are likely to be absent from genetic screens that relied on centrifugation to harvest bacteria. We also found that this anchored CAP form is not linked to LPS cores and may not be attached to the outer membrane.IMPORTANCEBacteria can partition in aqueous environments between surface-dwelling, planktonic, sedimentary, and biofilm forms. Residence in each location provides an advantage depending on nutritional and environmental stresses and a community of a single species is often observed to be distributed throughout two or more of these niches. Another adaptive strategy is to produce an extracellular capsule, which provides an environmental shield for the microbe and can allow escape from predators and immune systems. We discovered that bacteria can either shed or stably anchor capsules to dramatically alter their propensity to sediment. The degree to which the bacteria anchor their capsule is controlled by a stress sensing system, suggesting that anchoring may be used as an adaptive response to severe environmental challenges.
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31
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Saha S, Lach SR, Konovalova A. Homeostasis of the Gram-negative cell envelope. Curr Opin Microbiol 2021; 61:99-106. [PMID: 33901778 DOI: 10.1016/j.mib.2021.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 01/08/2023]
Abstract
The Gram-negative bacterial cell envelope is a complex structure and its homeostasis is essential for bacterial survival. Envelope stress responses (ESRs) are signal transduction pathways that monitor the fidelity of envelope assembly during normal growth and also detect and repair envelope damage caused by external assaults, including immune factors, protein toxins, and antibiotics. In this review, we focus on three best-studied ESRs and discuss the mechanisms by which ESRs detect various perturbations of envelope assembly and integrity and regulate envelope remodeling to promote bacterial survival. We will highlight the complex relationship of ESRs with envelope biogenesis pathways and discuss some of the challenges in this field on the road to mapping the global regulatory network of envelope homeostasis.
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Affiliation(s)
- Shreya Saha
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA
| | - Sarah R Lach
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, 6767 Bertner Avenue, Houston, TX, 77030, USA
| | - Anna Konovalova
- Department of Microbiology and Molecular Genetics, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), 6431 Fannin Street, Houston, TX, 77030, USA.
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32
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Mychack A, Janakiraman A. Defects in The First Step of Lipoprotein Maturation Underlie The Synthetic Lethality of Escherichia coli Lacking The Inner Membrane Proteins YciB And DcrB. J Bacteriol 2021; 203:JB.00640-20. [PMID: 33431434 PMCID: PMC8095458 DOI: 10.1128/jb.00640-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/14/2020] [Indexed: 11/20/2022] Open
Abstract
Nearly a quarter of the Escherichia coli genome encodes for inner membrane proteins of which approximately a third have unassigned or poorly understood function. We had previously demonstrated that the synergy between the functional roles of the inner membrane-spanning YciB and the inner membrane lipoprotein DcrB, is essential in maintaining cell envelope integrity. In yciB dcrB cells, the abundant outer membrane lipoprotein, Lpp, mislocalizes to the inner membrane where it forms toxic linkages to peptidoglycan. Here, we report that the aberrant localization of Lpp in this double mutant is due to inefficient lipid modification at the first step in lipoprotein maturation. Both Cpx and Rcs signaling systems are upregulated in response to the envelope stress. The phosphatidylglycerol-pre-prolipoprotein diacylglyceryl transferase, Lgt, catalyzes the initial step in lipoprotein maturation. Our results suggest that the attenuation in Lgt-mediated transacylation in the double mutant is not a consequence of lowered phosphatidylglycerol levels. Instead, we posit that altered membrane fluidity, perhaps due to changes in lipid homeostasis, may lead to the impairment in Lgt function. Consistent with this idea, a dcrB null is not viable when grown at low temperatures, conditions which impact membrane fluidity. Like the yciB dcrB double mutant, dcrB null-mediated toxicity can be overcome in distinct ways - by increased expression of Lgt, deletion of lpp, or removal of Lpp-peptidoglycan linkages. The last of these events leads to elevated membrane vesiculation and lipid loss, which may, in turn, impact membrane homeostasis in the double mutant.Importance A distinguishing feature of Gram-negative bacteria is their double-membraned cell envelope which presents a formidable barrier against environmental stress. In E. coli, more than a quarter of the cellular proteins reside at the inner membrane but about a third of these proteins are functionally unassigned or their function is incompletely understood. Here, we show that the synthetic lethality underlying the inactivation of two inner membrane proteins, a small integral membrane protein YciB, and a lipoprotein, DcrB, results from the attenuation of the first step of lipoprotein maturation at the inner membrane. We propose that these two inner membrane proteins YciB and DcrB play a role in membrane homeostasis in E. coli and related bacteria.
