1
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Stanley HM, Trent MS. Loss of YhcB results in overactive fatty acid biosynthesis. mBio 2024; 15:e0079024. [PMID: 38742872 DOI: 10.1128/mbio.00790-24] [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: 03/14/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Loss of the Escherichia coli inner membrane protein YhcB results in pleomorphic cell morphology and clear growth defects. Prior work suggested that YhcB was directly involved in cell division or peptidoglycan assembly. We found that loss of YhcB is detrimental in genetic backgrounds in which lipopolysaccharide (LPS) or glycerophospholipid (GPL) synthesis is altered. The growth defect of ΔyhcB could be rescued through inactivation of the Mla pathway, a system responsible for the retrograde transport of GPLs that are mislocalized to the outer leaflet of the outer membrane. Interestingly, this rescue was dependent upon the outer membrane phospholipase PldA that cleaves GPLs at the bacterial surface. Since the freed fatty acids resulting from PldA activity serve as a signal to the cell to increase LPS synthesis, this result suggested that outer membrane lipids are imbalanced in ΔyhcB. Mutations that arose in ΔyhcB populations during two independent suppressor screens were in genes encoding subunits of the acetyl coenzyme A carboxylase complex, which initiates fatty acid biosynthesis (FAB). These mutations fully restored cell morphology and reduced GPL levels, which were increased compared to wild-type bacteria. Growth of ΔyhcB with the FAB-targeting antibiotic cerulenin also increased cellular fitness. Furthermore, genetic manipulation of FAB and lipid biosynthesis showed that decreasing FAB rescued ΔyhcB filamentation, whereas increasing LPS alone could not. Altogether, these results suggest that YhcB may play a pivotal role in regulating FAB and, in turn, impact cell envelope assembly and cell division.IMPORTANCESynthesis of the Gram-negative cell envelope is a dynamic and complex process that entails careful coordination of many biosynthetic pathways. The inner and outer membranes are composed of molecules that are energy intensive to synthesize, and, accordingly, these synthetic pathways are under tight regulation. The robust nature of the Gram-negative outer membrane renders it naturally impermeable to many antibiotics and therefore a target of interest for antimicrobial design. Our data indicate that when the inner membrane protein YhcB is absent in Escherichia coli, the pathway for generating fatty acid substrates needed for all membrane lipid synthesis is dysregulated which leads to increased membrane material. These findings suggest a potentially novel regulatory mechanism for controlling the rate of fatty acid biosynthesis.
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Affiliation(s)
- Hannah M Stanley
- Department of Microbiology, College of Art and Sciences, University of Georgia, Athens, Georgia, USA
| | - M Stephen Trent
- Department of Microbiology, College of Art and Sciences, University of Georgia, Athens, Georgia, USA
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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2
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Fivenson EM, Dubois L, Bernhardt TG. Co-ordinated assembly of the multilayered cell envelope of Gram-negative bacteria. Curr Opin Microbiol 2024; 79:102479. [PMID: 38718542 DOI: 10.1016/j.mib.2024.102479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 06/11/2024]
Abstract
Bacteria surround themselves with complex cell envelopes to maintain their integrity and protect against external insults. The envelope of Gram-negative organisms is multilayered, with two membranes sandwiching the periplasmic space that contains the peptidoglycan cell wall. Understanding how this complicated surface architecture is assembled during cell growth and division is a major fundamental problem in microbiology. Additionally, because the envelope is an important antibiotic target and determinant of intrinsic antibiotic resistance, understanding the mechanisms governing its assembly is relevant to therapeutic development. In the last several decades, most of the factors required to build the Gram-negative envelope have been identified. However, surprisingly, little is known about how the biogenesis of the different cell surface layers is co-ordinated. Here, we provide an overview of recent work that is beginning to uncover the links connecting the different envelope biosynthetic pathways and assembly machines to ensure uniform envelope growth.
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Affiliation(s)
- Elayne M Fivenson
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Laurent Dubois
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States
| | - Thomas G Bernhardt
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, United States; Howard Hughes Medical Institute, Boston, United States.
