1
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Vashishth S, Ambasta RK, Kumar P. Deciphering the microbial map and its implications in the therapeutics of neurodegenerative disorder. Ageing Res Rev 2024; 100:102466. [PMID: 39197710 DOI: 10.1016/j.arr.2024.102466] [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: 07/31/2024] [Revised: 08/19/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
Every facet of biological anthropology, including development, ageing, diseases, and even health maintenance, is influenced by gut microbiota's significant genetic and metabolic capabilities. With current advancements in sequencing technology and with new culture-independent approaches, researchers can surpass older correlative studies and develop mechanism-based studies on microbiome-host interactions. The microbiota-gut-brain axis (MGBA) regulates glial functioning, making it a possible target for the improvement of development and advancement of treatments for neurodegenerative diseases (NDDs). The gut-brain axis (GBA) is accountable for the reciprocal communication between the gastrointestinal and central nervous system, which plays an essential role in the regulation of physiological processes like controlling hunger, metabolism, and various gastrointestinal functions. Lately, studies have discovered the function of the gut microbiome for brain health-different microbiota through different pathways such as immunological, neurological and metabolic pathways. Additionally, we review the involvement of the neurotransmitters and the gut hormones related to gut microbiota. We also explore the MGBA in neurodegenerative disorders by focusing on metabolites. Further, targeting the blood-brain barrier (BBB), intestinal barrier, meninges, and peripheral immune system is investigated. Lastly, we discuss the therapeutics approach and evaluate the pre-clinical and clinical trial data regarding using prebiotics, probiotics, paraprobiotics, fecal microbiota transplantation, personalised medicine, and natural food bioactive in NDDs. A comprehensive study of the GBA will felicitate the creation of efficient therapeutic approaches for treating different NDDs.
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Affiliation(s)
- Shrutikirti Vashishth
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India
| | - Rashmi K Ambasta
- Department of Medicine, School of Medicine, VUMC, Vanderbilt University, TN, USA
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly DCE), Delhi 110042, India.
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2
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Wu K, Lin X, Lu Y, Dong R, Jiang H, Svensson SL, Zheng J, Shen N, Camilli A, Chao Y. RNA interactome of hypervirulent Klebsiella pneumoniae reveals a small RNA inhibitor of capsular mucoviscosity and virulence. Nat Commun 2024; 15:6946. [PMID: 39138169 PMCID: PMC11322559 DOI: 10.1038/s41467-024-51213-z] [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: 04/26/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (HvKP) is an emerging bacterial pathogen causing invasive infection in immune-competent humans. The hypervirulence is strongly linked to the overproduction of hypermucoviscous capsule, but the underlying regulatory mechanisms of hypermucoviscosity (HMV) have been elusive, especially at the post-transcriptional level mediated by small noncoding RNAs (sRNAs). Using a recently developed RNA interactome profiling approach iRIL-seq, we interrogate the Hfq-associated sRNA regulatory network and establish an intracellular RNA-RNA interactome in HvKP. Our data reveal numerous interactions between sRNAs and HMV-related mRNAs, and identify a plethora of sRNAs that repress or promote HMV. One of the strongest HMV repressors is ArcZ, which is activated by the catabolite regulator CRP and targets many HMV-related genes including mlaA and fbp. We discover that MlaA and its function in phospholipid transport is crucial for capsule retention and HMV, inactivation of which abolishes Klebsiella virulence in mice. ArcZ overexpression drastically reduces bacterial burden in mice and reduces HMV in multiple hypervirulent and carbapenem-resistant clinical isolates, indicating ArcZ is a potent RNA inhibitor of bacterial pneumonia with therapeutic potential. Our work unravels a novel CRP-ArcZ-MlaA regulatory circuit of HMV and provides mechanistic insights into the posttranscriptional virulence control in a superbug of global concern.
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Affiliation(s)
- Kejing Wu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Xingyu Lin
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Lu
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Dong
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Hongnian Jiang
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sarah L Svensson
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jiajia Zheng
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Yanjie Chao
- Microbial RNA Systems Biology Unit, Center for Microbes, Development and Health (CMDH), Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of RNA Innovation, Science and Engineering (RISE), Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.
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3
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James VK, Voss BJ, Helms A, Trent MS, Brodbelt JS. Investigating Lipid Transporter Protein and Lipid Interactions Using Variable Temperature Electrospray Ionization, Ultraviolet Photodissociation Mass Spectrometry, and Collision Cross Section Analysis. Anal Chem 2024; 96:12676-12683. [PMID: 39038171 DOI: 10.1021/acs.analchem.4c01392] [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] [Indexed: 07/24/2024]
Abstract
Gram-negative bacteria develop and exhibit resistance to antibiotics, owing to their highly asymmetric outer membrane maintained by a group of six proteins comprising the Mla (maintenance of lipid asymmetry) pathway. Here, we investigate the lipid binding preferences of one Mla protein, MlaC, which transports lipids through the periplasm. We used ultraviolet photodissociation (UVPD) to identify and characterize modifications of lipids endogenously bound to MlaC expressed in three different bacteria strains. UVPD was also used to localize lipid binding to MlaC residues 130-140, consistent with the crystal structure reported for lipid-bound MlaC. The impact of removing the bound lipid from MlaC on its structure was monitored based on collision cross section measurements, revealing that the protein unfolded prior to release of the lipid. The lipid selectivity of MlaC was evaluated based on titrimetric experiments, indicating that MlaC-bound lipids in various classes (sphingolipids, glycerophospholipids, and fatty acids) as long as they possessed no more than two acyl chains.
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Affiliation(s)
- Virginia K James
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Bradley J Voss
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
| | - Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Stephen Trent
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, United States
- Department of Microbiology, College of Arts and Sciences, University of Georgia, Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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4
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Murphy BT, Wiepen JJ, Graham DE, Swanson SK, Kashipathy MM, Cooper A, Battaile KP, Johnson DK, Florens L, Blevins JS, Lovell S, Zückert WR. Borrelia burgdorferi BB0346 is an Essential, Structurally Variant LolA Homolog that is Primarily Required for Homeostatic Localization of Periplasmic Lipoproteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606844. [PMID: 39149330 PMCID: PMC11326224 DOI: 10.1101/2024.08.06.606844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
In diderm bacteria, the Lol pathway canonically mediates the periplasmic transport of lipoproteins from the inner membrane (IM) to the outer membrane (OM) and therefore plays an essential role in bacterial envelope homeostasis. After extrusion of modified lipoproteins from the IM via the LolCDE complex, the periplasmic chaperone LolA carries lipoproteins through the periplasm and transfers them to the OM lipoprotein insertase LolB, itself a lipoprotein with a LolA-like fold. Yet, LolB homologs appear restricted to γ-proteobacteria and are missing from spirochetes like the tick-borne Lyme disease pathogen Borrelia burgdorferi, suggesting a different hand-off mechanism at the OM. Here, we solved the crystal structure of the B. burgdorferi LolA homolog BB0346 (LolABb) at 1.9 Å resolution. We identified multiple structural deviations in comparative analyses to other solved LolA structures, particularly a unique LolB-like protruding loop domain. LolABb failed to complement an Escherichia coli lolA knockout, even after codon optimization, signal I peptide adaptation, and a C-terminal chimerization which had allowed for complementation with an α-proteobacterial LolA. Analysis of a conditional B. burgdorferi lolA knockout strain indicated that LolABb was essential for growth. Intriguingly, protein localization assays indicated that initial depletion of LolABb led to an emerging mislocalization of both IM and periplasmic OM lipoproteins, but not surface lipoproteins. Together, these findings further support the presence of two separate primary secretion pathways for periplasmic and surface OM lipoproteins in B. burgdorferi and suggest that the distinct structural features of LolABb allow it to function in a unique LolB-deficient lipoprotein sorting system.
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Affiliation(s)
- Bryan T. Murphy
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics & Immunology, Kansas City, Kansas
| | - Jacob J. Wiepen
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics & Immunology, Kansas City, Kansas
| | - Danielle E. Graham
- University of Arkansas for Medical Sciences, Department of Microbiology & Immunology, Little Rock, Arkansas
| | | | - Maithri M. Kashipathy
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, 98109, USA
| | - Anne Cooper
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, 98109, USA
- University of Kansas, Protein Structure and X-ray Crystallography Laboratory, Lawrence, Kansas
| | | | - David K. Johnson
- University of Kansas, Protein Structure and X-ray Crystallography Laboratory, Lawrence, Kansas
| | | | - Jon S. Blevins
- University of Arkansas for Medical Sciences, Department of Microbiology & Immunology, Little Rock, Arkansas
| | - Scott Lovell
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, 98109, USA
- University of Kansas, Protein Structure and X-ray Crystallography Laboratory, Lawrence, Kansas
| | - Wolfram R. Zückert
- University of Kansas School of Medicine, Department of Microbiology, Molecular Genetics & Immunology, Kansas City, Kansas
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5
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Wotherspoon P, Johnston H, Hardy DJ, Holyfield R, Bui S, Ratkevičiūtė G, Sridhar P, Colburn J, Wilson CB, Colyer A, Cooper BF, Bryant JA, Hughes GW, Stansfeld PJ, Bergeron JRC, Knowles TJ. Structure of the MlaC-MlaD complex reveals molecular basis of periplasmic phospholipid transport. Nat Commun 2024; 15:6394. [PMID: 39080293 PMCID: PMC11289387 DOI: 10.1038/s41467-024-50615-3] [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: 04/06/2023] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
The Maintenance of Lipid Asymmetry (Mla) pathway is a multicomponent system found in all gram-negative bacteria that contributes to virulence, vesicle blebbing and preservation of the outer membrane barrier function. It acts by removing ectopic lipids from the outer leaflet of the outer membrane and returning them to the inner membrane through three proteinaceous assemblies: the MlaA-OmpC complex, situated within the outer membrane; the periplasmic phospholipid shuttle protein, MlaC; and the inner membrane ABC transporter complex, MlaFEDB, proposed to be the founding member of a structurally distinct ABC superfamily. While the function of each component is well established, how phospholipids are exchanged between components remains unknown. This stands as a major roadblock in our understanding of the function of the pathway, and in particular, the role of ATPase activity of MlaFEDB is not clear. Here, we report the structure of E. coli MlaC in complex with the MlaD hexamer in two distinct stoichiometries. Utilising in vivo complementation assays, an in vitro fluorescence-based transport assay, and molecular dynamics simulations, we confirm key residues, identifying the MlaD β6-β7 loop as essential for MlaCD function. We also provide evidence that phospholipids pass between the C-terminal helices of the MlaD hexamer to reach the central pore, providing insight into the trajectory of GPL transfer between MlaC and MlaD.