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Affiliation(s)
- Aaron Mychack
- Department of Biology, 160 Convent Ave. MR 526, The City College of CUNY, New York, NY, 100031, USA
- Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
| | - Anuradha Janakiraman
- Department of Biology, 160 Convent Ave. MR 526, The City College of CUNY, New York, NY, 100031, USA
- Program in Biology, The Graduate Center, CUNY, Fifth Avenue, New York, NY, 10016, USA
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33
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Meng J, Young G, Chen J. The Rcs System in Enterobacteriaceae: Envelope Stress Responses and Virulence Regulation. Front Microbiol 2021; 12:627104. [PMID: 33658986 PMCID: PMC7917084 DOI: 10.3389/fmicb.2021.627104] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
The bacterial cell envelope is a protective barrier at the frontline of bacterial interaction with the environment, and its integrity is regulated by various stress response systems. The Rcs (regulator of capsule synthesis) system, a non-orthodox two-component regulatory system (TCS) found in many members of the Enterobacteriaceae family, is one of the envelope stress response pathways. The Rcs system can sense envelope damage or defects and regulate the transcriptome to counteract stress, which is particularly important for the survival and virulence of pathogenic bacteria. In this review, we summarize the roles of the Rcs system in envelope stress responses (ESRs) and virulence regulation. We discuss the environmental and intrinsic sources of envelope stress that cause activation of the Rcs system with an emphasis on the role of RcsF in detection of envelope stress and signal transduction. Finally, the different regulation mechanisms governing the Rcs system's control of virulence in several common pathogens are introduced. This review highlights the important role of the Rcs system in the environmental adaptation of bacteria and provides a theoretical basis for the development of new strategies for control, prevention, and treatment of bacterial infections.
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Affiliation(s)
- Jiao Meng
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Glenn Young
- Department of Food Science and Technology, University of California, Davis, Davis, CA, United States
| | - Jingyu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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34
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El Rayes J, Rodríguez-Alonso R, Collet JF. Lipoproteins in Gram-negative bacteria: new insights into their biogenesis, subcellular targeting and functional roles. Curr Opin Microbiol 2021; 61:25-34. [PMID: 33667939 DOI: 10.1016/j.mib.2021.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Bacterial lipoproteins are globular proteins anchored to a membrane by a lipid moiety. By discovering new functions carried out by lipoproteins, recent research has highlighted the crucial roles played by these proteins in the cell envelope of Gram-negative bacteria. Here, after discussing the wide range of activities carried out by lipoproteins in the model bacterium Escherichia coli, we review new insights into the essential mechanisms involved in lipoprotein maturation, sorting and targeting to their final destination. A special attention will also be given to the recent identification of lipoproteins on the surface of E. coli and of other bacteria. The renewed interest in lipoproteins is driven by the need to identify novel targets for antibiotic development.
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Affiliation(s)
- Jessica El Rayes
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Raquel Rodríguez-Alonso
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium
| | - Jean-François Collet
- WELBIO, Avenue Hippocrate 75, 1200 Brussels, Belgium; de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200 Brussels, Belgium.
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35
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Consoli E, Collet JF, den Blaauwen T. The Escherichia coli Outer Membrane β-Barrel Assembly Machinery (BAM) Anchors the Peptidoglycan Layer by Spanning It with All Subunits. Int J Mol Sci 2021; 22:ijms22041853. [PMID: 33673366 PMCID: PMC7918090 DOI: 10.3390/ijms22041853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Gram-negative bacteria possess a three-layered envelope composed of an inner membrane, surrounded by a peptidoglycan (PG) layer, enclosed by an outer membrane. The envelope ensures protection against diverse hostile milieus and offers an effective barrier against antibiotics. The layers are connected to each other through many protein interactions. Bacteria evolved sophisticated machineries that maintain the integrity and the functionality of each layer. The β-barrel assembly machinery (BAM), for example, is responsible for the insertion of the outer membrane integral proteins including the lipopolysaccharide transport machinery protein LptD. Labelling bacterial cells with BAM-specific fluorescent antibodies revealed the spatial arrangement between the machinery and the PG layer. The antibody detection of each BAM subunit required the enzymatic digestion of the PG layer. Enhancing the spacing between the outer membrane and PG does not abolish this prerequisite. This suggests that BAM locally sets the distance between OM and the PG layer. Our results shed new light on the local organization of the envelope.
