1
|
Mori S, Nomura K, Fujikawa K, Osawa T, Shionyu M, Yoda T, Shirai T, Tsuda S, Yoshizawa-Kumagaye K, Masuda S, Nishio H, Yoshiya T, Suzuki S, Muramoto M, Nishiyama KI, Shimamoto K. Intermolecular Interactions between a Membrane Protein and a Glycolipid Essential for Membrane Protein Integration. ACS Chem Biol 2022; 17:609-618. [PMID: 35239308 DOI: 10.1021/acschembio.1c00882] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inducing newly synthesized proteins to appropriate locations is an indispensable biological function in every organism. Integration of proteins into biomembranes in Escherichia coli is mediated by proteinaceous factors, such as Sec translocons and an insertase YidC. Additionally, a glycolipid named MPIase (membrane protein integrase), composed of a long sugar chain and pyrophospholipid, was proven essential for membrane protein integration. We reported that a synthesized minimal unit of MPIase possessing only one trisaccharide, mini-MPIase-3, involves an essential structure for the integration activity. Here, to elucidate integration mechanisms using MPIase, we analyzed intermolecular interactions of MPIase or its synthetic analogs with a model substrate, the Pf3 coat protein, using physicochemical methods. Surface plasmon resonance (SPR) analyses revealed the importance of a pyrophosphate for affinity to the Pf3 coat protein. Compared with mini-MPIase-3, natural MPIase showed faster association and dissociation due to its long sugar chain despite the slight difference in affinity. To focus on more detailed MPIase substructures, we performed docking simulations and saturation transfer difference-nuclear magnetic resonance. These experiments yielded that the 6-O-acetyl group on glucosamine and the phosphate of MPIase play important roles leading to interactions with the Pf3 coat protein. The high affinity of MPIase to the hydrophobic region and the basic amino acid residues of the protein was suggested by docking simulations and proven experimentally by SPR using protein mutants devoid of target regions. These results demonstrated the direct interactions of MPIase with a substrate protein and revealed detailed mechanisms of membrane protein integration.
Collapse
Affiliation(s)
- Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Tsukiho Osawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Masafumi Shionyu
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Takao Yoda
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Shugo Tsuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Kumiko Yoshizawa-Kumagaye
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Shun Masuda
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Hideki Nishio
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Taku Yoshiya
- Peptide Institute, Inc., 7-2-9 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan
| | - Sonomi Suzuki
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Maki Muramoto
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Ken-ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| |
Collapse
|
2
|
Fujikawa K, Mori S, Nishiyama KI, Shimamoto K. A bacterial glycolipid essential for membrane protein integration. Adv Carbohydr Chem Biochem 2022; 81:95-129. [DOI: 10.1016/bs.accb.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
3
|
Endo Y, Shimizu Y, Nishikawa H, Sawasato K, Nishiyama KI. Interplay between MPIase, YidC, and PMF during Sec-independent insertion of membrane proteins. Life Sci Alliance 2021; 5:5/1/e202101162. [PMID: 34642230 PMCID: PMC8548208 DOI: 10.26508/lsa.202101162] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/24/2022] Open
Abstract
Charges in the N-terminal region and the synthesis level of membrane proteins with N-out topology determine YidC and PMF dependencies with the interplay between glycolipid MPIase, YidC, and PMF. Integral membrane proteins with the N-out topology are inserted into membranes usually in YidC- and PMF-dependent manners. The molecular basis of the various dependencies on insertion factors is not fully understood. A model protein, Pf3-Lep, is inserted independently of both YidC and PMF, whereas the V15D mutant requires both YidC and PMF in vivo. We analyzed the mechanisms that determine the insertion factor dependency in vitro. Glycolipid MPIase was required for insertion of both proteins because MPIase depletion caused a significant defect in insertion. On the other hand, YidC depletion and PMF dissipation had no effects on Pf3-Lep insertion, whereas V15D insertion was reduced. We reconstituted (proteo)liposomes containing MPIase, YidC, and/or F0F1-ATPase. MPIase was essential for insertion of both proteins. YidC and PMF stimulated Pf3-Lep insertion as the synthesis level increased. V15D insertion was stimulated by both YidC and PMF irrespective of the synthesis level. These results indicate that charges in the N-terminal region and the synthesis level are the determinants of YidC and PMF dependencies with the interplay between MPIase, YidC, and PMF.