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3
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Möller AM, Vázquez-Hernández M, Kutscher B, Brysch R, Brückner S, Marino EC, Kleetz J, Senges CHR, Schäkermann S, Bandow JE, Narberhaus F. Common and varied molecular responses of Escherichia coli to five different inhibitors of the lipopolysaccharide biosynthetic enzyme LpxC. J Biol Chem 2024; 300:107143. [PMID: 38458396 PMCID: PMC10998244 DOI: 10.1016/j.jbc.2024.107143] [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: 01/10/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
A promising yet clinically unexploited antibiotic target in difficult-to-treat Gram-negative bacteria is LpxC, the key enzyme in the biosynthesis of lipopolysaccharides, which are the major constituents of the outer membrane. Despite the development of dozens of chemically diverse LpxC inhibitor molecules, it is essentially unknown how bacteria counteract LpxC inhibition. Our study provides comprehensive insights into the response against five different LpxC inhibitors. All compounds bound to purified LpxC from Escherichia coli. Treatment of E. coli with these compounds changed the cell shape and stabilized LpxC suggesting that FtsH-mediated proteolysis of the inactivated enzyme is impaired. LpxC inhibition sensitized E. coli to vancomycin and rifampin, which poorly cross the outer membrane of intact cells. Four of the five compounds led to an accumulation of lyso-phosphatidylethanolamine, a cleavage product of phosphatidylethanolamine, generated by the phospholipase PldA. The combined results suggested an imbalance in lipopolysaccharides and phospholipid biosynthesis, which was corroborated by the global proteome response to treatment with the LpxC inhibitors. Apart from LpxC itself, FabA and FabB responsible for the biosynthesis of unsaturated fatty acids were consistently induced. Upregulated compound-specific proteins are involved in various functional categories, such as stress reactions, nucleotide, or amino acid metabolism and quorum sensing. Our work shows that antibiotics targeting the same enzyme do not necessarily elicit identical cellular responses. Moreover, we find that the response of E. coli to LpxC inhibition is distinct from the previously reported response in Pseudomonas aeruginosa.
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Affiliation(s)
- Anna-Maria Möller
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | | | - Blanka Kutscher
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Raffael Brysch
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Simon Brückner
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Emily C Marino
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia Kleetz
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Christoph H R Senges
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Sina Schäkermann
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Julia E Bandow
- Applied Microbiology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany.
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4
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Mao Z, Zhang H, Cai W, Yang Y, Zhang X, Jiang F, Li G. NhaA facilitates the maintenance of bacterial envelope integrity and the evasion of complement attack contributing to extraintestinal pathogenic Escherichia coli virulence. Infect Immun 2023; 91:e0003923. [PMID: 37815368 PMCID: PMC10652942 DOI: 10.1128/iai.00039-23] [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: 01/24/2023] [Accepted: 09/01/2023] [Indexed: 10/11/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is responsible for severe bloodstream infections in humans and animals. However, the mechanisms underlying ExPEC's serum resistance remain incompletely understood. Through the transposon-directed insertion-site sequencing approach, our previous study identified nhaA, the gene encoding a Na+/H+ antiporter, as a crucial factor for infection in vivo. In this study, we investigated the role of NhaA in ExPEC virulence utilizing both in vitro models and systemic infection models involving avian and mammalian animals. Genetic mutagenesis analysis revealed that nhaA deletion resulted in filamentous bacterial morphology and rendered the bacteria more susceptible to sodium dodecyl sulfate, suggesting the role of nhaA in maintaining cell envelope integrity. The nhaA mutant also displayed heightened sensitivity to complement-mediated killing compared to the wild-type strain, attributed to augmented deposition of complement components (C3b and C9). Remarkably, NhaA played a more crucial role in virulence compared to several well-known factors, including Iss, Prc, NlpI, and OmpA. Our findings revealed that NhaA significantly enhanced virulence across diverse human ExPEC prototype strains within B2 phylogroups, suggesting widespread involvement in virulence. Given its pivotal role, NhaA could serve as a potential drug target for tackling ExPEC infections.