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Affiliation(s)
| | - Hannah Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - David J Hardy
- School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Soi Bui
- Randall Centre for Cell & Molecular Biophysics, School of Basic & Medical Biosciences, King's College London, London, UK
- Charles River Laboratories, 8-9 The Spire Green Centre, Harlow, UK
| | - Giedrė Ratkevičiūtė
- School of Biosciences, University of Birmingham, Birmingham, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Jonathan Colburn
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | | | - Adam Colyer
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Benjamin F Cooper
- School of Biosciences, University of Birmingham, Birmingham, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jack A Bryant
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Gareth W Hughes
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - Julien R C Bergeron
- Randall Centre for Cell & Molecular Biophysics, School of Basic & Medical Biosciences, King's College London, London, UK
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6
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Gerken H, Shetty D, Kern B, Kenney LJ, Misra R. Effects of pleiotropic ompR and envZ alleles of Escherichia coli on envelope stress and antibiotic sensitivity. J Bacteriol 2024; 206:e0017224. [PMID: 38809006 PMCID: PMC11332150 DOI: 10.1128/jb.00172-24] [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: 04/24/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024] Open
Abstract
The EnvZ-OmpR two-component system of Escherichia coli regulates the expression of the ompF and ompC porin genes in response to medium osmolarity. However, certain mutations in envZ confer pleiotropy by affecting the expression of genes of the iron and maltose regulons not normally controlled by EnvZ-OmpR. In this study, we obtained two novel envZ and ompR pleiotropic alleles, envZT15P and ompRL19Q, among revertants of a mutant with heightened envelope stress and an outer membrane (OM) permeability defect. Unlike envZ, pleiotropic mutations in ompR have not been described previously. The mutant alleles reduced the expression of several outer membrane proteins (OMPs), overcame the temperature-sensitive growth defect of a protease-deficient (ΔdegP) strain, and lowered envelope stress and OM permeability defects in a background lacking the BamB protein of an essential β-barrel assembly machinery complex. Biochemical analysis showed OmpRL19Q, like wild-type OmpR, is readily phosphorylated by EnvZ, but the EnvZ-dependent dephosphorylation of OmpRL19Q~P was drastically impaired compared to wild-type OmpR. This defect would lead to a prolonged half-life for OmpRL19Q~P, an outcome remarkably similar to what we had previously described for EnvZR397L, resulting in pleiotropy. By employing null alleles of the OMP genes, it was determined that the three pleiotropic alleles lowered envelope stress by reducing OmpF and LamB levels. The absence of LamB was principally responsible for lowering the OM permeability defect, as assessed by the reduced sensitivity of a ΔbamB mutant to vancomycin and rifampin. Possible mechanisms by which novel EnvZ and OmpR mutants influence EnvZ-OmpR interactions and activities are discussed.IMPORTANCEMaintenance of the outer membrane (OM) integrity is critical for the survival of Gram-negative bacteria. Several envelope homeostasis systems are activated when OM integrity is perturbed. Through the isolation and characterization of novel pleiotropic ompR/envZ alleles, this study highlights the involvement of the EnvZ-OmpR two-component system in lowering envelope stress and the OM permeability defect caused by the loss of proteins that are involved in OM biogenesis, envelope homeostasis, and structural integrity.
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Affiliation(s)
- Henri Gerken
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dasvit Shetty
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Brea Kern
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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7
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Stanley HM, Trent MS. Loss of YhcB results in overactive fatty acid biosynthesis. mBio 2024; 15:e0079024. [PMID: 38742872 PMCID: PMC11237625 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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8
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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. PLoS Genet 2024; 20:e1011335. [PMID: 38913742 PMCID: PMC11226057 DOI: 10.1371/journal.pgen.1011335] [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: 03/19/2024] [Revised: 07/05/2024] [Accepted: 06/07/2024] [Indexed: 06/26/2024] Open
Abstract
The outer membrane of gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. It remains unclear whether these functions are related to phospholipid metabolism. We investigated a synthetic cold sensitivity caused by deletion of fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, and yhdP, but not by ΔtamB ΔfadR or ΔydbH ΔfadR. Deletion of tamB recuses the ΔyhdP ΔfadR cold sensitivity further demonstrating the phenotype is related to functional diversification between these genes. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not. Moreover, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Together, our data clearly demonstrate that the diversification of function between YhdP and TamB is related to phospholipid metabolism. Although indirect regulatory effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential phospholipid-substrate transport preferences. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions based on regulation of abundance or activity of YhdP and TamB.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, United States of America
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9
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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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10
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Kaur M, Mingeot-Leclercq MP. Maintenance of bacterial outer membrane lipid asymmetry: insight into MlaA. BMC Microbiol 2024; 24:186. [PMID: 38802775 PMCID: PMC11131202 DOI: 10.1186/s12866-023-03138-8] [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: 03/28/2023] [Accepted: 11/29/2023] [Indexed: 05/29/2024] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria acts as an effective barrier to protect against toxic compounds. By nature, the OM is asymmetric with the highly packed lipopolysaccharide (LPS) at the outer leaflet and glycerophospholipids at the inner leaflet. OM asymmetry is maintained by the Mla system, in which is responsible for the retrograde transport of glycerophospholipids from the OM to the inner membrane. This system is comprised of six Mla proteins, including MlaA, an OM lipoprotein involved in the removal of glycerophospholipids that are mis-localized at the outer leaflet of the OM. Interestingly, MlaA was initially identified - and called VacJ - based on its role in the intracellular spreading of Shigella flexneri.Many open questions remain with respect to the Mla system and the mechanism involved in the translocation of mislocated glycerophospholipids at the outer leaflet of the OM, by MlaA. After summarizing the current knowledge on MlaA, we focus on the impact of mlaA deletion on OM lipid composition and biophysical properties of the OM. How changes in OM lipid composition and biophysical properties can impact the generation of membrane vesicles and membrane permeability is discussed. Finally, we explore whether and how MlaA might be a candidate for improving the activity of antibiotics and as a vaccine candidate.Efforts dedicated to understanding the relationship between the OM lipid composition and the mechanical strength of the bacterial envelope and, in turn, how such properties act against external stress, are needed for the design of new targets or drugs for Gram-negative infections.
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Affiliation(s)
- M Kaur
- Louvain Drug Research Institute, Université catholique de Louvain, Unité de Pharmacologie cellulaire et moléculaire, B1.73.05; 73 Av E. Mounier, Brussels, 1200, Belgium
| | - M-P Mingeot-Leclercq
- Louvain Drug Research Institute, Université catholique de Louvain, Unité de Pharmacologie cellulaire et moléculaire, B1.73.05; 73 Av E. Mounier, Brussels, 1200, Belgium.
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11
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Rai AK, Sawasato K, Bennett HC, Kozlova A, Sparagna GC, Bogdanov M, Mitchell AM. Genetic evidence for functional diversification of gram-negative intermembrane phospholipid transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.21.545913. [PMID: 37745482 PMCID: PMC10515749 DOI: 10.1101/2023.06.21.545913] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The outer membrane of Gram-negative bacteria is a barrier to chemical and physical stress. Phospholipid transport between the inner and outer membranes has been an area of intense investigation and, in E. coli K-12, it has recently been shown to be mediated by YhdP, TamB, and YdbH, which are suggested to provide hydrophobic channels for phospholipid diffusion, with YhdP and TamB playing the major roles. However, YhdP and TamB have different phenotypes suggesting distinct functions. We investigated these functions using synthetic cold sensitivity (at 30 °C) caused by deletion of yhdP and fadR, a transcriptional regulator controlling fatty acid degradation and unsaturated fatty acid production, but not by ΔtamB ΔfadR or ΔydbH ΔfadR,. Deletion of tamB suppresses the ΔyhdP ΔfadR cold sensitivity suggesting this phenotype is related to phospholipid transport. The ΔyhdP ΔfadR strain shows a greater increase in cardiolipin upon transfer to the non-permissive temperature and genetically lowering cardiolipin levels can suppress cold sensitivity. These data also reveal a qualitative difference between cardiolipin synthases in E. coli, as deletion of clsA and clsC suppresses cold sensitivity but deletion of clsB does not despite lower cardiolipin levels. In addition to increased cardiolipin, increased fatty acid saturation is necessary for cold sensitivity and lowering this level genetically or through supplementation of oleic acid suppresses the cold sensitivity of the ΔyhdP ΔfadR strain. Although indirect effects are possible, we favor the parsimonious hypothesis that YhdP and TamB have differential substrate transport preferences, most likely with YhdP preferentially transporting more saturated phospholipids and TamB preferentially transporting more unsaturated phospholipids. We envision cardiolipin contributing to this transport preference by sterically clogging TamB-mediated transport of saturated phospholipids. Thus, our data provide a potential mechanism for independent control of the phospholipid composition of the inner and outer membranes in response to changing conditions.
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Affiliation(s)
- Ashutosh K. Rai
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Katsuhiro Sawasato
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Haley C. Bennett
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Anastasiia Kozlova
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Genevieve C. Sparagna
- Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Angela M. Mitchell
- Department of Biology, Texas A&M University, College Station, Texas, USA
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12
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Liu C, Yazdani N, Moran CS, Salomon C, Seneviratne CJ, Ivanovski S, Han P. Unveiling clinical applications of bacterial extracellular vesicles as natural nanomaterials in disease diagnosis and therapeutics. Acta Biomater 2024; 180:18-45. [PMID: 38641182 DOI: 10.1016/j.actbio.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/03/2024] [Accepted: 04/11/2024] [Indexed: 04/21/2024]
Abstract
Bacterial extracellular vesicles (BEVs) are naturally occurring bioactive membrane-bound nanoparticles released by both gram-negative and gram-positive bacterial species, exhibiting a multifaceted role in mediating host-microbe interactions across various physiological conditions. Increasing evidence supports BEVs as essential mediators of cell-to-cell communicaiton, influencing bacterial pathogenicity, disease mechanisms, and modulating the host immune response. However, the extent to which these BEV-mediated actions can be leveraged to predict disease onset, guide treatment strategies, and determine clinical outcomes remains uncertain, particularly in terms of their clinical translation potentials. This review briefly describes BEV biogenesis and their internalisation by recipient cells and summarises methods for isolation and characterization, essential for understanding their composition and cargo. Further, it discusses the potential of biofluid-associated BEVs as biomarkers for various diseases, spanning both cancer and non-cancerous conditions. Following this, we outline the ongoing human clinical trials of using BEVs for vaccine development. In addition to disease diagnostics, this review explores the emerging research of using natural or engineered BEVs as smart nanomaterials for applications in anti-cancer therapy and bone regeneration. This discussion extends to key factors for unlocking the clinical potential of BEVs, such as standardization of BEV isolation and characterisation, as well as other hurdles in translating these findings to the clinical setting. We propose that addressing these hurdles through collaborative research efforts and well-designed clinical trials holds the key to fully harnessing the clinical potential of BEVs. As this field advances, this review suggests that BEV-based nanomedicine has the potential to revolutionize disease management, paving the way for innovative diagnosis, therapeutics, and personalized medicine approaches. STATEMENT OF SIGNIFICANCE: Extracellular vesicles (EVs) from both host cells and bacteria serve as multifunctional biomaterials and are emerging in the fields of biomedicine, bioengineering, and biomaterials. However, the majority of current studies focus on host-derived EVs, leaving a gap in comprehensive research on bacteria-derived EVs (BEVs). Although BEVs offer an attractive option as nanomaterials for drug delivery systems, their unique nanostructure and easy-to-modify functions make them a potential method for disease diagnosis and treatment as well as vaccine development. Our work among the pioneering studies investigating the potential of BEVs as natural nanobiomaterials plays a crucial role in both understanding the development of diseases and therapeutic interventions.
