1
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Wang Z, Chu Y, Li Q, Han X, Zhao L, Zhang H, Cai K, Zhang X, Wang X, Qin Y, Fan E. A minimum functional form of the Escherichia coli BAM complex constituted by BamADE assembles outer membrane proteins in vitro. J Biol Chem 2024; 300:107324. [PMID: 38677515 PMCID: PMC11130730 DOI: 10.1016/j.jbc.2024.107324] [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: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
The biogenesis of outer membrane proteins is mediated by the β-barrel assembly machinery (BAM), which is a heteropentomeric complex composed of five proteins named BamA-E in Escherichia coli. Despite great progress in the BAM structural analysis, the molecular details of BAM-mediated processes as well as the exact function of each BAM component during OMP assembly are still not fully understood. To enable a distinguishment of the function of each BAM component, it is the aim of the present work to examine and identify the effective minimum form of the E. coli BAM complex by use of a well-defined reconstitution strategy based on a previously developed versatile assay. Our data demonstrate that BamADE is the core BAM component and constitutes a minimum functional form for OMP assembly in E. coli, which can be stimulated by BamB and BamC. While BamB and BamC have a redundant function based on the minimum form, both together seem to cooperate with each other to substitute for the function of the missing BamD or BamE. Moreover, the BamAE470K mutant also requires the function of BamD and BamE to assemble OMPs in vitro, which vice verse suggests that BamADE are the effective minimum functional form of the E. coli BAM complex.
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Affiliation(s)
- Zhe Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yindi Chu
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Qingrong Li
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xiaochen Han
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Leyi Zhao
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Hanqing Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kun Cai
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xuyan Zhang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xingyuan Wang
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Youcai Qin
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Enguo Fan
- Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China; School of Medicine, Linyi University, Linyi, China.
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2
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Mallick B, Dutta A, Mondal P, Dutta M. Proteomic analysis and protein structure prediction of Shigella phage Sfk20 based on a comparative study using structure prediction approaches. Proteins 2024; 92:637-648. [PMID: 38146101 DOI: 10.1002/prot.26653] [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: 08/26/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 12/27/2023]
Abstract
Bacteriophages are the natural predators of bacteria and are available abundantly everywhere in nature. Lytic phages can specifically infect their bacterial host (through attachment to the receptor) and use their host replication machinery to replicate rapidly, a feature that enables them to kill a disease-causing bacteria. Hence, phage attachment to the host bacteria is the first important step of the infection process. It is reported in this study that the receptor could be an LPS which is responsible for the attachment of the Sfk20 phage to its host (Shigella flexneri 2a). Phage Sfk20 bacteriolytic activity was examined for preliminary optimization of phage titer. The phage Sfk20 viability at different saline conditions was conducted. The LC-MS/MS technique used here for detecting and identifying 40 Sfk20 phage proteins helped us to get an initial understanding of the structural landscape of phage Sfk20. From the identified proteins, six structurally significant proteins were selected for structure prediction using two neural network systems: AlphaFold2 and ESMFold, and one homology modeling software: Phyre2. Later the performance of these modeling systems was compared using various metrics. We conclude from the available and generated information that AlphaFold2 and Phyre2 perform better than ESMFold for predicting Sfk20 phage protein structures.
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Affiliation(s)
- Bani Mallick
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Aninda Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Payel Mondal
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
| | - Moumita Dutta
- Division of Electron Microscopy, ICMR-National Institute of Cholera & Enteric Diseases, Kolkata, West Bengal, India
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3
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George A, Patil AG, Mahalakshmi R. ATP-independent assembly machinery of bacterial outer membranes: BAM complex structure and function set the stage for next-generation therapeutics. Protein Sci 2024; 33:e4896. [PMID: 38284489 PMCID: PMC10804688 DOI: 10.1002/pro.4896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/30/2024]
Abstract
Diderm bacteria employ β-barrel outer membrane proteins (OMPs) as their first line of communication with their environment. These OMPs are assembled efficiently in the asymmetric outer membrane by the β-Barrel Assembly Machinery (BAM). The multi-subunit BAM complex comprises the transmembrane OMP BamA as its functional subunit, with associated lipoproteins (e.g., BamB/C/D/E/F, RmpM) varying across phyla and performing different regulatory roles. The ability of BAM complex to recognize and fold OM β-barrels of diverse sizes, and reproducibly execute their membrane insertion, is independent of electrochemical energy. Recent atomic structures, which captured BAM-substrate complexes, show the assembly function of BamA can be tailored, with different substrate types exhibiting different folding mechanisms. Here, we highlight common and unique features of its interactome. We discuss how this conserved protein complex has evolved the ability to effectively achieve the directed assembly of diverse OMPs of wide-ranging sizes (8-36 β-stranded monomers). Additionally, we discuss how darobactin-the first natural membrane protein inhibitor of Gram-negative bacteria identified in over five decades-selectively targets and specifically inhibits BamA. We conclude by deliberating how a detailed deduction of BAM complex-associated regulation of OMP biogenesis and OM remodeling will open avenues for the identification and development of effective next-generation therapeutics against Gram-negative pathogens.
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Affiliation(s)
- Anjana George
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Akanksha Gajanan Patil
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological SciencesIndian Institute of Science Education and ResearchBhopalIndia
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4
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Rath P, Hermann A, Schaefer R, Agustoni E, Vonach JM, Siegrist M, Miscenic C, Tschumi A, Roth D, Bieniossek C, Hiller S. High-throughput screening of BAM inhibitors in native membrane environment. Nat Commun 2023; 14:5648. [PMID: 37704632 PMCID: PMC10499997 DOI: 10.1038/s41467-023-41445-w] [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: 04/02/2022] [Accepted: 09/02/2023] [Indexed: 09/15/2023] Open
Abstract
The outer membrane insertase of Gram-negative bacteria, BAM, is a key target for urgently needed novel antibiotics. Functional reconstitutions of BAM have so far been limited to synthetic membranes and with low throughput capacity for inhibitor screening. Here, we describe a BAM functional assay in native membrane environment capable of high-throughput screening. This is achieved by employing outer membrane vesicles (OMVs) to present BAM directly in native membranes. Refolding of the model substrate OmpT by BAM was possible from the chaperones SurA and Skp, with the required SurA concentration three times higher than Skp. In the OMVs, the antibiotic darobactin had a tenfold higher potency than in synthetic membranes, highlighting the need for native conditions in antibiotics development. The assay is successfully miniaturized for 1536-well plates and upscaled using large scale fermentation, resulting in high-throughput capacities to screen large commercial compound libraries. Our OMV-based assay thus lays the basis for discovery, hit validation and lead expansion of antibiotics targeting BAM.
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Affiliation(s)
- Parthasarathi Rath
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Adrian Hermann
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Ramona Schaefer
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Elia Agustoni
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland
| | - Jean-Marie Vonach
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Martin Siegrist
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Christian Miscenic
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Andreas Tschumi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Doris Roth
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland.
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056, Basel, Switzerland.
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5
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Chen S, Zhou A, Xu Y. Symbiotic Bacteria Regulating Insect-Insect/Fungus/Virus Mutualism. INSECTS 2023; 14:741. [PMID: 37754709 PMCID: PMC10531535 DOI: 10.3390/insects14090741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/25/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023]
Abstract
Bacteria associated with insects potentially provide many beneficial services and have been well documented. Mutualism that relates to insects is widespread in ecosystems. However, the interrelation between "symbiotic bacteria" and "mutualism" has rarely been studied. We introduce three systems of mutualism that relate to insects (ants and honeydew-producing Hemiptera, fungus-growing insects and fungi, and plant persistent viruses and vector insects) and review the species of symbiotic bacteria in host insects, as well as their functions in host insects and the mechanisms underlying mutualism regulation. A deeper understanding of the molecular mechanisms and role of symbiotic bacteria, based on metagenomics, transcriptomics, proteomics, metabolomics, and microbiology, will be required for describing the entire interaction network.
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Affiliation(s)
- Siqi Chen
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou 510642, China;
| | - Aiming Zhou
- Hubei Insect Resources Utilization and Sustainable Pest Management, Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yijuan Xu
- Red Imported Fire Ant Research Center, South China Agricultural University, Guangzhou 510642, China;
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6
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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7
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Bobrovsky PA, Kharlampieva DD, Kirillin SA, Brovina KA, Grafskaia EN, Lazarev VN, Manuvera VA. Upregulation of YciM Expression Reduces Endotoxin Contamination of Recombinant Proteins Produced in Escherichia coli Cells. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1318-1325. [PMID: 37770398 DOI: 10.1134/s0006297923090110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/10/2023] [Indexed: 09/30/2023]
Abstract
Recombinant proteins produced in Escherichia coli are often contaminated with endotoxins, which can be a serious problem for their further application. One of the possible solutions is the use of modified strains with reduced lipopolysaccharide (LPS) levels. We compared two approaches to engineering such strains. The first commonly known approach was modification of LPS biosynthesis pathway by knocking out seven genes in the E. coli genome. The second approach, which has not been previously used, was to increase expression of E. coli protein YciM. According to the published data, elevated expression of YciM leads to the reduction in the amount of the LpxC enzyme involved in LPS biosynthesis. We investigated the impact of YciM coexpression with eGFP on the content of endotoxins in the purified recombinant eGFP samples. Both approaches provided similar outcomes, i.e., decreased the endotoxin levels in the purified protein samples.
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Affiliation(s)
- Pavel A Bobrovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology (National Research University), Moscow, 141701, Russia
| | - Daria D Kharlampieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Sergey A Kirillin
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Ksenia A Brovina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology (National Research University), Moscow, 141701, Russia
| | - Ekaterina N Grafskaia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Vassili N Lazarev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
- Moscow Institute of Physics and Technology (National Research University), Moscow, 141701, Russia
| | - Valentin A Manuvera
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia.