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Affiliation(s)
- Zhao Mao
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Haobo Zhang
- National Animal Tuberculosis Reference Laboratory, Division of Zoonoses Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Wentong Cai
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yan Yang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyang Zhang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fengwei Jiang
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ganwu Li
- Key Laboratory of Veterinary Public Health of Ministry of Agriculture, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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5
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Warner IA, Kok WJ, Martinelli N, Yang Z, Goodall ECA, Henderson I. Microbial Primer: Transposon directed insertion site sequencing (TraDIS): A high throughput method for linking genotype to phenotype. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 37909267 DOI: 10.1099/mic.0.001385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Genetic screens are a key tool for linking phenotype and genotype. Transposon mutagenesis was one of the first genetic methodologies to associate genetic loci with phenotypes. The advent of next-generation sequencing transformed the use of this technique allowing rapid interrogation of whole genomes for genes that correlate with phenotype. One method is transposon directed insertion-site sequencing (TraDIS). Here we describe the method, recent developments in technology, and the advantages and disadvantages of this method compared to other genetic screening tools.
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Affiliation(s)
- Isabel A Warner
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Weine J Kok
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Nicole Martinelli
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Zihao Yang
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Emily C A Goodall
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Ian Henderson
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
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6
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Maniyeri A, Wieczorek A, Ayyolath A, Sugalska W, Klein G, Raina S. Suppressors of lapC Mutation Identify New Regulators of LpxC, Which Mediates the First Committed Step in Lipopolysaccharide Biosynthesis. Int J Mol Sci 2023; 24:15174. [PMID: 37894855 PMCID: PMC10607373 DOI: 10.3390/ijms242015174] [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: 09/05/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Gram-negative bacteria, such as Escherichia coli, are characterized by an asymmetric outer membrane (OM) with lipopolysaccharide (LPS) located in the outer leaflet and phospholipids facing the inner leaflet. E. coli recruits LPS assembly proteins LapB, LapC and LapD in concert with FtsH protease to ensure a balanced biosynthesis of LPS and phospholipids. We recently reported that bacteria either lacking the periplasmic domain of the essential LapC protein (lapC190) or in the absence of LapD exhibit an elevated degradation of LpxC, which catalyzes the first committed step in LPS biosynthesis. To further understand the functions of LapC and LapD in regulating LPS biosynthesis, we show that the overproduction of the intact LapD suppresses the temperature sensitivity (Ts) of lapC190, but not when either its N-terminal transmembrane anchor or specific conserved amino acids in the C-terminal domain are mutated. Moreover, overexpression of srrA, marA, yceJ and yfgM genes can rescue the Ts phenotype of lapC190 bacteria by restoring LpxC amounts. We further show that MarA-mediated suppression requires the expression of mla genes, whose products participate in the maintenance of OM asymmetry, and the SrrA-mediated suppression requires the presence of cardiolipin synthase A.
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Affiliation(s)
| | | | | | | | - Gracjana Klein
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
| | - Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, 80-233 Gdansk, Poland; (A.M.); (A.W.); (A.A.); (W.S.)
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7
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Som N, Reddy M. Cross-talk between phospholipid synthesis and peptidoglycan expansion by a cell wall hydrolase. Proc Natl Acad Sci U S A 2023; 120:e2300784120. [PMID: 37276399 PMCID: PMC10268279 DOI: 10.1073/pnas.2300784120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
The Gram-negative bacterial cell envelope is a complex multilayered structure comprising a bilayered phospholipid (PL) membrane that surrounds the cytoplasm (inner membrane or IM) and an asymmetric outer membrane (OM) with PLs in the inner leaflet and lipopolysaccharides in the outer leaflet. Between these two layers is the periplasmic space, which contains a highly cross-linked mesh-like glycan polymer, peptidoglycan (PG). During cell expansion, coordinated synthesis of each of these components is required to maintain the integrity of the cell envelope; however, it is currently not clear how such coordination is achieved. In this study, we show that a cross-link-specific PG hydrolase couples the expansion of PG sacculus with that of PL synthesis in the Gram-negative model bacterium, Escherichia coli. We find that unregulated activity of a PG hydrolytic enzyme, MepS is detrimental for growth of E. coli during fatty acid (FA)-limiting conditions. Further genetic and biochemical analyses revealed that cellular availability of FA or PL alters the post-translational stability of MepS by modulating the proteolytic activity of a periplasmic adaptor-protease complex, NlpI-Prc toward MepS. Our results indicate that loss of OM lipid asymmetry caused by alterations in PL abundance leads to the generation of a signal to the NlpI-Prc complex for the stabilization of MepS, which subsequently cleaves the cross-links to facilitate expansion of PG. In summary, our study shows the existence of a molecular cross-talk that enables coordinated expansion of the PG sacculus with that of membrane synthesis for balanced cell-envelope biogenesis.