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Affiliation(s)
- Elisa Consoli
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Jean-François Collet
- de Duve Institute, Université Catholique de Louvain, B-1200 Brussels, Belgium;
- Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), B-1200 Brussels, Belgium
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
- Correspondence:
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36
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Tomasek D, Kahne D. The assembly of β-barrel outer membrane proteins. Curr Opin Microbiol 2021; 60:16-23. [PMID: 33561734 DOI: 10.1016/j.mib.2021.01.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/17/2021] [Accepted: 01/22/2021] [Indexed: 01/21/2023]
Abstract
The outer membranes of Gram-negative bacteria, mitochondria, and chloroplasts contain β-barrel integral membrane proteins. In bacteria, the five-protein β-barrel assembly machine (Bam) accelerates the folding and membrane integration of these proteins. The central component of the machine, BamA, contains a β-barrel domain that can adopt a lateral-open state with its N-terminal and C-terminal β-strands unpaired. Recently, strategies have been developed to capture β-barrel folding intermediates on the Bam complex. Biochemical and structural studies provide support for a model in which substrates assemble at the lateral opening of BamA. In this model, the N-terminal β-strand of BamA captures the C-terminal β-strand of substrates by hydrogen bonding to allow their directional folding and subsequent release into the membrane.
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Affiliation(s)
- David Tomasek
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel Kahne
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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37
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Smith LM, Jackson SA, Malone LM, Ussher JE, Gardner PP, Fineran PC. The Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages. Nat Microbiol 2021; 6:162-172. [PMID: 33398095 DOI: 10.1038/s41564-020-00822-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 10/23/2020] [Indexed: 12/16/2022]
Abstract
Bacteria harbour multiple innate defences and adaptive CRISPR-Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR-Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for ~300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR-Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR-Cas systems. Rcs-mediated repression of CRISPR-Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.
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Affiliation(s)
- Leah M Smith
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Simon A Jackson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Genetics Otago, University of Otago, Dunedin, New Zealand
| | - Lucia M Malone
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - James E Ussher
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Paul P Gardner
- Genetics Otago, University of Otago, Dunedin, New Zealand.,Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. .,Genetics Otago, University of Otago, Dunedin, New Zealand. .,Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand.
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38
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Rcs Phosphorelay Responses to Truncated Lipopolysaccharide-Induced Cell Envelope Stress in Yersinia enterocolitica. Molecules 2020; 25:molecules25235718. [PMID: 33287412 PMCID: PMC7730088 DOI: 10.3390/molecules25235718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 01/22/2023] Open
Abstract
Lipopolysaccharide (LPS) is the major component of the outer membrane of Gram-negative bacteria, and its integrity is monitored by various stress response systems. Although the Rcs system is involved in the envelope stress response and regulates genes controlling numerous bacterial cell functions of Yersinia enterocolitica, whether it can sense the truncated LPS in Y. enterocolitica remains unclear. In this study, the deletion of the Y. enterocolitica waaF gene truncated the structure of LPS and produced a deep rough LPS. The truncated LPS increased the cell surface hydrophobicity and outer membrane permeability, generating cell envelope stress. The truncated LPS also directly exposed the smooth outer membrane to the external environment and attenuated the resistance to adverse conditions, such as impaired survival under polymyxin B and sodium dodecyl sulfate (SDS) exposure. Further phenotypic experiment and gene expression analysis indicated that the truncated LPS was correlated with the activation of the Rcs phosphorelay, thereby repressing cell motility and biofilm formation. Our findings highlight the importance of LPS integrity in maintaining membrane function and broaden the understanding of Rcs phosphorelay signaling in response to cell envelope stress, thus opening new avenues to develop effective antimicrobial agents for combating Y. enterocolitica infections.