- Moscow Institute of Physics and Technology (National Research University), Moscow, 141701, Russia
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8
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Kuo K, Liu J, Pavlova A, Gumbart JC. Drug Binding to BamA Targets Its Lateral Gate. J Phys Chem B 2023; 127:7509-7517. [PMID: 37587651 PMCID: PMC10476194 DOI: 10.1021/acs.jpcb.3c04501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/30/2023] [Indexed: 08/18/2023]
Abstract
BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer-membrane protein (OMP) in Gram-negative bacteria. Its function is to insert and fold substrate OMPs into the outer membrane (OM). Evidence suggests that BamA follows the asymmetric hybrid-barrel model where the first and last strands of BamA separate, a process known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially insert and fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA's function have been identified. We modeled and then docked one of these compounds into either the extracellular loops of BamA or the open lateral gate. With the compound docked in the loops, we found that the lateral gate remains closed during 5 μs molecular dynamics simulations. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds. In these simulations, we observed a differing degree and/or frequency of opening of BamA's lateral gate compared to BamA-apo, suggesting that the mutations grant resistance by altering the dynamics at the gate. We conclude that the compounds act by inhibiting BamA lateral gate opening and/or binding of substrate, thus preventing subsequent OMP folding and insertion.
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Affiliation(s)
- Katie
M. Kuo
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jinchan Liu
- Department
of Molecular Biophysics and Biochemistry (MB&B), Yale University, New Haven, Connecticut 06510, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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9
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Rodriguez MT, McLaurin KA, Shtutman M, Kubinak JL, Mactutus CF, Booze RM. Therapeutically targeting the consequences of HIV-1-associated gastrointestinal dysbiosis: Implications for neurocognitive and affective alterations. Pharmacol Biochem Behav 2023; 229:173592. [PMID: 37390973 PMCID: PMC10494709 DOI: 10.1016/j.pbb.2023.173592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/16/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Approximately 50 % of the individuals living with human immunodeficiency virus type 1 (HIV-1) are plagued by debilitating neurocognitive impairments (NCI) and/or affective alterations. Sizeable alterations in the composition of the gut microbiome, or gastrointestinal dysbiosis, may underlie, at least in part, the NCI, apathy, and/or depression observed in this population. Herein, two interrelated aims will be critically addressed, including: 1) the evidence for, and functional implications of, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals; and 2) the potential for therapeutically targeting the consequences of this dysbiosis for the treatment of HIV-1-associated NCI and affective alterations. First, gastrointestinal microbiome dysbiosis in HIV-1 seropositive individuals is characterized by decreased alpha (α) diversity, a decreased relative abundance of bacterial species belonging to the Bacteroidetes phylum, and geographic-specific alterations in Bacillota (formerly Firmicutes) spp. Fundamentally, changes in the relative abundance of Bacteroidetes and Bacillota spp. may underlie, at least in part, the deficits in γ-aminobutyric acid and serotonin neurotransmission, as well as prominent synaptodendritic dysfunction, observed in this population. Second, there is compelling evidence for the therapeutic utility of targeting synaptodendritic dysfunction as a method to enhance neurocognitive function and improve motivational dysregulation in HIV-1. Further research is needed to determine whether the therapeutics enhancing synaptic efficacy exert their effects by altering the gut microbiome. Taken together, understanding gastrointestinal microbiome dysbiosis resulting from chronic HIV-1 viral protein exposure may afford insight into the mechanisms underlying HIV-1-associated neurocognitive and/or affective alterations; mechanisms which can be subsequently targeted via novel therapeutics.
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Affiliation(s)
- Mason T Rodriguez
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Kristen A McLaurin
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Michael Shtutman
- Drug Discovery and Biomedical Sciences, College of Pharmacy, 715 Sumter Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Jason L Kubinak
- Pathology, Microbiology & Immunology, School of Medicine Columbia, 6311 Garners Ferry Road, Building 2, Columbia, SC 29209, United States of America
| | - Charles F Mactutus
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America
| | - Rosemarie M Booze
- Cognitive and Neural Science Program, Department of Psychology, Barnwell College, 1512 Pendleton Street, University of South Carolina, Columbia, SC 29208, United States of America.
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10
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Schultz KM, Schneider JR, Fischer MA, Cina NP, Riegert MO, Frank DW, Klug CS. Binding and transport of LPS occurs through the coordinated combination of an array of sites across the entire Escherichia coli LPS transport protein LptA. Protein Sci 2023; 32:e4724. [PMID: 37417889 PMCID: PMC10360375 DOI: 10.1002/pro.4724] [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: 03/20/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/08/2023]
Abstract
The outer leaflet of the outer membrane (OM) of bacteria such as Escherichia coli, Pseudomonas aeruginosa, and other important pathogens is largely composed of lipopolysaccharide (LPS), which is essential to nearly all Gram-negative bacteria. LPS is transported to the outer leaflet of the OM through a yet unknown mechanism by seven proteins that comprise the LPS transport system. LptA, the only entirely periplasmic Lpt protein, bridges the periplasmic space between the IM LptB2 FGC and the OM LptDE complexes. LptA is postulated to protect the hydrophobic acyl chains of LPS as it crosses the hydrophilic periplasm, is essential to cell viability, and contains many conserved residues distributed across the protein. To identify which side chains are required for function of E. coli LptA in vivo, we performed a systematic, unbiased, high-throughput screen of the effect of 172 single alanine substitutions on cell viability utilizing an engineered BL21 derivative with a chromosomal knockout of the lptA gene. Remarkably, LptA is highly tolerant to amino acid substitution with alanine. Only four alanine mutants could not complement the chromosomal knockout; CD spectroscopy showed that these substitutions resulted in proteins with significantly altered secondary structure. In addition, 29 partial loss-of-function mutants were identified that led to OM permeability defects; interestingly, these sites were solely located within β-strands of the central core of the protein and each resulted in misfolding of the protein. Therefore, no single residue within LptA is responsible for LPS binding, supporting previous EPR spectroscopy data indicating that sites across the entire protein work in concert to bind and transport LPS.
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Affiliation(s)
- Kathryn M. Schultz
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - John R. Schneider
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Matthew A. Fischer
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Nicholas P. Cina
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Molly O. Riegert
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Dara W. Frank
- Department of Microbiology & ImmunologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Candice S. Klug
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
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11
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Kaiser KG, Delattre V, Frost VJ, Buck GW, Phu JV, Fernandez TG, Pavel IE. Nanosilver: An Old Antibacterial Agent with Great Promise in the Fight against Antibiotic Resistance. Antibiotics (Basel) 2023; 12:1264. [PMID: 37627684 PMCID: PMC10451389 DOI: 10.3390/antibiotics12081264] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Antibiotic resistance in bacteria is a major problem worldwide that costs 55 billion USD annually for extended hospitalization, resource utilization, and additional treatment expenditures in the United States. This review examines the roles and forms of silver (e.g., bulk Ag, silver salts (AgNO3), and colloidal Ag) from antiquity to the present, and its eventual incorporation as silver nanoparticles (AgNPs) in numerous antibacterial consumer products and biomedical applications. The AgNP fabrication methods, physicochemical properties, and antibacterial mechanisms in Gram-positive and Gram-negative bacterial models are covered. The emphasis is on the problematic ESKAPE pathogens and the antibiotic-resistant pathogens of the greatest human health concern according to the World Health Organization. This review delineates the differences between each bacterial model, the role of the physicochemical properties of AgNPs in the interaction with pathogens, and the subsequent damage of AgNPs and Ag+ released by AgNPs on structural cellular components. In closing, the processes of antibiotic resistance attainment and how novel AgNP-antibiotic conjugates may synergistically reduce the growth of antibiotic-resistant pathogens are presented in light of promising examples, where antibiotic efficacy alone is decreased.
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Affiliation(s)
- Kyra G. Kaiser
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoire Delattre
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Victoria J. Frost
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Gregory W. Buck
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
| | - Julianne V. Phu
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Timea G. Fernandez
- Department of Chemistry, Physics, Geology and the Environment, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA; (V.J.F.); (J.V.P.)
- Department of Biology, Winthrop University, 701 Oakland Avenue, Rock Hill, SC 29733, USA
| | - Ioana E. Pavel
- Department of Physical and Environmental Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA; (K.G.K.); (V.D.); (G.W.B.)
- Department of Life Sciences, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, TX 78412, USA
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12
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Wijesinghe WCB, Min D. Single-Molecule Force Spectroscopy of Membrane Protein Folding. J Mol Biol 2023; 435:167975. [PMID: 37330286 DOI: 10.1016/j.jmb.2023.167975] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 06/19/2023]
Abstract
Single-molecule force spectroscopy is a unique method that can probe the structural changes of single proteins at a high spatiotemporal resolution while mechanically manipulating them over a wide force range. Here, we review the current understanding of membrane protein folding learned by using the force spectroscopy approach. Membrane protein folding in lipid bilayers is one of the most complex biological processes in which diverse lipid molecules and chaperone proteins are intricately involved. The approach of single protein forced unfolding in lipid bilayers has produced important findings and insights into membrane protein folding. This review provides an overview of the forced unfolding approach, including recent achievements and technical advances. Progress in the methods can reveal more interesting cases of membrane protein folding and clarify general mechanisms and principles.
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Affiliation(s)
- W C Bhashini Wijesinghe
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Duyoung Min
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Center for Wave Energy Materials, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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13
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Selvam R, Lim IHY, Lewis JC, Lim CH, Yap MKK, Tan HS. Selecting antibacterial aptamers against the BamA protein in Pseudomonas aeruginosa by incorporating genetic algorithm to optimise computational screening method. Sci Rep 2023; 13:7582. [PMID: 37164985 PMCID: PMC10170454 DOI: 10.1038/s41598-023-34643-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023] Open
Abstract
Antibiotic resistance is one of the biggest threats to global health resulting in an increasing number of people suffering from severe illnesses or dying due to infections that were once easily curable with antibiotics. Pseudomonas aeruginosa is a major pathogen that has rapidly developed antibiotic resistance and WHO has categorised this pathogen under the critical list. DNA aptamers can act as a potential candidate for novel antimicrobial agents. In this study, we demonstrated that an existing aptamer is able to affect the growth of P. aeruginosa. A computational screen for aptamers that could bind to a well-conserved and essential outer membrane protein, BamA in Gram-negative bacteria was conducted. Molecular docking of about 100 functional DNA aptamers with BamA protein was performed via both local and global docking approaches. Additionally, genetic algorithm analysis was carried out to rank the aptamers based on their binding affinity. The top hits of aptamers with good binding to BamA protein were synthesised to investigate their in vitro antibacterial activity. Among all aptamers, Apt31, which is known to bind to an antitumor, Daunomycin, exhibited the highest HADDOCK score and resulted in a significant (p < 0.05) reduction in P. aeruginosa growth. Apt31 also induced membrane disruption that resulted in DNA leakage. Hence, computational screening may result in the identification of aptamers that bind to the desired active site with high affinity.