Collapse
Affiliation(s)
- Yuta Endo
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Yuko Shimizu
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - 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
| | - Ken-Ichi Nishiyama
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan .,Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| |
Collapse
|
4
|
Sekiya Y, Sawasato K, Nishiyama KI. Expression of Cds4/5 of Arabidopsis chloroplasts in E. coli reveals the membrane topology of the C-terminal region of CDP-diacylglycerol synthases. Genes Cells 2021; 26:727-738. [PMID: 34166546 DOI: 10.1111/gtc.12880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
CDP-diacylglycerol synthases (Cds) are conserved from bacteria to eukaryotes. Bacterial CdsA is involved not only in phospholipid biosynthesis but also in biosynthesis of glycolipid MPIase, an essential glycolipid that catalyzes membrane protein integration. We found that both Cds4 and Cds5 of Arabidopsis chloroplasts complement cdsA knockout by supporting both phospholipid and MPIase biosyntheses. Comparison of the sequences of CdsA and Cds4/5 suggests a difference in membrane topology at the C-termini, since the region assigned as the last transmembrane region of CdsA, which follows the conserved cytoplasmic domain, is missing in Cds4/5. Deletion of the C-terminal region abolished the function, indicating the importance of the region. Both 6 × His tag attachment to CdsA and substitution of the C-terminal 6 residues with 6 × His did not affect the function. These 6 × His tags were sensitive to protease added from the cytosolic side in vitro, indicating that this region is not a transmembrane one but forms a membrane-embedded reentrant loop. Thus, the C-terminal region of Cds homologues forms a reentrant loop, of which structure is important for the Cds function.
Collapse
Affiliation(s)
- Yusei Sekiya
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Katsuhiro Sawasato
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ken-Ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| |
Collapse
|
5
|
Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
Collapse
Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| |
Collapse
|
6
|
Nishikawa H, Kanno K, Endo Y, Nishiyama KI. Ring assembly of c subunits of F 0 F 1 -ATP synthase in Propionigenium modestum requires YidC and UncI following MPIase-dependent membrane insertion. FEBS Lett 2021; 595:647-654. [PMID: 33423295 DOI: 10.1002/1873-3468.14036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/20/2020] [Accepted: 12/31/2020] [Indexed: 01/25/2023]
Abstract
The c subunits of F0 F1 -ATP synthase (F0 c) assemble into a ring structure, following membrane insertion that is dependent on both glycolipid MPIase and protein YidC. We analyzed the insertion and assembly processes of Propionigenium modestum F0 c (Pm-F0 c), of which the ring structure is resistant to SDS. Ring assembly of Pm-F0 c requires P. modestum UncI (Pm-UncI). Ring assembly of in vitro synthesized Pm-F0 c was observed when both YidC and Pm-UncI were reconstituted into liposomes of Escherichia coli phospholipids. Under the physiological conditions where spontaneous insertion had been blocked by diacylglycerol, MPIase was necessary for Pm-F0 c insertion allowing the subsequent YidC/Pm-UncI-dependent ring assembly. Thus, we have succeeded in the complete reconstitution of membrane insertion and subsequent ring assembly of Pm-F0 c.
