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Hikage R, Tadika Y, Asanuma H, Han Y, Nishiyama KI. MucA is a small peptide encoded by an overlapping sequence with cdsA that upregulates the biosynthesis of glycolipid MPIase in the cold. Biochem Biophys Res Commun 2024; 721:150148. [PMID: 38781662 DOI: 10.1016/j.bbrc.2024.150148] [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: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
MPIase is a glycolipid involved in protein insertion into and preprotein translocation across the cytoplasmic membranes of E. coli. MPIase is upregulated in the cold conditions to overcome the cold-sensitive protein export. CdsA, a CDP-diacylglycerol synthase, catalyzes the first reaction in MPIase biosynthesis. An open reading frame for a peptide of 50 amino acids is encoded immediately after ispU, a neighboring upstream gene of cdsA, and overlaps cdsA to a large extent. Mutational analysis revealed that the expression of this peptide is essential for upregulation of MPIase in the cold. Consistently, expression of this peptide in trans resulted in cold upregulation of MPIase. We therefore named this peptide MucA after its function (MPIase upregulation in the cold). When the partially purified MucA was added to the reaction of the intermediate in MPIase biosynthesis, a significant increase in the product formation was observed, supporting the function of MucA. The possible role of MucA in MPIase biosynthesis is discussed.
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Affiliation(s)
- Runa Hikage
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Yuta Tadika
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Haruka Asanuma
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | - Youjung Han
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan
| | - Ken-Ichi Nishiyama
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan; Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan.
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2
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Hagino R, Kuwabara R, Komura N, Imamura A, Ishida H, Ando H, Tanaka HN. Protecting-Group-Free Synthesis of ADP-Ribose and Dinucleoside Di-/Triphosphate Derivatives via P(V)-P(V) Coupling Reaction. Chemistry 2024; 30:e202401302. [PMID: 38763895 DOI: 10.1002/chem.202401302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Biomolecules containing adenosine di- or triphosphate (ADP or ATP) are crucial for diverse biological processes. Synthesis of these biomolecules and development of their chemical probes are important to elucidate their functions. Enabling reproducible and high-yielding access to these ADP- and ATP-containing molecules via conventional P(III)-P(V) and P(V)-P(V) coupling reactions is challenging owing to water content in highly polar phosphate-containing substrates. Herein, we report an efficient and reliable method for protecting-group-free P(V)-P(V) coupling reaction through in situ activation of phosphates using hydrolysis-stable 2-[N-(2-methylimidazoyl)]-1,3-dimethylimidazolinium chloride (2-MeImIm-Cl), providing the corresponding electrophilic P(V) intermediates for subsequent nucleophilic attack using their coupling partners. This P(V)-P(V) coupling reaction proceeded even in a wet reaction medium and showed a broad substrate scope, accommodating protecting-group-free synthesis of ADP-ribose and nicotinamide adenine diphosphate analogs, ATP-containing biomolecules, and ADP-ribosyl peptides.
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Affiliation(s)
- Rui Hagino
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Ryo Kuwabara
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Naoko Komura
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Akihiro Imamura
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hideharu Ishida
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hiromune Ando
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| | - Hide-Nori Tanaka
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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3
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Ghotekar BK, Kulkarni SS. Total Synthesis of the Conjugation-Ready Tetrasaccharide Repeating Unit of Shewanella japonica Type Strain KMM 3299 T. Org Lett 2024; 26:4346-4350. [PMID: 38722236 DOI: 10.1021/acs.orglett.4c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Here we report the first total synthesis of the conjugation-ready tetrasaccharide repeating unit of Shewanella japonica type strain KMM 3299T. The presence of rare deoxyamino sugars and installation of three consecutive 1,2-cis glycosidic linkages makes the synthesis formidable. The challenging late-stage oxidation was overcome by using a galacturonate donor. The total synthesis was completed via a longest linear sequence of 22 steps in an overall yield of 3.5% starting from d-mannose.
