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Ariano K, Schweiger P. Determining the functional role of the Gluconobacter oxydans GOX1969 protein as a BamB homolog. Microbiol Spectr 2024; 12:e0106024. [PMID: 38916353 PMCID: PMC11302035 DOI: 10.1128/spectrum.01060-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
Acetic acid bacteria are used in many industrial processes such as the production of vinegar, vitamin C, the antidiabetic drug miglitol, and various artificial flavorings. These industrially important reactions are primarily carried out by an arsenal of periplasmic-facing membrane-bound dehydrogenases that incompletely oxidize their substrates and shuttle electrons directly into the respiratory chain. Among these dehydrogenases, GOX1969 in Gluconobacter oxydans was predicted to be a pyrroloquinoline quinone-dependent dehydrogenase of unknown function. However, after multiple analysis by a number of labs, no dehydrogenase activity has been detected. Reanalysis of GOX1969 sequence and structure reveals similarities to Escherichia coli BamB, which functions as a subunit of the β-barrel assembly machinery complex that is responsible for the assembly of β-barrel outer membrane proteins in Gram-negative bacteria. To test if the physiological function of GOX1969 is similar to BamB in E. coli, we introduced the gox1969 gene into an E. coli ∆bamB mutant. Growth deficiencies in the ∆bamB mutant were restored when gox1969 was expressed on the plasmid pGox1969. Furthermore, increased membrane permeability conferred by bamB deletion was restored upon gox1969 expression, which suggests a direct link between GOX1969 and a role in maintaining outer membrane stability. Together, this evidence strongly suggests that GOX1969 is functionally acting as a BamB in G. oxydans. As such, functional information on uncharacterized genes will provide new insights that will allow for more accurate modeling of acetic acid bacterial metabolism and further efforts to design rational strains for industrial use.IMPORTANCEGluconobacter oxydans is an industrially important member of the acetic acid bacteria. Experimental characterization of putative genes is necessary to identify targets for further engineering of rational acetic acid bacteria strains that can be used in the production of vitamin C, antidiabetic compounds, artificial flavorings, or novel compounds. In this study, we have identified an undefined dehydrogenase GOX1969 with no known substrate and defined structural similarities to outer membrane biogenesis protein BamB in E. coli K12. Furthermore, we demonstrate that GOX1969 is capable of complementing bamB knockout phenotypes in E. coli K12. Taken together, these findings enhance our understanding of G. oxydans physiology and expand the list of potential targets for future industrial strain design.
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Affiliation(s)
- Ky Ariano
- Department of Microbiology, University of Wisconsin–La Crosse, La Crosse, Wisconsin, USA
| | - Paul Schweiger
- Department of Microbiology, University of Wisconsin–La Crosse, La Crosse, Wisconsin, USA
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2
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Lu Z, Jiang H, Yang D, Tang H, Hamouda HI, Wang T, Mao X. Characterization of a λ-Carrageenase Mutant with the Generation of Long-Chain λ-Neocarrageenan Oligosaccharides. Foods 2024; 13:1923. [PMID: 38928863 PMCID: PMC11202985 DOI: 10.3390/foods13121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
λ-carrageenan oligosaccharides can be widely applied in the food, pharmaceutical, medicine and cosmetic industries due to their abundant bioactivities, and they are important products for the high-value utilization of λ-carrageenan. However, oligosaccharides with different degrees of polymerization have different properties, and the final products of λ-carrageenase reported so far are mainly λ-neocarrabiose, λ-neocarratetraose and λ-neocarrahexaose without longer-chain oligosaccharides. Further research is consequently required. Herein, a mutant λ-carrageenase was constructed by deleting the pyrroloquinoline quinone-like domain of OUC-CglA derived from Maribacter vaceletii. Interestingly, it was discovered that the majority of final products of the mutant OUC-CglA-DPQQ were long-chain oligosaccharides with a polymerization degree of 10-20, which underwent significant changes compared to that of OUC-CglA. Additionally, without the pyrroloquinoline quinone-like domain, fewer inclusion bodies were produced throughout the expression process, and the yield of the λ-carrageenase increased about five-fold. However, compared to its parental enzyme, significant changes were made to its enzymatic properties. Its optimal temperature and pH were 15 °C and pH 7.0, and its specific activity was 51.59 U/mg. The stability of the enzyme decreased. Thus, it was found that the deleting domain was related to the formation of inclusion bodies, the stability of the enzyme, the activity of the enzyme and the composition of the products.
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Affiliation(s)
- Zewei Lu
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Hong Jiang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
- Sanya Ocean Institute, Ocean University of China, Sanya 572024, China
| | - Dianqi Yang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hengxin Tang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Hamed I. Hamouda
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Tao Wang
- Sanya Ocean Institute, Ocean University of China, Sanya 572024, China
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, China
- Sanya Ocean Institute, Ocean University of China, Sanya 572024, China
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3
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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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4
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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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5
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Maseko SB, Brammerloo Y, Van Molle I, Sogues A, Martin C, Gorgulla C, Plant E, Olivet J, Blavier J, Ntombela T, Delvigne F, Arthanari H, El Hajj H, Bazarbachi A, Van Lint C, Salehi-Ashtiani K, Remaut H, Ballet S, Volkov AN, Twizere JC. Identification of small molecule antivirals against HTLV-1 by targeting the hDLG1-Tax-1 protein-protein interaction. Antiviral Res 2023; 217:105675. [PMID: 37481039 DOI: 10.1016/j.antiviral.2023.105675] [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: 06/24/2023] [Accepted: 07/15/2023] [Indexed: 07/24/2023]
Abstract
Human T-cell leukemia virus type-1 (HTLV-1) is the first pathogenic retrovirus discovered in human. Although HTLV-1-induced diseases are well-characterized and linked to the encoded Tax-1 oncoprotein, there is currently no strategy to target Tax-1 functions with small molecules. Here, we analyzed the binding of Tax-1 to the human homolog of the drosophila discs large tumor suppressor (hDLG1/SAP97), a multi-domain scaffolding protein involved in Tax-1-transformation ability. We have solved the structures of the PDZ binding motif (PBM) of Tax-1 in complex with the PDZ1 and PDZ2 domains of hDLG1 and assessed the binding of 10 million molecules by virtual screening. Among the 19 experimentally confirmed compounds, one systematically inhibited the Tax-1-hDLG1 interaction in different biophysical and cellular assays, as well as HTLV-1 cell-to-cell transmission in a T-cell model. Thus, our work demonstrates that interactions involving Tax-1 PDZ-domains are amenable to small-molecule inhibition, which provides a framework for the design of targeted therapies for HTLV-1-induced diseases.
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Affiliation(s)
- Sibusiso B Maseko
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Yasmine Brammerloo
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Adrià Sogues
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Estelle Plant
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Julien Olivet
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium
| | | | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hiba El Hajj
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Bazarbachi
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Carine Van Lint
- Service of Molecular Virology, Department of Molecular Biology (DBM), Université Libre de Bruxelles (ULB), Gosselies 6041, Belgium
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates
| | - Han Remaut
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Vrije Universiteit Brussel (VUB), Brussels Belgium.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Unit of Molecular Biology of Diseases, GIGA Institute, University of Liege, Liège, Belgium; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liege Belgium; Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University of Abu Dhabi, Abu Dhabi United Arab Emirates.
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6
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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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7
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Lu Z, Jiang H, Hamouda HI, Wang T, Dong Y, Mao X. Biochemical Characterization of a Cold-Adapted λ-Carrageenase OUC-CglA from Maribacter vaceletii: An Efficient Tool for λ-Carrageenan Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12135-12142. [PMID: 36112087 DOI: 10.1021/acs.jafc.2c05544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
λ-Carrageenase with high activity is an effective and environmentally friendly tool enzyme for the preparation of λ-carrageenan oligosaccharides with various biological activities. Herein, a novel GH150 (glycoside hydrolases family 150) λ-carrageenase OUC-CglA from Maribacter vaceletii was heterologously expressed, purified, and characterized. The recombinant OUC-CglA performs strict selectivity toward λ-carrageenan with a specific activity of 418.7 U/mg under its optimal reaction conditions of 20 °C and pH 7.0. Additionally, OUC-CglA is a typical cold-adapted λ-carrageenase because it unfolds 90% and 63% of its maximum activity at 15 and 10 °C, respectively. The hydrolysis process suggests that OUC-CglA is an endotype λ-carrageenase with the final products consisting of λ-neocarrabiose, λ-neocarratetraose, λ-neocarrahexaose, and other long-chain λ-neocarrageenan oligosaccharides. As a result, high activity, cold-adaptation, and principal products of OUC-CglA make it a potential biocatalyst for the effective preparation of λ-carrageenan oligosaccharides.
