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Nishikawa H, Sawasato K, Mori S, Fujikawa K, Nomura K, Shimamoto K, Nishiyama KI. Interaction between glycolipid MPIase and proteinaceous factors during protein integration into the cytoplasmic membrane of E. coli. Front Mol Biosci 2022; 9:986602. [PMID: 36060260 PMCID: PMC9437254 DOI: 10.3389/fmolb.2022.986602] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Protein integration into biomembranes is an essential biological phenomenon common to all organisms. While various factors involved in protein integration, such as SRP, SecYEG and YidC, are proteinaceous, we identified a glycolipid named MPIase (Membrane Protein Integrase), which is present in the cytoplasmic membrane of E. coli. In vitro experiments using inverted membrane vesicles prepared from MPIase-depleted strains, and liposomes containing MPIase showed that MPIase is required for insertion of a subset of membrane proteins, which has been thought to be SecYEG-independent and YidC-dependent. Also, SecYEG-dependent substrate membrane proteins require MPIase in addition. Furthermore, MPIase is also essential for insertion of proteins with multiple negative charges, which requires both YidC and the proton motive force (PMF). MPIase directly interacts with SecYEG and YidC on the membrane. MPIase not only cooperates with these factors but also has a molecular chaperone-like function specific to the substrate membrane proteins through direct interaction with the glycan chain. Thus, MPIase catalyzes membrane insertion by accepting nascent membrane proteins on the membrane through its chaperone-like function, i.e., direct interaction with the substrate proteins, and then MPIase functionally interacts with SecYEG and YidC for substrate delivery, and acts with PMF to facilitate and complete membrane insertion when necessary. In this review, we will outline the mechanisms underlying membrane insertion catalyzed by MPIase, which cooperates with proteinaceous factors and PMF.
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Affiliation(s)
- Hanako Nishikawa
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Katsuhiro Sawasato
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Ken-Ichi Nishiyama
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
- *Correspondence: Ken-Ichi Nishiyama,
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2
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SecY-mediated quality control prevents the translocation of non-gated porins. Sci Rep 2020; 10:16347. [PMID: 33004891 PMCID: PMC7530735 DOI: 10.1038/s41598-020-73185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/09/2020] [Indexed: 01/24/2023] Open
Abstract
OmpC and OmpF are among the most abundant outer membrane proteins in E. coli and serve as hydrophilic channels to mediate uptake of small molecules including antibiotics. Influx selectivity is controlled by the so-called constriction zone or eyelet of the channel. Mutations in the loop domain forming the eyelet can disrupt transport selectivity and thereby interfere with bacterial viability. In this study we show that a highly conserved motif of five negatively charged amino acids in the eyelet, which is critical to regulate pore selectivity, is also required for SecY-mediated transport of OmpC and OmpF into the periplasm. Variants with a deleted or mutated motif were expressed in the cytosol and translocation was initiated. However, after signal peptide cleavage, import into the periplasm was aborted and the mutated proteins were redirected to the cytosol. Strikingly, reducing the proof-reading capacity of SecY by introducing the PrlA4 substitutions restored transport of OmpC with a mutated channel domain into the periplasm. Our study identified a SecY-mediated quality control pathway to restrict transport of outer membrane porin proteins with a deregulated channel activity into the periplasm.