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Affiliation(s)
- Rupany Selvam
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ian Han Yan Lim
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | | | - Chern Hong Lim
- School of Information Technology, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | | | - Hock Siew Tan
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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14
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Xu Q, Guo M, Yu F. β-Barrel Assembly Machinery (BAM) Complex as Novel Antibacterial Drug Target. Molecules 2023; 28:molecules28093758. [PMID: 37175168 PMCID: PMC10180388 DOI: 10.3390/molecules28093758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 05/15/2023] Open
Abstract
The outer membrane of Gram-negative bacteria is closely related to the pathogenicity and drug resistance of bacteria. Outer membrane proteins (OMPs) are a class of proteins with important biological functions on the outer membrane. The β-barrel assembly machinery (BAM) complex plays a key role in OMP biogenesis, which ensures that the OMP is inserted into the outer membrane in a correct folding manner and performs nutrient uptake, antibiotic resistance, cell adhesion, cell signaling, and maintenance of membrane stability and other functions. The BAM complex is highly conserved among Gram-negative bacteria. The abnormality of the BAM complex will lead to the obstruction of OMP folding, affect the function of the outer membrane, and eventually lead to bacterial death. In view of the important role of the BAM complex in OMP biogenesis, the BAM complex has become an attractive target for the development of new antibacterial drugs against Gram-negative bacteria. Here, we summarize the structure and function of the BAM complex and review the latest research progress of antibacterial drugs targeting BAM in order to provide a new perspective for the development of antibiotics.
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Affiliation(s)
- Qian Xu
- Laboratory of Molecular Pathology, Department of Pathology, Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Min Guo
- Allergy Clinic, Zibo Central Hospital, Zibo 255000, China
| | - Feiyuan Yu
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China
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15
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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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16
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Dong A, Liu C, Hua X, Yu Y, Guo Y, Wang D, Liu X, Chen H, Wang H, Zhu L. Bioinformatic analysis of structures and encoding genes of Escherichia coli surface polysaccharides sheds light on the heterologous biosynthesis of glycans. BMC Genomics 2023; 24:168. [PMID: 37016299 PMCID: PMC10072801 DOI: 10.1186/s12864-023-09269-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 03/22/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Surface polysaccharides (SPs), such as lipopolysaccharide (O antigen) and capsular polysaccharide (K antigen), play a key role in the pathogenicity of Escherichia coli (E. coli). Gene cluster for polysaccharide antigen biosynthesis encodes various glycosyltransferases (GTs), which drive the process of SP synthesis and determine the serotype. RESULTS In this study, a total of 7,741 E. coli genomic sequences were chosen for systemic data mining. The monosaccharides in both O and K antigens were dominated by D-hexopyranose, and the SPs in 70-80% of the strains consisted of only the five most common hexoses (or some of them). The linkages between the two monosaccharides were mostly α-1,3 (23.15%) and β-1,3 (20.49%) bonds. Uridine diphosphate activated more than 50% of monosaccharides for glycosyltransferase reactions. These results suggest that the most common pathways could be integrated into chassis cells to promote glycan biosynthesis. We constructed a database (EcoSP, http://ecosp.dmicrobe.cn/ ) for browse this information, such as monosaccharide synthesis pathways. It can also be used for serotype analysis and GT annotation of known or novel E. coli sequences, thus facilitating the diagnosis and typing. CONCLUSIONS Summarizing and analyzing the properties of these polysaccharide antigens and GTs are of great significance for designing glycan-based vaccines and the synthetic glycobiology.
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Affiliation(s)
- Ao Dong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Chengzhi Liu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- Hangzhou Digital-Micro Biotech Co., Ltd, Hangzhou, People's Republic of China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People's Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Yan Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Dongshu Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Xiankai Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China
| | - Huan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.
- Hangzhou Digital-Micro Biotech Co., Ltd, Hangzhou, People's Republic of China.
- Zhejiang Chinese Medical University, Hangzhou, People's Republic of China.
| | - Hengliang Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China.
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, No. 20, Dongda Street, Fengtai District, Beijing, 100071, People's Republic of China.
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17
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Wang Z, Zeng J, Deng J, Hou X, Zhang J, Yan W, Cai Q. Pathogen-Derived Extracellular Vesicles: Emerging Mediators of Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:218-227. [PMID: 36574017 DOI: 10.1094/mpmi-08-22-0162-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Extracellular vesicles (EVs) are lipid bilayer-enclosed nanoparticles that deliver bioactive proteins, nucleic acids, lipids, and other small molecules from donor to recipient cells. They have attracted significant interest recently due to their important roles in regulating plant-microbe interaction. During microbial infection, plant EVs play a prominent role in defense by delivering small regulatory RNA into pathogens, resulting in the silencing of pathogen virulence genes. Pathogens also deliver small RNAs into plant cells to silence host immunity genes. Recent evidence indicates that microbial EVs may be involved in pathogenesis and host immunity modulation by transporting RNAs and other biomolecules. However, the biogenesis and function of microbial EVs in plant-microbe interaction remain ill-defined. In this review, we discuss various aspects of microbial EVs, with a particular focus on current methods for EV isolation, composition, biogenesis, and their roles in plant-microbe interaction. We also discussed the potential role of microbial EVs in cross-kingdom RNA trafficking from pathogens to plants, as it is a highly likely possibility to explore in the future. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zhangying Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Jiayue Zeng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Jiliang Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Xiangjie Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Jiefu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
| | - Wei Yan
- Department of Cell Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Hubei Hongshan Laboratory, Wuhan, 430072, China
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18
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Overly Cottom C, Stephenson R, Wilson L, Noinaj N. Targeting BAM for Novel Therapeutics against Pathogenic Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:679. [PMID: 37107041 PMCID: PMC10135246 DOI: 10.3390/antibiotics12040679] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/28/2023] [Accepted: 03/06/2023] [Indexed: 04/29/2023] Open
Abstract
The growing emergence of multidrug resistance in bacterial pathogens is an immediate threat to human health worldwide. Unfortunately, there has not been a matching increase in the discovery of new antibiotics to combat this alarming trend. Novel contemporary approaches aimed at antibiotic discovery against Gram-negative bacterial pathogens have expanded focus to also include essential surface-exposed receptors and protein complexes, which have classically been targeted for vaccine development. One surface-exposed protein complex that has gained recent attention is the β-barrel assembly machinery (BAM), which is conserved and essential across all Gram-negative bacteria. BAM is responsible for the biogenesis of β-barrel outer membrane proteins (β-OMPs) into the outer membrane. These β-OMPs serve essential roles for the cell including nutrient uptake, signaling, and adhesion, but can also serve as virulence factors mediating pathogenesis. The mechanism for how BAM mediates β-OMP biogenesis is known to be dynamic and complex, offering multiple modes for inhibition by small molecules and targeting by larger biologics. In this review, we introduce BAM and establish why it is a promising and exciting new therapeutic target and present recent studies reporting novel compounds and vaccines targeting BAM across various bacteria. These reports have fueled ongoing and future research on BAM and have boosted interest in BAM for its therapeutic promise in combatting multidrug resistance in Gram-negative bacterial pathogens.
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Affiliation(s)
- Claire Overly Cottom
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Robert Stephenson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Lindsey Wilson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
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19
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Pirhadi E, Vanegas JM, Farin M, Schertzer JW, Yong X. Effect of Local Stress on Accurate Modeling of Bacterial Outer Membranes Using All-Atom Molecular Dynamics. J Chem Theory Comput 2023; 19:363-372. [PMID: 36579901 DOI: 10.1021/acs.jctc.2c01026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Biological membranes are fundamental components of living organisms that play an undeniable role in their survival. Molecular dynamics (MD) serves as an essential computational tool for studying biomembranes on molecular and atomistic scales. The status quo of MD simulations of biomembranes studies a nanometer-sized membrane patch periodically extended under periodic boundary conditions (PBCs). In nature, membranes are usually composed of different lipids in their two layers (referred to as leaflets). This compositional asymmetry imposes a fixed ratio of lipid numbers between the two leaflets in a periodically constrained membrane, which needs to be set appropriately. The widely adopted methods of defining a leaflet lipid ratio suffer from the lack of control over the mechanical tension of each leaflet, which could significantly influence research findings. In this study, we investigate the role of membrane-building protocol and the resulting initial stress state on the interaction between small molecules and asymmetric membranes. We model the outer membrane of Pseudomonas aeruginosa bacteria using two different building protocols and probe their interactions with the Pseudomonas quinolone signal (PQS). Our results show that differential stress could shift the position of free energy minimum for the PQS molecule between the two leaflets of the asymmetric membrane. This work provides critical insights into the relationship between the initial per-leaflet tension and the spontaneous intercalation of PQS.
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Affiliation(s)
- Emad Pirhadi
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Juan M Vanegas
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-4003, United States
| | - Mithila Farin
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Jeffrey W Schertzer
- Department of Biological Sciences, Binghamton University, Binghamton, New York 13902-6000, United States
| | - Xin Yong
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902-6000, United States
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20
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Jin F, Chang Z. Uncovering the membrane-integrated SecA N protein that plays a key role in translocating nascent outer membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140865. [PMID: 36272538 DOI: 10.1016/j.bbapap.2022.140865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/08/2022]
Abstract
A large number of nascent polypeptides have to get across a membrane in targeting to the proper subcellular locations. The SecYEG protein complex, a homolog of the Sec61 complex in eukaryotic cells, has been viewed as the common translocon at the inner membrane for targeting proteins to three extracytoplasmic locations in Gram-negative bacteria, despite the lack of direct verification in living cells. Here, via unnatural amino acid-mediated protein-protein interaction analyses in living cells, in combination with genetic studies, we unveiled a hitherto unreported SecAN protein that seems to be directly involved in translocationg nascent outer membrane proteins across the plasma membrane; it consists of the N-terminal 375 residues of the SecA protein and exists as a membrane-integrated homooligomer. Our new findings place multiple previous observations related to bacterial protein targeting in proper biochemical and evolutionary contexts.