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Affiliation(s)
- Zewei Lu
- College of Food Science and Engineering, Ocean University of China, Qingdao266003, China
| | - Hong Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao266003, China
- Sanya Ocean Institute, Ocean University of China, Sanya572024, China
| | - Hamed I Hamouda
- College of Food Science and Engineering, Ocean University of China, Qingdao266003, China
- Processes Design and Development Department, Egyptian Petroleum Research Institute, Cairo11727, Egypt
| | - Tao Wang
- Sanya Ocean Institute, Ocean University of China, Sanya572024, China
| | - Yueyang Dong
- College of Food Science and Engineering, Ocean University of China, Qingdao266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- Sanya Ocean Institute, Ocean University of China, Sanya572024, China
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8
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Xiao L, Han L, Li B, Zhang M, Zhou H, Luo Q, Zhang X, Huang Y. Structures of the β-barrel assembly machine recognizing outer membrane protein substrates. FASEB J 2021; 35:e21207. [PMID: 33368572 DOI: 10.1096/fj.202001443rr] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/11/2022]
Abstract
β-barrel outer membrane proteins (β-OMPs) play critical roles in nutrition acquisition, protein import/export, and other fundamental biological processes. The assembly of β-OMPs in Gram-negative bacteria is mediated by the β-barrel assembly machinery (BAM) complex, yet its precise mechanism remains elusive. Here, we report two structures of the BAM complex in detergents and in nanodisks, and two crystal structures of the BAM complex with bound substrates. Structural analysis indicates that the membrane compositions surrounding the BAM complex could modulate its overall conformations, indicating low energy barriers between different conformational states and a highly dynamic nature of the BAM complex. Importantly, structures of the BAM complex with bound substrates and the related functional analysis show that the first β-strand of the BamA β-barrel (β1BamA ) in the BAM complex is associated with the last but not the first β-strand of a β-OMP substrate via antiparallel β-strand interactions. These observations are consistent with the β-signal hypothesis during β-OMP biogenesis, and suggest that the β1BamA strand in the BAM complex may interact with the last β-strand of an incoming β-OMP substrate upon their release from the chaperone-bound state.
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Affiliation(s)
- Le Xiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Long Han
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bufan Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 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
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qingshan Luo
- Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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9
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Diederichs KA, Buchanan SK, Botos I. Building Better Barrels - β-barrel Biogenesis and Insertion in Bacteria and Mitochondria. J Mol Biol 2021; 433:166894. [PMID: 33639212 PMCID: PMC8292188 DOI: 10.1016/j.jmb.2021.166894] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 01/20/2023]
Abstract
β-barrel proteins are folded and inserted into outer membranes by multi-subunit protein complexes that are conserved across different types of outer membranes. In Gram-negative bacteria this complex is the barrel-assembly machinery (BAM), in mitochondria it is the sorting and assembly machinery (SAM) complex, and in chloroplasts it is the outer envelope protein Oep80. Mitochondrial β-barrel precursor proteins are translocated from the cytoplasm to the intermembrane space by the translocase of the outer membrane (TOM) complex, and stabilized by molecular chaperones before interaction with the assembly machinery. Outer membrane bacterial BamA interacts with four periplasmic accessory proteins, whereas mitochondrial Sam50 interacts with two cytoplasmic accessory proteins. Despite these major architectural differences between BAM and SAM complexes, their core proteins, BamA and Sam50, seem to function the same way. Based on the new SAM complex structures, we propose that the mitochondrial β-barrel folding mechanism follows the budding model with barrel-switching aiding in the release of new barrels. We also built a new molecular model for Tom22 interacting with Sam37 to identify regions that could mediate TOM-SAM supercomplex formation.
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Affiliation(s)
- Kathryn A Diederichs
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes & Digestive & Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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10
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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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11
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Jin F. The transmembrane supercomplex mediating the biogenesis of OMPs in Gram-negative bacteria assumes a circular conformational change upon activation. FEBS Open Bio 2020; 10:1698-1715. [PMID: 32602996 PMCID: PMC7396438 DOI: 10.1002/2211-5463.12922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 11/06/2022] Open
Abstract
The cell envelope of Gram-negative bacteria is composed of the inner (plasma) and the outer membrane. In the outer membrane, the outer membrane β-barrel proteins (OMPs) serve multiple functions. They are synthesized in the cytoplasm and finally inserted into the outer membrane through a critical and complex pathway facilitated by many protein factors. Recently, a new model for the biogenesis of OMPs in Gram-negative bacteria was proposed, in which a supercomplex containing multiple proteins spans the inner and outer membrane, to mediate the biogenesis of OMPs. The core part of the transmembrane supercomplex is the inner membrane protein translocon and the outer membrane β-barrel assembly machinery (BAM) complex. Some components of the supercomplex, such as the BamA subunit of the BAM complex, are essential and conserved across species. The other components, for example, the BamB subunit and the primary periplasmic chaperone SurA, are also required for the supercomplex to gain complete function and full efficiency. How BamB and SurA behave in the supercomplex, however, is less well understood. Therefore, the crosstalk between BamA, BamB and SurA was investigated mainly through in vivo protein photo-cross-linking experiments and protein modeling. Moreover, theoretical structures for part of the supercomplex consisting of SurA and the BAM complex were constructed. The modeling data are consistent with the experimental results. The theoretical structures computed in this work provide a more comprehensive view of the mechanism of the supercomplex, demonstrating a circular conformational change of the supercomplex when it is active.
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Affiliation(s)
- Feng Jin
- School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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12
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Gunasinghe SD, Shiota T, Stubenrauch CJ, Schulze KE, Webb CT, Fulcher AJ, Dunstan RA, Hay ID, Naderer T, Whelan DR, Bell TDM, Elgass KD, Strugnell RA, Lithgow T. The WD40 Protein BamB Mediates Coupling of BAM Complexes into Assembly Precincts in the Bacterial Outer Membrane. Cell Rep 2019; 23:2782-2794. [PMID: 29847806 DOI: 10.1016/j.celrep.2018.04.093] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/05/2018] [Accepted: 04/23/2018] [Indexed: 01/28/2023] Open
Abstract
The β-barrel assembly machinery (BAM) complex is essential for localization of surface proteins on bacterial cells, but the mechanism by which it functions is unclear. We developed a direct stochastic optical reconstruction microscopy (dSTORM) methodology to view the BAM complex in situ. Single-cell analysis showed that discrete membrane precincts housing several BAM complexes are distributed across the E. coli surface, with a nearest neighbor distance of ∼200 nm. The auxiliary lipoprotein subunit BamB was crucial for this spatial distribution, and in situ crosslinking shows that BamB makes intimate contacts with BamA and BamB in neighboring BAM complexes within the precinct. The BAM complex precincts swell when outer membrane protein synthesis is maximal, visual proof that the precincts are active in protein assembly. This nanoscale interrogation of the BAM complex in situ suggests a model whereby bacterial outer membranes contain highly organized assembly precincts to drive integral protein assembly.
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Affiliation(s)
- Sachith D Gunasinghe
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Takuya Shiota
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Christopher J Stubenrauch
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Keith E Schulze
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Chaille T Webb
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Alex J Fulcher
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Iain D Hay
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Thomas Naderer
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Biochemistry & Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Donna R Whelan
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Toby D M Bell
- School of Chemistry, Monash University, Clayton, VIC 3800, Australia
| | - Kirstin D Elgass
- Monash Micro Imaging, Monash University, Clayton, VIC 3800, Australia; Hudson Institute of Medical Research, Clayton, VIC 3800, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
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13
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Wu R, Stephenson R, Gichaba A, Noinaj N. The big BAM theory: An open and closed case? BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183062. [PMID: 31520605 DOI: 10.1016/j.bbamem.2019.183062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
The β-barrel assembly machinery (BAM) is responsible for the biogenesis of outer membrane proteins (OMPs) into the outer membranes of Gram-negative bacteria. These OMPs have a membrane-embedded domain consisting of a β-barrel fold which can vary from 8 to 36 β-strands, with each serving a diverse role in the cell such as nutrient uptake and virulence. BAM was first identified nearly two decades ago, but only recently has the molecular structure of the full complex been reported. Together with many years of functional characterization, we have a significantly clearer depiction of BAM's structure, the intra-complex interactions, conformational changes that BAM may undergo during OMP biogenesis, and the role chaperones may play. But still, despite advances over the past two decades, the mechanism for BAM-mediated OMP biogenesis remains elusive. Over the years, several theories have been proposed that have varying degrees of support from the literature, but none has of yet been conclusive enough to be widely accepted as the sole mechanism. We will present a brief history of BAM, the recent work on the structures of BAM, and a critical analysis of the current theories for how it may function.