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Affiliation(s)
- Chun Liu
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia
| | - Negar Yazdani
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia
| | - Corey S Moran
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, The University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Brisbane, QLD, 4029 Australia
| | - Chaminda Jayampath Seneviratne
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia
| | - Sašo Ivanovski
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia.
| | - Pingping Han
- The University of Queensland, School of Dentistry, Centre for Oralfacial Regeneration, Rehabilitation and Reconstruction (COR3), Epigenetics Nanodiagnostic and Therapeutic Group, Brisbane, QLD 4006, Australia.
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13
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Muñoz-Echeverri LM, Benavides-López S, Geiger O, Trujillo-Roldán MA, Valdez-Cruz NA. Bacterial extracellular vesicles: biotechnological perspective for enhanced productivity. World J Microbiol Biotechnol 2024; 40:174. [PMID: 38642254 PMCID: PMC11032300 DOI: 10.1007/s11274-024-03963-7] [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: 01/17/2024] [Accepted: 03/19/2024] [Indexed: 04/22/2024]
Abstract
Bacterial extracellular vesicles (BEVs) are non-replicative nanostructures released by Gram-negative and Gram-positive bacteria as a survival mechanism and inter- and intraspecific communication mechanism. Due to BEVs physical, biochemical, and biofunctional characteristics, there is interest in producing and using them in developing new therapeutics, vaccines, or delivery systems. However, BEV release is typically low, limiting their application. Here, we provide a biotechnological perspective to enhance BEV production, highlighting current strategies. The strategies include the production of hypervesiculating strains through gene modification, bacteria culture under stress conditions, and artificial vesicles production. We discussed the effect of these production strategies on BEVs types, morphology, composition, and activity. Furthermore, we summarized general aspects of BEV biogenesis, functional capabilities, and applications, framing their current importance and the need to produce them in abundance. This review will expand the knowledge about the range of strategies associated with BEV bioprocesses to increase their productivity and extend their application possibilities.
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Affiliation(s)
- Laura M Muñoz-Echeverri
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México AP. 70228, Ciudad de México, C.P. 04510, México
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán CDMX, C.P. 04510, México
| | - Santiago Benavides-López
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México AP. 70228, Ciudad de México, C.P. 04510, México
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio B, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán CDMX, C.P. 04510, México
| | - Otto Geiger
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Cuernavaca, Morelos, CP 62210, México
| | - Mauricio A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México AP. 70228, Ciudad de México, C.P. 04510, México
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 Carretera, Tijuana-Ensenada, Baja California, 22860, México
| | - Norma A Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México AP. 70228, Ciudad de México, C.P. 04510, México.
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 Carretera, Tijuana-Ensenada, Baja California, 22860, México.
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14
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Dutta A, Kanaujia SP. The Structural Features of MlaD Illuminate its Unique Ligand-Transporting Mechanism and Ancestry. Protein J 2024; 43:298-315. [PMID: 38347327 DOI: 10.1007/s10930-023-10179-5] [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] [Accepted: 12/22/2023] [Indexed: 05/01/2024]
Abstract
The membrane-associated solute-binding protein (SBP) MlaD of the maintenance of lipid asymmetry (Mla) system has been reported to help the transport of phospholipids (PLs) between the outer and inner membranes of Gram-negative bacteria. Despite the availability of structural information, the molecular mechanism underlying the transport of PLs and the ancestry of the protein MlaD remain unclear. In this study, we report the crystal structures of the periplasmic region of MlaD from Escherichia coli (EcMlaD) at a resolution range of 2.3-3.2 Å. The EcMlaD protomer consists of two distinct regions, viz. N-terminal β-barrel fold consisting of seven strands (referred to as MlaD domain) and C-terminal α-helical domain (HD). The protein EcMlaD oligomerizes to give rise to a homo-hexameric ring with a central channel that is hydrophobic and continuous with a variable diameter. Interestingly, the structural analysis revealed that the HD, instead of the MlaD domain, plays a critical role in determining the oligomeric state of the protein. Based on the analysis of available structural information, we propose a working mechanism of PL transport, viz. "asymmetric protomer movement (APM)". Wherein half of the EcMlaD hexamer would rise in the periplasmic side along with an outward movement of pore loops, resulting in the change of the central channel geometry. Furthermore, this study highlights that, unlike typical SBPs, EcMlaD possesses a fold similar to EF/AMT-type beta(6)-barrel and a unique ancestry. Altogether, the findings firmly establish EcMlaD to be a non-canonical SBP with a unique ligand-transport mechanism.
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Affiliation(s)
- Angshu Dutta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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15
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Xiu L, Wu Y, Lin G, Zhang Y, Huang L. Bacterial membrane vesicles: orchestrators of interkingdom interactions in microbial communities for environmental adaptation and pathogenic dynamics. Front Immunol 2024; 15:1371317. [PMID: 38576623 PMCID: PMC10991846 DOI: 10.3389/fimmu.2024.1371317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Bacterial membrane vesicles (MVs) have attracted increasing attention due to their significant roles in bacterial physiology and pathogenic processes. In this review, we provide an overview of the importance and current research status of MVs in regulating bacterial physiology and pathogenic processes, as well as their crucial roles in environmental adaptation and pathogenic infections. We describe the formation mechanism, composition, structure, and functions of MVs, and discuss the various roles of MVs in bacterial environmental adaptation and pathogenic infections. Additionally, we analyze the limitations and challenges of MV-related research and prospect the potential applications of MVs in environmental adaptation, pathogenic mechanisms, and novel therapeutic strategies. This review emphasizes the significance of understanding and studying MVs for the development of new insights into bacterial environmental adaptation and pathogenic processes. Overall, this review contributes to our understanding of the intricate interplay between bacteria and their environment and provides valuable insights for the development of novel therapeutic strategies targeting bacterial pathogenicity.
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Affiliation(s)
- Lijun Xiu
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, Fujian, China
| | - Yuwei Wu
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, Fujian, China
| | - Gongshi Lin
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, Fujian, China
- Xiamen Marine & Fisheries Research Institute, Xiamen, Fujian, China
| | - Youyu Zhang
- Institute of Electromagnetics and Acoustics, School of Electronic Science and Engineering, Xiamen University, Xiamen, Fujian, China
| | - Lixing Huang
- State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, Xiamen, Fujian, China
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16
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Noel HR, Keerthi S, Ren X, Winkelman JD, Troutman JM, Palmer LD. Genetic synergy between Acinetobacter baumannii undecaprenyl phosphate biosynthesis and the Mla system impacts cell envelope and antimicrobial resistance. mBio 2024; 15:e0280423. [PMID: 38364179 PMCID: PMC10936186 DOI: 10.1128/mbio.02804-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/17/2024] [Indexed: 02/18/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacterial pathogen that poses a major health concern due to increasing multidrug resistance. The Gram-negative cell envelope is a key barrier to antimicrobial entry and includes an inner and outer membrane. The maintenance of lipid asymmetry (Mla) system is the main homeostatic mechanism by which Gram-negative bacteria maintain outer membrane asymmetry. Loss of the Mla system in A. baumannii results in attenuated virulence and increased susceptibility to membrane stressors and some antibiotics. We recently reported two strain variants of the A. baumannii type strain ATCC 17978: 17978VU and 17978UN. Here, ∆mlaF mutants in the two ATCC 17978 strains display different phenotypes for membrane stress resistance, antibiotic resistance, and pathogenicity in a murine pneumonia model. Although allele differences in obgE were previously reported to synergize with ∆mlaF to affect growth and stringent response, obgE alleles do not affect membrane stress resistance. Instead, a single-nucleotide polymorphism (SNP) in the essential gene encoding undecaprenyl pyrophosphate (Und-PP) synthase, uppS, results in decreased enzymatic rate and decrease in total Und-P levels in 17978UN compared to 17978VU. The UppSUN variant synergizes with ∆mlaF to reduce capsule and lipooligosaccharide (LOS) levels, increase susceptibility to membrane stress and antibiotics, and reduce persistence in a mouse lung infection. Und-P is a lipid glycan carrier required for the biosynthesis of A. baumannii capsule, cell wall, and glycoproteins. These findings uncover synergy between Und-P and the Mla system in maintaining the A. baumannii cell envelope and antibiotic resistance.IMPORTANCEAcinetobacter baumannii is a critical threat to global public health due to its multidrug resistance and persistence in hospital settings. Therefore, novel therapeutic approaches are urgently needed. We report that a defective undecaprenyl pyrophosphate synthase (UppS) paired with a perturbed Mla system leads to synthetically sick cells that are more susceptible to clinically relevant antibiotics and show reduced virulence in a lung infection model. These results suggest that targeting UppS or undecaprenyl species and the Mla system may resensitize A. baumannii to antibiotics in combination therapies. This work uncovers a previously unknown synergistic relationship in cellular envelope homeostasis that could be leveraged for use in combination therapy against A. baumannii.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Sowmya Keerthi
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | | | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, North Carolina, USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
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17
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Harrison GA. mSphere of Influence: The discovery of a missing link in bacterial cell envelope biogenesis. mSphere 2024; 9:e0063123. [PMID: 38299856 PMCID: PMC10900875 DOI: 10.1128/msphere.00631-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Gregory Harrison is a bacteriologist researching essential pathways in bacteria as potential therapeutic targets. In this mSphere of Influence article, he reflects on a series of studies that employ complementary genetic approaches to define the crucial role of AsmA-family proteins in transporting phospholipids between the inner and outer membranes of Gram-negative bacteria. The authors of these three studies identify this family of lipid transporters through the means of bacterial genetics, answering a long-standing question in bacterial physiology, and serving as a reminder that a well-designed genetic strategy can go a long way in uncovering new biology.
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Affiliation(s)
- Gregory A. Harrison
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
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18
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Sposato D, Mercolino J, Torrini L, Sperandeo P, Lucidi M, Alegiani R, Varone I, Molesini G, Leoni L, Rampioni G, Visca P, Imperi F. Redundant essentiality of AsmA-like proteins in Pseudomonas aeruginosa. mSphere 2024; 9:e0067723. [PMID: 38305166 PMCID: PMC10900882 DOI: 10.1128/msphere.00677-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
The outer membrane (OM) is an essential structure of Gram-negative bacteria that provides mechanical strength and protection from large and/or hydrophobic toxic molecules, including many antibiotics. The OM is composed of glycerophospholipids (GPLs) and lipopolysaccharide (LPS) in the inner and outer leaflets, respectively, and hosts integral β-barrel proteins and lipoproteins. While the systems responsible for translocation and insertion of LPS and OM proteins have been elucidated, the mechanism(s) mediating transport of GPLs from the inner membrane to the OM has remained elusive for decades. Very recently, studies performed in Escherichia coli proposed a role in this process for AsmA-like proteins that are predicted to share structural features with eukaryotic lipid transporters. In this study, we provide the first systematic investigation of AsmA-like proteins in a bacterium other than E. coli, the opportunistic human pathogen Pseudomonas aeruginosa. Bioinformatic analyses revealed that P. aeruginosa possesses seven AsmA-like proteins. Deletion of asmA-like genes in many different combinations, coupled with conditional mutagenesis, revealed that four AsmA-like proteins are redundantly essential for growth and OM integrity in P. aeruginosa, including a novel AsmA-like protein (PA4735) that is not present in E. coli. Cells depleted of AsmA-like proteins showed severe defects in the OM permeability barrier that were partially rescued by lowering the synthesis or transport of LPS. Since fine balancing of GPL and LPS levels is crucial for OM integrity, this evidence supports the role of AsmA-like proteins in GPL transport toward the OM. IMPORTANCE Given the importance of the outer membrane (OM) for viability and antibiotic resistance in Gram-negative bacteria, in the last decades, several studies have focused on the characterization of the systems involved in OM biogenesis, which have also been explored as targets for antibacterial drug development. However, the mechanism mediating translocation of glycerophospholipids (GPLs) to the OM remained unknown until recent studies provided evidence that AsmA-like proteins could be responsible for this process. Here, we demonstrate for the first time that AsmA-like proteins are essential and redundant for growth and OM integrity in a Gram-negative bacterium other than the model organism Escherichia coli and demonstrate that the human pathogen Pseudomonas aeruginosa has an additional essential AsmA-like protein that is not present in E. coli, thus expanding the range of AsmA-like proteins that play key functions in Gram-negative bacteria.