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Affiliation(s)
- Feng Jin
- State key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing 100871, China
| | - Zengyi Chang
- State key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Protein Science, Peking University, Beijing 100871, China.
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21
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Chen Q, Ren D, Liu L, Xu J, Wu Y, Yu H, Liu M, Zhang Y, Wang T. Ginsenoside Compound K Ameliorates Development of Diabetic Kidney Disease through Inhibiting TLR4 Activation Induced by Microbially Produced Imidazole Propionate. Int J Mol Sci 2022; 23:ijms232112863. [PMID: 36361652 PMCID: PMC9656537 DOI: 10.3390/ijms232112863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 12/31/2022] Open
Abstract
Diabetic kidney disease (DKD) is a common and devastating complication in diabetic patients, which is recognized as a large and growing problem leading to end-stage kidney disease. As dietary-mediated therapies are gradually becoming more acceptable to patients with DKD, we planned to find active compounds on preventing DKD progression from dietary material. The present paper reports the renoprotective properties and underlying mechanisms of ginsenoside compound K (CK), a major metabolite in serum after oral administration of ginseng. CK supplementation for 16 weeks could improve urine microalbumin, the ratio of urinary albumin/creatinine and renal morphological abnormal changes in db/db mice. In addition, CK supplementation reshaped the gut microbiota by decreasing the contents of Bacteroides and Paraprevotella and increasing the contents of Lactobacillu and Akkermansia at the genus level, as well as reduced histidine-derived microbial metabolite imidazole propionate (IMP) in the serum. We first found that IMP played a significant role in the progression of DKD through activating toll-like receptor 4 (TLR4). We also confirmed CK supplementation can down-regulate IMP-induced protein expression of the TLR4 signaling pathway in vivo and in vitro. This study suggests that dietary CK could offer a better health benefit in the early intervention of DKD. From a nutrition perspective, CK or dietary material containing CK can possibly be developed as new adjuvant therapy products for DKD.
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Affiliation(s)
- Qian Chen
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Dongwen Ren
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Luokun Liu
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Jingge Xu
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Yuzheng Wu
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Haiyang Yu
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Mengyang Liu
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Yi Zhang
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Correspondence: (Y.Z.); (T.W.); Tel.: +86-22-59596163 (Y.Z.); +86-22-59596572 (T.W.)
| | - Tao Wang
- State Key Laboratory of Component Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Haihe Laboratory of Modern Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Correspondence: (Y.Z.); (T.W.); Tel.: +86-22-59596163 (Y.Z.); +86-22-59596572 (T.W.)
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22
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Dai X, Yuan M, Lu Y, Zhu X, Liu C, Zheng Y, Si S, Yuan L, Zhang J, Li Y. Identification of a Small Molecule That Inhibits the Interaction of LPS Transporters LptA and LptC. Antibiotics (Basel) 2022; 11:1385. [PMID: 36290043 PMCID: PMC9598311 DOI: 10.3390/antibiotics11101385] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 10/15/2023] Open
Abstract
The need for novel antibiotics has become imperative with the increasing prevalence of antibiotic resistance in Gram-negative bacteria in clinics. Acting as a permeability barrier, lipopolysaccharide (LPS) protects Gram-negative bacteria against drugs. LPS is synthesized in cells and transported to the outer membrane (OM) via seven lipopolysaccharide transport (Lpt) proteins (LptA-LptG). Of these seven Lpt proteins, LptC interacts with LptA to transfer LPS from the inner membrane (IM) to the OM, and assembly is aided by LptD/LptE. This interaction among the Lpt proteins is important for the biosynthesis of LPS; therefore, the Lpt proteins, which are significant in the assembly process of LPS, can be a potential target for new antibiotics. In this study, a yeast two-hybrid (Y2H) system was used to screen compounds that could block LPS transport by inhibiting LptA/LptC interaction, which finally disrupts the biosynthesis of the OM. We selected the compound IMB-0042 for this study. Our results suggest that IMB-0042 disrupts LptA/LptC interaction by binding to both LptA and LptC. Escherichia coli cells, when treated with IMB-0042, showed filament morphology, impaired OM integrity, and an accumulation of LPS in the periplasm. IMB-0042 inhibited the growth of Gram-negative bacteria and showed synergistic sensitization to other antibiotics, with low cytotoxicity. Thus, we successfully identified a potential antibacterial agent by using a Y2H system, which blocks the transport of LPS by targeting LptA/LptC interaction in Escherichia coli.
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Affiliation(s)
- Xiaowei Dai
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Min Yuan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yu Lu
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Xiaohong Zhu
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Chao Liu
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yifan Zheng
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Shuyi Si
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Lijie Yuan
- Hebei Key Laboratory for Chronic Diseases, Tangshan Key Laboratory for Preclinical and Basic Research on Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Jing Zhang
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yan Li
- Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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23
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022; 61:e202203319. [PMID: 35712982 PMCID: PMC9540533 DOI: 10.1002/anie.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Indexed: 11/18/2022]
Abstract
Membrane proteins are known to exert many essential biological functions by forming complexes in cell membranes. An example refers to the β‐barrel assembly machinery (BAM), a 200 kDa pentameric complex containing BAM proteins A–E that catalyzes the essential process of protein insertion into the outer membrane of gram‐negative bacteria. While progress has been made in capturing three‐dimensional structural snapshots of the BAM complex, the role of the lipoprotein BamC in the complex assembly in functional lipid bilayers has remained unclear. We have devised a component‐selective preparation scheme to directly study BamC as part of the entire BAM complex in lipid bilayers. Combination with proton‐detected solid‐state NMR methods allowed us to probe the structure, dynamics, and supramolecular topology of full‐length BamC embedded in the entire complex in lipid bilayers. Our approach may help decipher how individual proteins contribute to the dynamic formation and functioning of membrane protein complexes in membranes.
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Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- MOE Key Lab for Cellular Dynamics School of Life Sciences University of Science and Technology of China 96 Jinzhai Road Hefei 230026 Anhui China
| | - Cecilia Pinto
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Current address: Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Van der Maasweg 9 2629 H. Z. Delft The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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24
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Groeger S, Wu F, Wagenlehner F, Dansranjav T, Ruf S, Denter F, Meyle J. PD-L1 Up-Regulation in Prostate Cancer Cells by Porphyromonas gingivalis. Front Cell Infect Microbiol 2022; 12:935806. [PMID: 35846769 PMCID: PMC9277116 DOI: 10.3389/fcimb.2022.935806] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/30/2022] [Indexed: 12/24/2022] Open
Abstract
Chronic inflammation is known to contribute to various human cancers. Porphyromonas gingivalis (P. gingivalis), is a gram-negative oral keystone pathogen that may cause severe periodontitis and expresses several virulence factors to affect the host immune system. Periodontitis is a chronic infectious disease that while progression, may cause loss of attachment and destruction of the tooth supporting tissues. Prostate cancer is one of the most common malignancies in men. Increasing evidence links periodontitis with prostate cancer, however the mechanisms explaining this relationship remain unclear. The aim of this study was to investigate the expression and signaling pathway of programmed death ligand 1 (PD-L1) in a prostate cancer cell line after infection with P. gingivalis and stimulation with P. gingivalis components to reveal the mechanism of tumor-induced immune evasion associated with bacterial infection in the tumor environment. Prostate cancer cells were infected with different concentrations of viable P. gingivalis and treated with different concentrations of heat-killed P. gingivalis and P. gingivalis cell components, including the total membrane fraction, inner membrane fraction, outer membrane fraction, cytosolic fraction and peptidoglycan (PGN). Chemical inhibitors were used to block different important molecules of signaling pathways to assess the participating signal transduction mechanisms. PD-L1 expression was detected by Western blot after 24 h of infection. PD-L1 was demonstrated to be upregulated in prostate cancer cells after infection with viable and with heat-killed P. gingivalis membrane fractions. Also isolated PGN induced PD-L1 up-regulation. The upregulation was mediated by the NOD1/NOD2 signaling pathway. No upregulation could be detected after treatment of the cells with P. gingivalis lipopolysaccharide (LPS). These results indicate, that chronic inflammatory disease can contribute to tumor immune evasion by modifying the tumor microenvironment. Thus, chronic infection possibly plays an essential role in the immune response and may promote the development and progression of prostate cancer.
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Affiliation(s)
- Sabine Groeger
- Dept. of Periodontology, Justus-Liebig University, Giessen, Germany
- Dept. of Orthodontics, Justus-Liebig University, Giessen, Germany
- *Correspondence: Sabine Groeger,
| | - Fan Wu
- Dept. of Periodontology, Justus-Liebig University, Giessen, Germany
| | | | | | - Sabine Ruf
- Dept. of Orthodontics, Justus-Liebig University, Giessen, Germany
| | - Fabian Denter
- Dept. of Periodontology, Justus-Liebig University, Giessen, Germany
| | - Joerg Meyle
- Dept. of Periodontology, Justus-Liebig University, Giessen, Germany
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25
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Xiang S, Pinto C, Baldus M. Divide and Conquer: A Tailored Solid‐state NMR Approach to Study Large Membrane Protein Complexes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- ShengQi Xiang
- University of Science and Technology of China, Anhui, MOE Key lab for Cellular Dynamics CHINA
| | - Cecilia Pinto
- Delft University of Technology: Technische Universiteit Delft Department of Bionanoscience NETHERLANDS
| | - Marc Baldus
- Utrecht University Bijvoet Center for Biomolecular Research Padualaan 8 3584 Utrecht NETHERLANDS
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26
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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27
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Ferrous Iron Uptake Is Required for Salmonella to Persist within Vacuoles of Host Cells. Infect Immun 2022; 90:e0014922. [PMID: 35536027 DOI: 10.1128/iai.00149-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Iron is an essential oligoelement that incorporates into proteins as a biocatalyst or electron carrier. The intracellular pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) takes iron as free reduced ferrous cation or as oxidized ferric cation complexed to siderophores or ferrichromes. Deficiencies in ferrous or ferric iron uptake attenuate S. Typhimurium virulence, but how the uptake systems are used in the intracellular environment remains poorly understood. Here, using S. Typhimurium mutants deficient in multiple iron uptake systems, we show that SitABCD and FeoABC, involved in ferrous iron uptake, are central for this pathogen to persist within vacuoles of fibroblasts. Assays at the protein level showed that components of these two uptake systems, SitD and FeoB, are produced at high levels by intravacuolar bacteria. Despite not being essential for viability inside the vacuole, intracellular bacteria also upregulate transporters involved in ferric iron uptake such as IroN, FepA, and CirA. In addition, an unprecedented cleavage at the N-terminal region of FepA was observed as a distinctive feature of nonproliferating intravacuolar bacteria. Collectively, our findings indicate that SitABCD and FeoABC contribute to S. Typhimurium virulence by promoting iron acquisition within the vacuolar compartment.