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Affiliation(s)
- Runrun Wu
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert Stephenson
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Abigail Gichaba
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA.
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14
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Leibiger K, Schweers JM, Schütz M. Biogenesis and function of the autotransporter adhesins YadA, intimin and invasin. Int J Med Microbiol 2019; 309:331-337. [PMID: 31176600 DOI: 10.1016/j.ijmm.2019.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/06/2019] [Accepted: 05/31/2019] [Indexed: 01/15/2023] Open
Abstract
Bacteria often express numerous virulence factors. These virulence factors make them successful pathogens, by e.g. mediating attachment to host cells and thereby facilitating persistence or invasion, or by contributing to the evasion of the host immune system to allow proliferation and spread within the host and in the environment. The site of first contact of Gram negative bacteria with the host is the bacterial outer membrane (OM). Consisting of an asymmetrical lipid bilayer with phospholipids forming the inner, and lipopolysaccharides forming the outer leaflet, the OM harbors numerous integral membrane proteins that are almost exclusively β-barrel proteins. One distinct family of OM β-barrel proteins strongly linked to bacterial virulence are the autotransporter (AT) proteins. During the last years huge progress has been made to better understand the mechanisms underlying the insertion of AT proteins into the OM and also AT function for interaction with the host. This review shortly summarizes our current knowledge about outer membrane protein (OMP) and more specifically AT biogenesis and function. We focused on the AT proteins that we haved studied in most detail: i.e. the Yersinia adhesin A (YadA) and invasin of Yersinia enterocolitica (Ye) as well as its homolog intimin (Int) expressed by enteropathogenic Escherichia coli. In addition, this review provides a short outlook about how we could possibly use this knowledge to fight infection.
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Affiliation(s)
- Karolin Leibiger
- Institut für Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Str. 6, 72076, Tübingen, Germany
| | - Jonas Malte Schweers
- Institut für Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Str. 6, 72076, Tübingen, Germany
| | - Monika Schütz
- Institut für Medizinische Mikrobiologie und Hygiene, Elfriede-Aulhorn-Str. 6, 72076, Tübingen, Germany.
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15
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Brouwer E, Ngo G, Yadav S, Ladig R, Schleiff E. Tic22 from
Anabaena
sp. PCC 7120 with holdase function involved in outer membrane protein biogenesis shuttles between plasma membrane and Omp85. Mol Microbiol 2019; 111:1302-1316. [DOI: 10.1111/mmi.14222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Eva‐Maria Brouwer
- Institute for Molecular Biosciences Goethe University Frankfurt am Main Frankfurt am Main Germany
| | - Giang Ngo
- Institute for Molecular Biosciences Goethe University Frankfurt am Main Frankfurt am Main Germany
| | - Shivam Yadav
- Institute for Molecular Biosciences Goethe University Frankfurt am Main Frankfurt am Main Germany
- Centre of Advanced Studies in Botany, Institute of Science Banaras Hindu University Varanasi India
| | - Roman Ladig
- Institute for Molecular Biosciences Goethe University Frankfurt am Main Frankfurt am Main Germany
| | - Enrico Schleiff
- Institute for Molecular Biosciences Goethe University Frankfurt am Main Frankfurt am Main Germany
- Buchman Institute for Molecular Life Sciences Goethe University Frankfurt am Main Frankfurt am Main Germany
- Frankfurt Institute of Advanced Studies Frankfurt am Main Germany
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16
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Ricci DP, Silhavy TJ. Outer Membrane Protein Insertion by the β-barrel Assembly Machine. EcoSal Plus 2019; 8:10.1128/ecosalplus.ESP-0035-2018. [PMID: 30869065 PMCID: PMC6419762 DOI: 10.1128/ecosalplus.esp-0035-2018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Like all outer membrane (OM) constituents, integral OM β-barrel proteins in Gram-negative bacteria are synthesized in the cytoplasm and trafficked to the OM, where they are locally assembled into the growing OM by the ubiquitous β-barrel assembly machine (Bam). While the identities and structures of all essential and accessory Bam components have been determined, the basic mechanism of Bam-assisted OM protein integration remains elusive. Here we review mechanistic analyses of OM β-barrel protein folding and Bam dynamics and summarize recent insights that inform a general model for OM protein recognition and assembly by the Bam complex.
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Affiliation(s)
- Dante P Ricci
- Department of Early Research, Achaogen, Inc., South San Francisco, CA 94080
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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17
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Klein K, Sonnabend MS, Frank L, Leibiger K, Franz-Wachtel M, Macek B, Trunk T, Leo JC, Autenrieth IB, Schütz M, Bohn E. Deprivation of the Periplasmic Chaperone SurA Reduces Virulence and Restores Antibiotic Susceptibility of Multidrug-Resistant Pseudomonas aeruginosa. Front Microbiol 2019; 10:100. [PMID: 30846971 PMCID: PMC6394205 DOI: 10.3389/fmicb.2019.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main causative agents of nosocomial infections and the spread of multidrug-resistant strains is rising. Therefore, novel strategies for therapy are urgently required. The outer membrane composition of Gram-negative pathogens and especially of Pa restricts the efficacy of antibiotic entry into the cell and determines virulence. For efficient outer membrane protein biogenesis, the β-barrel assembly machinery (BAM) complex in the outer membrane and periplasmic chaperones like Skp and SurA are crucial. Previous studies indicated that the importance of individual proteins involved in outer membrane protein biogenesis may vary between different Gram-negative species. In addition, since multidrug-resistant Pa strains pose a serious global threat, the interference with both virulence and antibiotic resistance by disturbing outer membrane protein biogenesis might be a new strategy to cope with this challenge. Therefore, deletion mutants of the non-essential BAM complex components bamB and bamC, of the skp homolog hlpA as well as a conditional mutant of surA were investigated. The most profound effects for both traits were associated with reduced levels of SurA, characterized by increased membrane permeability, enhanced sensitivity to antibiotic treatment and attenuation of virulence in a Galleria mellonella infection model. Strikingly, the depletion of SurA in a multidrug-resistant clinical bloodstream isolate re-sensitized the strain to antibiotic treatment. From our data we conclude that SurA of Pa serves as a promising target for developing a drug that shows antiinfective activity and re-sensitizes multidrug-resistant strains to antibiotics.
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Affiliation(s)
- Kristina Klein
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Michael S. Sonnabend
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Lisa Frank
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Karolin Leibiger
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, Universität Tübingen, Tübingen, Germany
| | - Thomas Trunk
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C. Leo
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ingo B. Autenrieth
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Monika Schütz
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Erwin Bohn
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
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18
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Robinson JA. Folded Synthetic Peptides and Other Molecules Targeting Outer Membrane Protein Complexes in Gram-Negative Bacteria. Front Chem 2019; 7:45. [PMID: 30788339 PMCID: PMC6372539 DOI: 10.3389/fchem.2019.00045] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Conformationally constrained peptidomimetics have been developed to mimic interfacial epitopes and target a wide selection of protein-protein interactions. ß-Hairpin mimetics based on constrained macrocyclic peptides have provided access to excellent structural mimics of ß-hairpin epitopes and found applications as interaction inhibitors in many areas of biology and medicinal chemistry. Recently, ß-hairpin peptidomimetics and naturally occurring ß-hairpin-shaped peptides have also been discovered with potent antimicrobial activity and novel mechanisms of action, targeting essential outer membrane protein (OMP) complexes in Gram-negative bacteria. This includes the Lpt complex, required for transporting LPS to the cell surface during OM biogenesis and the BAM complex that folds OMPs and inserts them into the OM bilayer. The Lpt complex is a macromolecular superstructure comprising seven different proteins (LptA-LptG) that spans the entire bacterial cell envelope, whereas the BAM complex is a folding machine comprising a ß-barrel OMP (BamA) and four different lipoproteins (BamB-BamE). Folded synthetic and natural ß-hairpin-shaped peptides appear well-suited for interacting with proteins within the Lpt and BAM complexes that are rich in ß-structure. Recent progress in identifying antibiotics targeting these complexes are reviewed here. Already a clinical candidate has been developed (murepavadin) that targets LptD, with potent antimicrobial activity specifically against pseudmonads. The ability of folded synthetic ß-hairpin epitope mimetics to interact with ß-barrel and ß-jellyroll domains in the Lpt and Bam complexes represent new avenues for antibiotic discovery, which may lead to the development of much needed new antimicrobials to combat the rise of drug-resistant pathogenic Gram-negative bacteria.