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Affiliation(s)
| | | | - Luisa Torrini
- Department of Science, University Roma Tre, Rome, Italy
| | - Paola Sperandeo
- Department of Pharmacological and Biomolecular Sciences, University of Milano, Milan, Italy
| | - Massimiliano Lucidi
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Ilaria Varone
- Department of Science, University Roma Tre, Rome, Italy
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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Coves X, Mamat U, Conchillo-Solé O, Huedo P, Bravo M, Gómez AC, Krohn I, Streit WR, Schaible UE, Gibert I, Daura X, Yero D. The Mla system and its role in maintaining outer membrane barrier function in Stenotrophomonas maltophilia. Front Cell Infect Microbiol 2024; 14:1346565. [PMID: 38469346 PMCID: PMC10925693 DOI: 10.3389/fcimb.2024.1346565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Stenotrophomonas maltophilia are ubiquitous Gram-negative bacteria found in both natural and clinical environments. It is a remarkably adaptable species capable of thriving in various environments, thanks to the plasticity of its genome and a diverse array of genes that encode a wide range of functions. Among these functions, one notable trait is its remarkable ability to resist various antimicrobial agents, primarily through mechanisms that regulate the diffusion across cell membranes. We have investigated the Mla ABC transport system of S. maltophilia, which in other Gram-negative bacteria is known to transport phospholipids across the periplasm and is involved in maintaining outer membrane homeostasis. First, we structurally and functionally characterized the periplasmic substrate-binding protein MlaC, which determines the specificity of this system. The predicted structure of the S. maltophilia MlaC protein revealed a hydrophobic cavity of sufficient size to accommodate the phospholipids commonly found in this species. Moreover, recombinant MlaC produced heterologously demonstrated the ability to bind phospholipids. Gene knockout experiments in S. maltophilia K279a revealed that the Mla system is involved in baseline resistance to antimicrobial and antibiofilm agents, especially those with divalent-cation chelating activity. Co-culture experiments with Pseudomonas aeruginosa also showed a significant contribution of this system to the cooperation between both species in the formation of polymicrobial biofilms. As suggested for other Gram-negative pathogenic microorganisms, this system emerges as an appealing target for potential combined antimicrobial therapies.
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Affiliation(s)
- Xavier Coves
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Uwe Mamat
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Leibniz Research Alliance INFECTIONS, Borstel, Germany
| | - Oscar Conchillo-Solé
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Pol Huedo
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Marc Bravo
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Andromeda-Celeste Gómez
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Ines Krohn
- Department of Microbiology and Biotechnology, University Institute of Plant Science and Microbiology, of Hamburg, Hamburg, Germany
| | - Wolfgang R. Streit
- Department of Microbiology and Biotechnology, University Institute of Plant Science and Microbiology, of Hamburg, Hamburg, Germany
| | - Ulrich E. Schaible
- Cellular Microbiology, Priority Research Area Infections, Research Center Borstel, Leibniz Lung Center, Leibniz Research Alliance INFECTIONS, Borstel, Germany
| | - Isidre Gibert
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Cerdanyola del Vallès, Spain
| | - Daniel Yero
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, Spain
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20
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Tiwari V, Sharma A, Braga R, Garcia E, Appiah R, Fleeman R, Abuaita BH, Patrauchan M, Doerrler WT. Klebsiella pneumoniae DedA family proteins have redundant roles in divalent cation homeostasis and resistance to phagocytosis. Microbiol Spectr 2024; 12:e0380723. [PMID: 38214522 PMCID: PMC10846249 DOI: 10.1128/spectrum.03807-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 12/04/2023] [Indexed: 01/13/2024] Open
Abstract
The DedA superfamily is a highly conserved family of membrane proteins. Deletion of Escherichia coli yqjA and yghB, encoding related DedA family proteins, results in sensitivity to elevated temperature, antibiotics, and alkaline pH. The human pathogen Klebsiella pneumoniae possesses genes encoding DedA family proteins with >90% amino acid identity to E. coli YqjA and YghB. We hypothesized that the deletion of K. pneumoniae yqjA and yghB will impact its physiology and may reduce its virulence. The K. pneumoniae ΔyqjA ΔyghB mutant (strain VT101) displayed a growth defect at 42°C and alkaline pH sensitivity, not unlike its E. coli counterpart. However, VT101 retained mostly wild-type resistance to antibiotics. We found VT101 was sensitive to the chelating agent EDTA, the anionic detergent SDS, and agents capable of alkalizing the bacterial cytoplasm such as bicarbonate or chloroquine. We could restore growth at alkaline pH and at elevated temperature by addition of 0.5-2 mM Ca2+ or Mg2+ to the culture media. VT101 displayed a slower uptake of calcium, which was dependent upon calcium channel activity. VT201, with similar deletions as VT101 but derived from a virulent K. pneumoniae strain, was highly susceptible to phagocytosis by alveolar macrophages and displayed a defect in the production of capsule. These findings suggest divalent cation homeostasis and virulence are interlinked by common functions of the DedA family.IMPORTANCEKlebsiella pneumoniae is a dangerous human pathogen. The DedA protein family is found in all bacteria and is a membrane transporter often required for virulence and antibiotic resistance. K. pneumoniae possesses homologs of E. coli YqjA and YghB, with 60% amino acid identity and redundant functions, which we have previously shown to be required for tolerance to biocides and alkaline pH. A K. pneumoniae strain lacking yqjA and yghB was found to be sensitive to alkaline pH, elevated temperature, and EDTA/SDS and displayed a defect in calcium uptake. Sensitivity to these conditions was reversed by addition of calcium or magnesium to the growth medium. Introduction of ΔyqjA and ΔyghB mutations into virulent K. pneumoniae resulted in the loss of capsule, increased phagocytosis by macrophages, and a partial loss of virulence. These results show that targeting the Klebsiella DedA family results in impaired divalent cation transport and, in turn, loss of virulence.
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Affiliation(s)
- Vijay Tiwari
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Amit Sharma
- Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Reygan Braga
- Department of Microbiology and Molecular Genetics, College of Arts and Science, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Emily Garcia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Ridhwana Appiah
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Renee Fleeman
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Basel H. Abuaita
- Department of Pathobiological Sciences, LSU School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, College of Arts and Science, Oklahoma State University, Stillwater, Oklahoma, USA
| | - William T. Doerrler
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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21
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Cooper BF, Ratkevičiūtė G, Clifton LA, Johnston H, Holyfield R, Hardy DJ, Caulton SG, Chatterton W, Sridhar P, Wotherspoon P, Hughes GW, Hall SC, Lovering AL, Knowles TJ. An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system. EMBO Rep 2024; 25:82-101. [PMID: 38228789 PMCID: PMC10897342 DOI: 10.1038/s44319-023-00014-4] [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: 08/02/2023] [Revised: 10/31/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer membrane lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide a continuous channel between the inner and outer membranes of diderms. Here, we present X-ray structures of both the native and a truncated, soluble construct of the PqiC lipoprotein, providing insight into its biological assembly, and utilise neutron reflectometry to characterise the nature of the PqiB-PqiC-membrane interaction. Finally, we employ phenotypic complementation assays to probe specific PqiC residues, which imply the interaction between PqiB and PqiC is less intimate than previously anticipated.
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Affiliation(s)
- Benjamin F Cooper
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | | | - Luke A Clifton
- ISIS Pulsed Neutron & Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Harwell Oxford Campus, OX11 OQX, Didcot, UK
| | - Hannah Johnston
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Rachel Holyfield
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - David J Hardy
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Simon G Caulton
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - William Chatterton
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Peter Wotherspoon
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Gareth W Hughes
- Institute of Cancer and Genomic Sciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Stephen Cl Hall
- ISIS Pulsed Neutron & Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory Harwell Oxford Campus, OX11 OQX, Didcot, UK
| | - Andrew L Lovering
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, B15 2TT, Birmingham, UK.
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22
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Scheeder A, Brockhoff M, Ward EN, Kaminski Schierle GS, Mela I, Kaminski CF. Molecular Mechanisms of Cationic Fusogenic Liposome Interactions with Bacterial Envelopes. J Am Chem Soc 2023; 145:28240-28250. [PMID: 38085801 PMCID: PMC10755748 DOI: 10.1021/jacs.3c11463] [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: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Although fusogenic liposomes offer a promising approach for the delivery of antibiotic payloads across the cell envelope of Gram-negative bacteria, there is still a limited understanding of the individual nanocarrier interactions with the bacterial target. Using super-resolution microscopy, we characterize the interaction dynamics of positively charged fusogenic liposomes with Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The liposomes merge with the outer membrane (OM) of Gram-negative bacteria, while attachment or lipid internalization is observed in Gram-positive cells. Employing total internal reflection fluorescence microscopy, we demonstrated liposome fusion with model supported lipid bilayers. For whole E. coli cells, however, we observed heterogeneous membrane integrations, primarily involving liposome attachment and hemifusion events. With increasing lipopolysaccharide length, the likelihood of full-fusion events was reduced. The integration of artificial lipids into the OM of Gram-negative cells led to membrane destabilization, resulting in decreased bacterial vitality, membrane detachment, and improved codelivery of vancomycin─an effective antibiotic against Gram-positive cells. These findings provide significant insights into the interactions of individual nanocarriers with bacterial envelopes at the single-cell level, uncovering effects that would be missed in bulk measurements. This highlights the importance of conducting single-particle and single-cell investigations to assess the performance of next-generation drug delivery platforms.
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Affiliation(s)
- Anna Scheeder
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Marius Brockhoff
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Edward N. Ward
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Gabriele S. Kaminski Schierle
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Ioanna Mela
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K.