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Affiliation(s)
- Nilanjan Som
- Centre for Cellular and Molecular Biology, Hyderabad, 500007Telangana, India
| | - Manjula Reddy
- Centre for Cellular and Molecular Biology, Hyderabad, 500007Telangana, India
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8
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Li S, Yan P, Mu B, Kang Y, Wang A. Preparation of Hybrid Nanopigments with Excellent Environmental Stability, Antibacterial and Antioxidant Properties Based on Monascus Red and Sepiolite by One-Step Grinding Process. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:nano13111792. [PMID: 37299695 DOI: 10.3390/nano13111792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
This study is focused on the preparation, characterization, and multifunctional properties of intelligent hybrid nanopigments. The hybrid nanopigments with excellent environmental stability and antibacterial and antioxidant properties were fabricated based on natural Monascus red, surfactant, and sepiolite via a facile one-step grinding process. The density functional theory calculations demonstrated that the surfactants loaded on sepiolite were in favor of enhancing the electrostatic, coordination, and hydrogen bonding interactions between Monascus red and sepiolite. Thus, the obtained hybrid nanopigments exhibited excellent antibacterial and antioxidant properties, with an inhibition effect on Gram-positive bacteria that was superior to that of Gram-negative bacteria. In addition, the scavenging activity on DPPH and hydroxyl free radicals as well as the reducing power of hybrid nanopigments were higher than those of hybrid nanopigments prepared without the addition of the surfactant. Inspired by nature, gas-sensitive reversible alochroic superamphiphobic coatings with excellent thermal and chemical stability were successfully designed by combining hybrid nanopigments and fluorinated polysiloxane. Therefore, intelligent multifunctional hybrid nanopigments have great application foreground in related fields.
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Affiliation(s)
- Shue Li
- Key Laboratory of Clay Mineral Applied Research of Gansu Province, Center of Eco-Material and Green Chemistry, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Penji Yan
- College of Chemistry and Chemical Engineering, Key Laboratory of Hexi Corridor Resources Utilization of Gansu Province, Hexi University, Zhangye 734000, China
| | - Bin Mu
- Key Laboratory of Clay Mineral Applied Research of Gansu Province, Center of Eco-Material and Green Chemistry, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yuru Kang
- Key Laboratory of Clay Mineral Applied Research of Gansu Province, Center of Eco-Material and Green Chemistry, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Aiqin Wang
- Key Laboratory of Clay Mineral Applied Research of Gansu Province, Center of Eco-Material and Green Chemistry, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, China
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9
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Nakamoto R, Bamyaci S, Blomqvist K, Normark S, Henriques-Normark B, Sham LT. The divisome but not the elongasome organizes capsule synthesis in Streptococcus pneumoniae. Nat Commun 2023; 14:3170. [PMID: 37264013 DOI: 10.1038/s41467-023-38904-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
The bacterial cell envelope consists of multiple layers, including the peptidoglycan cell wall, one or two membranes, and often an external layer composed of capsular polysaccharides (CPS) or other components. How the synthesis of all these layers is precisely coordinated remains unclear. Here, we identify a mechanism that coordinates the synthesis of CPS and peptidoglycan in Streptococcus pneumoniae. We show that CPS synthesis initiates from the division septum and propagates along the long axis of the cell, organized by the tyrosine kinase system CpsCD. CpsC and the rest of the CPS synthesis complex are recruited to the septum by proteins associated with the divisome (a complex involved in septal peptidoglycan synthesis) but not the elongasome (involved in peripheral peptidoglycan synthesis). Assembly of the CPS complex starts with CpsCD, then CpsA and CpsH, the glycosyltransferases, and finally CpsJ. Remarkably, targeting CpsC to the cell pole is sufficient to reposition CPS synthesis, leading to diplococci that lack CPS at the septum. We propose that septal CPS synthesis is important for chain formation and complement evasion, thereby promoting bacterial survival inside the host.