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39
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Choi E, Jeon H, Oh C, Hwang J. Elucidation of a Novel Role of YebC in Surface Polysaccharides Regulation of Escherichia coli bipA-Deletion. Front Microbiol 2020; 11:597515. [PMID: 33240252 PMCID: PMC7682190 DOI: 10.3389/fmicb.2020.597515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/23/2020] [Indexed: 12/19/2022] Open
Abstract
The BipA (BPI-inducible protein A) protein is ubiquitously conserved in various bacterial species and belongs to the translational GTPase family. Interestingly, the function of Escherichia coli BipA is not essential for cell growth under normal growth conditions. However, cultivation of bipA-deleted cells at 20°C leads to cold-sensitive growth defect and several phenotypic changes in ribosome assembly, capsule production, and motility, suggesting its global regulatory roles. Previously, our genomic library screening revealed that the overexpressed ribosomal protein (r-protein) L20 partially suppressed cold-sensitive growth defect by resolving the ribosomal abnormality in bipA-deleted cells at low temperature. Here, we explored another genomic library clone containing yebC, which encodes a predicted transcriptional factor that is not directly associated with ribosome biogenesis. Interestingly, overexpression of yebC in bipA-deleted cells diminished capsule synthesis and partially restored lipopolysaccharide (LPS) core maturation at a low temperature without resolving defects in ribosome assembly or motility, indicating that YebC may be specifically involved in the regulation of exopolysaccharide and LPS core synthesis. In this study, we collectively investigated the impacts of bipA-deletion on E. coli capsule, LPS, biofilm formation, and motility and revealed novel roles of YebC in extracellular polysaccharide production and LPS core synthesis at low temperature using this mutant strain. Furthermore, our findings suggest that ribosomal defects as well as increased capsule synthesis, and changes in LPS composition may contribute independently to the cold-sensitivity of bipA-deleted cells, implying multiple regulatory roles of BipA.
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Affiliation(s)
- Eunsil Choi
- Microbiological Resource Research Institute, Pusan National University, Busan, South Korea.,Department of Microbiology, Pusan National University, Busan, South Korea
| | - Hyerin Jeon
- Microbiological Resource Research Institute, Pusan National University, Busan, South Korea
| | - Changmin Oh
- Microbiological Resource Research Institute, Pusan National University, Busan, South Korea
| | - Jihwan Hwang
- Microbiological Resource Research Institute, Pusan National University, Busan, South Korea.,Department of Microbiology, Pusan National University, Busan, South Korea
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40
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Steenhuis M, ten Hagen-Jongman CM, van Ulsen P, Luirink J. Stress-Based High-Throughput Screening Assays to Identify Inhibitors of Cell Envelope Biogenesis. Antibiotics (Basel) 2020; 9:antibiotics9110808. [PMID: 33202774 PMCID: PMC7698014 DOI: 10.3390/antibiotics9110808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/16/2022] Open
Abstract
The structural integrity of the Gram-negative cell envelope is guarded by several stress responses, such as the σE, Cpx and Rcs systems. Here, we report on assays that monitor these responses in E. coli upon addition of antibacterial compounds. Interestingly, compromised peptidoglycan synthesis, outer membrane biogenesis and LPS integrity predominantly activated the Rcs response, which we developed into a robust HTS (high-throughput screening) assay that is suited for phenotypic compound screening. Furthermore, by interrogating all three cell envelope stress reporters, and a reporter for the cytosolic heat-shock response as control, we found that inhibitors of specific envelope targets induce stress reporter profiles that are distinct in quality, amplitude and kinetics. Finally, we show that by using a host strain with a more permeable outer membrane, large-scaffold antibiotics can also be identified by the reporter assays. Together, the data suggest that stress profiling is a useful first filter for HTS aimed at inhibitors of cell envelope processes.
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41
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Hu L, Yu F, Liu M, Chen J, Zong B, Zhang Y, Chen T, Wang C, Zhang T, Zhang J, Zhu Y, Wang X, Chen H, Tan C. RcsB-dependent regulation of type VI secretion system in porcine extra-intestinal pathogenic Escherichia coli. Gene 2020; 768:145289. [PMID: 33181257 DOI: 10.1016/j.gene.2020.145289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 02/02/2023]
Abstract
Signal transduction system and specialized secretory devices are crucial for bacteria to sense and adequately adapt in adverse environmental conditions. Therefore, it's crucial for microbes to detect and respond to lethal attacks when envelope is perturbed so as to minimize and fix the damage in milieu. We investigated the adaptive response of porcine extra-intestinal pathogenic Escherichia coli PCN033 to polymyxin B challenge. Treatment with polymyxin B led to rapid and robust activation of Rcs system via RcsF, as well as the accumulation of reactive oxygen species. ExPEC T6SS expression was strongly induced by RcsB in Rcs system, resulting in the reduction in the damage to constitute a survival strategy. Finally, we show that T6SS of ExPEC is involved in its pathogenicity in mouse model. Compared with the wild type strain, the deletion of T6SS genes led to a decrease in the organ colonization ability, and the RcsFS2DM3Q mutant that caused Rcs activation had a stronger colonization ability than the wild type strain. In conclusion, Rcs system orchestrates Rcs cascade to trigger antioxidant defense of T6SS, and presents a typical model in which a bacterium reschedule its transcription network via the Rcs phosphorelay pathway in response to membrane perturbations for survival and pathogenesis.