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
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23
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Vinacour M, Moiana M, Forné I, Jung K, Bertea M, Calero Valdayo PM, Nikel PI, Imhof A, Palumbo MC, Fernández Do Porto D, Ruiz JA. Genetic dissection of the degradation pathways for the mycotoxin fusaric acid in Burkholderia ambifaria T16. Appl Environ Microbiol 2023; 89:e0063023. [PMID: 38054732 PMCID: PMC10734416 DOI: 10.1128/aem.00630-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Fusaric acid (FA) is an important virulence factor produced by several Fusarium species. These fungi are responsible for wilt and rot diseases in a diverse range of crops. FA is toxic for animals, humans and soil-borne microorganisms. This mycotoxin reduces the survival and competition abilities of bacterial species able to antagonize Fusarium spp., due to its negative effects on viability and the production of antibiotics effective against these fungi. FA biodegradation is not a common characteristic among bacteria, and the determinants of FA catabolism have not been identified so far in any microorganism. In this study, we identified genes, enzymes, and metabolic pathways involved in the degradation of FA in the soil bacterium Burkholderia ambifaria T16. Our results provide insights into the catabolism of a pyridine-derivative involved in plant pathogenesis by a rhizosphere bacterium.
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Affiliation(s)
- Matias Vinacour
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mauro Moiana
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kirsten Jung
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Micaela Bertea
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Patricia M. Calero Valdayo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I. Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Miranda C. Palumbo
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario Fernández Do Porto
- Instituto de Cálculo (IC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jimena A. Ruiz
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales (INBA), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Faculty Biology, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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24
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Abstract
Gram-negative bacteria are intrinsically resistant to many antibiotics, due in large part to the permeability barrier formed by their cell envelope. The complex and synergistic interplay of the two Gram-negative membranes and active efflux prevents the accumulation of a diverse range of compounds that are effective against Gram-positive bacteria. A lack of detailed information on how components of the cell envelope contribute to this has been identified as a key barrier to the rational development of new antibiotics with efficacy against Gram-negative species. This review describes the current understanding of the role of the different components of the Gram-negative cell envelope in preventing compound accumulation and the state of efforts to describe properties that allow compounds to overcome this barrier and apply them to the development of new broad-spectrum antibiotics.
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Affiliation(s)
- Claire Maher
- College of Engineering, Science and Environment, University of Newcastle, Newcastle, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - Karl A. Hassan
- College of Engineering, Science and Environment, University of Newcastle, Newcastle, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
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25
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Yeow J, Luo M, Chng SS. Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun 2023; 14:8285. [PMID: 38092770 PMCID: PMC10719372 DOI: 10.1038/s41467-023-44144-8] [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: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117558, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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26
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Machin JM, Kalli AC, Ranson NA, Radford SE. Protein-lipid charge interactions control the folding of outer membrane proteins into asymmetric membranes. Nat Chem 2023; 15:1754-1764. [PMID: 37710048 PMCID: PMC10695831 DOI: 10.1038/s41557-023-01319-6] [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: 08/09/2022] [Accepted: 08/08/2023] [Indexed: 09/16/2023]
Abstract
Biological membranes consist of two leaflets of phospholipid molecules that form a bilayer, each leaflet comprising a distinct lipid composition. This asymmetry is created and maintained in vivo by dedicated biochemical pathways, but difficulties in creating stable asymmetric membranes in vitro have restricted our understanding of how bilayer asymmetry modulates the folding, stability and function of membrane proteins. In this study, we used cyclodextrin-mediated lipid exchange to generate liposomes with asymmetric bilayers and characterize the stability and folding kinetics of two bacterial outer membrane proteins (OMPs), OmpA and BamA. We found that excess negative charge in the outer leaflet of a liposome impedes their insertion and folding, while excess negative charge in the inner leaflet accelerates their folding relative to symmetric liposomes with the same membrane composition. Using molecular dynamics, mutational analysis and bioinformatics, we identified a positively charged patch critical for folding and stability. These results rationalize the well-known 'positive-outside' rule of OMPs and suggest insights into the mechanisms that drive OMP folding and assembly in vitro and in vivo.
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Affiliation(s)
- Jonathan M Machin
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Antreas C Kalli
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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27
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Grasekamp KP, Beaud Benyahia B, Taib N, Audrain B, Bardiaux B, Rossez Y, Izadi-Pruneyre N, Lejeune M, Trivelli X, Chouit Z, Guerardel Y, Ghigo JM, Gribaldo S, Beloin C. The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking. Nat Commun 2023; 14:7642. [PMID: 37993432 PMCID: PMC10665443 DOI: 10.1038/s41467-023-43411-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
E. coli and most other diderm bacteria (those with two membranes) have an inner membrane enriched in glycerophospholipids (GPLs) and an asymmetric outer membrane (OM) containing GPLs in its inner leaflet and primarily lipopolysaccharides in its outer leaflet. In E. coli, this lipid asymmetry is maintained by the Mla system which consists of six proteins: the OM lipoprotein MlaA extracts GPLs from the outer leaflet, and the periplasmic chaperone MlaC transfers them across the periplasm to the inner membrane complex MlaBDEF. However, GPL trafficking still remains poorly understood, and has only been studied in a handful of model species. Here, we investigate GPL trafficking in Veillonella parvula, a diderm Firmicute with an Mla system that lacks MlaA and MlaC, but contains an elongated MlaD. V. parvula mla mutants display phenotypes characteristic of disrupted lipid asymmetry which can be suppressed by mutations in tamB, supporting that these two systems have opposite GPL trafficking functions across diverse bacterial lineages. Structural modelling and subcellular localisation assays suggest that V. parvula MlaD forms a transenvelope bridge, comprising a typical inner membrane-localised MCE domain and, in addition, an outer membrane ß-barrel. Phylogenomic analyses indicate that this elongated MlaD type is widely distributed across diderm bacteria and likely forms part of the ancestral functional core of the Mla system, which would be composed of MlaEFD only.
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Affiliation(s)
- Kyrie P Grasekamp
- Institut Pasteur, Université Paris Cité, Genetics of Biofilms Laboratory, Paris, France
| | - Basile Beaud Benyahia
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Laboratory, Paris, France
| | - Najwa Taib
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Laboratory, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, F-75015, Paris, France
| | - Bianca Audrain
- Institut Pasteur, Université Paris Cité, Genetics of Biofilms Laboratory, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, Structural Bioinformatics Unit, CNRS UMR 3528, Paris, France
- Institut Pasteur, Université Paris Cité, Bacterial Transmembrane Systems Unit, CNRS UMR 3528, Paris, France
| | - Yannick Rossez
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, Structural Bioinformatics Unit, CNRS UMR 3528, Paris, France
- Institut Pasteur, Université Paris Cité, Bacterial Transmembrane Systems Unit, CNRS UMR 3528, Paris, France
| | - Maylis Lejeune
- Institut Pasteur, Université Paris Cité, Structural Bioinformatics Unit, CNRS UMR 3528, Paris, France
- Institut Pasteur, Université Paris Cité, Bacterial Transmembrane Systems Unit, CNRS UMR 3528, Paris, France
| | - Xavier Trivelli
- Université de Lille, CNRS, INRAE, Centrale Lille, Université d'Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, Lille, 59000, France
| | - Zina Chouit
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Yann Guerardel
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, Japan
| | - Jean-Marc Ghigo
- Institut Pasteur, Université Paris Cité, Genetics of Biofilms Laboratory, Paris, France
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, Evolutionary Biology of the Microbial Cell Laboratory, Paris, France.
| | - Christophe Beloin
- Institut Pasteur, Université Paris Cité, Genetics of Biofilms Laboratory, Paris, France.
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28
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Kaur M, Buyck JM, Goormaghtigh F, Decout JL, Mozaheb N, Mingeot-Leclercq MP. Deficient Pseudomonas aeruginosa in MlaA/VacJ outer membrane lipoprotein shows decrease in rhamnolipids secretion, motility, and biofilm formation, and increase in fluoroquinolones susceptibility and innate immune response. Res Microbiol 2023; 174:104132. [PMID: 37660742 DOI: 10.1016/j.resmic.2023.104132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Pseudomonas aeruginosa, a Gram-negative bacterium that causes severe hospital acquired infections poses threat by its ability for adaptation to various growth modes and environmental conditions and by its intrinsic resistance to antibiotics. The latter is mainly due to the outer membrane (OM) asymmetry which is maintained by the Mla pathway resulting in the retrograde transport of glycerophospholipids from the OM to the inner membrane. It comprises six Mla proteins, including MlaA, an OM lipoprotein involved in the removal of glycerophospholipids mislocalized at the outer leaflet of OM. To investigate the role of P. aeruginosa OM asymmetry especially MlaA, this study investigated the effect of mlaA deletion on (i) the susceptibility to antibiotics, (ii) the secretion of virulence factors, the motility, biofilm formation, and (iii) the inflammatory response. mlaA deletion in P. aeruginosa ATCC27853 results in phenotypic changes including, an increase in fluoroquinolones susceptibility and in PQS (Pseudomonas Quinolone Signal) and TNF-α release and a decrease in rhamnolipids secretion, motility and biofilm formation. Investigating how the mlaA knockout impacts on antibiotic susceptibility, bacterial virulence and innate immune response will help to elucidate the biological significance of the Mla system and contribute to the understanding of MlaA in P. aeruginosa OM asymmetry.
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Affiliation(s)
- M Kaur
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - J M Buyck
- University of Poitiers, INSERM U1070, Poitiers, France.
| | - F Goormaghtigh
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - J-L Decout
- Université Grenoble Alpes, CNRS, Département de Pharmacochimie Moléculaire, Rue de la Chimie, F-38041 Grenoble, France.
| | - N Mozaheb
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
| | - M-P Mingeot-Leclercq
- Université catholique de Louvain, Louvain Drug Research Institute, Pharmacologie Cellulaire et Moléculaire, Avenue E. Mounier 73, UCL B1.73.05, 1200 Brussels, Belgium.
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29
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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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30
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Cooper BF, Clark R, Kudhail A, Bhabha G, Ekiert DC, Khalid S, Isom GL. Phospholipid transport to the bacterial outer membrane through an envelope-spanning bridge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561070. [PMID: 37873249 PMCID: PMC10592960 DOI: 10.1101/2023.10.05.561070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The outer membrane of Gram-negative bacteria provides a formidable barrier, essential for both pathogenesis and antimicrobial resistance. Biogenesis of the outer membrane requires the transport of phospholipids across the cell envelope. Recently, YhdP was implicated as a major protagonist in the transport of phospholipids from the inner membrane to the outer membrane however the molecular mechanism of YhdP mediated transport remains elusive. Here, utilising AlphaFold, we observe YhdP to form an elongated assembly of 60 β strands that curve to form a continuous hydrophobic groove. This architecture is consistent with our negative stain electron microscopy data which reveals YhdP to be approximately 250 Å in length and thus sufficient to span the bacterial cell envelope. Furthermore, molecular dynamics simulations and in vivo bacterial growth assays indicate essential helical regions at the N- and C-termini of YhdP, that may embed into the inner and outer membranes respectively, reinforcing its envelope spanning nature. Our in vivo crosslinking data reveal phosphate-containing substrates captured along the length of the YhdP groove, providing direct evidence that YhdP transports phospholipids. This finding is congruent with our molecular dynamics simulations which demonstrate the propensity for inner membrane lipids to spontaneously enter the groove of YhdP. Collectively, our results support a model in which YhdP bridges the cell envelope, providing a hydrophobic environment for the transport of phospholipids to the outer membrane.