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Affiliation(s)
- John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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19
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Abstract
The transport of small molecules across membranes is essential for the import of nutrients and other energy sources into the cell and, for the export of waste and other potentially harmful byproducts out of the cell. While hydrophobic molecules are permeable to membranes, ions and other small polar molecules require transport via specialized membrane transport proteins . The two major classes of membrane transport proteins are transporters and channels. With our focus here on porins-major class of non-specific diffusion channel proteins , we will highlight some recent structural biology reports and functional assays that have substantially contributed to our understanding of the mechanism that mediates uptake of small molecules, including antibiotics, across the outer membrane of Enterobacteriaceae . We will also review advances in the regulation of porin expression and porin biogenesis and discuss these pathways as new therapeutic targets.
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Affiliation(s)
- Muriel Masi
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
| | | | - Jean-Marie Pagès
- UMR_MD1, Inserm U1261, IRBA, Membranes et Cibles Thérapeutiques, Facultés de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France.
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20
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Hartmann JB, Zahn M, Burmann IM, Bibow S, Hiller S. Sequence-Specific Solution NMR Assignments of the β-Barrel Insertase BamA to Monitor Its Conformational Ensemble at the Atomic Level. J Am Chem Soc 2018; 140:11252-11260. [PMID: 30125090 DOI: 10.1021/jacs.8b03220] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
β-barrel outer membrane proteins (Omps) are key functional components of the outer membranes of Gram-negative bacteria, mitochondria, and plastids. In bacteria, their biogenesis requires the β-barrel-assembly machinery (Bam) with the central insertase BamA, but the exact translocation and insertion mechanism remains elusive. The BamA insertase features a loosely closed gating region between the first and last β-strand 16. Here, we describe ∼70% complete sequence-specific NMR resonance assignments of the transmembrane region of the BamA β-barrel in detergent micelles. On the basis of the assignments, NMR spectra show that the BamA barrel populates a conformational ensemble in slow exchange equilibrium, both in detergent micelles and lipid bilayer nanodiscs. Individual conformers can be selected from the ensemble by the introduction of a C-terminal strand extension, single-point mutations, or specific disulfide cross-linkings, and these modifications at the barrel seam are found to be allosterically coupled to sites at the entire barrel circumference. The resonance assignment provides a platform for mechanistic studies of BamA at atomic resolution, as well as for investigating interactions with potential antibiotic drugs and partner proteins.
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Affiliation(s)
| | - Michael Zahn
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | | | - Stefan Bibow
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | - Sebastian Hiller
- Biozentrum , University of Basel , Klingelbergstrasse 70 , 4056 Basel , Switzerland
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21
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Ranava D, Caumont-Sarcos A, Albenne C, Ieva R. Bacterial machineries for the assembly of membrane-embedded β-barrel proteins. FEMS Microbiol Lett 2018; 365:4961134. [DOI: 10.1093/femsle/fny087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/03/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
- David Ranava
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Anne Caumont-Sarcos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Cécile Albenne
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
| | - Raffaele Ieva
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse, France
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22
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Chaturvedi D, Mahalakshmi R. Folding Determinants of Transmembrane β-Barrels Using Engineered OMP Chimeras. Biochemistry 2018. [DOI: 10.1021/acs.biochem.8b00012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepti Chaturvedi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal − 462066, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal − 462066, India
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23
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Sikora AE, Wierzbicki IH, Zielke RA, Ryner RF, Korotkov KV, Buchanan SK, Noinaj N. Structural and functional insights into the role of BamD and BamE within the β-barrel assembly machinery in Neisseria gonorrhoeae. J Biol Chem 2018; 293:1106-1119. [PMID: 29229778 PMCID: PMC5787791 DOI: 10.1074/jbc.ra117.000437] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/18/2017] [Indexed: 12/22/2022] Open
Abstract
The β-barrel assembly machinery (BAM) is a conserved multicomponent protein complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Given its role in the production of OMPs for survival and pathogenesis, BAM represents an attractive target for the development of therapeutic interventions, including drugs and vaccines against multidrug-resistant bacteria such as Neisseria gonorrhoeae The first structure of BamA, the central component of BAM, was from N. gonorrhoeae, the etiological agent of the sexually transmitted disease gonorrhea. To aid in pharmaceutical targeting of BAM, we expanded our studies to BamD and BamE within BAM of this clinically relevant human pathogen. We found that the presence of BamD, but not BamE, is essential for gonococcal viability. However, BamE, but not BamD, was cell-surface-displayed under native conditions; however, in the absence of BamE, BamD indeed becomes surface-exposed. Loss of BamE altered cell envelope composition, leading to slower growth and an increase in both antibiotic susceptibility and formation of membrane vesicles containing greater amounts of vaccine antigens. Both BamD and BamE are expressed in diverse gonococcal isolates, under host-relevant conditions, and throughout different phases of growth. The solved structures of Neisseria BamD and BamE share overall folds with Escherichia coli proteins but contain differences that may be important for function. Together, these studies highlight that, although BAM is conserved across Gram-negative bacteria, structural and functional differences do exist across species, which may be leveraged in the development of species-specific therapeutics in the effort to combat multidrug resistance.
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Affiliation(s)
- Aleksandra E Sikora
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330,
| | - Igor H Wierzbicki
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Ryszard A Zielke
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Rachael F Ryner
- From the Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon 97330
| | - Konstantin V Korotkov
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536
| | - Susan K Buchanan
- NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907
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24
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Abstract
In Gram-negative bacteria, the biogenesis of β-barrel outer membrane proteins (OMPs) is mediated by the β-barrel assembly machinery (BAM) complex. During the past decade, structural and functional studies have collectively contributed to advancing our understanding of the structure and function of the BAM complex; however, the exact mechanism that is involved remains elusive. In this Progress article, we discuss recent structural studies that have revealed that the accessory proteins may regulate essential unprecedented conformational changes in the core component BamA during function. We also detail the mechanistic insights that have been gained from structural data, mutagenesis studies and molecular dynamics simulations, and explore two emerging models for the BAM-mediated biogenesis of OMPs in bacteria.
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Affiliation(s)
- Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences and the Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
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25
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Weirich J, Bräutigam C, Mühlenkamp M, Franz-Wachtel M, Macek B, Meuskens I, Skurnik M, Leskinen K, Bohn E, Autenrieth I, Schütz M. Identifying components required for OMP biogenesis as novel targets for antiinfective drugs. Virulence 2017; 8:1170-1188. [PMID: 28118090 PMCID: PMC5711350 DOI: 10.1080/21505594.2016.1278333] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The emergence of multiresistant Gram-negative bacteria requires new therapies for combating bacterial infections. Targeting the biogenesis of virulence factors could be an alternative strategy instead of killing bacteria with antibiotics. The outer membrane (OM) of Gram-negative bacteria acts as a physical barrier. At the same time it facilitates the exchange of molecules and harbors a multitude of proteins associated with virulence. In order to insert proteins into the OM, an essential oligomeric membrane-associated protein complex, the ß-barrel assembly machinery (BAM) is required. Being essential for the biogenesis of outer membrane proteins (OMPs) the BAM and also periplasmic chaperones may serve as attractive targets to develop novel antiinfective agents. Herein, we aimed to elucidate which proteins belonging to the OMP biogenesis machinery have the most important function in granting bacterial fitness, OM barrier function, facilitating biogenesis of dedicated virulence factors and determination of overall virulence. To this end we used the enteropathogen Yersinia enterocolitica as a model system. We individually knocked out all non-essential components of the BAM (BamB, C and E) as well as the periplasmic chaperones DegP, SurA and Skp. In summary, we found that the most profound phenotypes were produced by the loss of BamB or SurA with both knockouts resulting in significant attenuation or even avirulence of Ye in a mouse infection model. Thus, we assume that both BamB and SurA are promising targets for the development of new antiinfective drugs in the future.
