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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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Hikage R, Sekiya Y, Sawasato K, Nishiyama KI. CdsA, a CDP-diacylglycerol synthase involved in phospholipid and glycolipid MPIase biosynthesis, possesses multiple initiation codons. Genes Cells 2024; 29:347-355. [PMID: 38351722 DOI: 10.1111/gtc.13104] [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: 01/08/2024] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 04/04/2024]
Abstract
CdsA is a CDP-diacylglycerol synthase essential for phospholipid and glycolipid MPIase biosynthesis, and therefore for growth. The initiation codon of CdsA has been assigned as "TTG," while methionine at the 37th codon was reported to be an initiation codon in the original report. Since a vector containing the open reading frame starting with "TTG" under a controllable promoter complemented the cdsA knockout, "TTG" could function as an initiation codon. However, no evidence supporting that this "TTG" is the sole initiation codon has been reported. We determined the initiation codon by examining the ability of mutants around the N-terminal region to complement cdsA mutants. Even if the "TTG" was substituted with a stop codon, the clear complementation was observed. Moreover, the clones with multiple mutations of stop codons complemented the cdsA mutant up to the 37th codon, indicating that cdsA possesses multiple codons that can function as initiation codons. We constructed an experimental system in which the chromosomal expression of cdsA can be analyzed. By means of this system, we found that the cdsA mutant with substitution of "TTG" with a stop codon is fully functional. Thus, we concluded that CdsA contains multiple initiation codons.
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Affiliation(s)
- Runa Hikage
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yusei Sekiya
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Katsuhiro Sawasato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ken-Ichi Nishiyama
- Department of Applied Biological Chemistry, Faculty of Agriculture, Iwate University, Morioka, Japan
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3
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Zhou Y, Tu T, Yao X, Luo Y, Yang Z, Ren M, Zhang G, Yu Y, Lu A, Wang Y. Pan-genome analysis of Streptococcus suis serotype 2 highlights genes associated with virulence and antibiotic resistance. Front Microbiol 2024; 15:1362316. [PMID: 38450165 PMCID: PMC10915096 DOI: 10.3389/fmicb.2024.1362316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Streptococcus suis serotype 2 (SS2) is a Gram-positive bacterium. It is a common and significant pathogen in pigs and a common cause of zoonotic meningitis in humans. It can lead to sepsis, endocarditis, arthritis, and pneumonia. If not diagnosed and treated promptly, it has a high mortality rate. The pan-genome of SS2 is open, and with an increasing number of genes, the core genome and accessory genome may exhibit more pronounced differences. Due to the diversity of SS2, the genes related to its virulence and resistance are still unclear. In this study, a strain of SS2 was isolated from a pig farm in Sichuan Province, China, and subjected to whole-genome sequencing and characterization. Subsequently, we conducted a Pan-Genome-Wide Association Study (Pan-GWAS) on 230 strains of SS2. Our analysis indicates that the core genome is composed of 1,458 genes related to the basic life processes of the bacterium. The accessory genome, consisting of 4,337 genes, is highly variable and a major contributor to the genetic diversity of SS2. Furthermore, we identified important virulence and resistance genes in SS2 through pan-GWAS. The virulence genes of SS2 are mainly associated with bacterial adhesion. In addition, resistance genes in the core genome may confer natural resistance of SS2 to fluoroquinolone and glycopeptide antibiotics. This study lays the foundation for further research on the virulence and resistance of SS2, providing potential new drug and vaccine targets against SS2.
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Affiliation(s)
- You Zhou
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Teng Tu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xueping Yao
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yan Luo
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Zexiao Yang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Meishen Ren
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery (HKAP), Kowloon Tong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery (HKAP), Kowloon Tong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery (HKAP), Kowloon Tong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery (HKAP), Kowloon Tong, Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
| | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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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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5
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Kobayashi K, Jimbo H, Nakamura Y, Wada H. Biosynthesis of phosphatidylglycerol in photosynthetic organisms. Prog Lipid Res 2024; 93:101266. [PMID: 38040200 DOI: 10.1016/j.plipres.2023.101266] [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: 10/04/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
Phosphatidylglycerol (PG) is a unique phospholipid class with its indispensable role in photosynthesis and growth in land plants, algae, and cyanobacteria. PG is the only major phospholipid in the thylakoid membrane of cyanobacteria and plant chloroplasts and a main lipid component in photosynthetic protein-cofactor complexes such as photosystem I and photosystem II. In plants and algae, PG is also essential as a substrate for the biosynthesis of cardiolipin, which is a unique lipid present only in mitochondrial membranes and crucial for the functions of mitochondria. PG biosynthesis pathways in plants include three membranous organelles, plastids, mitochondria, and the endoplasmic reticulum in a complex manner. While the molecular biology underlying the role of PG in photosynthetic functions is well established, many enzymes responsible for the PG biosynthesis are only recently cloned and functionally characterized in the model plant species including Arabidopsis thaliana and Chlamydomonas reinhardtii and cyanobacteria such as Synechocystis sp. PCC 6803. The characterization of those enzymes helps understand not only the metabolic flow for PG production but also the crosstalk of biosynthesis pathways between PG and other lipids. This review aims to summarize recent advances in the understanding of the PG biosynthesis pathway and functions of involved enzymes.