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Affiliation(s)
- Benjamin F. Cooper
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Robert Clark
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anju Kudhail
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016
| | - Damian C. Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016
- Department of Microbiology, New York University School of Medicine, New York, NY, 10016
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Georgia L. Isom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
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Yin L, Wang X, Xu H, Yin B, Wang X, Zhang Y, Li X, Luo Y, Chen Z. Unrecognized risk of perfluorooctane sulfonate in promoting conjugative transfers of bacterial antibiotic resistance genes. Appl Environ Microbiol 2023; 89:e0053323. [PMID: 37565764 PMCID: PMC10537727 DOI: 10.1128/aem.00533-23] [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: 03/29/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
Antibiotic resistance is a major global health crisis facing humanity, with horizontal gene transfer (HGT) as a principal dissemination mechanism in the natural and clinical environments. Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse effects on humans. However, it is unknown whether PFASs affect the HGT of bacterial antibiotic resistance. Using a genetically engineered Escherichia coli MG1655 as the donor of plasmid-encoded antibiotic resistance genes (ARGs), E. coli J53 and soil bacterial community as two different recipients, this study demonstrated that the conjugation frequency of ARGs between two E. coli strains was (1.45 ± 0.17) × 10-5 and perfluorooctane sulfonate (PFOS) at environmentally relevant concentrations (2-50 μg L-1) increased conjugation transfer between E. coli strains by up to 3.25-fold. Increases in reactive oxygen species production, cell membrane permeability, biofilm formation capacity, and cell contact in two E. coli strains were proposed as major promotion mechanisms from PFOS exposure. Weighted gene co-expression network analysis of transcriptome data identified a series of candidate genes whose expression changes could contribute to the increase in conjugation transfer induced by PFOS. Furthermore, PFOS also generally increased the ARG transfer into the studied soil bacterial community, although the uptake ability of different community members of the plasmid either increased or decreased upon PFOS exposure depending on specific bacterial taxa. Overall, this study reveals an unrecognized risk of PFOS in accelerating the dissemination of antibiotic resistance. IMPORTANCE Perfluoroalkyl substances (PFASs) are emerging contaminants of global concern due to their high persistence in the environment and adverse health effects. Although the influence of environmental pollutants on the spread of antibiotic resistance, one of the biggest threats to global health, has attracted increasing attention in recent years, it is unknown whether environmental residues of PFASs affect the dissemination of bacterial antibiotic resistance. Considering PFASs, often called "forever" compounds, have significantly higher environmental persistence than most emerging organic contaminants, exploring the effect of PFASs on the spread of antibiotic resistance is more environmentally relevant and has essential ecological and health significance. By systematically examining the influence of perfluorooctane sulfonate on the antibiotic resistance gene conjugative transfer, not only at the single-strain level but also at the community level, this study has uncovered an unrecognized risk of PFASs in promoting conjugative transfers of bacterial antibiotic resistance genes, which could be incorporated into the risk assessment framework of PFASs.
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Affiliation(s)
- Lichun Yin
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Xiaolong Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Han Xu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Bo Yin
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Xingshuo Wang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yulin Zhang
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Xinyao Li
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Zeyou Chen
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin, China
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32
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Noel HR, Keerthi S, Ren X, Winkelman JD, Troutman JM, Palmer LD. Genetic synergy in Acinetobacter baumannii undecaprenyl biosynthesis and maintenance of lipid asymmetry impacts outer membrane and antimicrobial resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.556980. [PMID: 37790371 PMCID: PMC10542541 DOI: 10.1101/2023.09.22.556980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Acinetobacter baumannii is a Gram-negative healthcare-associated pathogen that poses a major health concern due to increasing multidrug resistance. The Gram-negative cell envelope is a key barrier to antimicrobial entry and includes an inner and outer membrane. The outer membrane has an asymmetric composition that is important for structural integrity and barrier to the environment. Therefore, Gram-negative bacteria have mechanisms to uphold this asymmetry such as the maintenance of lipid asymmetry system (Mla), which removes glycerophospholipids from the outer leaflet of the outer membrane and transports them to the inner membrane. Loss of this system in A. baumannii results in attenuated virulence and increased susceptibility to membrane stressors and some antibiotics. We recently reported two strain variants of the A. baumannii type strain ATCC 17978, 17978VU and 17978UN. We show here that ΔmlaF mutants in the two strains display different phenotypes for membrane stress resistance, antibiotic resistance, and pathogenicity in a murine pneumonia model. We used comparative genetics to identify interactions between ATCC 17978 strain alleles and mlaF to uncover the cause behind the phenotypic differences. Although allele differences in obgE were previously reported to synergize with ΔmlaF to affect growth and stringent response, we show that obgE alleles do not affect membrane stress resistance. Instead, a single nucleotide polymorphism (SNP) in the essential gene encoding undecaprenyl pyrophosphate (Und-PP) synthase, uppS, synergizes with ΔmlaF to increase susceptibility to membrane stress and antibiotics, and reduce persistence in a mouse lung infection. Und-P is a lipid glycan carrier known to be required for biosynthesis of A. baumannii capsule, cell wall, and glycoproteins. Our data suggest that in the absence of the Mla system, the cellular level of Und-P is critical for envelope integrity, antibiotic resistance, and lipooligosaccharide abundance. These findings uncover synergy between Und-P and the Mla system in maintaining the A. baumannii outer membrane and stress resistance.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | - Sowmya Keerthi
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC, USA
| | - Xiaomei Ren
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
| | | | - Jerry M. Troutman
- Department of Chemistry, University of North Carolina Charlotte, Charlotte, NC, USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL, USA
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Chen Y, Wang Y, Chng SS. A conserved membrane protein negatively regulates Mce1 complexes in mycobacteria. Nat Commun 2023; 14:5897. [PMID: 37736771 PMCID: PMC10517005 DOI: 10.1038/s41467-023-41578-y] [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: 03/04/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Tuberculosis continues to pose a serious threat to global health. Mycobacterium tuberculosis, the causative agent of tuberculosis, is an intracellular pathogen that relies on various mechanisms to survive and persist within the host. Among their many virulence factors, mycobacteria encode Mce systems. Some of these systems are implicated in lipid uptake, but the molecular basis for Mce function(s) is poorly understood. To gain insights into the composition and architecture of Mce systems, we characterized the putative Mce1 complex involved in fatty acid transport. We show that the Mce1 system in Mycobacterium smegmatis comprises a canonical ATP-binding cassette transporter associated with distinct heterohexameric assemblies of substrate-binding proteins. Furthermore, we establish that the conserved membrane protein Mce1N negatively regulates Mce1 function via a unique mechanism involving blocking transporter assembly. Our work offers a molecular understanding of Mce complexes, sheds light on mycobacterial lipid metabolism and its regulation, and informs future anti-mycobacterial strategies.
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Affiliation(s)
- Yushu Chen
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Yuchun Wang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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Mikheyeva IV, Sun J, Huang KC, Silhavy TJ. Mechanism of outer membrane destabilization by global reduction of protein content. Nat Commun 2023; 14:5715. [PMID: 37714857 PMCID: PMC10504340 DOI: 10.1038/s41467-023-40396-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 07/26/2023] [Indexed: 09/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria such as Escherichia coli is an asymmetric bilayer with the glycolipid lipopolysaccharide (LPS) in the outer leaflet and glycerophospholipids in the inner. Nearly all integral OM proteins (OMPs) have a characteristic β-barrel fold and are assembled in the OM by the BAM complex, which contains one essential β-barrel protein (BamA), one essential lipoprotein (BamD), and three non-essential lipoproteins (BamBCE). A gain-of-function mutation in bamA enables survival in the absence of BamD, showing that the essential function of this protein is regulatory. Here, we demonstrate that the global reduction in OMPs caused by BamD loss weakens the OM, altering cell shape and causing OM rupture in spent medium. To fill the void created by OMP loss, phospholipids (PLs) flip into the outer leaflet. Under these conditions, mechanisms that remove PLs from the outer leaflet create tension between the OM leaflets, which contributes to membrane rupture. Rupture is prevented by suppressor mutations that release the tension by halting PL removal from the outer leaflet. However, these suppressors do not restore OM stiffness or normal cell shape, revealing a possible connection between OM stiffness and cell shape.
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Affiliation(s)
- Irina V Mikheyeva
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08540, USA.
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35
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Wang Z, Zhao A, Qiao J, Yu J, He F, Bi Y, Yu L, Wang X. Engineering Escherichia coli MG1655 to Efficiently Produce 3-Deacyl-4'-monophosphoryl Lipid A. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13376-13390. [PMID: 37656614 DOI: 10.1021/acs.jafc.3c00681] [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: 09/03/2023]
Abstract
Monophosphoryl lipid A, derived from Salmonella minnesota R595, has been used in various adjuvant formulations. Escherichia coli can produce lipid A, but its structure is different. In this study, E. coli MG1655 has been engineered to efficiently produce the monophosphoryl lipid A. First, 126 genes relevant to the biosynthesis of the fimbriae, flagella, and ECA were deleted in MG1655, resulting in WQM027. Second, the genes pldA, mlaA, and mlaC related to the phospholipid transport system, the gene ptsG related to the carbohydrate phosphotransferase system, and the gene eptA encoding phosphoethanolamine transferase for lipid A modification were further deleted from WQM027, resulting in MW020. Third, lpxE from Francisella novicida and pagP and pagL from Salmonella were overexpressed in pFT24, resulting in pTEPL. pTEPL was transformed into MW020, resulting in MW020/pTEPL. Finally, fabI encoding an enoyl-ACP reductase was deleted from the genome of MW020/pTEPL, resulting in MW021/pTEPL. MW021/pTEPL could produce 85.31 mg/L of lipid A species after 26 h of fed-batch fermentation. Mainly two monophosphoryl lipid A species were produced in MW021/pTEPL, one is 3-deacyl-2-acyloxyacyl-4'-monophosphoryl lipid A and the other is 3-deacyl-4'-monophosphoryl lipid A. E. coli MW021/pTEPL constructed in this study could be an ideal host for the industrial production of monophosphoryl lipid A.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Aizhen Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jun Qiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jing Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fenfang He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yibing Bi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Letong Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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36
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Ng D, Moraes TF. Dynamic players and intricate interactions: An integrated investigation of the Mla lipid transport system. J Biol Chem 2023; 299:105146. [PMID: 37562569 PMCID: PMC10474453 DOI: 10.1016/j.jbc.2023.105146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2023] [Indexed: 08/12/2023] Open
Abstract
The Maintenance of outer membrane (OM) Lipid Asymmetry system mediates retrograde phospholipid transport from the OM to the inner membrane (IM) in Gram-negative bacteria. However, the interactions between the various subunits of the IM and OM complexes are not well understood. In a recent study in 2023 by MacRae et al. in the Journal of Biological Chemistry, the authors examine components in the Maintenance of OM Lipid Asymmetry complex, define the interaction interfaces between members of the pathway, and propose a molecular model of the lipid transfer process from the OM to the IM that will help elucidate intricacies of lipid transport.