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Affiliation(s)
- Johanna Weirich
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | - Cornelia Bräutigam
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | - Melanie Mühlenkamp
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | | | - Boris Macek
- b Proteome Center Tübingen, Universität Tübingen , Tübingen , Germany
| | - Ina Meuskens
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | - Mikael Skurnik
- c Department of Bacteriology and Immunology , Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki , Helsinki , Finland
| | - Katarzyna Leskinen
- c Department of Bacteriology and Immunology , Medicum, Research Programs Unit, Immunobiology Research Program, University of Helsinki , Helsinki , Finland
| | - Erwin Bohn
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | - Ingo Autenrieth
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
| | - Monika Schütz
- a Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen , Tübingen , Germany
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26
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Bakelar J, Buchanan SK, Noinaj N. Structural snapshots of the β-barrel assembly machinery. FEBS J 2016; 284:1778-1786. [PMID: 27862971 DOI: 10.1111/febs.13960] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/01/2016] [Accepted: 11/10/2016] [Indexed: 11/29/2022]
Abstract
The β-barrel assembly machinery (BAM) is a multicomponent complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria, with conserved systems in both mitochondria and chloroplasts. Given its importance in the integrity of the outer membrane and in the assembly of surface exposed virulence factors, BAM is an attractive therapeutic target against pathogenic bacteria, particularly multidrug-resistant strains. While the mechanism for how BAM functions remains elusive, previous structural studies have described each of the individual components of BAM, offering only a few clues to how the complex functions. Recently, a number of structures have been reported of complexes, including that of fully assembled BAM in differing conformational states. These studies have provided the molecular blueprint detailing the atomic interactions between the components and have revealed new details about BAM, which suggest a dynamic mechanism that may use conformational changes to assist in the biogenesis of new OMPs.
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Affiliation(s)
- Jeremy Bakelar
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN, USA
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicholas Noinaj
- Department of Biological Sciences, Markey Center for Structural Biology, Purdue Institute for Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN, USA
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27
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Iqbal H, Kenedy MR, Lybecker M, Akins DR. The TamB ortholog of Borrelia burgdorferi interacts with the β-barrel assembly machine (BAM) complex protein BamA. Mol Microbiol 2016; 102:757-774. [PMID: 27588694 PMCID: PMC5582053 DOI: 10.1111/mmi.13492] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2016] [Indexed: 12/29/2022]
Abstract
Two outer membrane protein (OMP) transport systems in diderm bacteria assist in assembly and export of OMPs. These two systems are the β-barrel assembly machine (BAM) complex and the translocation and assembly module (TAM). The BAM complex consists of the OMP component BamA along with several outer membrane associated proteins. The TAM also consists of an OMP, designated TamA, and a single inner membrane (IM) protein, TamB. Together TamA and TamB aid in the secretion of virulence-associated OMPs. In this study we characterized the hypothetical protein BB0794 in Borrelia burgdorferi. BB0794 contains a conserved DUF490 domain, which is a motif found in all TamB proteins. All spirochetes lack a TamA ortholog, but computational and physicochemical characterization of BB0794 revealed it is a TamB ortholog. Interestingly, BB0794 was observed to interact with BamA and a BB0794 regulatable mutant displayed altered cellular morphology and antibiotic sensitivity. The observation that B. burgdorferi contains a TamB ortholog that interacts with BamA and is required for proper outer membrane biogenesis not only identifies a novel role for TamB-like proteins, but also may explain why most diderms harbor a TamB-like protein while only a select group encodes TamA.
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Affiliation(s)
- Henna Iqbal
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Meghan Lybecker
- Department of Biology, University of Colorado - Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Darrin R Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
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28
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Rollauer SE, Sooreshjani MA, Noinaj N, Buchanan SK. Outer membrane protein biogenesis in Gram-negative bacteria. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2015.0023. [PMID: 26370935 DOI: 10.1098/rstb.2015.0023] [Citation(s) in RCA: 160] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gram-negative bacteria contain a double membrane which serves for both protection and for providing nutrients for viability. The outermost of these membranes is called the outer membrane (OM), and it contains a host of fully integrated membrane proteins which serve essential functions for the cell, including nutrient uptake, cell adhesion, cell signalling and waste export. For pathogenic strains, many of these outer membrane proteins (OMPs) also serve as virulence factors for nutrient scavenging and evasion of host defence mechanisms. OMPs are unique membrane proteins in that they have a β-barrel fold and can range in size from 8 to 26 strands, yet can still serve many different functions for the cell. Despite their essential roles in cell survival and virulence, the exact mechanism for the biogenesis of these OMPs into the OM has remained largely unknown. However, the past decade has witnessed significant progress towards unravelling the pathways and mechanisms necessary for moulding a nascent polypeptide into a functional OMP within the OM. Here, we will review some of these recent discoveries that have advanced our understanding of the biogenesis of OMPs in Gram-negative bacteria, starting with synthesis in the cytoplasm to folding and insertion into the OM.
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Affiliation(s)
- Sarah E Rollauer
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Moloud A Sooreshjani
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Han L, Zheng J, Wang Y, Yang X, Liu Y, Sun C, Cao B, Zhou H, Ni D, Lou J, Zhao Y, Huang Y. Structure of the BAM complex and its implications for biogenesis of outer-membrane proteins. Nat Struct Mol Biol 2016; 23:192-6. [PMID: 26900875 DOI: 10.1038/nsmb.3181] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/02/2016] [Indexed: 11/09/2022]
Abstract
In Gram-negative bacteria, the assembly of β-barrel outer-membrane proteins (OMPs) requires the β-barrel-assembly machinery (BAM) complex. We determined the crystal structure of the 200-kDa BAM complex from Escherichia coli at 3.55-Å resolution. The structure revealed that the BAM complex assembles into a hat-like shape, in which the BamA β-barrel domain forms the hat's crown embedded in the outer membrane, and its five polypeptide transport-associated (POTRA) domains interact with the four lipoproteins BamB, BamC, BamD and BamE, thus forming the hat's brim in the periplasm. The assembly of the BAM complex creates a ring-like apparatus beneath the BamA β-barrel in the periplasm and a potential substrate-exit pore located at the outer membrane-periplasm interface. The complex structure suggests that the chaperone-bound OMP substrates may feed into the chamber of the ring-like apparatus and insert into the outer membrane via the potential substrate-exit pore in an energy-independent manner.
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Affiliation(s)
- Long Han
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiangge Zheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xu Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanqing Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chuanqi Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Baohua Cao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haizhen Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongchun Ni
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yongfang Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yihua Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
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30
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Gu Y, Li H, Dong H, Zeng Y, Zhang Z, Paterson NG, Stansfeld PJ, Wang Z, Zhang Y, Wang W, Dong C. Structural basis of outer membrane protein insertion by the BAM complex. Nature 2016; 531:64-9. [PMID: 26901871 DOI: 10.1038/nature17199] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/05/2016] [Indexed: 02/06/2023]
Abstract
All Gram-negative bacteria, mitochondria and chloroplasts have outer membrane proteins (OMPs) that perform many fundamental biological processes. The OMPs in Gram-negative bacteria are inserted and folded into the outer membrane by the β-barrel assembly machinery (BAM). The mechanism involved is poorly understood, owing to the absence of a structure of the entire BAM complex. Here we report two crystal structures of the Escherichia coli BAM complex in two distinct states: an inward-open state and a lateral-open state. Our structures reveal that the five polypeptide transport-associated domains of BamA form a ring architecture with four associated lipoproteins, BamB-BamE, in the periplasm. Our structural, functional studies and molecular dynamics simulations indicate that these subunits rotate with respect to the integral membrane β-barrel of BamA to induce movement of the β-strands of the barrel and promote insertion of the nascent OMP.