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3
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Kamemoto Y, Funaba N, Kawakami M, Sawasato K, Kanno K, Suzuki S, Nishikawa H, Sato R, Nishiyama KI. Biosynthesis of glycolipid MPIase (membrane protein integrase) is independent of the genes for ECA (enterobacterial common antigen). J GEN APPL MICROBIOL 2020; 66:169-174. [DOI: 10.2323/jgam.2019.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yuki Kamemoto
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
| | - Nanaka Funaba
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
| | - Mayu Kawakami
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
| | | | - Kotoka Kanno
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
| | - Sonomi Suzuki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
| | - Hanako Nishikawa
- The United Graduate School of Agricultural Sciences, Iwate University
| | - Ryo Sato
- The United Graduate School of Agricultural Sciences, Iwate University
| | - Ken-ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University
- The United Graduate School of Agricultural Sciences, Iwate University
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4
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Jauss B, Petriman NA, Drepper F, Franz L, Sachelaru I, Welte T, Steinberg R, Warscheid B, Koch HG. Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli. J Biol Chem 2019; 294:19167-19183. [PMID: 31699901 DOI: 10.1074/jbc.ra119.010686] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The SecYEG translocon constitutes the major protein transport channel in bacteria and transfers an enormous variety of different secretory and inner-membrane proteins. The minimal core of the SecYEG translocon consists of three inner-membrane proteins, SecY, SecE, and SecG, which, together with appropriate targeting factors, are sufficient for protein transport in vitro However, in vivo the SecYEG translocon has been shown to associate with multiple partner proteins, likely allowing the SecYEG translocon to process its diverse substrates. To obtain a global view on SecYEG plasticity in Escherichia coli, here we performed a quantitative interaction proteomic analysis, which identified several known SecYEG-interacting proteins, verified the interaction of SecYEG with quality-control proteins, and revealed several previously unknown putative SecYEG-interacting proteins. Surprisingly, we found that the chaperone complex PpiD/YfgM is the most prominent interaction partner of SecYEG. Detailed analyses of the PpiD-SecY interaction by site-directed cross-linking revealed that PpiD and the established SecY partner protein YidC use almost completely-overlapping binding sites on SecY. Both PpiD and YidC contacted the lateral gate, the plug domain, and the periplasmic cavity of SecY. However, quantitative MS and cross-linking analyses revealed that despite having almost identical binding sites, their binding to SecY is noncompetitive. This observation suggests that the SecYEG translocon forms different substrate-independent subassemblies in which SecYEG either associates with YidC or with the PpiD/YfgM complex. In summary, the results of this study indicate that the PpiD/YfgM chaperone complex is a primary interaction partner of the SecYEG translocon.
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Affiliation(s)
- Benjamin Jauss
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Narcis-Adrian Petriman
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Lisa Franz
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ilie Sachelaru
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Thomas Welte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Bettina Warscheid
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Institute of Biology II, Biochemistry and Functional Proteomics, Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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5
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Kater L, Frieg B, Berninghausen O, Gohlke H, Beckmann R, Kedrov A. Partially inserted nascent chain unzips the lateral gate of the Sec translocon. EMBO Rep 2019; 20:e48191. [PMID: 31379073 PMCID: PMC6776908 DOI: 10.15252/embr.201948191] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/10/2019] [Accepted: 07/16/2019] [Indexed: 12/25/2022] Open
Abstract
The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
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Affiliation(s)
- Lukas Kater
- Gene Center MunichLudwig‐Maximilian‐UniversityMunichGermany
| | - Benedikt Frieg
- John von Neumann Institute for ComputingJülich Supercomputing CentreInstitute for Complex Systems ‐ Structural Biochemistry (ICS‐6)Forschungszentrum Jülich GmbHJülichGermany
| | | | - Holger Gohlke
- John von Neumann Institute for ComputingJülich Supercomputing CentreInstitute for Complex Systems ‐ Structural Biochemistry (ICS‐6)Forschungszentrum Jülich GmbHJülichGermany
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | | | - Alexej Kedrov
- Gene Center MunichLudwig‐Maximilian‐UniversityMunichGermany
- Synthetic Membrane SystemsInstitute for BiochemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
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6
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Sawasato K, Suzuki S, Nishiyama KI. Increased expression of the bacterial glycolipid MPIase is required for efficient protein translocation across membranes in cold conditions. J Biol Chem 2019; 294:8403-8411. [PMID: 30936205 DOI: 10.1074/jbc.ra119.008457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
Protein integration into and translocation across biological membranes are vital events for organismal survival and are fundamentally conserved among many organisms. Membrane protein integrase (MPIase) is a glycolipid that drives membrane protein integration into the cytoplasmic membrane in Escherichia coli MPIase also stimulates protein translocation across the membrane, but how its expression is regulated is incompletely understood. In this study, we found that the expression level of MPIase significantly increases in the cold (<25 °C), whereas that of the SecYEG translocon does not. Using previously created gene-knockout E. coli strains, we also found that either the cdsA or ynbB gene, both encoding rate-limiting enzymes for MPIase biosynthesis, is responsible for the increase in the MPIase expression. Furthermore, using pulse-chase experiments and protein integration assays, we demonstrated that the increase in MPIase levels is important for efficient protein translocation, but not for protein integration. We conclude that MPIase expression is required to stimulate protein translocation in cold conditions and is controlled by cdsA and ynbB gene expression.