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28
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Mobed A, Hasanzadeh M. Environmental protection based on the nanobiosensing of bacterial lipopolysaccharides (LPSs): material and method overview. RSC Adv 2022; 12:9704-9724. [PMID: 35424904 PMCID: PMC8959448 DOI: 10.1039/d1ra09393b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/08/2022] [Indexed: 12/13/2022] Open
Abstract
Lipopolysaccharide (LPS) or endotoxin control is critical for environmental and healthcare issues. LPSs are responsible for several infections, including septic and shock sepsis, and are found in water samples. Accurate and specific diagnosis of endotoxin is one of the most challenging issues in medical bacteriology. Enzyme-linked immunosorbent assay (ELISA), plating and culture-based methods, and Limulus amebocyte lysate (LAL) assay are the conventional techniques in quantifying LPS in research and medical laboratories. However, these methods have been restricted due to their disadvantages, such as low sensitivity and time-consuming and complicated procedures. Therefore, the development of new and advanced methods is demanding, particularly in the biological and medical fields. Biosensor technology is an innovative method that developed extensively in the past decade. Biosensors are classified based on the type of transducer and bioreceptor. So in this review, various types of biosensors, such as optical (fluorescence, SERS, FRET, and SPR), electrochemical, photoelectrochemical, and electrochemiluminescence, on the biosensing of LPs were investigated. Also, the critical role of advanced nanomaterials on the performance of the above-mentioned biosensors is discussed. In addition, the application of different labels on the efficient usage of biosensors for LPS is surveyed comprehensively. Also, various bio-elements (aptamer, DNA, miRNA, peptide, enzyme, antibody, etc.) on the structure of the LPS biosensor are investigated. Finally, bio-analytical parameters that affect the performance of LPS biosensors are surveyed.
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Affiliation(s)
- Ahmad Mobed
- Aging Research Institute, Faculty of Medicine, Tabriz University of Medical Sciences Iran
- Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences Tabriz Iran
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences Tabriz 51664 Iran
| | - Mohammad Hasanzadeh
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences Tabriz 51664 Iran
- Nutrition Research Center, Tabriz University of Medical Sciences Tabriz Iran
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29
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Lee YJ, Inzana TJ. Extraction and Electrophoretic Analysis of Bacterial Lipopolysaccharides and Outer Membrane Proteins. Bio Protoc 2021; 11:e4263. [PMID: 35087922 PMCID: PMC8720528 DOI: 10.21769/bioprotoc.4263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 10/19/2023] Open
Abstract
Lipopolysaccharides (LPS) (or lipooligosaccharides [LOS], which lack the O-antigen side chains characteristic of LPS), and outer membrane proteins (OMP) are major cell-surface molecules in the outer membrane (OM) of gram-negative bacteria. The LPS is responsible for causing endotoxic shock in infected hosts and, in conjunction with some OMPs, provides protection to the bacterium against host innate immune defenses and attachment to host cells. Electrophoretic analysis can provide valuable information regarding the size, number, and variability of LPS/LOS and OMP components between bacterial strains and mutants, which aids in understanding the basic biology and virulence factors of a particular species. Furthermore, highly purified extracts are normally not required if only electrophoretic analysis is to be done, and various methods have been established for such procedures. Here, we review ameliorated procedures for fast and convenient extraction of LPS/LOS and protein-enriched outer membranes (PEOM) for optimal electrophoretic resolution. Specifically, we will describe the phenol-based micro-method for LPS/LOS extraction, a differential extraction procedure with sodium lauryl sarcosinate for PEOM, and gel preparation for electrophoretic analysis of LPS/LOS samples in detail. Graphic abstract: Workflow for the preparation and analysis of LPS/LOS and PEOM.
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Affiliation(s)
- Yue-Jia Lee
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
| | - Thomas J. Inzana
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Brookville, NY, United States
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30
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Paulucci NS, Cesari AB, Biasutti MA, Dardanelli MS, Perillo MA. Membrane Homeoviscous Adaptation in Sinorhizobium Submitted to a Stressful Thermal Cycle Contributes to the Maintenance of the Symbiotic Plant–Bacteria Interaction. Front Microbiol 2021; 12:652477. [PMID: 34975776 PMCID: PMC8718912 DOI: 10.3389/fmicb.2021.652477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 11/15/2021] [Indexed: 12/02/2022] Open
Abstract
Here, we estimate fast changes in the fluidity of Sinorhizobium meliloti membranes submitted to cyclic temperature changes (10°C–40°C–10°C) by monitoring the fluorescence polarization (P) of DPH and TMA-DPH of the whole cell (WC) as well as in its outer (OM) and inner (IM) membranes. Additionally, the long-term response to thermal changes is demonstrated through the dynamics of the phospholipid and fatty acid composition in each membrane. This allowed membrane homeoviscous adaptation by the return to optimal fluidity levels as measured by the PDPH/TMA-DPH in WC, OM, IM, and multilamellar vesicles of lipids extracted from OM and IM. Due to probe-partitioning preferences and membranes’ compositional characteristics, DPH and TMA-DPH exhibit different behaviors in IM and OM. The rapid effect of cyclic temperature changes on the P was the opposite in both membranes with the IM being the one that exhibited the thermal behavior expected for lipid bilayers. Interestingly, only after the incubation at 40°C, cells were unable to recover the membrane preheating P levels when cooled up to 10°C. Solely in this condition, the formation of threads and nodular structures in Medicago sativa infected with S. meliloti were delayed, indicating that the symbiotic interaction was partially altered but not halted.
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Affiliation(s)
- Natalia Soledad Paulucci
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
- Instituto de Biotecnología Ambiental y Salud (INBIAS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Argentina
- *Correspondence: Natalia Soledad Paulucci,
| | - Adriana Belén Cesari
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
- Instituto de Biotecnología Ambiental y Salud (INBIAS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Argentina
| | - María Alicia Biasutti
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Departamento de Química, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
- Instituto para el Desarrollo Agroindustrial y de la Salud (IDAS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Argentina
| | - Marta Susana Dardanelli
- Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Argentina
- Instituto de Biotecnología Ambiental y Salud (INBIAS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Río Cuarto, Argentina
- Marta Susana Dardanelli,
| | - María Angélica Perillo
- Facultad de Ciencias Exactas, Físicas y Naturales, Instituto de Ciencia y Tecnología de Alimentos (ICTA), Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- María Angélica Perillo,
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31
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Abdollahi S, Raoufi Z, Fakoor MH. Physicochemical and structural characterization, epitope mapping and vaccine potential investigation of a new protein containing Tetratrico Peptide Repeats of Acinetobacter baumannii: An in-silico and in-vivo approach. Mol Immunol 2021; 140:22-34. [PMID: 34649027 DOI: 10.1016/j.molimm.2021.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022]
Abstract
Acinetobacter baumannii is an opportunistic multidrug-resistant pathogen that causes a significant mortality rate. The proteins containing Tetratrico Peptide Repeats (TPRs) are involved in the pathogenicity and virulence of bacteria and have different roles such as transfer of bacterial virulence factors to host cells, binding to the host cells and inhibition of phagolysosomal maturation. So, in this study, physicochemical properties of a new protein containing TPRs in A. baumannii which was named PcTPRs1 by this study were characterized and its 3D structure was predicted by in-silico tools. The protein B and T cell epitopes were mapped and its vaccine potential was in-silico and in-vivo investigated. Domain analysis indicated that the protein contains the Flp pilus assembly protein TadD domain which has three TPRs. The helix is dominant in the protein structure, and this protein is an outer membrane antigen which, is extremely conserved among A. baumannii strains; thus, has good properties to be applied as a recombinant vaccine. The best-predicted and refined model was applied in ligand-binding sites and conformational epitopes prediction. Based on epitope mapping results, several epitopes were characterized which could stimulate both immune systems. BLAST results showed the introduced epitopes are completely conserved among A. baumannii strains. The in-vivo analysis indicates that a 101 amino acid fragment of the protein which contains the best selected epitope, can produce a good protectivity against A. baumannii as well as the whole TPR protein and thus could be investigated as an effective subunit and potential vaccines.
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Affiliation(s)
- Sajad Abdollahi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
| | - Zeinab Raoufi
- Department of Biology, Faculty of Basic Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Iran.
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32
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Abstract
Gram-negative bacteria have a multicomponent and constitutively active periplasmic chaperone system to ensure the quality control of their outer membrane proteins (OMPs). Recently, OMPs have been identified as a new class of vulnerable targets for antibiotic development, and therefore a comprehensive understanding of OMP quality control network components will be critical for discovering antimicrobials. Here, we demonstrate that the periplasmic chaperone Spy protects certain OMPs against protein-unfolding stress and can functionally compensate for other periplasmic chaperones, namely Skp and FkpA, in the Escherichia coli K-12 MG1655 strain. After extensive in vivo genetic experiments for functional characterization of Spy, we use nuclear magnetic resonance and circular dichroism spectroscopy to elucidate the mechanism by which Spy binds and folds two different OMPs. Along with holding OMP substrates in a dynamic conformational ensemble, Spy binding enables OmpX to form a partially folded β-strand secondary structure. The bound OMP experiences temperature-dependent conformational exchange within the chaperone, pointing to a multitude of local dynamics. Our findings thus deepen the understanding of functional compensation among periplasmic chaperones during OMP biogenesis and will promote the development of innovative antimicrobials against pathogenic Gram-negative bacteria.