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Affiliation(s)
- Koichi Kobayashi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, Sakai, Japan.
| | - Haruhiko Jimbo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuki Nakamura
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hajime Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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6
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Phosphatidylglycerol Is the Lipid Donor for Synthesis of Phospholipid-Linked Enterobacterial Common Antigen. J Bacteriol 2023; 205:e0040322. [PMID: 36622229 PMCID: PMC9879101 DOI: 10.1128/jb.00403-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The Gram-negative outer membrane (OM) is an asymmetric bilayer with phospholipids in its inner leaflet and mainly lipopolysaccharide (LPS) in its outer leaflet and is largely impermeable to many antibiotics. In Enterobacterales (e.g., Escherichia, Salmonella, Klebsiella, and Yersinia), the outer leaflet of the OM also contains phosphoglyceride-linked enterobacterial common antigen (ECAPG). This molecule consists of the conserved ECA carbohydrate linked to diacylglycerol-phosphate (DAG-P) through a phosphodiester bond. ECAPG contributes to the OM permeability barrier and modeling suggests that it may alter the packing of LPS molecules in the OM. Here, we investigate, in Escherichia coli K-12, the reaction synthesizing ECAPG from ECA precursor linked to an isoprenoid carrier to identify the lipid donor that provides the DAG-P moiety to ECAPG. Through overexpression of phospholipid biosynthesis genes, we observed alterations expected to increase levels of phosphatidylglycerol (PG) increased the synthesis of ECAPG, whereas alterations expected to decrease levels of PG decreased the synthesis of ECAPG. We discovered depletion of PG levels in strains that could synthesize ECAPG, but not other forms of ECA, causes additional growth defects, likely due to the buildup of ECA precursor on the isoprenoid carrier inhibiting peptidoglycan biosynthesis. Our results demonstrate ECAPG can be synthesized in the absence of the other major phospholipids (phosphatidylethanolamine and cardiolipin). Overall, these results conclusively demonstrate PG is the lipid donor for the synthesis of ECAPG and provide a key insight into the reaction producing ECAPG. In addition, these results provide an interesting parallel to lipoprotein acylation, which also uses PG as its DAG donor. IMPORTANCE The Gram-negative outer membrane is a permeability barrier preventing cellular entry of antibiotics. However, outer membrane biogenesis pathways are targets for small molecule development. Here, we investigate the synthesis of a form of enterobacterial common antigen (ECA), ECAPG, found in the outer membrane of Enterobacterales (e.g., Escherichia, Salmonella, and Klebsiella). ECAPG consists of the conserved ECA carbohydrate unit linked to diacylglycerol-phosphate-ECA is a phospholipid headgroup. The details of the reaction forming this molecule from polymerized ECA precursor are unknown. We determined the lipid donor providing the phospholipid moiety is phosphatidylglycerol. Understanding the synthesis of outer membrane constituents such as ECAPG provides the opportunity for development of molecules to increase outer membrane permeability, expanding the antibiotics available to treat Gram-negative infections.
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7
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Kamemoto Y, Hikage R, Han Y, Sekiya Y, Sawasato K, Nishiyama KI. Coordinated upregulation of two CDP-diacylglycerol synthases, YnbB and CdsA, is essential for cell growth and membrane protein export in the cold. FEMS Microbiol Lett 2023; 370:fnad131. [PMID: 38070879 DOI: 10.1093/femsle/fnad131] [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: 10/19/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/29/2023] Open
Abstract
YnbB is a paralogue of CdsA, a CDP-diacylglycerol synthase. While the cdsA gene is essential, the ynbB gene is dispensable. So far, no phenotype of ynbB knockout has been observed. We found that a ynbB knockout strain acquired cold-sensitivity on growth under CdsA-limited conditions. We found that MPIase, a glycolipid involved in protein export, is cold-upregulated to facilitate protein export in the cold, by increasing the mRNA levels of not only CdsA but also that of YnbB. Under non-permissive conditions, phospholipid biosynthesis proceeded normally, however, MPIase upregulation was inhibited with accumulation of precursors of membrane and secretory proteins such as M13 procoat and proOmpA, indicating that YnbB is dedicated to MPIase biosynthesis, complementing the CdsA function.