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Affiliation(s)
- Katsuhiro Sawasato
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Sonomi Suzuki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Ken-Ichi Nishiyama
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.
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7
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Sato R, Sawasato K, Nishiyama KI. YnbB is a CdsA paralogue dedicated to biosynthesis of glycolipid MPIase involved in membrane protein integration. Biochem Biophys Res Commun 2019; 510:636-642. [DOI: 10.1016/j.bbrc.2019.01.145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
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8
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Zheng J, Wang X, Li Q, Yuan S, Wei S, Tian X, Huang Y, Wang W, Yang H. Characterization of Five Molecular Markers for Pathotype Identification of the Clubroot Pathogen Plasmodiophora brassicae. PHYTOPATHOLOGY 2018; 108:1486-1492. [PMID: 29996697 DOI: 10.1094/phyto-11-17-0362-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Clubroot disease is an important disease on cruciferous crops caused by Plasmodiophora brassicae infections. The pathotypes have been classified based on the reactions of differential hosts. However, molecular markers of particular pathotypes for P. brassicae are limited. In this study, we found five genetic markers in association with different pathotypes. Different gene expression patterns among different pathotypes (P4, P7, P9, and P11) were assayed according to the transcriptome data. The assay indicated that molecular markers PBRA_007750 and PBRA_009348 could be used to distinguish P11 from P4, P7, and P9; PBRA_009348 and Novel342 could distinguish P9 from P4, P7, and P11; and PBRA_008439 and Novel342 could represent a kind of P4. Polymerase chain reaction cycles ranging from 25 to 30 were able to identify the predominant pathotype in general. Therefore, these molecular markers would be a valuable tool to identify and discriminate pathotypes in P. brassicae population.
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Affiliation(s)
- Jing Zheng
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Xuliang Wang
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Qian Li
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Shu Yuan
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Shiqing Wei
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Xiyu Tian
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Yun Huang
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Wenming Wang
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
| | - Hui Yang
- First, second, third, fifth, sixth, seventh, and ninth authors: College of Agronomy; fourth author: College of Resources; and eighth author: Rice Research Institute and Research Center for Major Crop Diseases, Sichuan Agricultural University Chengdu Campus, Chengdu 611130, China
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9
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Crane JM, Randall LL. The Sec System: Protein Export in Escherichia coli. EcoSal Plus 2017; 7:10.1128/ecosalplus.ESP-0002-2017. [PMID: 29165233 PMCID: PMC5807066 DOI: 10.1128/ecosalplus.esp-0002-2017] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/20/2022]
Abstract
In Escherichia coli, proteins found in the periplasm or the outer membrane are exported from the cytoplasm by the general secretory, Sec, system before they acquire stably folded structure. This dynamic process involves intricate interactions among cytoplasmic and membrane proteins, both peripheral and integral, as well as lipids. In vivo, both ATP hydrolysis and proton motive force are required. Here, we review the Sec system from the inception of the field through early 2016, including biochemical, genetic, and structural data.