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Affiliation(s)
- Linlin Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Feifei Yu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Manli Liu
- Hubei Biopesticide Engineering Research Centre, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
| | - Jing Chen
- Guangzhou Medical University, Guangzhou 511436, Guangdong, China
| | - Bingbing Zong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Tumei Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Chenchen Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Tongchao Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Junli Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yongwei Zhu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Centre for Sustainable Pig Production, Wuhan, Hubei 430070, China.
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42
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Mutalik VK, Adler BA, Rishi HS, Piya D, Zhong C, Koskella B, Kutter EM, Calendar R, Novichkov PS, Price MN, Deutschbauer AM, Arkin AP. High-throughput mapping of the phage resistance landscape in E. coli. PLoS Biol 2020; 18:e3000877. [PMID: 33048924 PMCID: PMC7553319 DOI: 10.1371/journal.pbio.3000877] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
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Affiliation(s)
- Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
| | - Benjamin A. Adler
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Harneet S. Rishi
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Denish Piya
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
| | - Crystal Zhong
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Britt Koskella
- Department of Integrative Biology, University of California – Berkeley, Berkeley, California, United States of America
| | | | - Richard Calendar
- Department of Molecular and Cell Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Pavel S. Novichkov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Morgan N. Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California – Berkeley, Berkeley, California, United States of America
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Innovative Genomics Institute, Berkeley, California, United States of America
- Department of Bioengineering, University of California – Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California – Berkeley, Berkeley, California, United States of America
- Designated Emphasis Program in Computational and Genomic Biology, University of California – Berkeley, Berkeley, California, United States of America
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43
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Dekoninck K, Létoquart J, Laguri C, Demange P, Bevernaegie R, Simorre JP, Dehu O, Iorga BI, Elias B, Cho SH, Collet JF. Defining the function of OmpA in the Rcs stress response. eLife 2020; 9:60861. [PMID: 32985973 PMCID: PMC7553776 DOI: 10.7554/elife.60861] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/26/2020] [Indexed: 01/18/2023] Open
Abstract
OmpA, a protein commonly found in the outer membrane of Gram-negative bacteria, has served as a paradigm for the study of β-barrel proteins for several decades. In Escherichia coli, OmpA was previously reported to form complexes with RcsF, a surface-exposed lipoprotein that triggers the Rcs stress response when damage occurs in the outer membrane and the peptidoglycan. How OmpA interacts with RcsF and whether this interaction allows RcsF to reach the surface has remained unclear. Here, we integrated in vivo and in vitro approaches to establish that RcsF interacts with the C-terminal, periplasmic domain of OmpA, not with the N-terminal β-barrel, thus implying that RcsF does not reach the bacterial surface via OmpA. Our results suggest a novel function for OmpA in the cell envelope: OmpA competes with the inner membrane protein IgaA, the downstream Rcs component, for RcsF binding across the periplasm, thereby regulating the Rcs response.
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Affiliation(s)
- Kilian Dekoninck
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Juliette Létoquart
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | | | - Pascal Demange
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Robin Bevernaegie
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Olivia Dehu
- de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Bogdan I Iorga
- de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium.,Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Seung-Hyun Cho
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - Jean-Francois Collet
- WELBIO, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
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44
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A Trimeric Autotransporter Enhances Biofilm Cohesiveness in Yersinia pseudotuberculosis but Not in Yersinia pestis. J Bacteriol 2020; 202:JB.00176-20. [PMID: 32778558 DOI: 10.1128/jb.00176-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/01/2020] [Indexed: 12/17/2022] Open
Abstract