Collapse
Affiliation(s)
- Hanako Nishikawa
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Kotoka Kanno
- Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yuta Endo
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Ken-Ichi Nishiyama
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan.,Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Japan
| |
Collapse
|
7
|
Cardiolipin is required in vivo for the stability of bacterial translocon and optimal membrane protein translocation and insertion. Sci Rep 2020; 10:6296. [PMID: 32286407 PMCID: PMC7156725 DOI: 10.1038/s41598-020-63280-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/25/2020] [Indexed: 01/05/2023] Open
Abstract
Translocation of preproteins across the Escherichia coli inner membrane requires anionic lipids by virtue of their negative head-group charge either in vivo or in situ. However, available results do not differentiate between the roles of monoanionic phosphatidylglycerol and dianionic cardiolipin (CL) in this essential membrane-related process. To define in vivo the molecular steps affected by the absence of CL in protein translocation and insertion, we analyzed translocon activity, SecYEG stability and its interaction with SecA in an E. coli mutant devoid of CL. Although no growth defects were observed, co- and post-translational translocation of α-helical proteins across inner membrane and the assembly of outer membrane β-barrel precursors were severely compromised in CL-lacking cells. Components of proton-motive force which could impair protein insertion into and translocation across the inner membrane, were unaffected. However, stability of the dimeric SecYEG complex and oligomerization properties of SecA were strongly compromised while the levels of individual SecYEG translocon components, SecA and insertase YidC were largely unaffected. These results demonstrate that CL is required in vivo for the stability of the bacterial translocon and its efficient function in co-translational insertion into and translocation across the inner membrane of E. coli.
Collapse
|
8
|
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
| |
Collapse
|
9
|
Fujikawa K, Nomura K, Nishiyama KI, Shimamoto K. Novel Glycolipid Involved in Membrane Protein Integration: Structure and Mode of Action. J SYN ORG CHEM JPN 2019. [DOI: 10.5059/yukigoseikyokaishi.77.1096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences
| | - Ken-ichi Nishiyama
- Department of Biological Chemistry, Faculty of Agriculture, Iwate University
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences
| |
Collapse
|
10
|
Sasaki M, Nishikawa H, Suzuki S, Moser M, Huber M, Sawasato K, Matsubayashi HT, Kumazaki K, Tsukazaki T, Kuruma Y, Nureki O, Ueda T, Nishiyama KI. The bacterial protein YidC accelerates MPIase-dependent integration of membrane proteins. J Biol Chem 2019; 294:18898-18908. [PMID: 31662434 DOI: 10.1074/jbc.ra119.011248] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/25/2019] [Indexed: 01/06/2023] Open
Abstract
Bacterial membrane proteins are integrated into membranes through the concerted activities of a series of integration factors, including membrane protein integrase (MPIase). However, how MPIase activity is complemented by other integration factors during membrane protein integration is incompletely understood. Here, using inverted inner-membrane vesicle and reconstituted (proteo)liposome preparations from Escherichia coli cells, along with membrane protein integration assays and the PURE system to produce membrane proteins, we found that anti-MPIase IgG inhibits the integration of both the Sec-independent substrate 3L-Pf3 coat and the Sec-dependent substrate MtlA into E. coli membrane vesicles. MPIase-depleted membrane vesicles lacked both 3L-Pf3 coat and MtlA integration, indicating that MPIase is involved in the integration of both proteins. We developed a reconstitution system in which disordered spontaneous integration was precluded, which revealed that SecYEG, YidC, or both, are not sufficient for Sec-dependent and -independent integration. Although YidC had no effect on MPIase-dependent integration of Sec-independent substrates in the conventional assay system, YidC significantly accelerated the integration when the substrate amounts were increased in our PURE system-based assay. Similar acceleration by YidC was observed for MtlA integration. YidC mutants with amino acid substitutions in the hydrophilic cavity inside the membrane were defective in the acceleration of the Sec-independent integration. Of note, MPIase was up-regulated upon YidC depletion. These results indicate that YidC accelerates the MPIase-dependent integration of membrane proteins, suggesting that MPIase and YidC function sequentially and cooperatively during the catalytic cycle of membrane protein integration.