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Affiliation(s)
- Jennine M. Crane
- Department of Biochemistry, University of Missouri, Columbia, Missouri
| | - Linda L. Randall
- Department of Biochemistry, University of Missouri, Columbia, Missouri
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10
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Cui P, Li X, Zhu M, Wang B, Liu J, Chen H. Design, synthesis and antibacterial activities of thiouracil derivatives containing acyl thiourea as SecA inhibitors. Bioorg Med Chem Lett 2017; 27:2234-2237. [DOI: 10.1016/j.bmcl.2016.11.060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/11/2016] [Accepted: 11/22/2016] [Indexed: 12/28/2022]
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11
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Cui P, Li X, Zhu M, Wang B, Liu J, Chen H. Design, synthesis and antimicrobial activities of thiouracil derivatives containing triazolo-thiadiazole as SecA inhibitors. Eur J Med Chem 2016; 127:159-165. [PMID: 28039774 DOI: 10.1016/j.ejmech.2016.12.053] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 11/28/2022]
Abstract
A series of novel thiouracil derivatives containing a triazolo-thiadiazole moiety (7a-7l) have been synthesized by structural modifications on a lead SecA inhibitor, 2. All the compounds have been evaluated for their antibacterial activities against Bacillus amyloliquefaciens, Staphylococcus aureus, and Bacillus subtilis. Compounds 7d and 7g were also tested for their inhibitory activities against SecA ATPase due to their promising antimicrobial activities. The inhibitory activity of compound 7d was found to be higher than that of 2. Molecular docking work suggests that compound 7d might bind at a pocket close to the ATPase ATP-binding domain.
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Affiliation(s)
- Penglei Cui
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China; College of Science, Agricultural University of Hebei, Baoding 071001, China
| | - Xiaoliu Li
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
| | - Mengyuan Zhu
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Jing Liu
- College of Veterinary Medicine, Agricultural University of Hebei, Baoding 071001, China
| | - Hua Chen
- Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China.
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12
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Nishiyama KI, Tokuda H. Novel translocation intermediate allows re-evaluation of roles of ATP, proton motive force and SecG at the late stage of preprotein translocation. Genes Cells 2016; 21:1353-1364. [PMID: 27813233 DOI: 10.1111/gtc.12447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/05/2016] [Indexed: 11/30/2022]
Abstract
Presecretory proteins such as pOmpA are translocated across the inner membrane of Escherichia coli by Sec translocase powered by ATP and proton motive force (PMF). Translocation activity has been determined by protease protection assaying in vitro. We identified a new translocation intermediate at a late stage, which was protected by proteinase K (PK), but became PK sensitive upon urea extraction. At a late stage of pOmpA translocation driven by PMF in the presence of a nonhydrolyzable ATP analogue, the PK-protected materials arose, but were pulled back upon urea extraction, indicating that completion of translocation requires ATP hydrolysis. When inverted membrane vesicles prepared from secG-null strain (ΔSecG IMV) were used in the absence of PMF, the translocation intermediate was accumulated. When the ATP concentration was low in the absence of PMF, the translocation intermediate was also accumulated. Imposition of PMF in the presence of a low ATP concentration caused recovery of pOmpA translocation and resistance to urea extraction for SecG+ IMV, but not for ΔSecG IMV. Thus, analysis of the late translocation intermediate showed that two of three constituents, physiological concentration of ATP, PMF and SecG, are required for the catalytic cycle of preprotein translocation, that is, completion and subsequent initiation of translocation.
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Affiliation(s)
- Ken-Ichi Nishiyama
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan.,Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan
| | - Hajime Tokuda
- Faculty of Nutritional Sciences, The University of Morioka, Takizawa, 020-0694, Japan
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13
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De Marothy MT, Elofsson A. Marginally hydrophobic transmembrane α-helices shaping membrane protein folding. Protein Sci 2015; 24:1057-74. [PMID: 25970811 DOI: 10.1002/pro.2698] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/24/2015] [Indexed: 01/12/2023]
Abstract
Cells have developed an incredible machinery to facilitate the insertion of membrane proteins into the membrane. While we have a fairly good understanding of the mechanism and determinants of membrane integration, more data is needed to understand the insertion of membrane proteins with more complex insertion and folding pathways. This review will focus on marginally hydrophobic transmembrane helices and their influence on membrane protein folding. These weakly hydrophobic transmembrane segments are by themselves not recognized by the translocon and therefore rely on local sequence context for membrane integration. How can such segments reside within the membrane? We will discuss this in the light of features found in the protein itself as well as the environment it resides in. Several characteristics in proteins have been described to influence the insertion of marginally hydrophobic helices. Additionally, the influence of biological membranes is significant. To begin with, the actual cost for having polar groups within the membrane may not be as high as expected; the presence of proteins in the membrane as well as characteristics of some amino acids may enable a transmembrane helix to harbor a charged residue. The lipid environment has also been shown to directly influence the topology as well as membrane boundaries of transmembrane helices-implying a dynamic relationship between membrane proteins and their environment.