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Affiliation(s)
- Dixon Ng
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Trevor F Moraes
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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37
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Fan Q, Dong X, Wang Z, Yue Y, Yuan Y, Wang Z, Yue T. TMT-Based Quantitative Proteomics and Non-targeted Metabolomic Analyses Reveal the Antibacterial Mechanism of Hexanal against Vibrio parahaemolyticus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12105-12115. [PMID: 37498004 DOI: 10.1021/acs.jafc.3c00009] [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: 07/28/2023]
Abstract
Hexanal is a phytochemical with antimicrobial activity. However, its antibacterial effect and mechanism against Vibrio parahaemolyticus (V. parahaemolyticus) remain unclear. The study aims to elucidate the associated mechanism using tandem mass tag quantitative proteomics and non-targeted metabolomics. Hexanal treatment reduced intracellular ATP concentration, increased membrane permeability, and destroyed the morphology and ultrastructure of V. parahaemolyticus cells. Proteomics and metabolomics data indicated that 572 differentially expressed proteins (DEPs) and 241 differential metabolites (DMs) were identified in hexanal-treated V. parahaemolyticus. These DEPs and DMs were involved in multiple biological pathways including amino acid metabolism, purine and pyrimidine biosynthesis, etc. Bioinformatics analysis revealed that hexanal damaged the structure and function of cell membranes, inhibited nucleotide metabolism, and disturbed carbohydrate metabolism and tricarboxylic acid cycle (TCA) cycle, which ultimately resulted in growth inhibition and bacterial death. The study is conducive to better understand the mode of action of hexanal against V. parahaemolyticus and offers experimental foundation for the application of hexanal as the antibacterial agent in the seafood-associated industry.
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Affiliation(s)
- Qiuxia Fan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinru Dong
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zewei Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Yue
- Xi'an Gaoxin No.1 High School, Xian 710000, People's Republic of China
| | - Yahong Yuan
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
| | - Zhouli Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
- College of Food Science and Technology, Northwest University, Xi'an 710069, China
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38
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Hogan AM, Rahman ASMZ, Motnenko A, Natarajan A, Maydaniuk DT, León B, Batun Z, Palacios A, Bosch A, Cardona ST. Profiling cell envelope-antibiotic interactions reveals vulnerabilities to β-lactams in a multidrug-resistant bacterium. Nat Commun 2023; 14:4815. [PMID: 37558695 PMCID: PMC10412643 DOI: 10.1038/s41467-023-40494-5] [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: 02/13/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023] Open
Abstract
The cell envelope of Gram-negative bacteria belonging to the Burkholderia cepacia complex (Bcc) presents unique restrictions to antibiotic penetration. As a consequence, Bcc species are notorious for causing recalcitrant multidrug-resistant infections in immunocompromised individuals. Here, we present the results of a genome-wide screen for cell envelope-associated resistance and susceptibility determinants in a Burkholderia cenocepacia clinical isolate. For this purpose, we construct a high-density, randomly-barcoded transposon mutant library and expose it to 19 cell envelope-targeting antibiotics. By quantifying relative mutant fitness with BarSeq, followed by validation with CRISPR-interference, we profile over a hundred functional associations and identify mediators of antibiotic susceptibility in the Bcc cell envelope. We reveal connections between β-lactam susceptibility, peptidoglycan synthesis, and blockages in undecaprenyl phosphate metabolism. The synergy of the β-lactam/β-lactamase inhibitor combination ceftazidime/avibactam is primarily mediated by inhibition of the PenB carbapenemase. In comparison with ceftazidime, avibactam more strongly potentiates the activity of aztreonam and meropenem in a panel of Bcc clinical isolates. Finally, we characterize in Bcc the iron and receptor-dependent activity of the siderophore-cephalosporin antibiotic, cefiderocol. Our work has implications for antibiotic target prioritization, and for using additional combinations of β-lactam/β-lactamase inhibitors that can extend the utility of current antibacterial therapies.
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Affiliation(s)
- Andrew M Hogan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Aakash Natarajan
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Dustin T Maydaniuk
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Beltina León
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Zayra Batun
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Armando Palacios
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alejandra Bosch
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvia T Cardona
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
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39
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Bekale LA, Sharma D, Bacacao B, Chen J, Santa Maria PL. Eradication of Bacterial Persister Cells By Leveraging Their Low Metabolic Activity Using Adenosine Triphosphate Coated Gold Nanoclusters. NANO TODAY 2023; 51:101895. [PMID: 37575958 PMCID: PMC10421611 DOI: 10.1016/j.nantod.2023.101895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Bacteria first develop tolerance after antibiotic exposure; later genetic resistance emerges through the population of tolerant bacteria. Bacterial persister cells are the multidrug-tolerant subpopulation within an isogenic bacteria culture that maintains genetic susceptibility to antibiotics. Because of this link between antibiotic tolerance and resistance and the rise of antibiotic resistance, there is a pressing need to develop treatments to eradicate persister cells. Current anti persister cell strategies are based on the paradigm of "awakening" them from their low metabolic state before attempting eradication with traditional antibiotics. Herein, we demonstrate that the low metabolic activity of persister cells can be exploited for eradication over their metabolically active counterparts. We engineered gold nanoclusters coated with adenosine triphosphate (AuNC@ATP) as a benchmark nanocluster that kills persister cells over exponential growth bacterial cells and prove the feasibility of this new concept. Finally, using AuNC@ATP as a new research tool, we demonstrated that it is possible to prevent the emergence of antibiotic-resistant superbugs with an anti-persister compound. Eradicating persister cells with AuNC@ATP in an isogenic culture of bacteria stops the emergence of superbug bacteria mediated by the sub-lethal dose of conventional antibiotics. Our findings lay the groundwork for developing novel nano-antibiotics targeting persister cells, which promise to prevent the emergence of superbugs and prolong the lifespan of currently available antibiotics.
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Affiliation(s)
- Laurent A. Bekale
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Devesh Sharma
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Brian Bacacao
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Jing Chen
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
| | - Peter L. Santa Maria
- Department of Otolaryngology, Head and Neck Surgery, Stanford University, 801 Welch Road Stanford, CA 94305-5739, USA
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40
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Chen J, Fruhauf A, Fan C, Ponce J, Ueberheide B, Bhabha G, Ekiert DC. Structure of an endogenous mycobacterial MCE lipid transporter. Nature 2023; 620:445-452. [PMID: 37495693 DOI: 10.1038/s41586-023-06366-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 06/22/2023] [Indexed: 07/28/2023]
Abstract
To replicate inside macrophages and cause tuberculosis, Mycobacterium tuberculosis must scavenge a variety of nutrients from the host1,2. The mammalian cell entry (MCE) proteins are important virulence factors in M. tuberculosis1,3, where they are encoded by large gene clusters and have been implicated in the transport of fatty acids4-7 and cholesterol1,4,8 across the impermeable mycobacterial cell envelope. Very little is known about how cargos are transported across this barrier, and it remains unclear how the approximately ten proteins encoded by a mycobacterial mce gene cluster assemble to transport cargo across the cell envelope. Here we report the cryo-electron microscopy (cryo-EM) structure of the endogenous Mce1 lipid-import machine of Mycobacterium smegmatis-a non-pathogenic relative of M. tuberculosis. The structure reveals how the proteins of the Mce1 system assemble to form an elongated ABC transporter complex that is long enough to span the cell envelope. The Mce1 complex is dominated by a curved, needle-like domain that appears to be unrelated to previously described protein structures, and creates a protected hydrophobic pathway for lipid transport across the periplasm. Our structural data revealed the presence of a subunit of the Mce1 complex, which we identified using a combination of cryo-EM and AlphaFold2, and name LucB. Our data lead to a structural model for Mce1-mediated lipid import across the mycobacterial cell envelope.
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Affiliation(s)
- James Chen
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Alice Fruhauf
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Catherine Fan
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jackeline Ponce
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
- Department of Neurology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
- Department of Microbiology, New York University School of Medicine, New York, NY, USA.
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41
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Thapa HB, Ebenberger SP, Schild S. The Two Faces of Bacterial Membrane Vesicles: Pathophysiological Roles and Therapeutic Opportunities. Antibiotics (Basel) 2023; 12:1045. [PMID: 37370364 PMCID: PMC10295235 DOI: 10.3390/antibiotics12061045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial membrane vesicles (MVs) are nanosized lipid particles secreted by lysis or blebbing mechanisms from Gram-negative and -positive bacteria. It is becoming increasingly evident that MVs can promote antimicrobial resistance but also provide versatile opportunities for therapeutic exploitation. As non-living facsimiles of parent bacteria, MVs can carry multiple bioactive molecules such as proteins, lipids, nucleic acids, and metabolites, which enable them to participate in intra- and interspecific communication. Although energetically costly, the release of MVs seems beneficial for bacterial fitness, especially for pathogens. In this review, we briefly discuss the current understanding of diverse MV biogenesis routes affecting MV cargo. We comprehensively highlight the physiological functions of MVs derived from human pathogens covering in vivo adaptation, colonization fitness, and effector delivery. Emphasis is given to recent findings suggesting a vicious cycle of MV biogenesis, pathophysiological function, and antibiotic therapy. We also summarize potential therapeutical applications, such as immunotherapy, vaccination, targeted delivery, and antimicrobial potency, including their experimental validation. This comparative overview identifies common and unique strategies for MV modification used along diverse applications. Thus, the review summarizes timely aspects of MV biology in a so far unprecedented combination ranging from beneficial function for bacterial pathogen survival to future medical applications.
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Affiliation(s)
- Himadri B. Thapa
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Stephan P. Ebenberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
- BioTechMed Graz, 8010 Graz, Austria
- Field of Excellence Biohealth, University of Graz, 8010 Graz, Austria
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42
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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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43
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MacRae MR, Puvanendran D, Haase MAB, Coudray N, Kolich L, Lam C, Baek M, Bhabha G, Ekiert DC. Protein-protein interactions in the Mla lipid transport system probed by computational structure prediction and deep mutational scanning. J Biol Chem 2023; 299:104744. [PMID: 37100290 PMCID: PMC10245069 DOI: 10.1016/j.jbc.2023.104744] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 04/28/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric bilayer that protects the cell from external stressors, such as antibiotics. The Mla transport system is implicated in the Maintenance of OM Lipid Asymmetry by mediating retrograde phospholipid transport across the cell envelope. Mla uses a shuttle-like mechanism to move lipids between the MlaFEDB inner membrane complex and the MlaA-OmpF/C OM complex, via a periplasmic lipid-binding protein, MlaC. MlaC binds to MlaD and MlaA, but the underlying protein-protein interactions that facilitate lipid transfer are not well understood. Here, we take an unbiased deep mutational scanning approach to map the fitness landscape of MlaC from Escherichia coli, which provides insights into important functional sites. Combining this analysis with AlphaFold2 structure predictions and binding experiments, we map the MlaC-MlaA and MlaC-MlaD protein-protein interfaces. Our results suggest that the MlaD and MlaA binding surfaces on MlaC overlap to a large extent, leading to a model in which MlaC can only bind one of these proteins at a time. Low-resolution cryo-electron microscopy (cryo-EM) maps of MlaC bound to MlaFEDB suggest that at least two MlaC molecules can bind to MlaD at once, in a conformation consistent with AlphaFold2 predictions. These data lead us to a model for MlaC interaction with its binding partners and insights into lipid transfer steps that underlie phospholipid transport between the bacterial inner and OMs.