Collapse
Affiliation(s)
- Masaru Sasaki
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hanako Nishikawa
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Sonomi Suzuki
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Michael Moser
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Maria Huber
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Katsuhiro Sawasato
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hideaki T Matsubayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kaoru Kumazaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | | | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Ken-Ichi Nishiyama
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan; Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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]
|
13
|
Sawasato K, Sato R, Nishikawa H, Iimura N, Kamemoto Y, Fujikawa K, Yamaguchi T, Kuruma Y, Tamura Y, Endo T, Ueda T, Shimamoto K, Nishiyama KI. CdsA is involved in biosynthesis of glycolipid MPIase essential for membrane protein integration in vivo. Sci Rep 2019; 9:1372. [PMID: 30718729 PMCID: PMC6362211 DOI: 10.1038/s41598-018-37809-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 12/07/2018] [Indexed: 11/17/2022] Open
Abstract
MPIase is a glycolipid that is involved in membrane protein integration. Despite evaluation of its functions in vitro, the lack of information on MPIase biosynthesis hampered verification of its involvement in vivo. In this study, we found that depletion of CdsA, a CDP-diacylglycerol synthase, caused not only a defect in phospholipid biosynthesis but also MPIase depletion with accumulation of the precursors of both membrane protein M13 coat protein and secretory protein OmpA. Yeast Tam41p, a mitochondrial CDP-diacylglycerol synthase, suppressed the defect in phospholipid biosynthesis, but restored neither MPIase biosynthesis, precursor processing, nor cell growth, indicating that MPIase is essential for membrane protein integration and therefore for cell growth. Consistently, we observed a severe defect in protein integration into MPIase-depleted membrane vesicles in vitro. Thus, the function of MPIase as a factor involved in protein integration was proven in vivo as well as in vitro. Moreover, Cds1p, a eukaryotic CdsA homologue, showed a potential for MPIase biosynthesis. From these results, we speculate the presence of a eukaryotic MPIase homologue.
Collapse
Affiliation(s)
- Katsuhiro Sawasato
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Ryo Sato
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Hanako Nishikawa
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Naoki Iimura
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Yuki Kamemoto
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Kyoto, 619-0284, Japan
| | - Toshiyuki Yamaguchi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Kyoto, 619-0284, Japan
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yasushi Tamura
- Faculty of Science, Yamagata University, Yamagata, Yamagata, 990-8560, Japan
| | - Toshiya Endo
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, 603-8555, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Kyoto, 619-0284, Japan
| | - Ken-Ichi Nishiyama
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, 020-8550, Japan. .,Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan. .,Department of Biological Chemistry and Food Science, Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan.
| |
Collapse
|
14
|
Fujikawa K, Suzuki S, Nagase R, Ikeda S, Mori S, Nomura K, Nishiyama KI, Shimamoto K. Syntheses and Activities of the Functional Structures of a Glycolipid Essential for Membrane Protein Integration. ACS Chem Biol 2018; 13:2719-2727. [PMID: 30064209 DOI: 10.1021/acschembio.8b00654] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MPIase is the first known glycolipid that is essential for membrane protein integration in the inner membrane of E. coli. Since the amount of natural MPIase available for analysis is limited and it contains structural heterogeneity, precisely designed synthetic derivatives are promising tools for further elucidation of its membrane protein integration mechanism. Thus, we synthesized the minimal unit of MPIase, a trisaccharyl pyrophospholipid termed mini-MPIase-3, and its derivatives. Integration assays revealed that the chemically synthesized trisaccharyl pyrophospholipid possesses significant activity, indicating that it includes the essential structure for membrane integration. Structure-activity relationship studies demonstrated that the number of trisaccharide units and the 6- O-acetyl group on N-acetylglucosamine contribute to efficient integration. Furthermore, anchoring in the membrane by a lipid moiety was essential for the integration. However, the addition of phosphorylated glycans devoid of the lipid moiety in the assay solution modulated the integration activity of MPIase embedded in liposomes, suggesting an interaction between phosphorylated glycans and substrate proteins in aqueous solutions. The prevention of protein aggregation required the 6- O-acetyl group on N-acetylglucosamine, a phosphate group at the reducing end of the glycan, and a long glycan chain. Taken together, we verified the mechanism of the initial step of the translocon-independent pathway in which a membrane protein is captured by a glycan of MPIase, which maintains its structure to be competent for integration, and then MPIase integrates it into the membrane by hydrophobic interactions with membrane lipids.
Collapse
Affiliation(s)
- Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Sonomi Suzuki
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Ryohei Nagase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Shiori Ikeda
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Ken-ichi Nishiyama
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Shimamoto K. Elucidation of Excitatory Neurotransmission and Membrane Protein Integration Mechanisms. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences
| |
Collapse
|