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Affiliation(s)
- Minttu T De Marothy
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
| | - Arne Elofsson
- Department of Biochemistry and Biophysics Science for Life Laboratory, Stockholm University, Solna, SE-171 21, Sweden
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14
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Bogdanov M, Dowhan W, Vitrac H. Lipids and topological rules governing membrane protein assembly. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1843:1475-88. [PMID: 24341994 PMCID: PMC4057987 DOI: 10.1016/j.bbamcr.2013.12.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/08/2013] [Indexed: 10/25/2022]
Abstract
Membrane protein folding and topogenesis are tuned to a given lipid profile since lipids and proteins have co-evolved to follow a set of interdependent rules governing final protein topological organization. Transmembrane domain (TMD) topology is determined via a dynamic process in which topogenic signals in the nascent protein are recognized and interpreted initially by the translocon followed by a given lipid profile in accordance with the Positive Inside Rule. The net zero charged phospholipid phosphatidylethanolamine and other neutral lipids dampen the translocation potential of negatively charged residues in favor of the cytoplasmic retention potential of positively charged residues (Charge Balance Rule). This explains why positively charged residues are more potent topological signals than negatively charged residues. Dynamic changes in orientation of TMDs during or after membrane insertion are attributed to non-sequential cooperative and collective lipid-protein charge interactions as well as long-term interactions within a protein. The proportion of dual topological conformers of a membrane protein varies in a dose responsive manner with changes in the membrane lipid composition not only in vivo but also in vitro and therefore is determined by the membrane lipid composition. Switching between two opposite TMD topologies can occur in either direction in vivo and also in liposomes (designated as fliposomes) independent of any other cellular factors. Such lipid-dependent post-insertional reversibility of TMD orientation indicates a thermodynamically driven process that can occur at any time and in any cell membrane driven by changes in the lipid composition. This dynamic view of protein topological organization influenced by the lipid environment reveals previously unrecognized possibilities for cellular regulation and understanding of disease states resulting from mis-folded proteins. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Mikhail Bogdanov
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA.
| | - Heidi Vitrac
- Department of Biochemistry and Molecular Biology, University of Texas Medical School-Houston, Houston, TX 77030, USA
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Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Kudva R, Denks K, Kuhn P, Vogt A, Müller M, Koch HG. Protein translocation across the inner membrane of Gram-negative bacteria: the Sec and Tat dependent protein transport pathways. Res Microbiol 2013; 164:505-34. [DOI: 10.1016/j.resmic.2013.03.016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/11/2013] [Indexed: 11/28/2022]
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Glycolipozyme MPIase is essential for topology inversion of SecG during preprotein translocation. Proc Natl Acad Sci U S A 2013; 110:9734-9. [PMID: 23716687 DOI: 10.1073/pnas.1303160110] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Presecretory proteins are translocated across biological membranes through protein-conducting channels such as Sec61 (eukaryotes) and SecYEG (bacteria). SecA, a translocation ATPase, pushes preproteins out with dynamic structural changes through SecYEG. SecG, a subunit of the SecYEG channel possessing two transmembrane stretches (TMs), undergoes topology inversion coupled with SecA-dependent translocation. Recently, we characterized membrane protein integrase (MPIase), a glycolipozyme involved in not only protein integration into membranes but also preprotein translocation. We report here that SecG inversion occurs only when MPIase associates with SecYEG. We also found that MPIase modulates the dimer orientation of SecYEG. Cysteine-scanning mutagenesis mapped SecG TM 2 to a relatively hydrophilic environment. The dimer formation of SecG, crosslinked at TM 2, was not observed on SecG inversion, indicating that SecYEG undergoes a dynamic structural change during preprotein translocation.