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Affiliation(s)
- Rei Nakamoto
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Sarp Bamyaci
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Karin Blomqvist
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-17177, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, SE-17176, Stockholm, Sweden
| | - Staffan Normark
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-17177, Sweden
| | - Birgitta Henriques-Normark
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, SE-17177, Sweden
- Clinical Microbiology, Karolinska University Hospital Solna, SE-17176, Stockholm, Sweden
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
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10
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Zeng X, Hinenoya A, Guan Z, Xu F, Lin J. Critical role of the RpoE stress response pathway in polymyxin resistance of Escherichia coli. J Antimicrob Chemother 2023; 78:732-746. [PMID: 36658759 PMCID: PMC10396327 DOI: 10.1093/jac/dkad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/31/2022] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVES Polymyxins, including colistin, are the drugs of last resort to treat MDR bacterial infections in humans. In-depth understanding of the molecular basis and regulation of polymyxin resistance would provide new therapeutic opportunities to combat increasing polymyxin resistance. Here we aimed to identify novel targets that are crucial for polymyxin resistance using Escherichia coli BL21(DE3), a unique colistin-resistant model strain. METHODS BL21(DE3) was subjected to random transposon mutagenesis for screening colistin-susceptible mutants. The insertion sites of desired mutants were mapped; the key genes of interest were also inactivated in different strains to examine functional conservation. Specific genes in the known PmrAB and PhoPQ regulatory network were inactivated to examine crosstalk among different pathways. Lipid A species and membrane phospholipids were analysed by normal phase LC/MS. RESULTS Among eight mutants with increased susceptibility to colistin, five mutants contained different mutations in three genes (rseP, degS and surA) that belong to the RpoE stress response pathway. Inactivation of rpoE, pmrB, eptA or pmrD led to significantly increased susceptibility to colistin; however, inactivation of phoQ or eptB did not change colistin MIC. RpoE mutation in different E. coli and Salmonella resistant strains all led to significant reduction in colistin MIC (16-32-fold). Inactivation of rpoE did not change the lipid A profile but significantly altered the phospholipid profile. CONCLUSIONS Inactivation of the important members of the RpoE regulon in polymyxin-resistant strains led to a drastic reduction in polymyxin MIC and an increase of lysophospholipids with no change in lipid A modifications.
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Affiliation(s)
- Ximin Zeng
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Atsushi Hinenoya
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- Asian Health Science Research Institute, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
| | - Fuzhou Xu
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
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11
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Möller AM, Brückner S, Tilg LJ, Kutscher B, Nowaczyk MM, Narberhaus F. LapB (YciM) orchestrates protein-protein interactions at the interface of lipopolysaccharide and phospholipid biosynthesis. Mol Microbiol 2023; 119:29-43. [PMID: 36464488 DOI: 10.1111/mmi.15005] [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: 09/29/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria functions as an essential barrier and is characterized by an asymmetric bilayer with lipopolysaccharide (LPS) in the outer leaflet. The enzyme LpxC catalyzes the first committed step in LPS biosynthesis. It plays a critical role in maintaining the balance between LPS and phospholipids (PL), which are both derived from the same biosynthetic precursor. The essential inner membrane proteins YejM (PbgA, LapC), LapB (YciM), and the protease FtsH are known to account for optimal LpxC levels, but the mechanistic details are poorly understood. LapB is thought to be a bi-functional protein serving as an adaptor for FtsH-mediated turnover of LpxC and acting as a scaffold in the coordination of LPS biosynthesis. Here, we provide experimental evidence for the physical interaction of LapB with proteins at the biosynthetic node from where the LPS and PL biosynthesis pathways diverge. By a total of four in vivo and in vitro assays, we demonstrate protein-protein interactions between LapB and the LPS biosynthesis enzymes LpxA, LpxC, and LpxD, between LapB and YejM, the anti-adaptor protein regulating LapB activity, and between LapB and FabZ, the first PL biosynthesis enzyme. Moreover, we uncovered a new adaptor function of LapB in destabilizing not only LpxC but also LpxD. Overall, our study shows that LapB is a multi-functional protein that serves as a protein-protein interaction hub for key enzymes in LPS and PL biogenesis presumably by virtue of multiple tetratricopeptide repeat (TPR) motifs in its cytoplasmic C-terminal region.