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Affiliation(s)
- Yuki Kamemoto
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Runa Hikage
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Youjung Han
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Yusei Sekiya
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Katsuhiro Sawasato
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Ken-Ichi Nishiyama
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
- Department of Applied Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, 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: 2] [Impact Index Per Article: 1.0] [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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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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10
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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.
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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
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11
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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.
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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
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12
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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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Ito K, Shimokawa-Chiba N, Chiba S. Sec translocon has an insertase-like function in addition to polypeptide conduction through the channel. F1000Res 2020; 8. [PMID: 32025287 PMCID: PMC6971846 DOI: 10.12688/f1000research.21065.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 11/20/2022] Open
Abstract
The Sec translocon provides a polypeptide-conducting channel, which is insulated from the hydrophobic lipidic environment of the membrane, for translocation of hydrophilic passenger polypeptides. Its lateral gate allows a downstream hydrophobic segment (stop-transfer sequence) to exit the channel laterally for integration into the lipid phase. We note that this channel model only partly accounts for the translocon function. The other essential role of translocon is to facilitate de novo insertion of the N-terminal topogenic segment of a substrate polypeptide into the membrane. Recent structural studies suggest that de novo insertion does not use the polypeptide-conducting channel; instead, it takes place directly at the lateral gate, which is prone to opening. We propose that the de novo insertion process, in concept, is similar to that of insertases (such as YidC in bacteria and EMC3 in eukaryotes), in which an intramembrane surface of the machinery provides the halfway point of insertion.
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Affiliation(s)
- Koreaki Ito
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Naomi Shimokawa-Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
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14
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Blunsom NJ, Cockcroft S. CDP-Diacylglycerol Synthases (CDS): Gateway to Phosphatidylinositol and Cardiolipin Synthesis. Front Cell Dev Biol 2020; 8:63. [PMID: 32117988 PMCID: PMC7018664 DOI: 10.3389/fcell.2020.00063] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Cytidine diphosphate diacylglycerol (CDP-DAG) is a key intermediate in the synthesis of phosphatidylinositol (PI) and cardiolipin (CL). Both PI and CL have highly specialized roles in cells. PI can be phosphorylated and these phosphorylated derivatives play major roles in signal transduction, membrane traffic, and maintenance of the actin cytoskeletal network. CL is the signature lipid of mitochondria and has a plethora of functions including maintenance of cristae morphology, mitochondrial fission, and fusion and for electron transport chain super complex formation. Both lipids are synthesized in different organelles although they share the common intermediate, CDP-DAG. CDP-DAG is synthesized from phosphatidic acid (PA) and CTP by enzymes that display CDP-DAG synthase activities. Two families of enzymes, CDS and TAMM41, which bear no sequence or structural relationship, have now been identified. TAMM41 is a peripheral membrane protein localized in the inner mitochondrial membrane required for CL synthesis. CDS enzymes are ancient integral membrane proteins found in all three domains of life. In mammals, they provide CDP-DAG for PI synthesis and for phosphatidylglycerol (PG) and CL synthesis in prokaryotes. CDS enzymes are critical for maintaining phosphoinositide levels during phospholipase C (PLC) signaling. Hydrolysis of PI (4,5) bisphosphate by PLC requires the resynthesis of PI and CDS enzymes catalyze the rate-limiting step in the process. In mammals, the protein products of two CDS genes (CDS1 and CDS2) localize to the ER and it is suggested that CDS2 is the major CDS for this process. Expression of CDS enzymes are regulated by transcription factors and CDS enzymes may also contribute to CL synthesis in mitochondria. Studies of CDS enzymes in protozoa reveal spatial segregation of CDS enzymes from the rest of the machinery required for both PI and CL synthesis identifying a key gap in our understanding of how CDP-DAG can cross the different membrane compartments in protozoa and in mammals.
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Affiliation(s)
| | - Shamshad Cockcroft
- Division of Biosciences, Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
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15
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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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16
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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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17
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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: 11] [Impact Index Per Article: 2.2] [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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18
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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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19
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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: 10] [Impact Index Per Article: 2.0] [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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20
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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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