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Lycklama A Nijeholt JA, Driessen AJM. The bacterial Sec-translocase: structure and mechanism. Philos Trans R Soc Lond B Biol Sci 2012; 367:1016-28. [PMID: 22411975 DOI: 10.1098/rstb.2011.0201] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Most bacterial secretory proteins pass across the cytoplasmic membrane via the translocase, which consists of a protein-conducting channel SecYEG and an ATP-dependent motor protein SecA. The ancillary SecDF membrane protein complex promotes the final stages of translocation. Recent years have seen a major advance in our understanding of the structural and biochemical basis of protein translocation, and this has led to a detailed model of the translocation mechanism.
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Affiliation(s)
- Jelger A Lycklama A Nijeholt
- Department of Molecular Microbiology, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands.
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Morita K, Tokuda H, Nishiyama KI. Multiple SecA molecules drive protein translocation across a single translocon with SecG inversion. J Biol Chem 2011; 287:455-464. [PMID: 22074917 DOI: 10.1074/jbc.m111.301754] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SecA is a translocation ATPase that drives protein translocation. D209N SecA, a dominant-negative mutant, binds ATP but is unable to hydrolyze it. This mutant was inactive to proOmpA translocation. However, it generated a translocation intermediate of 18 kDa. Further addition of wild-type SecA caused its translocation into either mature OmpA or another intermediate of 28 kDa that can be translocated into mature by a proton motive force. The addition of excess D209N SecA during translocation caused a topology inversion of SecG. Moreover, an intermediate of SecG inversion was identified when wild-type and D209N SecA were used in the same amounts. These results indicate that multiple SecA molecules drive translocation across a single translocon with SecG inversion. Here, we propose a revised model of proOmpA translocation in which a single catalytic cycle of SecA causes translocation of 10-13 kDa with ATP binding and hydrolysis, and SecG inversion is required when the next SecA cycle begins with additional ATP hydrolysis.
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Affiliation(s)
- Kazuhiro Morita
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hajime Tokuda
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ken-Ichi Nishiyama
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.
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Nishiyama KI, Tokuda H. Preparation of a highly translocation-competent proOmpA/SecB complex. Protein Sci 2011; 19:2402-8. [PMID: 20945359 DOI: 10.1002/pro.520] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Methods for reproducibly preparing highly translocation-competent proOmpA were developed. Only a competent form of proOmpA was sorted out from incompetent one using SecB, a translocation-dedicated chaperone, as a probe. Trypsin digestion revealed that the incompetent form of proOmpA was partially folded at its N-terminus, consistent with the jamming of proOmpA within translocon. Although the incompetent form of proOmpA was not active as to topology inversion of SecG, the isolated proOmpA/SecB complex had recovered the ability of SecG inversion. These results let us prepare a proOmpA/SecB complex both in vivo and in vitro that is highly translocation-competent. E. coli cells harboring a plasmid, in which ompA and secB were encoded as a synthetic operon, accumulated the proOmpA/SecB complex in the cytosol. The complex, purified by means of a His tag attached to SecB, was found to be translocation-competent as revealed by the occurrence of SecG inversion, although the signal peptide of proOmpA was sensitive to proteolytic digestion. ProOmpA, in vitro synthesized by means of a continuous exchange cell free system in the presence of SecB-His, was purified as a complex with SecB, which was active as to SecG inversion as well.
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Affiliation(s)
- Ken-Ichi Nishiyama
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.
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Das S, Oliver DB. Mapping of the SecA·SecY and SecA·SecG interfaces by site-directed in vivo photocross-linking. J Biol Chem 2011; 286:12371-80. [PMID: 21317284 DOI: 10.1074/jbc.m110.182931] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The two major components of the Eubacteria Sec-dependent protein translocation system are the heterotrimeric channel-forming component SecYEG and its binding partner, the SecA ATPase nanomotor. Once bound to SecYEG, the preprotein substrate, and ATP, SecA undergoes ATP-hydrolytic cycles that drive the stepwise translocation of proteins. Although a previous site-directed in vivo photocross-linking study (Mori, H., and Ito, K. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 16159-16164) elucidated residues of SecY needed for interaction with SecA, no reciprocal study for SecA protein has been reported to date. In the present study we mapped residues of SecA that interact with SecY or SecG utilizing this approach. Our results show that distinct domains of SecA on two halves of the molecule interact with two corresponding SecY partners as well as with the central cytoplasmic domain of SecG. Our data support the in vivo relevance of the Thermotoga maritima SecA·SecYEG crystal structure that visualized SecYEG interaction for only one-half of SecA as well as previous studies indicating that SecA normally binds two molecules of SecYEG.