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Affiliation(s)
- Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Dhenesh Puvanendran
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Max A B Haase
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Nicolas Coudray
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA; Applied Bioinformatics Laboratories, New York University School of Medicine, New York, New York, USA
| | - Ljuvica Kolich
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Cherry Lam
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA
| | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, Washington, USA; Institute for Protein Design, University of Washington, Seattle, Washington, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA.
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, New York, USA; Department of Microbiology, New York University School of Medicine, New York, New York, USA.
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44
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Ahmed AAQ, Besio R, Xiao L, Forlino A. Outer Membrane Vesicles (OMVs) as Biomedical Tools and Their Relevance as Immune-Modulating Agents against H. pylori Infections: Current Status and Future Prospects. Int J Mol Sci 2023; 24:ijms24108542. [PMID: 37239888 DOI: 10.3390/ijms24108542] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/26/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Outer membrane vesicles (OMVs) are lipid-membrane-bounded nanoparticles that are released from Gram-negative bacteria via vesiculation of the outer membrane. They have vital roles in different biological processes and recently, they have received increasing attention as possible candidates for a broad variety of biomedical applications. In particular, OMVs have several characteristics that enable them to be promising candidates for immune modulation against pathogens, such as their ability to induce the host immune responses given their resemblance to the parental bacterial cell. Helicobacter pylori (H. pylori) is a common Gram-negative bacterium that infects half of the world's population and causes several gastrointestinal diseases such as peptic ulcer, gastritis, gastric lymphoma, and gastric carcinoma. The current H. pylori treatment/prevention regimens are poorly effective and have limited success. This review explores the current status and future prospects of OMVs in biomedicine with a special focus on their use as a potential candidate in immune modulation against H. pylori and its associated diseases. The emerging strategies that can be used to design OMVs as viable immunogenic candidates are discussed.
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Affiliation(s)
- Abeer Ahmed Qaed Ahmed
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Roberta Besio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
| | - Lin Xiao
- School of Biomedical Engineering, Shenzhen Campus, Sun Yat-sen University, Shenzhen 518107, China
| | - Antonella Forlino
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
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45
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Borchert AJ, Bleem A, Beckham GT. RB-TnSeq identifies genetic targets for improved tolerance of Pseudomonas putida towards compounds relevant to lignin conversion. Metab Eng 2023; 77:208-218. [PMID: 37059293 DOI: 10.1016/j.ymben.2023.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/21/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
Lignin-derived mixtures intended for bioconversion commonly contain high concentrations of aromatic acids, aliphatic acids, and salts. The inherent toxicity of these chemicals places a significant bottleneck upon the effective use of microbial systems for the valorization of these mixtures. Pseudomonas putida KT2440 can tolerate stressful quantities of several lignin-related compounds, making this bacterium a promising host for converting these chemicals to valuable bioproducts. Nonetheless, further increasing P. putida tolerance to chemicals in lignin-rich substrates has the potential to improve bioprocess performance. Accordingly, we employed random barcoded transposon insertion sequencing (RB-TnSeq) to reveal genetic determinants in P. putida KT2440 that influence stress outcomes during exposure to representative constituents found in lignin-rich process streams. The fitness information obtained from the RB-TnSeq experiments informed engineering of strains via deletion or constitutive expression of several genes. Namely, ΔgacAS, ΔfleQ, ΔlapAB, ΔttgR::Ptac:ttgABC, Ptac:PP_1150:PP_1152, ΔrelA, and ΔPP_1430 mutants showed growth improvement in the presence of single compounds, and some also exhibited greater tolerance when grown using a complex chemical mixture representative of a lignin-rich chemical stream. Overall, this work demonstrates the successful implementation of a genome-scale screening tool for the identification of genes influencing stress tolerance against notable compounds within lignin-enriched chemical streams, and the genetic targets identified herein offer promising engineering targets for improving feedstock tolerance in lignin valorization strains of P. putida KT2440.
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Affiliation(s)
- Andrew J Borchert
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Alissa Bleem
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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46
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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47
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Bilsing FL, Anlauf MT, Hachani E, Khosa S, Schmitt L. ABC Transporters in Bacterial Nanomachineries. Int J Mol Sci 2023; 24:ijms24076227. [PMID: 37047196 PMCID: PMC10094684 DOI: 10.3390/ijms24076227] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Members of the superfamily of ABC transporters are found in all domains of life. Most of these primary active transporters act as isolated entities and export or import their substrates in an ATP-dependent manner across biological membranes. However, some ABC transporters are also part of larger protein complexes, so-called nanomachineries that catalyze the vectorial transport of their substrates. Here, we will focus on four bacterial examples of such nanomachineries: the Mac system providing drug resistance, the Lpt system catalyzing vectorial LPS transport, the Mla system responsible for phospholipid transport, and the Lol system, which is required for lipoprotein transport to the outer membrane of Gram-negative bacteria. For all four systems, we tried to summarize the existing data and provide a structure-function analysis highlighting the mechanistical aspect of the coupling of ATP hydrolysis to substrate translocation.
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48
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Arrieta-Ortiz ML, Pan M, Kaur A, Pepper-Tunick E, Srinivas V, Dash A, Immanuel SRC, Brooks AN, Shepherd TR, Baliga NS. Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli. mSystems 2023; 8:e0090422. [PMID: 36537814 PMCID: PMC9948699 DOI: 10.1128/msystems.00904-22] [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: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 02/24/2023] Open
Abstract
There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (TetR) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of TetR E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of TetR E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized TetR E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the TetR strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics. IMPORTANCE Antimicrobial resistance (AMR) is projected to be the cause of >10 million deaths annually by 2050. While efforts to find new potent antibiotics are effective, they are expensive and outpaced by the rate at which new resistant strains emerge. There is desperate need for a rational approach to accelerate the discovery of drugs and drug combinations that effectively clear AMR pathogens and even prevent the emergence of new resistant strains. Using tetracycline-resistant (TetR) Escherichia coli, we demonstrate that gaining resistance is accompanied by loss of fitness, which is restored by compensatory physiological changes. We demonstrate that transcriptional regulators of the compensatory physiologic state are promising drug targets because their disruption increases the susceptibility of TetR E. coli to tetracycline. Thus, we describe a generalizable systems biology approach to identify new vulnerabilities within AMR strains to rationally accelerate the discovery of therapeutics that extend the life span of existing antibiotics.
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Affiliation(s)
| | - Min Pan
- Institute for Systems Biology, Seattle, Washington, USA
| | - Amardeep Kaur
- Institute for Systems Biology, Seattle, Washington, USA
| | - Evan Pepper-Tunick
- Institute for Systems Biology, Seattle, Washington, USA
- Molecular Engineering Sciences Institute, University of Washington, Seattle, Washington, USA
| | | | - Ananya Dash
- Institute for Systems Biology, Seattle, Washington, USA
| | | | | | | | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, USA
- Molecular Engineering Sciences Institute, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
- Lawrence Berkeley National Lab, Berkeley, California, USA
- Department of Microbiology, University of Washington, Seattle Washington, USA
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49
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Mikheyeva IV, Sun J, Huang KC, Silhavy TJ. Mechanism of outer membrane destabilization by global reduction of protein content. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.19.529137. [PMID: 36865163 PMCID: PMC9980000 DOI: 10.1101/2023.02.19.529137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria such as Escherichia coli is an asymmetric bilayer with the glycolipid lipopolysaccharide (LPS) in the outer leaflet and glycerophospholipids in the inner. Nearly all integral OM proteins (OMPs) have a characteristic β-barrel fold and are assembled in the OM by the BAM complex, which contains one essential β-barrel protein (BamA), one essential lipoprotein (BamD), and three non-essential lipoproteins (BamBCE). A gain-of-function mutation in bamA enables survival in the absence of BamD, showing that the essential function of this protein is regulatory. We demonstrate that the global reduction in OMPs caused by BamD loss weakens the OM, altering cell shape and causing OM rupture in spent medium. To fill the void created by OMP loss, PLs flip into the outer leaflet. Under these conditions, mechanisms that remove PLs from the outer leaflet create tension between the OM leaflets, which contributes to membrane rupture. Rupture is prevented by suppressor mutations that release the tension by halting PL removal from the outer leaflet. However, these suppressors do not restore OM stiffness or normal cell shape, revealing a possible connection between OM stiffness and cell shape. Significance Statement The outer membrane (OM) is a selective permeability barrier that contributes to the intrinsic antibiotic resistance of Gram-negative bacteria. Biophysical characterization of the roles of the component proteins, lipopolysaccharides, and phospholipids is limited by both the essentiality of the OM and its asymmetrical organization. In this study, we dramatically change OM physiology by limiting the protein content, which requires phospholipid localization to the outer leaflet and thus disrupts OM asymmetry. By characterizing the perturbed OM of various mutants, we provide novel insight into the links among OM composition, OM stiffness, and cell shape regulation. These findings deepen our understanding of bacterial cell envelope biology and provide a platform for further interrogation of OM properties.
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Affiliation(s)
- Irina V. Mikheyeva
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Thomas J. Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
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50
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Gregg KA, Wang Y, Warfel J, Schoenfeld E, Jankowska E, Cipollo JF, Mayho M, Boinett C, Prasad D, Brickman TJ, Armstrong SK, Parkhill J, Da Silva Antunes R, Sette A, Papin JF, Wolf R, Merkel TJ. Antigen Discovery for Next-Generation Pertussis Vaccines Using Immunoproteomics and Transposon-Directed Insertion Sequencing. J Infect Dis 2023; 227:583-591. [PMID: 36575950 PMCID: PMC10169431 DOI: 10.1093/infdis/jiac502] [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: 08/26/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Despite high vaccination rates, the United States has experienced a resurgence in reported cases of pertussis after switching to the acellular pertussis vaccine, indicating a need for improved vaccines that enhance infection control. METHODS Bordetella pertussis antigens recognized by convalescent-baboon serum and nasopharyngeal wash were identified by immunoproteomics and their subcellular localization predicted. Genes essential or important for persistence in the baboon airway were identified by transposon-directed insertion-site sequencing (TraDIS) analysis. RESULTS In total, 314 B. pertussis antigens were identified by convalescent baboon serum and 748 by nasopharyngeal wash. Thirteen antigens were identified as immunogenic in baboons, essential for persistence in the airway by TraDIS, and membrane-localized: BP0840 (OmpP), Pal, OmpA2, BP1485, BamA, Pcp, MlaA, YfgL, BP2197, BP1569, MlaD, ComL, and BP0183. CONCLUSIONS The B. pertussis antigens identified as immunogenic, essential for persistence in the airway, and membrane-localized warrant further investigation for inclusion in vaccines designed to reduce or prevent carriage of bacteria in the airway of vaccinated individuals.
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Affiliation(s)
- Kelsey A Gregg
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Yihui Wang
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jason Warfel
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Elizabeth Schoenfeld
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Ewa Jankowska
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - John F Cipollo
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | | | | | - Deepika Prasad
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Timothy J Brickman
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sandra K Armstrong
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | | | | | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA.,Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - James F Papin
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Roman Wolf
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Tod J Merkel
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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