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Affiliation(s)
- Yinghong Gu
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Huanyu Li
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Haohao Dong
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Yi Zeng
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Zhengyu Zhang
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Neil G Paterson
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Zhongshan Wang
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical College, Xuzhou 221004, China.,Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yizheng Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Wenjian Wang
- Laboratory of Department of Surgery, the First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080, China
| | - Changjiang Dong
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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31
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Chen Z, Zhan LH, Hou HF, Gao ZQ, Xu JH, Dong C, Dong YH. Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:236-44. [PMID: 26894671 DOI: 10.1107/s2059798315024729] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/23/2015] [Indexed: 11/10/2022]
Abstract
In Escherichia coli, the Omp85 protein BamA and four lipoproteins (BamBCDE) constitute the BAM complex, which is essential for the assembly and insertion of outer membrane proteins into the outer membrane. Here, the crystal structure of BamB in complex with the POTRA3-4 domains of BamA is reported at 2.1 Å resolution. Based on this structure, the POTRA3 domain is associated with BamB via hydrogen-bonding and hydrophobic interactions. Structural and biochemical analysis revealed that the conserved residues Arg77, Glu127, Glu150, Ser167, Leu192, Leu194 and Arg195 of BamB play an essential role in interaction with the POTRA3 domain.
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Affiliation(s)
- Zhen Chen
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Li Hong Zhan
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Hai Feng Hou
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Zeng Qiang Gao
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Jian Hua Xu
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Cheng Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yu Hui Dong
- Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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32
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Abstract
β-Barrel outer membrane proteins (OMPs) are found in the outer membranes of Gram-negative bacteria and are essential for nutrient import, signaling, and adhesion. A 200-kilodalton five-component complex called the β-barrel assembly machinery (BAM) complex has been implicated in the biogenesis of OMPs. We report the structure of the BAM complex from Escherichia coli, revealing that binding of BamCDE modulates the conformation of BamA, the central component, which may serve to regulate the BAM complex. The periplasmic domain of BamA was in a closed state that prevents access to the barrel lumen, which indicates substrate OMPs may not be threaded through the barrel during biogenesis. Further, conformational shifts in the barrel domain lead to opening of the exit pore and rearrangement at the lateral gate.
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Affiliation(s)
- Jeremy Bakelar
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
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33
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Bergal HT, Hopkins AH, Metzner SI, Sousa MC. The Structure of a BamA-BamD Fusion Illuminates the Architecture of the β-Barrel Assembly Machine Core. Structure 2015; 24:243-51. [PMID: 26749448 DOI: 10.1016/j.str.2015.10.030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022]
Abstract
The β-barrel assembly machine (BAM) mediates folding and insertion of integral β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria. Of the five BAM subunits, only BamA and BamD are essential for cell viability. Here we present the crystal structure of a fusion between BamA POTRA4-5 and BamD from Rhodothermus marinus. The POTRA5 domain binds BamD between its tetratricopeptide repeats 3 and 4. The interface structural elements are conserved in the Escherichia coli proteins, which allowed structure validation by mutagenesis and disulfide crosslinking in E. coli. Furthermore, the interface is consistent with previously reported mutations that impair BamA-BamD binding. The structure serves as a linchpin to generate a BAM model where POTRA domains and BamD form an elongated periplasmic ring adjacent to the membrane with a central cavity approximately 30 × 60 Å wide. We propose that nascent OMPs bind this periplasmic ring prior to insertion and folding by BAM.
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Affiliation(s)
- Hans Thor Bergal
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Alex Hunt Hopkins
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Sandra Ines Metzner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Marcelo Carlos Sousa
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.
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34
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O'Neil PK, Rollauer SE, Noinaj N, Buchanan SK. Fitting the Pieces of the β-Barrel Assembly Machinery Complex. Biochemistry 2015; 54:6303-11. [PMID: 26394220 PMCID: PMC4631317 DOI: 10.1021/acs.biochem.5b00852] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
β-Barrel membrane proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria; however, exactly how they are folded and inserted remains unknown. Over the past decade, both functional and structural studies have greatly contributed to addressing this elusive mechanism. It is known that a conserved core machinery is required for each organelle, though the overall composition varies significantly. The vast majority of studies that aimed to understand the biogenesis of β-barrel membrane proteins has been conducted in Gram-negative bacteria. Here, it is the task of a multicomponent complex known as the β-barrel assembly machinery (BAM) complex to fold and insert new β-barrel membrane proteins into the outer membrane. In this review, we will discuss recent discoveries with the goal of utilizing all reported structural and functional studies to piece together a current structural model for the fully assembled BAM complex.
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Affiliation(s)
- Patrick K O'Neil
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Sarah E Rollauer
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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35
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Bodelón G, Marín E, Fernández LÁ. Analyzing the Role of Periplasmic Folding Factors in the Biogenesis of OMPs and Members of the Type V Secretion System. Methods Mol Biol 2015; 1329:77-110. [PMID: 26427678 DOI: 10.1007/978-1-4939-2871-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The outer membrane (OM) of gram-negative bacteria is highly packed with OM proteins (OMPs) and the trafficking and assembly of OMPs in gram-negative bacteria is a subject of intense research. Structurally, OMPs vary in the number of β-strands and in the size and complexity of extra-membrane domains, with extreme examples being the members of the type V protein secretion system (T5SS), such as the autotransporter (AT) and intimin/invasin families of secreted proteins, in which a large extracellular "passenger" domain is linked to a β-barrel that inserts in the OM. Despite their structural and functional diversity, OMPs interact in the periplasm with a relatively small set of protein chaperones that facilitate their transport from the inner membrane (IM) to the β-barrel assembly machinery (BAM complex), preventing aggregation and assisting their folding in various aspects including disulfide bond formation. This chapter is focused on the periplasmic folding factors involved in the biogenesis of integral OMPs and members of T5SS in E. coli, which are used as a model system in this field. Background information on these periplasmic folding factors is provided along with genetic methods to generate conditional mutants that deplete these factors from E. coli and biochemical methods to analyze the folding, surface display, disulfide formation and oligomerization state of OMPs/T5SS in these mutants.
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Affiliation(s)
- Gustavo Bodelón
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
| | - Elvira Marín
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
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36
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Computational redesign of the lipid-facing surface of the outer membrane protein OmpA. Proc Natl Acad Sci U S A 2015. [PMID: 26199411 DOI: 10.1073/pnas.1501836112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Advances in computational design methods have made possible extensive engineering of soluble proteins, but designed β-barrel membrane proteins await improvements in our understanding of the sequence determinants of folding and stability. A subset of the amino acid residues of membrane proteins interact with the cell membrane, and the design rules that govern this lipid-facing surface are poorly understood. We applied a residue-level depth potential for β-barrel membrane proteins to the complete redesign of the lipid-facing surface of Escherichia coli OmpA. Initial designs failed to fold correctly, but reversion of a small number of mutations indicated by backcross experiments yielded designs with substitutions to up to 60% of the surface that did support folding and membrane insertion.
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Noinaj N, Rollauer SE, Buchanan SK. The β-barrel membrane protein insertase machinery from Gram-negative bacteria. Curr Opin Struct Biol 2015; 31:35-42. [PMID: 25796031 PMCID: PMC4476940 DOI: 10.1016/j.sbi.2015.02.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/06/2015] [Accepted: 02/23/2015] [Indexed: 12/25/2022]
Abstract
The outer membranes (OM) of Gram-negative bacteria contain a host of β-barrel outer membrane proteins (OMPs) which serve many functions for cell survival and virulence. The biogenesis of these OMPs is mediated by the β-barrel assembly machinery (BAM) complex which is composed of five components including the essential core component called BamA that mediates the insertase function within the OM. The crystal structure of BamA has recently been reported from three different species, including a full-length structure from Neisseria gonorrhoeae. Mutagenesis and functional studies identified several conformational changes within BamA that are required for function, providing a significant advancement towards unraveling exactly how BamA and the BAM complex are able to fold and insert new OMPs in the OM.
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Affiliation(s)
- Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States
| | - Sarah E Rollauer
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Susan K Buchanan
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States.