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Affiliation(s)
- Sanchaita Das
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06457, USA
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22
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Synthetic effects of secG and secY2 mutations on exoproteome biogenesis in Staphylococcus aureus. J Bacteriol 2010; 192:3788-800. [PMID: 20472795 DOI: 10.1128/jb.01452-09] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gram-positive pathogen Staphylococcus aureus secretes various proteins into its extracellular milieu. Bioinformatics analyses have indicated that most of these proteins are directed to the canonical Sec pathway, which consists of the translocation motor SecA and a membrane-embedded channel composed of the SecY, SecE, and SecG proteins. In addition, S. aureus contains an accessory Sec2 pathway involving the SecA2 and SecY2 proteins. Here, we have addressed the roles of the nonessential channel components SecG and SecY2 in the biogenesis of the extracellular proteome of S. aureus. The results show that SecG is of major importance for protein secretion by S. aureus. Specifically, the extracellular accumulation of nine abundant exoproteins and seven cell wall-bound proteins was significantly affected in an secG mutant. No secretion defects were detected for strains with a secY2 single mutation. However, deletion of secY2 exacerbated the secretion defects of secG mutants, affecting the extracellular accumulation of one additional exoprotein and one cell wall protein. Furthermore, an secG secY2 double mutant displayed a synthetic growth defect. This might relate to a slightly elevated expression of sraP, encoding the only known substrate for the Sec2 pathway, in cells lacking SecG. Additionally, the results suggest that SecY2 can interact with the Sec1 channel, which would be consistent with the presence of a single set of secE and secG genes in S. aureus.
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Nishiyama KI, Tokuda H. Development of a functional in vitro integration system for an integral membrane protein, SecG. Biochem Biophys Res Commun 2009; 390:920-4. [PMID: 19853580 DOI: 10.1016/j.bbrc.2009.10.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
Abstract
A functional in vitro integration system for an integral membrane protein, SecG, comprising an efficient translation system supplemented with inverted membrane vesicles (IMV) was developed. When SecG was synthesized in the presence of IMV prepared from a DeltasecG strain (DeltaSecG IMV), the synthesized SecG was recovered with the IMV. A population of SecG was resistant to urea extraction, indicating that the synthesized SecG was integrated into DeltaSecG IMV. Addition of signal recognition particle and its receptor (SRP) and SecA caused an increase in the amount of the urea-resistant form of SecG. When IMV into which SecG had been integrated were subjected to the translocation assay, the translocation activity was found to be significantly stimulated compared with for DeltaSecG IMV. Moreover, when SRP and SecA had been supplemented, the translocation activity nearly recovered to the level in IMV prepared from the wild type strain. These results indicate that the in vitro synthesized SecG could be functionally integrated into DeltaSecG IMV with the help of SRP and SecA. We also present evidence that the membrane targeting and integration of SecG is stimulated by externally added SecA and SecG itself.
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Affiliation(s)
- Ken-ichi Nishiyama
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.
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Abstract
The topology of polytopic membrane proteins is determined by topogenic sequences in the protein, protein-translocon interactions, and interactions during folding within the protein and between the protein and the lipid environment. Orientation of transmembrane domains is dependent on membrane phospholipid composition during initial assembly as well as on changes in lipid composition postassembly. The membrane translocation potential of negative amino acids working in opposition to the positive-inside rule is largely dampened by the normal presence of phosphatidylethanolamine, thus explaining the dominance of positive residues as retention signals. Phosphatidylethanolamine provides the appropriate charge density that permits the membrane surface to maintain a charge balance between membrane translocation and retention signals and also allows the presence of negative residues in the cytoplasmic face of proteins for other purposes.