Cohesion of biofilms made by Yersinia pestis and Yersinia pseudotuberculosis has been attributed solely to an extracellular polysaccharide matrix encoded by the hms genes (Hms-dependent extracellular matrix [Hms-ECM]). However, mutations in the Y. pseudotuberculosis BarA/UvrY/CsrB regulatory cascade enhance biofilm stability without dramatically increasing Hms-ECM production. We found that treatment with proteinase K enzyme effectively destabilized Y. pseudotuberculosis csrB mutant biofilms, suggesting that cell-cell interactions might be mediated by protein adhesins or extracellular matrix proteins. We identified an uncharacterized trimeric autotransporter lipoprotein (YPTB2394), repressed by csrB, which has been referred to as YadE. Biofilms made by a ΔyadE mutant strain were extremely sensitive to mechanical disruption. Overexpression of yadE in wild-type Y. pseudotuberculosis increased biofilm cohesion, similar to biofilms made by csrB or uvrY mutants. We found that the Rcs signaling cascade, which represses Hms-ECM production, activated expression of yadE The yadE gene appears to be functional in Y. pseudotuberculosis but is a pseudogene in modern Y. pestis strains. Expression of functional yadE in Y. pestis KIM6+ weakened biofilms made by these bacteria. This suggests that although the YadE autotransporter protein increases Y. pseudotuberculosis biofilm stability, it may be incompatible with the Hms-ECM production that is essential for Y. pestis biofilm production in fleas. Inactivation of yadE in Y. pestis may be another instance of selective gene loss in the evolution of flea-borne transmission by this species.IMPORTANCE The evolution of Yersinia pestis from its Y. pseudotuberculosis ancestor involved gene acquisition and gene losses, leading to differences in biofilm production. Characterizing the unique biofilm features of both species may provide better understanding of how each adapts to its specific niches. This study identifies a trimeric autotransporter, YadE, that promotes biofilm stability of Y. pseudotuberculosis but which has been inactivated in Y. pestis, perhaps because it is not compatible with the Hms polysaccharide that is crucial for biofilms inside fleas. We also reveal that the Rcs signaling cascade, which represses Hms expression, activates YadE in Y. pseudotuberculosis The ability of Y. pseudotuberculosis to use polysaccharide or YadE protein for cell-cell adhesion may help it produce biofilms in different environments.
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45
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Kimkes TEP, Heinemann M. How bacteria recognise and respond to surface contact. FEMS Microbiol Rev 2020; 44:106-122. [PMID: 31769807 PMCID: PMC7053574 DOI: 10.1093/femsre/fuz029] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/23/2019] [Indexed: 12/27/2022] Open
Abstract
Bacterial biofilms can cause medical problems and issues in technical systems. While a large body of knowledge exists on the phenotypes of planktonic and of sessile cells in mature biofilms, our understanding of what happens when bacteria change from the planktonic to the sessile state is still very incomplete. Fundamental questions are unanswered: for instance, how do bacteria sense that they are in contact with a surface, and what are the very initial cellular responses to surface contact. Here, we review the current knowledge on the signals that bacteria could perceive once they attach to a surface, the signal transduction systems that could be involved in sensing the surface contact and the cellular responses that are triggered as a consequence to surface contact ultimately leading to biofilm formation. Finally, as the main obstacle in investigating the initial responses to surface contact has been the difficulty to experimentally study the dynamic response of single cells upon surface attachment, we also review recent experimental approaches that could be employed to study bacterial surface sensing, which ultimately could lead to an improved understanding of how biofilm formation could be prevented.
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Affiliation(s)
- Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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46
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Collet JF, Cho SH, Iorga BI, Goemans CV. How the assembly and protection of the bacterial cell envelope depend on cysteine residues. J Biol Chem 2020; 295:11984-11994. [PMID: 32487747 PMCID: PMC7443483 DOI: 10.1074/jbc.rev120.011201] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/02/2020] [Indexed: 12/15/2022] Open
Abstract
The cell envelope of Gram-negative bacteria is a multilayered structure essential for bacterial viability; the peptidoglycan cell wall provides shape and osmotic protection to the cell, and the outer membrane serves as a permeability barrier against noxious compounds in the external environment. Assembling the envelope properly and maintaining its integrity are matters of life and death for bacteria. Our understanding of the mechanisms of envelope assembly and maintenance has increased tremendously over the past two decades. Here, we review the major achievements made during this time, giving central stage to the amino acid cysteine, one of the least abundant amino acid residues in proteins, whose unique chemical and physical properties often critically support biological processes. First, we review how cysteines contribute to envelope homeostasis by forming stabilizing disulfides in crucial bacterial assembly factors (LptD, BamA, and FtsN) and stress sensors (RcsF and NlpE). Second, we highlight the emerging role of enzymes that use cysteine residues to catalyze reactions that are necessary for proper envelope assembly, and we also explain how these enzymes are protected from oxidative inactivation. Finally, we suggest future areas of investigation, including a discussion of how cysteine residues could contribute to envelope homeostasis by functioning as redox switches. By highlighting the redox pathways that are active in the envelope of Escherichia coli, we provide a timely overview of the assembly of a cellular compartment that is the hallmark of Gram-negative bacteria.