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33
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Steenhuis M, Corona F, ten Hagen-Jongman CM, Vollmer W, Lambin D, Selhorst P, Klaassen H, Versele M, Chaltin P, Luirink J. Combining Cell Envelope Stress Reporter Assays in a Screening Approach to Identify BAM Complex Inhibitors. ACS Infect Dis 2021; 7:2250-2263. [PMID: 34125508 PMCID: PMC8369490 DOI: 10.1021/acsinfecdis.0c00728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Indexed: 12/11/2022]
Abstract
The development of new antibiotics is particularly problematic in Gram-negative bacteria due to the presence of the outer membrane (OM), which serves as a permeability barrier. Recently, the β-barrel assembly machine (BAM), located in the OM and responsible for β-barrel type OM protein (OMP) assembly, has been validated as a novel target for antibiotics. Here, we identified potential BAM complex inhibitors using a screening approach that reports on cell envelope σE and Rcs stress in Escherichia coli. Screening a library consisting of 316 953 compounds yielded five compounds that induced σE and Rcs stress responses, while not inducing the intracellular heat-shock response. Two of the five compounds (compounds 2 and 14) showed the characteristics of known BAM complex inhibitors: synergy with OMP biogenesis mutants, decrease in the abundance of various OMPs, and loss of OM integrity. Importantly, compound 2 also inhibited BAM-dependent OMP folding in an in vitro refolding assay using purified BAM complex reconstituted in proteoliposomes.
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Affiliation(s)
- Maurice Steenhuis
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Federico Corona
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, United
Kingdom
| | - Corinne M. ten Hagen-Jongman
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Waldemar Vollmer
- Centre
for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle
upon Tyne NE2 4HH, United
Kingdom
| | - Dominique Lambin
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Philippe Selhorst
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Hugo Klaassen
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Matthias Versele
- Centre
for Innovation and Stimulation of Drug Discovery (CISTIM), Gaston Geenslaan 2, B-3001 Leuven, Belgium
| | - Patrick Chaltin
- Center
for Drug Design and Development (CD3), KU
Leuven R&D, Waaistraat 6, B-3000 Leuven, Belgium
| | - Joen Luirink
- Department
of Molecular Microbiology, Amsterdam Institute
of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
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34
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Olona A, Hateley C, Muralidharan S, Wenk MR, Torta F, Behmoaras J. Sphingolipid metabolism during Toll-like receptor 4 (TLR4)-mediated macrophage activation. Br J Pharmacol 2021; 178:4575-4587. [PMID: 34363204 DOI: 10.1111/bph.15642] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/18/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Macrophage activation in response to stimulation of Toll-like receptor 4 (TLR4) provides a paradigm for investigating energy metabolism that regulates the inflammatory response. TLR4-mediated pro-inflammatory macrophage activation is characterized by increased glycolysis and altered mitochondrial metabolism, supported by selective amino acid uptake and/or usage. Fatty acid metabolism remains as a highly complex rewiring that accompanies classical macrophage activation. TLR4 activation leads to de novo synthesis of fatty acids, which flux into sphingolipids, complex lipids that form the building blocks of eukaryotic cell membranes and regulate cell function. Here, we review the importance of TLR4-mediated de novo synthesis of membrane sphingolipids in macrophages. We first highlight fatty acid metabolism during TLR4-driven macrophage immunometabolism. We then focus on the temporal dynamics of sphingolipid biosynthesis and emphasize the modulatory role of some sphingolipid species (i.e. sphingomyelins, ceramides and glycosphingolipids) on the pro-inflammatory and pro-resolution phases of LPS/TLR4 activation in macrophages.
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Affiliation(s)
- Antoni Olona
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK
| | - Charlotte Hateley
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK
| | | | - Markus R Wenk
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- SLING, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jacques Behmoaras
- Faculty of Medicine, Imperial College London, Hammersmith Hospital, London, UK.,Programme in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Medical School Singapore, Republic of Singapore
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35
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Aye SM, Galani I, Han ML, Karaiskos I, Creek DJ, Zhu Y, Lin YW, Velkov T, Giamarellou H, Li J. Lipid A profiling and metabolomics analysis of paired polymyxin-susceptible and -resistant MDR Klebsiella pneumoniae clinical isolates from the same patients before and after colistin treatment. J Antimicrob Chemother 2021; 75:2852-2863. [PMID: 32696049 DOI: 10.1093/jac/dkaa245] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The increased incidence of polymyxin-resistant MDR Klebsiella pneumoniae has become a major global health concern. OBJECTIVES To characterize the lipid A profiles and metabolome differences between paired polymyxin-susceptible and -resistant MDR K. pneumoniae clinical isolates. METHODS Three pairs of K. pneumoniae clinical isolates from the same patients were examined [ATH 7 (polymyxin B MIC 0.25 mg/L) versus ATH 8 (64 mg/L); ATH 15 (0.5 mg/L) versus ATH 16 (32 mg/L); and ATH 17 (0.5 mg/L) versus ATH 18 (64 mg/L)]. Lipid A and metabolomes were analysed using LC-MS and bioinformatic analysis was conducted. RESULTS The predominant species of lipid A in all three paired isolates were hexa-acylated and 4-amino-4-deoxy-l-arabinose-modified lipid A species were detected in the three polymyxin-resistant isolates. Significant metabolic differences were evident between the paired isolates. Compared with their corresponding polymyxin-susceptible isolates, the levels of metabolites in amino sugar metabolism (UDP-N-acetyl-α-d-glucosamine and UDP-N-α-acetyl-d-mannosaminuronate) and central carbon metabolism (e.g. pentose phosphate pathway and tricarboxylic acid cycle) were significantly reduced in all polymyxin-resistant isolates [fold change (FC) > 1.5, P < 0.05]. Similarly, nucleotides, amino acids and key metabolites in glycerophospholipid metabolism, namely sn-glycerol-3-phosphate and sn-glycero-3-phosphoethanolamine, were significantly reduced across all polymyxin-resistant isolates (FC > 1.5, P < 0.05) compared with polymyxin-susceptible isolates. However, higher glycerophospholipid levels were evident in polymyxin-resistant ATH 8 and ATH 16 (FC > 1.5, P < 0.05) compared with their corresponding susceptible isolates. CONCLUSIONS To our knowledge, this study is the first to reveal significant metabolic perturbations associated with polymyxin resistance in K. pneumoniae.
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Affiliation(s)
- Su Mon Aye
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Irene Galani
- Fourth Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Mei-Ling Han
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Ilias Karaiskos
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, 3052 Victoria, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Yu-Wei Lin
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Helen Giamarellou
- First Department of Internal Medicine-Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Jian Li
- Biomedicine Discovery Institute, Infection and Immunity Program and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Alegun O, Pandeya A, Cui J, Ojo I, Wei Y. Donnan Potential across the Outer Membrane of Gram-Negative Bacteria and Its Effect on the Permeability of Antibiotics. Antibiotics (Basel) 2021; 10:701. [PMID: 34208097 PMCID: PMC8230823 DOI: 10.3390/antibiotics10060701] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
The cell envelope structure of Gram-negative bacteria is unique, composed of two lipid bilayer membranes and an aqueous periplasmic space sandwiched in between. The outer membrane constitutes an extra barrier to limit the exchange of molecules between the cells and the exterior environment. Donnan potential is a membrane potential across the outer membrane, resulted from the selective permeability of the membrane, which plays a pivotal role in the permeability of many antibiotics. In this review, we discussed factors that affect the intensity of the Donnan potential, including the osmotic strength and pH of the external media, the osmoregulated periplasmic glucans trapped in the periplasmic space, and the displacement of cell surface charges. The focus of our discussion is the impact of Donnan potential on the cellular permeability of selected antibiotics including fluoroquinolones, tetracyclines, β-lactams, and trimethoprim.
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Affiliation(s)
| | | | | | | | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, USA; (O.A.); (A.P.); (J.C.); (I.O.)
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Steenhuis M, van Ulsen P, Martin NI, Luirink J. A ban on BAM: an update on inhibitors of the β-barrel assembly machinery. FEMS Microbiol Lett 2021; 368:6287571. [PMID: 34048543 DOI: 10.1093/femsle/fnab059] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Gram-negative pathogens are a rapidly increasing threat to human health worldwide due to high rates of antibiotic resistance and the lack of development of novel antibiotics. The protective cell envelope of gram-negative bacteria is a major permeability barrier that contributes to the problem by restricting the uptake of antibiotics. On the other hand, its unique architecture also makes it a suitable target for antibiotic interference. In particular, essential multiprotein machines that are required for biogenesis of the outer membrane have attracted attention in antibacterial design strategies. Recently, significant progress has been made in the development of inhibitors of the β-barrel assembly machine (BAM) complex. Here, we summarize the current state of drug development efforts targeting the BAM complex in pursuit of new antibiotics.