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Affiliation(s)
- William Dowhan
- Department of Biochemistry and Molecular Biology, University of Texas-Houston Medical School, Houston, TX 77030, USA.
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Yusa F, Steiner JM, Löffelhardt W. Evolutionary conservation of dual Sec translocases in the cyanelles of Cyanophora paradoxa. BMC Evol Biol 2008; 8:304. [PMID: 18976493 PMCID: PMC2600650 DOI: 10.1186/1471-2148-8-304] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 11/01/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanelles, the peptidoglycan-armored plastids of glaucocystophytes, occupy a unique bridge position in between free-living cyanobacteria and chloroplasts. In some respects they side with cyanobacteria whereas other features are clearly shared with chloroplasts. The Sec translocase, an example for "conservative sorting" in the course of evolution, is found in the plasma membrane of all prokaryotes, in the thylakoid membrane of chloroplasts and in both these membrane types of cyanobacteria. RESULTS In this paper we present evidence for a dual location of the Sec translocon in the thylakoid as well as inner envelope membranes of the cyanelles from Cyanophora paradoxa, i. e. conservative sorting sensu stricto. The prerequisite was the generation of specific antisera directed against cyanelle SecY that allowed immunodetection of the protein on SDS gels from both membrane types separated by sucrose density gradient floatation centrifugation. Immunoblotting of blue-native gels yielded positive but differential results for both the thylakoid and envelope Sec complexes, respectively. In addition, heterologous antisera directed against components of the Toc/Tic translocons and binding of a labeled precursor protein were used to discriminate between inner and outer envelope membranes. CONCLUSION The envelope translocase can be envisaged as a prokaryotic feature missing in higher plant chloroplasts but retained in cyanelles, likely for protein transport to the periplasm. Candidate passengers are cytochrome c6 and enzymes of peptidoglycan metabolism. The minimal set of subunits of the Toc/Tic translocase of a primitive plastid is proposed.
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Affiliation(s)
- Fumie Yusa
- SLT, Nagahama-city, Shiga-ken 526-0829, Japan.
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Gatsos X, Perry AJ, Anwari K, Dolezal P, Wolynec PP, Likić VA, Purcell AW, Buchanan SK, Lithgow T. Protein secretion and outer membrane assembly in Alphaproteobacteria. FEMS Microbiol Rev 2008; 32:995-1009. [PMID: 18759741 PMCID: PMC2635482 DOI: 10.1111/j.1574-6976.2008.00130.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/18/2008] [Indexed: 11/17/2022] Open
Abstract
The assembly of beta-barrel proteins into membranes is a fundamental process that is essential in Gram-negative bacteria, mitochondria and plastids. Our understanding of the mechanism of beta-barrel assembly is progressing from studies carried out in Escherichia coli and Neisseria meningitidis. Comparative sequence analysis suggests that while many components mediating beta-barrel protein assembly are conserved in all groups of bacteria with outer membranes, some components are notably absent. The Alphaproteobacteria in particular seem prone to gene loss and show the presence or absence of specific components mediating the assembly of beta-barrels: some components of the pathway appear to be missing from whole groups of bacteria (e.g. Skp, YfgL and NlpB), other proteins are conserved but are missing characteristic domains (e.g. SurA). This comparative analysis is also revealing important structural signatures that are vague unless multiple members from a protein family are considered as a group (e.g. tetratricopeptide repeat (TPR) motifs in YfiO, beta-propeller signatures in YfgL). Given that the process of the beta-barrel assembly is conserved, analysis of outer membrane biogenesis in Alphaproteobacteria, the bacterial group that gave rise to mitochondria, also promises insight into the assembly of beta-barrel proteins in eukaryotes.
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Affiliation(s)
- Xenia Gatsos
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Andrew J Perry
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Khatira Anwari
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Pavel Dolezal
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - P Peter Wolynec
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Vladimir A Likić
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Trevor Lithgow
- Department of Biochemistry and Molecular Biology, University of MelbourneMelbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneMelbourne, Australia
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