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Affiliation(s)
| | - Seung-Hyun Cho
- de Duve Institute, UCLouvain, Brussels, Belgium; WELBIO, Brussels, Belgium
| | - Bogdan I Iorga
- de Duve Institute, UCLouvain, Brussels, Belgium; Université Paris-Saclay, CNRS UPR 2301, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
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47
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Envelope Stress and Regulation of the Salmonella Pathogenicity Island 1 Type III Secretion System. J Bacteriol 2020; 202:JB.00272-20. [PMID: 32571967 DOI: 10.1128/jb.00272-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/15/2020] [Indexed: 01/19/2023] Open
Abstract
Salmonella enterica serovar Typhimurium uses a type three secretion system (T3SS) encoded on the Salmonella pathogenicity island 1 (SPI1) to invade intestinal epithelial cells and induce inflammatory diarrhea. The SPI1 T3SS is regulated by numerous environmental and physiological signals, integrated to either activate or repress invasion. Transcription of hilA, encoding the transcriptional activator of the SPI1 structural genes, is activated by three AraC-like regulators, HilD, HilC, and RtsA, that act in a complex feed-forward loop. Deletion of bamB, encoding a component of the β-barrel assembly machinery, causes a dramatic repression of SPI1, but the mechanism was unknown. Here, we show that partially defective β-barrel assembly activates the RcsCDB regulon, leading to decreased hilA transcription. This regulation is independent of RpoE activation. Though Rcs has been previously shown to repress SPI1 when disulfide bond formation is impaired, we show that activation of Rcs in a bamB background is dependent on the sensor protein RcsF, whereas disulfide bond status is sensed independently. Rcs decreases transcription of the flagellar regulon, including fliZ, the product of which indirectly activates HilD protein activity. Rcs also represses hilD, hilC, and rtsA promoters by an unknown mechanism. Both dsbA and bamB mutants have motility defects, though this is simply regulatory in a bamB background; motility is restored in the absence of Rcs. Effector secretion assays show that repression of SPI1 in a bamB background is also regulatory; if expressed, the SPI1 T3SS is functional in a bamB background. This emphasizes the sensitivity of SPI1 regulation to overall envelope homeostasis.IMPORTANCE Salmonella causes worldwide foodborne illness, leading to massive disease burden and an estimated 600,000 deaths per year. Salmonella infects orally and invades intestinal epithelial cells using a type 3 secretion system that directly injects effector proteins into host cells. This first step in invasion is tightly regulated by a variety of inputs. In this work, we demonstrate that Salmonella senses the functionality of outer membrane assembly in determining regulation of invasion machinery, and we show that Salmonella uses distinct mechanisms to detect specific perturbations in envelope assembly.
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48
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Wall EA, Majdalani N, Gottesman S. IgaA negatively regulates the Rcs Phosphorelay via contact with the RcsD Phosphotransfer Protein. PLoS Genet 2020; 16:e1008610. [PMID: 32716926 PMCID: PMC7418988 DOI: 10.1371/journal.pgen.1008610] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/11/2020] [Accepted: 06/10/2020] [Indexed: 01/13/2023] Open
Abstract
Two-component systems and phosphorelays play central roles in the ability of bacteria to rapidly respond to changing environments. In E. coli and related enterobacteria, the complex Rcs phosphorelay is a critical player in the bacterial response to antimicrobial peptides, beta-lactam antibiotics, and other disruptions at the cell surface. The Rcs system is unusual in that an inner membrane protein, IgaA, is essential due to its negative regulation of the RcsC/RcsD/RcsB phosphorelay. While it is known that IgaA transduces signals from the outer membrane lipoprotein RcsF, how it interacts with the phosphorelay has remained unknown. Here we performed in vivo interaction assays and genetic dissection of the critical proteins and found that IgaA interacts with the phosphorelay protein RcsD, and that this interaction is necessary for regulation. Interactions between IgaA and RcsD within their respective periplasmic domains of these two proteins anchor repression of signaling. However, the signaling response depends on a second interaction between cytoplasmic loop 1 of IgaA and a truncated Per-Arndt-Sim (PAS-like) domain in RcsD. A single point mutation in the PAS-like domain increased interactions between the two proteins and blocked induction of the phosphorelay. IgaA may regulate RcsC, the histidine kinase that initiates phosphotransfer through the phosphorelay, indirectly, via its contacts with RcsD. Unlike RcsD, and unlike many other histidine kinases, the periplasmic domain of RcsC is dispensable for the response to signals that induce the Rcs phosphorelay system. The multiple contacts between IgaA and RcsD constitute a poised sensing system, preventing potentially toxic over-activation of this phosphorelay while enabling it to rapidly and quantitatively respond to signals. The Rcs phosphorelay system plays a central role in allowing enterobacteria to sense and respond to antibiotics, host-produced antimicrobials, and interactions with surfaces. A unique negative regulator, IgaA, attenuates signaling from this pathway when it is not needed, but how IgaA controls the phosphorelay has been unclear. We define a set of critical interactions between IgaA and the phosphotransfer protein RcsD, including a periplasmic contact between IgaA and RcsD that mediates a necessary inhibition of Rcs signaling. Inhibition is further modulated by regulated interactions between the cytoplasmic domains of each protein, providing a sensitive regulatory switch.