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Dunn JP, Kenedy MR, Iqbal H, Akins DR. Characterization of the β-barrel assembly machine accessory lipoproteins from Borrelia burgdorferi. BMC Microbiol 2015; 15:70. [PMID: 25887384 PMCID: PMC4377024 DOI: 10.1186/s12866-015-0411-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/12/2015] [Indexed: 12/26/2022] Open
Abstract
Background Like all diderm bacteria studied to date, Borrelia burgdorferi possesses a β-barrel assembly machine (BAM) complex. The bacterial BAM complexes characterized thus far consist of an essential integral outer membrane protein designated BamA and one or more accessory proteins. The accessory proteins are typically lipid-modified proteins anchored to the inner leaflet of the outer membrane through their lipid moieties. We previously identified and characterized the B. burgdorferi BamA protein in detail and more recently identified two lipoproteins encoded by open reading frames bb0324 and bb0028 that associate with the borrelial BamA protein. The role(s) of the BAM accessory lipoproteins in B. burgdorferi is currently unknown. Results Structural modeling of B. burgdorferi BB0028 revealed a distinct β-propeller fold similar to the known structure for the E. coli BAM accessory lipoprotein BamB. Additionally, the structural model for BB0324 was highly similar to the known structure of BamD, which is consistent with the prior finding that BB0324 contains tetratricopeptide repeat regions similar to other BamD orthologs. Consistent with BB0028 and BB0324 being BAM accessory lipoproteins, mutants lacking expression of each protein were found to exhibit altered membrane permeability and enhanced sensitivity to various antimicrobials. Additionally, BB0028 mutants also exhibited significantly impaired in vitro growth. Finally, immunoprecipitation experiments revealed that BB0028 and BB0324 each interact specifically and independently with BamA to form the BAM complex in B. burgdorferi. Conclusions Combined structural studies, functional assays, and co-immunoprecipitation experiments confirmed that BB0028 and BB0324 are the respective BamB and BamD orthologs in B. burgdorferi, and are important in membrane integrity and/or outer membrane protein localization. The borrelial BamB and BamD proteins both interact specifically and independently with BamA to form a tripartite BAM complex in B. burgdorferi. A working model has been developed to further analyze outer membrane biogenesis and outer membrane protein transport in this pathogenic spirochete.
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Affiliation(s)
- Joshua P Dunn
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Melisha R Kenedy
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Henna Iqbal
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| | - Darrin R Akins
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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39
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Garnett JA, Muhl D, Douse CH, Hui K, Busch A, Omisore A, Yang Y, Simpson P, Marchant J, Waksman G, Matthews S, Filloux A. Structure-function analysis reveals that the Pseudomonas aeruginosa Tps4 two-partner secretion system is involved in CupB5 translocation. Protein Sci 2015; 24:670-87. [PMID: 25641651 PMCID: PMC4420518 DOI: 10.1002/pro.2640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 01/11/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium, synonymous with cystic fibrosis patients, which can cause chronic infection of the lungs. This pathogen is a model organism to study biofilms: a bacterial population embedded in an extracellular matrix that provide protection from environmental pressures and lead to persistence. A number of Chaperone-Usher Pathways, namely CupA-CupE, play key roles in these processes by assembling adhesive pili on the bacterial surface. One of these, encoded by the cupB operon, is unique as it contains a nonchaperone-usher gene product, CupB5. Two-partner secretion (TPS) systems are comprised of a C-terminal integral membrane β-barrel pore with tandem N-terminal POTRA (POlypeptide TRansport Associated) domains located in the periplasm (TpsB) and a secreted substrate (TpsA). Using NMR we show that TpsB4 (LepB) interacts with CupB5 and its predicted cognate partner TpsA4 (LepA), an extracellular protease. Moreover, using cellular studies we confirm that TpsB4 can translocate CupB5 across the P. aeruginosa outer membrane, which contrasts a previous observation that suggested the CupB3 P-usher secretes CupB5. In support of our findings we also demonstrate that tps4/cupB operons are coregulated by the RocS1 sensor suggesting P. aeruginosa has developed synergy between these systems. Furthermore, we have determined the solution-structure of the TpsB4-POTRA1 domain and together with restraints from NMR chemical shift mapping and in vivo mutational analysis we have calculated models for the entire TpsB4 periplasmic region in complex with both TpsA4 and CupB5 secretion motifs. The data highlight specific residues for TpsA4/CupB5 recognition by TpsB4 in the periplasm and suggest distinct roles for each POTRA domain.
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Affiliation(s)
- James A Garnett
- Department of Life Sciences, Centre for Structural Biology, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom; Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
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40
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Hagan CL, Wzorek JS, Kahne D. Inhibition of the β-barrel assembly machine by a peptide that binds BamD. Proc Natl Acad Sci U S A 2015; 112:2011-6. [PMID: 25646443 PMCID: PMC4343090 DOI: 10.1073/pnas.1415955112] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The protein complex that assembles integral membrane β-barrel proteins in the outer membranes of Gram-negative bacteria is an attractive target in the development of new antibiotics. This complex, the β-barrel assembly machine (Bam), contains two essential proteins, BamA and BamD. We have identified a peptide that inhibits the assembly of β-barrel proteins in vitro by characterizing the interaction of BamD with an unfolded substrate protein. This peptide is a fragment of the substrate protein and contains a conserved amino acid sequence. We have demonstrated that mutations of this sequence in the full-length substrate protein impair the protein's assembly, implying that BamD's interaction with this sequence is an important part of the assembly mechanism. Finally, we have found that in vivo expression of a peptide containing this sequence causes growth defects and sensitizes Escherichia coli to antibiotics to which they are normally resistant. Therefore, inhibiting the binding of substrates to BamD is a viable strategy for developing new antibiotics directed against Gram-negative bacteria.
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Affiliation(s)
- Christine L Hagan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; and
| | - Joseph S Wzorek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; and
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138; and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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41
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Abstract
Outer membrane protein biogenesis is a fundamental and essential process in all Gram-negative bacteria. The key players conducting this process are organized in the β-barrel assembly machinery (BAM) complex. This complex has recently attracted a lot of attention due to its importance in cell wall generation, maintenance, and the fascinating yet partially unknown mechanism. The currently best studied example is the BAM complex from E. coli which comprises five proteins, BamA-BamE, two of which, BamA and BamD, are essential for cell survival. Four of the complex proteins, BamB-BamE, are lipoproteins and are attached to the outer membrane via N-terminal lipid anchors. Two of them, BamB and BamD, comprise protein folds known to mediate protein-protein interactions through WD40 and TPR domains, respectively. Structures of BamB to BamE have been determined using X-ray crystallography, NMR and SAXS techniques. Details on protein preparation, crystallization, data acquisition, and determination of structures are given here along with the brief summary of the currently available structural Bam protein repertoire.
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Affiliation(s)
- Kornelius Zeth
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.
- Ikerbasque, Basque Foundation of Science, Maria Diaz de Haro 3, Floor 6, Bilbao, 48013, Spain.
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42
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Expression and Purification of the Individual Bam Components BamB-E. Methods Mol Biol 2015; 1329:179-88. [PMID: 26427685 DOI: 10.1007/978-1-4939-2871-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BamB, BamC, BamD, and BamE are lipoproteins that, along with the integral membrane protein BamA, form the β-barrel assembly machinery (BAM) complex in the outer-membrane of Gram-negative bacteria. Elucidating the roles that these lipoproteins play in the β-barrel assembly process requires both structural and functional studies that rely on milligram quantities of pure protein. Here, we describe a simple protocol for expressing individual BamB-BamE proteins in Escherichia coli and purifying them by nickel affinity and size-exclusion chromatography. This protocol yields pure proteins in amounts that are sufficient for crystallization trials, in vitro protein-protein interaction studies, NMR, and other biochemical experiments.
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43
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Abstract
The outer membranes of gram-negative bacteria contain integral membrane proteins, most of which are of β-barrel structure, and critical for bacterial survival. These β-barrel proteins rely on the β-barrel assembly machinery (BAM) complex for their integration into the outer membrane as folded species. The central and essential subunit of the BAM complex, BamA, is a β-barrel protein conserved in all gram-negative bacteria and also found in eukaryotic organelles derived from bacterial endosymbionts. In Escherichia coli, BamA docks with four peripheral lipoproteins, BamB, BamC, BamD and BamE, partner subunits that add to the function of the BAM complex in outer membrane protein biogenesis. By way of introduction to this volume, we provide an overview of the work that has illuminated the mechanism by which the BAM complex drives β-barrel assembly. The protocols and methodologies associated with these studies as well as the challenges encountered and their elegant solutions are discussed in subsequent chapters.