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Affiliation(s)
- Maurice Steenhuis
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Peter van Ulsen
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology Leiden, Leiden University, Nonnensteeg 3, 2311 VJ, Leiden, The Netherlands
| | - Joen Luirink
- Department of Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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38
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Zhou C, Shi H, Zhang M, Zhou L, Xiao L, Feng S, Im W, Zhou M, Zhang X, Huang Y. Structural Insight into Phospholipid Transport by the MlaFEBD Complex from P. aeruginosa. J Mol Biol 2021; 433:166986. [PMID: 33845086 DOI: 10.1016/j.jmb.2021.166986] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 11/27/2022]
Abstract
The outer membrane (OM) of Gram-negative bacteria, which consists of lipopolysaccharides (LPS) in the outer leaflet and phospholipids (PLs) in the inner leaflet, plays a key role in antibiotic resistance and pathogen virulence. The maintenance of lipid asymmetry (Mla) pathway is known to be involved in PL transport and contributes to the lipid homeostasis of the OM, yet the underlying molecular mechanism and the directionality of PL transport in this pathway remain elusive. Here, we reported the cryo-EM structures of the ATP-binding cassette (ABC) transporter MlaFEBD from P. areuginosa, the core complex in the Mla pathway, in nucleotide-free (apo)-, ADP (ATP + vanadate)- and ATP (AMPPNP)-bound states as well as the structures of MlaFEB from E. coli in apo- and AMPPNP-bound states at a resolution range of 3.4-3.9 Å. The structures show that the MlaFEBD complex contains a total of twelve protein molecules with a stoichiometry of MlaF2E2B2D6, and binds a plethora of PLs at different locations. In contrast to canonical ABC transporters, nucleotide binding fails to trigger significant conformational changes of both MlaFEBD and MlaFEB in the nucleotide-binding and transmembrane domains of the ABC transporter, correlated with their low ATPase activities exhibited in both detergent micelles and lipid nanodiscs. Intriguingly, PLs or detergents appeared to relocate to the membrane-proximal end from the distal end of the hydrophobic tunnel formed by the MlaD hexamer in MlaFEBD upon addition of ATP, indicating that retrograde PL transport might occur in the tunnel in an ATP-dependent manner. Site-specific photocrosslinking experiment confirms that the substrate-binding pocket in the dimeric MlaE and the MlaD hexamer are able to bind PLs in vitro, in line with the notion that MlaFEBD complex functions as a PL transporter.
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Affiliation(s)
- Changping Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Manfeng Zhang
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lijun Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiao Ling Wei Street, Nanjing 210094, China
| | - Le Xiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China
| | - Shasha Feng
- Departments of Biological Sciences and Chemistry, Lehigh University, PA 18015, USA
| | - Wonpil Im
- Departments of Biological Sciences and Chemistry, Lehigh University, PA 18015, USA
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiao Ling Wei Street, Nanjing 210094, China.
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China.
| | - Yihua Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing100101, China.
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Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
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Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
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40
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Wadhawan A, Reynolds MA, Makkar H, Scott AJ, Potocki E, Hoisington AJ, Brenner LA, Dagdag A, Lowry CA, Dwivedi Y, Postolache TT. Periodontal Pathogens and Neuropsychiatric Health. Curr Top Med Chem 2021; 20:1353-1397. [PMID: 31924157 DOI: 10.2174/1568026620666200110161105] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
Increasing evidence incriminates low-grade inflammation in cardiovascular, metabolic diseases, and neuropsychiatric clinical conditions, all important causes of morbidity and mortality. One of the upstream and modifiable precipitants and perpetrators of inflammation is chronic periodontitis, a polymicrobial infection with Porphyromonas gingivalis (P. gingivalis) playing a central role in the disease pathogenesis. We review the association between P. gingivalis and cardiovascular, metabolic, and neuropsychiatric illness, and the molecular mechanisms potentially implicated in immune upregulation as well as downregulation induced by the pathogen. In addition to inflammation, translocation of the pathogens to the coronary and peripheral arteries, including brain vasculature, and gut and liver vasculature has important pathophysiological consequences. Distant effects via translocation rely on virulence factors of P. gingivalis such as gingipains, on its synergistic interactions with other pathogens, and on its capability to manipulate the immune system via several mechanisms, including its capacity to induce production of immune-downregulating micro-RNAs. Possible targets for intervention and drug development to manage distal consequences of infection with P. gingivalis are also reviewed.
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Affiliation(s)
- Abhishek Wadhawan
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, United States.,Department of Psychiatry, Saint Elizabeths Hospital, Washington, D.C. 20032, United States
| | - Mark A Reynolds
- Department of Advanced Oral Sciences & Therapeutics, University of Maryland School of Dentistry, Baltimore 21201, United States
| | - Hina Makkar
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, United States
| | - Alison J Scott
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, United States
| | - Eileen Potocki
- VA Maryland Healthcare System, Baltimore VA Medical Center, Baltimore, United States
| | - Andrew J Hoisington
- Air Force Institute of Technology, Wright-Patterson Air Force Base, United States
| | - Lisa A Brenner
- Departments of Psychiatry, Neurology, and Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, United States.,Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, United States
| | - Aline Dagdag
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, United States
| | - Christopher A Lowry
- Departments of Psychiatry, Neurology, and Physical Medicine & Rehabilitation, University of Colorado Anschutz Medical Campus, Aurora, United States.,Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, United States.,Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, United States.,Department of Integrative Physiology, Center for Neuroscience and Center for Microbial Exploration, University of Colorado Boulder, Boulder, United States.,Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Rocky Mountain Regional Veterans Affairs Medical Center (RMRVAMC), Aurora, United States
| | - Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Alabama, United States
| | - Teodor T Postolache
- Mood and Anxiety Program, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, United States.,Rocky Mountain Mental Illness Research Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 19, Aurora, United States.,Military and Veteran Microbiome: Consortium for Research and Education (MVM-CoRE), Aurora, United States.,Mental Illness Research, Education and Clinical Center (MIRECC), Veterans Integrated Service Network (VISN) 5, VA Capitol Health Care Network, Baltimore, United States
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Chen X, Ding Y, Bamert RS, Le Brun AP, Duff AP, Wu CM, Hsu HY, Shiota T, Lithgow T, Shen HH. Substrate-dependent arrangements of the subunits of the BAM complex determined by neutron reflectometry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183587. [PMID: 33639106 DOI: 10.1016/j.bbamem.2021.183587] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/22/2022]
Abstract
In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex catalyses the assembly of β-barrel proteins into the outer membrane, and is composed of five subunits: BamA, BamB, BamC, BamD and BamE. Once assembled, - β-barrel proteins can be involved in various functions including uptake of nutrients, export of toxins and mediating host-pathogen interactions, but the precise mechanism by which these ubiquitous and often essential β-barrel proteins are assembled is yet to be established. In order to determine the relative positions of BAM subunits in the membrane environment we reconstituted each subunit into a biomimetic membrane, characterizing their interaction and structural changes by Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) and neutron reflectometry. Our results suggested that the binding of BamE, or a BamDE dimer, to BamA induced conformational changes in the polypeptide transported-associated (POTRA) domains of BamA, but that BamB or BamD alone did not promote any such changes. As monitored by neutron reflectometry, addition of an unfolded substrate protein extended the length of POTRA domains further away from the membrane interface as part of the mechanism whereby the substrate protein was folded into the membrane.
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Affiliation(s)
- Xiaoyu Chen
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Yue Ding
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Rebecca S Bamert
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Anthony P Duff
- National Deuteration Facility, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Chun-Ming Wu
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Road, Lucas Heights, NSW 2234, Australia; National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
| | - Hsien-Yi Hsu
- School of Energy and Environment & Department of Materials Science and Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong, PR China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, PR China
| | - Takuya Shiota
- Institute for Tenure Track Promotion, Organization for Promotion of Career Management, University of Miyazaki, Miyazaki, Japan
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
| | - Hsin-Hui Shen
- Department of Materials Science & Engineering, Monash University, Clayton, VIC 3800, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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Diversification of OmpA and OmpF of Yersinia ruckeri is independent of the underlying species phylogeny and evidence of virulence-related selection. Sci Rep 2021; 11:3493. [PMID: 33568758 PMCID: PMC7876001 DOI: 10.1038/s41598-021-82925-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 01/27/2021] [Indexed: 01/30/2023] Open
Abstract
Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM) which causes economically significant losses in farmed salmonids, especially Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss, Walbaum). However, very little is known about the genetic relationships of disease-causing isolates in these two host species or about factors responsible for disease. Phylogenetic analyses of 16 representative isolates based on the nucleotide sequences of 19 housekeeping genes suggests that pathogenic Atlantic salmon and rainbow trout isolates represent distinct host-specific lineages. However, the apparent phylogenies of certain isolates has been influenced by horizontal gene transfer and recombinational exchange. Splits decomposition analysis demonstrated a net-like phylogeny based on the housekeeping genes, characteristic of recombination. Comparative analysis of the distribution of individual housekeeping gene alleles across the isolates demonstrated evidence of genomic mosaicism and recombinational exchange involving certain Atlantic salmon and rainbow trout isolates. Comparative nucleotide sequence analysis of the key outer membrane protein genes ompA and ompF revealed that the corresponding gene trees were both non-congruent with respect to the housekeeping gene phylogenies providing evidence that horizontal gene transfer has influenced the evolution of both these surface protein-encoding genes. Analysis of inferred amino acid sequence variation in OmpA identified a single variant, OmpA.1, that was present in serotype O1 and O8 isolates representing typical pathogenic strains in rainbow trout and Atlantic salmon, respectively. In particular, the sequence of surface-exposed loop 3 differed by seven amino acids to that of other Y. ruckeri isolates. These findings suggest that positive selection has likely influenced the presence of OmpA.1 in these isolates and that loop 3 may play an important role in virulence. Amino acid sequence variation of OmpF was greater than that of OmpA and was similarly restricted mainly to the surface-exposed loops. Two OmpF variants, OmpF.1 and OmpF.2, were associated with pathogenic rainbow trout and Atlantic salmon isolates, respectively. These OmpF proteins had very similar amino acid sequences suggesting that positive evolutionary pressure has also favoured the selection of these variants in pathogenic strains infecting both species.
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Molecular mechanism of networking among DegP, Skp and SurA in periplasm for biogenesis of outer membrane proteins. Biochem J 2021; 477:2949-2965. [PMID: 32729902 DOI: 10.1042/bcj20200483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/13/2022]
Abstract
The biogenesis of outer membrane proteins (OMPs) is an extremely challenging process. In the periplasm of Escherichia coli, a group of quality control factors work together to exercise the safe-guard and quality control of OMPs. DegP, Skp and SurA are the three most prominent ones. Although extensive investigations have been carried out, the molecular mechanism regarding the networking among these proteins remains mostly mysterious. Our group has previously studied the molecular interactions of OMPs with SurA and Skp, using single-molecule detection (SMD). In this work, again using SMD, we studied how OmpC, a representative of OMPs, interacts with DegP, Skp and SurA collectively. Several important discoveries were made. The self-oligomerization of DegP to form hexamer occurs over hundred micromolars. When OmpC is in a monomer state at a low concentration, the OmpC·DegP6 and OmpC·DegP24 complexes form when the DegP concentration is around sub-micromolars and a hundred micromolars, respectively. High OmpC concentration promotes the binding affinity of DegP to OmpC by ∼100 folds. Skp and SurA behave differently when they interact synergistically with DegP in the presence of substrate. DegP can degrade SurA-protected OmpC, but Skp-protected OmpC forms the ternary complex OmpC·(Skp3)n·DegP6 (n = 1,2) to resist the DegP-mediated degradation. Combined with previous results, we were able to depict a comprehensive picture regarding the molecular mechanism of the networking among DegP, Skp and SurA in the periplasm for the OMPs biogenesis under physiological and stressed conditions.