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Affiliation(s)
- Balasaheb K Ghotekar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Suvarn S Kulkarni
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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4
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Mori S, Shionyu M, Shimamoto K, Nomura K. Bacterial Glycolipid Acting on Protein Transport Across Membranes. Chembiochem 2024; 25:e202300808. [PMID: 38400776 DOI: 10.1002/cbic.202300808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/11/2024] [Accepted: 02/22/2024] [Indexed: 02/26/2024]
Abstract
The process of protein transport across membranes involves a variety of factors and has been extensively investigated. Traditionally, proteinaceous translocons and chaperones have been recognized as crucial factors in this process. However, recent studies have highlighted the significant roles played by lipids and a glycolipid present in biological membranes in membrane protein transport. Membrane lipids can influence transport efficiency by altering the physicochemical properties of membranes. Notably, our studies have revealed that diacylglycerol (DAG) attenuates mobility in the membrane core region, leading to a dramatic suppression of membrane protein integration. Conversely, a glycolipid in Escherichia coli inner membranes, named membrane protein integrase (MPIase), enhances integration not only through the alteration of membrane properties but also via direct interactions with membrane proteins. This review explores the mechanisms of membrane protein integration mediated by membrane lipids, specifically DAG, and MPIase. Our results, along with the employed physicochemical analysis methods such as fluorescence measurements, nuclear magnetic resonance, surface plasmon resonance, and docking simulation, are presented to elucidate these mechanisms.
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Affiliation(s)
- Shoko Mori
- 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, Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga, 526-0829, 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
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284, Japan
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5
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Nomura K, Mori S, Shimamoto K. Roles of a Glycolipid MPIase in Sec-Independent Membrane Protein Insertion. MEMBRANES 2024; 14:48. [PMID: 38392675 PMCID: PMC10890265 DOI: 10.3390/membranes14020048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Membrane protein integrase (MPIase), an endogenous glycolipid in Escherichia coli (E. coli) membranes, is essential for membrane protein insertion in E. coli. We have examined Sec-independent membrane protein insertion mechanisms facilitated by MPIase using physicochemical analytical techniques, namely solid-state nuclear magnetic resonance, fluorescence measurements, and surface plasmon resonance. In this review, we outline the physicochemical characteristics of membranes that may affect membrane insertion of proteins. Subsequently, we introduce our results verifying the effects of membrane lipids on insertion and estimate the impact of MPIase. Although MPIase is a minor component of E. coli membranes, it regulates insertion by altering the physicochemical properties of the membrane. In addition, MPIase promotes insertion by interacting with substrate proteins. We propose comprehensive mechanisms for the membrane insertion of proteins involving MPIase, which provide a physicochemical basis for understanding the roles of glycolipids in protein translocation.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, 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
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6
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Osawa T, Fujikawa K, Shimamoto K. Structures, functions, and syntheses of glycero-glycophospholipids. Front Chem 2024; 12:1353688. [PMID: 38389730 PMCID: PMC10881803 DOI: 10.3389/fchem.2024.1353688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Biological membranes consist of integral and peripheral protein-associated lipid bilayers. Although constituent lipids vary among cells, membrane lipids are mainly classified as phospholipids, glycolipids, and sterols. Phospholipids are further divided into glycerophospholipids and sphingophospholipids, whereas glycolipids are further classified as glyceroglycolipids and sphingoglycolipids. Both glycerophospholipids and glyceroglycolipids contain diacylglycerol as the common backbone, but their head groups differ. Most glycerolipids have polar head groups containing phosphate esters or sugar moieties. However, trace components termed glycero-glycophospholipids, each possessing both a phosphate ester and a sugar moiety, exist in membranes. Recently, the unique biological activities of glycero-glycophospholipids have attracted considerable attention. In this review, we describe the structure, distribution, function, biosynthesis, and chemical synthetic approaches of representative glycero-glycophospholipids-phosphatidylglucoside (PtdGlc) and enterobacterial common antigen (ECA). In addition, we introduce our recent studies on the rare glycero-glyco"pyrophospho"lipid, membrane protein integrase (MPIase), which is involved in protein translocation across biomembranes.