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Affiliation(s)
| | - Simon Brückner
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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12
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Goodall ECA, Morris FC, McKeand SA, Sullivan R, Warner IA, Sheehan E, Boelter G, Icke C, Cunningham AF, Cole JA, Banzhaf M, Bryant JA, Henderson IR. LI-Detector: a Method for Curating Ordered Gene-Replacement Libraries. Microbiol Spectr 2022; 10:e0083322. [PMID: 35856675 PMCID: PMC9431181 DOI: 10.1128/spectrum.00833-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/01/2022] [Indexed: 12/04/2022] Open
Abstract
In recent years the availability of genome sequence information has grown logarithmically resulting in the identification of a plethora of uncharacterized genes. To address this gap in functional annotation, many high-throughput screens have been devised to uncover novel gene functions. Gene-replacement libraries are one such tool that can be screened in a high-throughput way to link genotype and phenotype and are key community resources. However, for a phenotype to be attributed to a specific gene, there needs to be confidence in the genotype. Construction of large libraries can be laborious and occasionally errors will arise. Here, we present a rapid and accurate method for the validation of any ordered library where a gene has been replaced or disrupted by a uniform linear insertion (LI). We applied our method (LI-detector) to the well-known Keio library of Escherichia coli gene-deletion mutants. Our method identified 3,718 constructed mutants out of a total of 3,728 confirmed isolates, with a success rate of 99.7% for identifying the correct kanamycin cassette position. This data set provides a benchmark for the purity of the Keio mutants and a screening method for mapping the position of any linear insertion, such as an antibiotic resistance cassette in any ordered library. IMPORTANCE The construction of ordered gene replacement libraries requires significant investment of time and resources to create a valuable community resource. During construction, technical errors may result in a limited number of incorrect mutants being made. Such mutants may confound the output of subsequent experiments. Here, using the remarkable E. coli Keio knockout library, we describe a method to rapidly validate the construction of every mutant.
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Affiliation(s)
- Emily C. A. Goodall
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Faye C. Morris
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Samantha A. McKeand
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Rudi Sullivan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Isabel A. Warner
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Emma Sheehan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Adam F. Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jeffrey A. Cole
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Jack A. Bryant
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
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A New Factor LapD Is Required for the Regulation of LpxC Amounts and Lipopolysaccharide Trafficking. Int J Mol Sci 2022; 23:ijms23179706. [PMID: 36077106 PMCID: PMC9456370 DOI: 10.3390/ijms23179706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Lipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex with several proteins involved in LPS and phospholipid biosynthesis, including FtsH-LapA/B and Fab enzymes. Loss of LapD causes a reduction in LpxC amounts and vancomycin sensitivity, which can be restored by mutations that stabilize LpxC (mutations in lapB, ftsH and lpxC genes), revealing that LapD acts upstream of LapB-FtsH in regulating LpxC amounts. Interestingly, LapD absence results in the substantial retention of LPS in the inner membranes and synthetic lethality when either the lauroyl or the myristoyl acyl transferase is absent, which can be overcome by single-amino acid suppressor mutations in LPS flippase MsbA, suggesting LPS translocation defects in ΔlapD bacteria. Several genes whose products are involved in cell envelope homeostasis, including clsA, waaC, tig and micA, become essential in LapD’s absence. Furthermore, the overproduction of acyl carrier protein AcpP or transcriptional factors DksA, SrrA can overcome certain defects of the LapD-lacking strain.
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