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Extracellular RNAs in Bacterial Infections: From Emerging Key Players on Host-Pathogen Interactions to Exploitable Biomarkers and Therapeutic Targets. Int J Mol Sci 2020; 21:ijms21249634. [PMID: 33348812 PMCID: PMC7766527 DOI: 10.3390/ijms21249634] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are key regulators of post-transcriptional gene expression in prokaryotic and eukaryotic organisms. These molecules can interact with mRNAs or proteins, affecting a variety of cellular functions. Emerging evidence shows that intra/inter-species and trans-kingdom regulation can also be achieved with exogenous RNAs, which are exported to the extracellular medium, mainly through vesicles. In bacteria, membrane vesicles (MVs) seem to be the more common way of extracellular communication. In several bacterial pathogens, MVs have been described as a delivery system of ncRNAs that upon entry into the host cell, regulate their immune response. The aim of the present work is to review this recently described mode of host-pathogen communication and to foster further research on this topic envisaging their exploitation in the design of novel therapeutic and diagnostic strategies to fight bacterial infections.
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Taheri F, Nazarian S, Ahmadi TS, Gargari SLM. Protective effects of egg yolk immunoglobulins (IgYs) developed against recombinant immunogens CtxB, OmpW and TcpA on infant mice infected with Vibrio cholerae. Int Immunopharmacol 2020; 89:107054. [DOI: 10.1016/j.intimp.2020.107054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
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46
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Kong X, Song W, Hua Y, Li X, Chen Y, Zhang C, Chen Y. Insights into the antibacterial activity of cottonseed protein-derived peptide against Escherichia coli. Food Funct 2020; 11:10047-10057. [PMID: 33135695 DOI: 10.1039/d0fo01279c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In the study, antibacterial peptides were separated and identified from cottonseed protein hydrolysates and the interactions between antibacterial peptides and Escherichia coli were further investigated. Firstly, by using a combined strategy of Amberlite CG-50 ion exchange chromatography and reversed-phase high-performance liquid chromatography, three peptides with antibacterial activity were purified and identified, including HHRRFSLY, KFMPT, and RRLFSDY. Interestingly, HHRRFSLY and RRLFSDY exhibited higher inhibition activity with the IC50 value of 0.26 mg mL-1 and 0.58 mg mL-1 (p < 0.05), respectively. Flow cytometry results showed that the incubation of antibacterial peptides with E. coli could cause damage to the integrity of the E. coli cell membrane. Transmission electron microscopy and scanning electron microscopy results revealed the damage caused to the bacterial cell surface and the leakage of cytoplasmic content by the antibacterial peptides. Molecular docking studies indicated that HHRRFSLY, KFMPT, and RRLFSDY have a good binding affinity to the active sites of the surface protein (OmpF) mainly through a hydrogen bond and salt bridge. The results here showed that the antibacterial peptides derived from cottonseed protein could be used as a good choice for functional foods or related drugs, and also shed light on further studies of antibacterial mechanism.
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Affiliation(s)
- Xiangzhen Kong
- State Key Laboratory of Food Science and Technology, Jiangnan University, China.
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Zamani E, Johnson TJ, Chatterjee S, Immethun C, Sarella A, Saha R, Dishari SK. Cationic π-Conjugated Polyelectrolyte Shows Antimicrobial Activity by Causing Lipid Loss and Lowering Elastic Modulus of Bacteria. ACS APPLIED MATERIALS & INTERFACES 2020; 12:49346-49361. [PMID: 33089982 PMCID: PMC8926324 DOI: 10.1021/acsami.0c12038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Cationic, π-conjugated oligo-/polyelectrolytes (CCOEs/CCPEs) have shown great potential as antimicrobial materials to fight against antibiotic resistance. In this work, we treated wild-type and ampicillin-resistant (amp-resistant) Escherichia coli (E. coli) with a promising cationic, π-conjugated polyelectrolyte (P1) with a phenylene-based backbone and investigated the resulting morphological, mechanical, and compositional changes of the outer membrane of bacteria in great detail. The cationic quaternary amine groups of P1 led to electrostatic interactions with negatively charged moieties within the outer membrane of bacteria. Using atomic force microscopy (AFM), high-resolution transmission electron microscopy (TEM), we showed that due to this treatment, the bacterial outer membrane became rougher, decreased in stiffness/elastic modulus (AFM nanoindentation), formed blebs, and released vesicles near the cells. These evidences, in addition to increased staining of the P1-treated cell membrane by lipophilic dye Nile Red (confocal laser scanning microscopy (CLSM)), suggested loosening/disruption of packing of the outer cell envelope and release and exposure of lipid-based components. Lipidomics and fatty acid analysis confirmed a significant loss of phosphate-based outer membrane lipids and fatty acids, some of which are critically needed to maintain cell wall integrity and mechanical strength. Lipidomics and UV-vis analysis also confirmed that the extracellular vesicles released upon treatment (AFM) are composed of lipids and cationic P1. Such surface alterations (vesicle/bleb formation) and release of lipids/fatty acids upon treatment were effective enough to inhibit further growth of E. coli cells without completely disintegrating the cells and have been known as a defense mechanism of the cells against cationic antimicrobial agents.
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Affiliation(s)
- Ehsan Zamani
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Tyler J. Johnson
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Shyambo Chatterjee
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Cheryl Immethun
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Anandakumar Sarella
- Nebraska Center for Materials and Nanoscience, Voelte-Keegan Nanoscience Research Center, University of Nebraska-Lincoln, Lincoln, NE 68588-0298, United States
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Shudipto Konika Dishari
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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48
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Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition. Nat Ecol Evol 2020; 4:1661-1672. [PMID: 33077930 DOI: 10.1038/s41559-020-01299-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/05/2020] [Indexed: 11/08/2022]
Abstract
The transition between cell envelopes with one membrane (Gram-positive or monoderm) and those with two membranes (Gram-negative or diderm) is a fundamental open question in the evolution of Bacteria. Evidence of the presence of two independent diderm lineages, the Halanaerobiales and the Negativicutes, within the classically monoderm Firmicutes has blurred the monoderm/diderm divide and specifically anticipated that other members with an outer membrane (OM) might exist in this phylum. Here, by screening 1,639 genomes of uncultured Firmicutes for signatures of an OM, we highlight a third and deep branching diderm clade, the Limnochordia, strengthening the hypothesis of a diderm ancestor and the occurrence of independent transitions leading to the monoderm phenotype. Phyletic patterns of over 176,000 protein families constituting the Firmicutes pan-proteome identify those that strongly correlate with the diderm phenotype and suggest the existence of new potential players in OM biogenesis. In contrast, we find practically no largely conserved core of monoderms, a fact possibly linked to different ways of adapting to repeated OM losses. Phylogenetic analysis of a concatenation of main OM components totalling nearly 2,000 amino acid positions illustrates the common origin and vertical evolution of most diderm bacterial envelopes. Finally, mapping the presence/absence of OM markers onto the tree of Bacteria shows the overwhelming presence of diderm phyla and the non-monophyly of monoderm ones, pointing to an early origin of two-membraned cells and the derived nature of the Gram-positive envelope following multiple OM losses.
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Pandeya A, Ojo I, Alegun O, Wei Y. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria. ACS Infect Dis 2020; 6:2337-2354. [PMID: 32786281 PMCID: PMC8187054 DOI: 10.1021/acsinfecdis.0c00384] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance has emerged as a serious threat to global public health in recent years. Lack of novel antimicrobials, especially new classes of compounds, further aggravates the situation. For Gram-negative bacteria, their double layered cell envelope and an array of efflux pumps act as formidable barriers for antimicrobials to penetrate. While cytoplasmic targets are hard to reach, proteins in the periplasm are clearly more accessible, as the drug only needs to breach the outer membrane. In this review, we summarized recent efforts on the validation and testing of periplasmic proteins as potential antimicrobial targets and the development of related inhibitors that either inhibit the growth of a bacterial pathogen or reduce its virulence during interaction with host cells. We conclude that the periplasm contains a promising pool of novel antimicrobial targets that should be scrutinized more closely for the development of effective treatment against multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Olaniyi Alegun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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50
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Jia M, Wu B, Yang Z, Chen C, Zhao M, Hou X, Niu X, Jin C, Hu Y. Conformational Dynamics of the Periplasmic Chaperone SurA. Biochemistry 2020; 59:3235-3246. [PMID: 32786408 DOI: 10.1021/acs.biochem.0c00507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The periplasmic protein SurA is the primary chaperone involved in the biogenesis of bacterial outer membrane proteins and is a potential antibacterial drug target. The three-dimensional structure of SurA can be divided into three parts, a core module formed by the N- and C-terminal regions and two peptidyl-prolyl isomerase (PPIase) domains, P1 and P2. Despite the determination of the structures of several SurA-peptide complexes, the functional mechanism of this chaperone remains elusive and the roles of the two PPIase domains are yet unclear. Herein, we characterize the conformational dynamics of SurA by using solution nuclear magnetic resonance and single-molecule fluorescence resonance energy transfer methods. We demonstrate a "closed-to-open" structural transition of the P1 domain that is correlated with both chaperone activity and peptide binding and show that the flexible P2 domain can also occupy conformations that closely contact the NC core module. Our results offer a structural basis for the counteracting roles of the two PPIase domains in regulating the SurA chaperone activity.
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Affiliation(s)
- Moye Jia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bo Wu
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Ziyu Yang
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.,MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xianhui Hou
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Yunfei Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, Innovation Academy for Precision Measurement Science and Technology, CAS, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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