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Affiliation(s)
- Erin A. Wall
- National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nadim Majdalani
- National Cancer Institute, Bethesda, Maryland, United States of America
| | - Susan Gottesman
- National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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49
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Meng J, Bai J, Xu J, Huang C, Chen J. Differential regulation of physiological activities by RcsB and OmpR in Yersinia enterocolitica. FEMS Microbiol Lett 2020; 366:5584338. [PMID: 31598670 DOI: 10.1093/femsle/fnz210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
A thorough understanding of the mechanisms of Rcs and EnvZ/OmpR phosphorelay systems that allow Yersinia enterocolitica to thrive in various environments is crucial to prevent and control Y. enterocolitica infections. In this study, we showed that RcsB and OmpR have the ability to function differently in modulating a diverse array of physiological processes in Y. enterocolitica. The rcsB mutant stimulated flagella biosynthesis and increased motility, biofilm formation and c-di-GMP production by upregulating flhDC, hmsHFRS and hmsT. However, mutation in ompR exhibited a non-motile phenotype due to the lack of flagella. Biofilm formation was reduced and less c-di-GMP was produced through the downregulation of flhDC, hmsHFRS and hmsT expression when Y. enterocolitica was exposed to low osmolarity conditions. Furthermore, OmpR was identified to be important for Y. enterocolitica to grow in extreme temperature conditions. Importantly, ompR mutations in Y. enterocolitica were more sensitive to polymyxin B and sodium dodecyl sulfate than rcsB mutations. Since motility, biofilm formation and environmental tolerance are critical for bacterial colonization of the host, these findings indicated that OmpR is more critical than RcsB in shaping the pathogenic phenotype of Y. enterocolitica.
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Affiliation(s)
- Jiao Meng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.,Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jiaqi Bai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.,Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Junhong Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.,Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Can Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.,Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jingyu Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.,Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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50
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Rodríguez-Alonso R, Létoquart J, Nguyen VS, Louis G, Calabrese AN, Iorga BI, Radford SE, Cho SH, Remaut H, Collet JF. Structural insight into the formation of lipoprotein-β-barrel complexes. Nat Chem Biol 2020; 16:1019-1025. [PMID: 32572278 PMCID: PMC7610366 DOI: 10.1038/s41589-020-0575-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/15/2020] [Indexed: 12/14/2022]
Abstract
The β-barrel assembly machinery (BAM) inserts outer membrane β-barrel proteins (OMPs) in the outer membrane of Gram-negative bacteria. In Enterobacteriacea, BAM also mediates export of the stress sensor lipoprotein RcsF to the cell surface by assembling RcsF-OMP complexes. Here, we report the crystal structure of the key BAM component BamA in complex with RcsF. BamA adopts an inward-open conformation, with the lateral gate to the membrane closed. RcsF is lodged deep inside the lumen of the BamA barrel, binding regions proposed to undergo an outward and lateral opening during OMP insertion. On the basis of our structural and biochemical data, we propose a push-and-pull model for RcsF export upon conformational cycling of BamA and provide a mechanistic explanation for how RcsF uses its interaction with BamA to detect envelope stress. Our data also suggest that the flux of incoming OMP substrates is involved in the control of BAM activity.
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Affiliation(s)
- Raquel Rodríguez-Alonso
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Juliette Létoquart
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Van Son Nguyen
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium
| | - Gwennaelle Louis
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium.,de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Antonio N Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Bogdan I Iorga
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium.,Université Paris-Saclay, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Seung-Hyun Cho
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium. .,Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Brussels, Belgium.
| | - Jean-François Collet
- Walloon Excellence in Life Sciences and Biotechnology, Brussels, Belgium. .,de Duve Institute, Université catholique de Louvain, Brussels, Belgium.
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