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Affiliation(s)
- Tsukiho Osawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, Osaka, Japan
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7
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Shimamoto K, Fujikawa K, Osawa T, Mori S, Nomura K, Nishiyama KI. Key contributions of a glycolipid to membrane protein integration. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2024; 100:387-413. [PMID: 39085064 DOI: 10.2183/pjab.100.026] [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: 08/02/2024]
Abstract
Regulation of membrane protein integration involves molecular devices such as Sec-translocons or the insertase YidC. We have identified an integration-promoting factor in the inner membrane of Escherichia coli called membrane protein integrase (MPIase). Structural analysis revealed that, despite its enzyme-like name, MPIase is a glycolipid with a long glycan comprising N-acetyl amino sugars, a pyrophosphate linker, and a diacylglycerol (DAG) anchor. Additionally, we found that DAG, a minor membrane component, blocks spontaneous integration. In this review, we demonstrate how they contribute to Sec-independent membrane protein integration in bacteria using a comprehensive approach including synthetic chemistry and biophysical analyses. DAG blocks unfavorable spontaneous integrations by suppressing mobility in the membrane core, whereas MPIase compensates for this. Moreover, MPIase plays critical roles in capturing a substrate protein to prevent its aggregation, attracting it to the membrane surface, facilitating its insertion into the membrane, and delivering it to other factors. The combination of DAG and MPIase efficiently regulates the integration of membrane proteins.
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Affiliation(s)
- Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Soraku-gun, Kyoto, Japan
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Soraku-gun, Kyoto, Japan
| | - Tsukiho Osawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Soraku-gun, Kyoto, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Soraku-gun, Kyoto, Japan
| | - Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Seika-cho, Soraku-gun, Kyoto, Japan
| | - Ken-Ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
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8
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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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9
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Role of a bacterial glycolipid in Sec-independent membrane protein insertion. Sci Rep 2022; 12:12231. [PMID: 35851412 PMCID: PMC9293918 DOI: 10.1038/s41598-022-16304-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/07/2022] [Indexed: 11/08/2022] Open
Abstract
Non-proteinaceous components in membranes regulate membrane protein insertion cooperatively with proteinaceous translocons. An endogenous glycolipid in the Escherichia coli membrane called membrane protein integrase (MPIase) is one such component. Here, we focused on the Sec translocon-independent pathway and examined the mechanisms of MPIase-facilitated protein insertion using physicochemical techniques. We determined the membrane insertion efficiency of a small hydrophobic protein using solid-state nuclear magnetic resonance, which showed good agreement with that determined by the insertion assay using an in vitro translation system. The observed insertion efficiency was strongly correlated with membrane physicochemical properties measured using fluorescence techniques. Diacylglycerol, a trace component of E. coli membrane, reduced the acyl chain mobility in the core region and inhibited the insertion, whereas MPIase restored them. We observed the electrostatic intermolecular interactions between MPIase and the side chain of basic amino acids in the protein, suggesting that the negatively charged pyrophosphate of MPIase attracts the positively charged residues of a protein near the membrane surface, which triggers the insertion. Thus, this study demonstrated the ingenious approach of MPIase to support membrane insertion of proteins by using its unique molecular structure in various ways.
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10
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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.
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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
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11
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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]
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12
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Alex C, Demchenko AV. Recent Advances in Stereocontrolled Mannosylation: Focus on Glycans Comprising Acidic and/or Amino Sugars. CHEM REC 2021; 21:3278-3294. [PMID: 34661961 DOI: 10.1002/tcr.202100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/20/2022]
Abstract
The main focus of this review is to describe accomplishments made in the stereoselective synthesis of β-linked mannosides functionalized with carboxyls or amines/amides. These ManNAc, ManA and ManNAcA residues found in many glycoconjugates, bacterial polysaccharides, and alginates have consistently captured interest of the glycoscience community both due to synthetic challenge and therapeutic potential.
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Affiliation(s)
- Catherine Alex
- Department of Chemistry and Biochemistry, University of Missouri - St. Louis, One University Blvd., St. Louis, MO 63121, USA
| | - Alexei V Demchenko
- Department of Chemistry and Biochemistry, University of Missouri - St. Louis, One University Blvd., St. Louis, MO 63121, USA.,Department of Chemistry, Saint Louis University, 3501 Laclede Ave, St. Louis, MO 63103, USA
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13
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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.