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44
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Simmerman RF, Dave AM, Bruce BD. Structure and function of POTRA domains of Omp85/TPS superfamily. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 308:1-34. [PMID: 24411168 DOI: 10.1016/b978-0-12-800097-7.00001-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Omp85/TPS (outer-membrane protein of 85 kDa/two-partner secretion) superfamily is a ubiquitous and major class of β-barrel proteins. This superfamily is restricted to the outer membranes of gram-negative bacteria, mitochondria, and chloroplasts. The common architecture, with an N-terminus consisting of repeats of soluble polypeptide-transport-associated (POTRA) domains and a C-terminal β-barrel pore is highly conserved. The structures of multiple POTRA domains and one full-length TPS protein have been solved, yet discovering roles of individual POTRA domains has been difficult. This review focuses on similarities and differences between POTRA structures, emphasizing POTRA domains in autotrophic organisms including plants and cyanobacteria. Unique roles, specific for certain POTRA domains, are examined in the context of POTRA location with respect to their attachment to the β-barrel pore, and their degree of biological dispensability. Finally, because many POTRA domains may have the ability to interact with thousands of partner proteins, possible modes of these interactions are also explored.
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Affiliation(s)
- Richard F Simmerman
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA
| | - Ashita M Dave
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA
| | - Barry D Bruce
- Department of Biochemistry and Cellular and Molecular Biology, Knoxville, Tennessee, USA; Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.
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45
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McMorran LM, Brockwell DJ, Radford SE. Mechanistic studies of the biogenesis and folding of outer membrane proteins in vitro and in vivo: what have we learned to date? Arch Biochem Biophys 2014; 564:265-80. [PMID: 24613287 PMCID: PMC4262575 DOI: 10.1016/j.abb.2014.02.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/16/2014] [Accepted: 02/20/2014] [Indexed: 11/17/2022]
Abstract
Research into the mechanisms by which proteins fold into their native structures has been on-going since the work of Anfinsen in the 1960s. Since that time, the folding mechanisms of small, water-soluble proteins have been well characterised. By contrast, progress in understanding the biogenesis and folding mechanisms of integral membrane proteins has lagged significantly because of the need to create a membrane mimetic environment for folding studies in vitro and the difficulties in finding suitable conditions in which reversible folding can be achieved. Improved knowledge of the factors that promote membrane protein folding and disfavour aggregation now allows studies of folding into lipid bilayers in vitro to be performed. Consequently, mechanistic details and structural information about membrane protein folding are now emerging at an ever increasing pace. Using the panoply of methods developed for studies of the folding of water-soluble proteins. This review summarises current knowledge of the mechanisms of outer membrane protein biogenesis and folding into lipid bilayers in vivo and in vitro and discusses the experimental techniques utilised to gain this information. The emerging knowledge is beginning to allow comparisons to be made between the folding of membrane proteins with current understanding of the mechanisms of folding of water-soluble proteins.
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Affiliation(s)
- Lindsay M McMorran
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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46
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Jansen KB, Baker SL, Sousa MC. Crystal structure of BamB bound to a periplasmic domain fragment of BamA, the central component of the β-barrel assembly machine. J Biol Chem 2014; 290:2126-36. [PMID: 25468906 DOI: 10.1074/jbc.m114.584524] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The β-barrel assembly machinery (BAM) mediates folding and insertion of β-barrel outer membrane proteins (OMPs) into the outer membrane of Gram-negative bacteria. BAM is a five-protein complex consisting of the β-barrel OMP BamA and lipoproteins BamB, -C, -D, and -E. High resolution structures of all the individual BAM subunits and a BamD-BamC complex have been determined. However, the overall complex architecture remains elusive. BamA is the central component of BAM and consists of a membrane-embedded β-barrel and a periplasmic domain with five polypeptide translocation-associated (POTRA) motifs thought to interact with the accessory lipoproteins. Here we report the crystal structure of a fusion between BamB and a POTRA3-5 fragment of BamA. Extended loops 13 and 17 protruding from one end of the BamB β-propeller contact the face of the POTRA3 β-sheet in BamA. The interface is stabilized by several hydrophobic contacts, a network of hydrogen bonds, and a cation-π interaction between BamA Tyr-255 and BamB Arg-195. Disruption of BamA-BamB binding by BamA Y255A and probing of the interface by disulfide bond cross-linking validate the physiological relevance of the observed interface. Furthermore, the structure is consistent with previously published mutagenesis studies. The periplasmic five-POTRA domain of BamA is flexible in solution due to hinge motions in the POTRA2-3 linker. Modeling BamB in complex with full-length BamA shows BamB binding at the POTRA2-3 hinge, suggesting a role in modulation of BamA flexibility and the conformational changes associated with OMP folding and insertion.
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Affiliation(s)
- Katarina Bartoš Jansen
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - Susan Lynn Baker
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - Marcelo Carlos Sousa
- From the Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
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47
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Selkrig J, Leyton DL, Webb CT, Lithgow T. Assembly of β-barrel proteins into bacterial outer membranes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1542-50. [DOI: 10.1016/j.bbamcr.2013.10.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 12/30/2022]
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48
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Heinz E, Lithgow T. A comprehensive analysis of the Omp85/TpsB protein superfamily structural diversity, taxonomic occurrence, and evolution. Front Microbiol 2014; 5:370. [PMID: 25101071 PMCID: PMC4104836 DOI: 10.3389/fmicb.2014.00370] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 01/25/2023] Open
Abstract
Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins.
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Affiliation(s)
- Eva Heinz
- Department of Microbiology, Monash University Melbourne, VIC, Australia ; Victorian Bioinformatics Consortium, Monash University Melbourne, VIC, Australia
| | - Trevor Lithgow
- Department of Microbiology, Monash University Melbourne, VIC, Australia
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49
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Noinaj N, Kuszak AJ, Balusek C, Gumbart JC, Buchanan SK. Lateral opening and exit pore formation are required for BamA function. Structure 2014; 22:1055-62. [PMID: 24980798 DOI: 10.1016/j.str.2014.05.008] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/06/2014] [Accepted: 05/14/2014] [Indexed: 10/25/2022]
Abstract
The outer membrane of Gram-negative bacteria is replete with a host of β-barrel outer membrane proteins (OMPs). Despite serving a variety of essential functions, including immune response evasion, the exact mechanism of OMP folding and membrane insertion remains largely unclear. The β-barrel assembly machinery complex is required for OMP biogenesis. Crystal structures and molecular dynamics (MD) simulations of the central and essential component, BamA, suggest a mechanism involving lateral opening of its barrel domain. MD simulations reported here reveal an additional feature of BamA: a substrate exit pore positioned above the lateral opening site. Disulfide crosslinks that prevent lateral opening and exit pore formation result in a loss of BamA function, which can be fully rescued by the reductant tris(2-carboxyethyl)phosphine. These data provide strong evidence that lateral opening and exit pore formation are required for BamA function.
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Affiliation(s)
- Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam J Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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50
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Misra R, Stikeleather R, Gabriele R. In vivo roles of BamA, BamB and BamD in the biogenesis of BamA, a core protein of the β-barrel assembly machine of Escherichia coli. J Mol Biol 2014; 427:1061-74. [PMID: 24792419 DOI: 10.1016/j.jmb.2014.04.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/18/2014] [Accepted: 04/22/2014] [Indexed: 11/24/2022]
Abstract
Assembly of the β-barrel outer membrane proteins (OMPs) is an essential cellular process in Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes--two organelles of bacterial origin. Central to this process is the conserved β-barrel OMP that belongs to the Omp85 superfamily. In Escherichia coli, BamA is the core β-barrel OMP and, together with four outer membrane lipoproteins, BamBCDE, constitutes the β-barrel assembly machine (BAM). In this paper, we investigated the roles of BamD, an essential lipoprotein, and BamB in BamA biogenesis. Depletion of BamD caused impairment in BamA biogenesis and cessation of cell growth. These defects of BamD depletion were partly reversed by single-amino-acid substitutions mapping within the β-barrel domain of BamA. However, in the absence of BamB, the positive effects of the β-barrel substitutions on BamA biogenesis under BamD depletion conditions were nullified. By employing a BamA protein bearing one such substitution, F474L, it was demonstrated that the mutant BamA protein could not only assemble without BamD but also facilitate the assembly of wild-type BamA expressed in trans. Based on these data, we propose a model in which the Bam lipoproteins, which are localized to the outer membrane by the BAM-independent Lol pathway, aid in the creation of new BAM complexes by serving as outer membrane receptors and folding factors for nascent BamA molecules. The newly assembled BAM holocomplex then catalyzes the assembly of substrate OMPs and BamA. These in vivo findings are corroborated by recently published in vitro data.
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Affiliation(s)
- Rajeev Misra
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Ryan Stikeleather
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Rebecca Gabriele
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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