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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
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14
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Sun H, Ren Q, Zhao X, Tian Y, Pan J, Wei Q, Li Y, Chen Y, Zhang H, Zhang W, Jiang S. Regional similarities and differences in mature human milk fatty acids in Chinese population: A systematic review. Prostaglandins Leukot Essent Fatty Acids 2020; 162:102184. [PMID: 33045533 DOI: 10.1016/j.plefa.2020.102184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022]
Abstract
Maternal factors such as the diet can impact human milk fatty acid profiles. We hypothesized that mature human milk fatty acid profiles differ among regions of China. To test our hypothesis, we conducted a systematic review to calculate regional average contents of fatty acids and the statistical significance of regional differences in fatty acids. We searched both Chinese and English literature databases and selected 21 articles, including 11 in Chinese and 10 in English. We categorized regions of China by 3 ways: 1) north vs. south; 2) inland vs. coastal; 3) socioeconomic development levels. The ratios of ΣSFAs:ΣMUFAs:ΣPUFAs were similar between regions and the average was 1:1:0.7. Contents of palmitic, oleic, and linoleic acids were also similar between regions and together they accounted for more than 70% of all fatty acids in mature human milk. Conversely, concentrations of ALA and DHA differed more than palmitic, oleic, and linoleic acids. We also found that it might be necessary to reduce maternal dietary contents of potentially harmful fatty acids such as erucic acid to minimize detrimental effects on infant health. To our knowledge, this study represents the first systematic review that quantitatively investigated the regional similarities and differences in mature human milk fatty acid contents and is therefore significant for academia and policy makers.
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Affiliation(s)
- Han Sun
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Qiqi Ren
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Xuejun Zhao
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yueyue Tian
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Jiancun Pan
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Qiaosi Wei
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yuanyuan Li
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yong Chen
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Huaqin Zhang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Wei Zhang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China.
| | - Shilong Jiang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China.
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15
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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
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16
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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.
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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.
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17
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Sawasato K, Sekiya Y, Nishiyama K. Two‐step induction ofcdsApromoters leads to upregulation of the glycolipidMPIase at cold temperature. FEBS Lett 2019; 593:1711-1723. [DOI: 10.1002/1873-3468.13460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Katsuhiro Sawasato
- The United Graduate School of Agricultural Sciences Iwate University Morioka Japan
| | - Yusei Sekiya
- 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
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18
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Nomura K, Yamaguchi T, Mori S, Fujikawa K, Nishiyama KI, Shimanouchi T, Tanimoto Y, Morigaki K, Shimamoto K. Alteration of Membrane Physicochemical Properties by Two Factors for Membrane Protein Integration. Biophys J 2019; 117:99-110. [PMID: 31164197 PMCID: PMC6626835 DOI: 10.1016/j.bpj.2019.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/01/2022] Open
Abstract
After a nascent chain of a membrane protein emerges from the ribosomal tunnel, the protein is integrated into the cell membrane. This process is controlled by a series of proteinaceous molecular devices, such as signal recognition particles and Sec translocons. In addition to these proteins, we discovered two endogenous components regulating membrane protein integration in the inner membrane of Escherichia coli. The integration is blocked by diacylglycerol (DAG), whereas the blocking is relieved by a glycolipid named membrane protein integrase (MPIase). Here, we investigated the influence of these integration-blocking and integration-promoting factors on the physicochemical properties of membrane lipids via solid-state NMR and fluorescence measurements. These factors did not have destructive effects on membrane morphology because the membrane maintained its lamellar structure and did not fuse in the presence of DAG and/or MPIase at their effective concentrations. We next focused on membrane flexibility. DAG did not affect the mobility of the membrane surface, whereas the sugar chain in MPIase was highly mobile and enhanced the flexibility of membrane lipid headgroups. Comparison with a synthetic MPIase analog revealed the effects of the long sugar chain on membrane properties. The acyl chain order inside the membrane was increased by DAG, whereas the increase was cancelled by the addition of MPIase. MPIase also loosened the membrane lipid packing. Focusing on the transbilayer movement, MPIase reduced the rapid flip-flop motion of DAG. On the other hand, MPIase could not compensate for the diminished lateral diffusion by DAG. These results suggest that by manipulating the membrane lipids dynamics, DAG inhibits the protein from contacting the inner membrane, whereas the flexible long sugar chain of MPIase increases the opportunity for interaction between the membrane and the protein, leading to membrane integration of the newly formed protein.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
| | - Toshiyuki Yamaguchi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, 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
| | - Ken-Ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | | | - Yasushi Tanimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
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19
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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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