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Okuda A, Shimizu M, Inoue R, Urade R, Sugiyama M. Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance. Angew Chem Int Ed Engl 2023; 62:e202214412. [PMID: 36347766 DOI: 10.1002/anie.202214412] [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] [Received: 09/30/2022] [Indexed: 11/10/2022]
Abstract
Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.
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Affiliation(s)
- Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masahiro Shimizu
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
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Tanikawa Y, Kanemura S, Ito D, Lin Y, Matsusaki M, Kuroki K, Yamaguchi H, Maenaka K, Lee YH, Inaba K, Okumura M. Ca 2+ Regulates ERp57-Calnexin Complex Formation. Molecules 2021; 26:molecules26102853. [PMID: 34064874 PMCID: PMC8151781 DOI: 10.3390/molecules26102853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/01/2021] [Accepted: 05/09/2021] [Indexed: 11/20/2022] Open
Abstract
ERp57, a member of the protein disulfide isomerase family, is a ubiquitous disulfide catalyst that functions in the oxidative folding of various clients in the mammalian endoplasmic reticulum (ER). In concert with ER lectin-like chaperones calnexin and calreticulin (CNX/CRT), ERp57 functions in virtually all folding stages from co-translation to post-translation, and thus plays a critical role in maintaining protein homeostasis, with direct implication for pathology. Here, we present mechanisms by which Ca2+ regulates the formation of the ERp57-calnexin complex. Biochemical and isothermal titration calorimetry analyses revealed that ERp57 strongly interacts with CNX via a non-covalent bond in the absence of Ca2+. The ERp57-CNX complex not only promoted the oxidative folding of human leukocyte antigen heavy chains, but also inhibited client aggregation. These results suggest that this complex performs both enzymatic and chaperoning functions under abnormal physiological conditions, such as Ca2+ depletion, to effectively guide proper oxidative protein folding. The findings shed light on the molecular mechanisms underpinning crosstalk between the chaperone network and Ca2+.
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Affiliation(s)
- Yuya Tanikawa
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
| | - Shingo Kanemura
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
| | - Dai Ito
- Department of Brain and Cognitive Science, Daegu Gyeongbuk Institute of Science and Technology, 333 Techno Jungang Daero, Daegu 42988, Korea;
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Cheongju 28119, Korea; (Y.L.); (Y.-H.L.)
| | - Motonori Matsusaki
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
- Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Kimiko Kuroki
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan; (K.K.); (K.M.)
| | - Hiroshi Yamaguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan; (Y.T.); (S.K.); (H.Y.)
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan; (K.K.); (K.M.)
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences and Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Nishi 6, Kita 12, Kita-ku, Sapporo 060-0812, Japan
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang, Cheongju 28119, Korea; (Y.L.); (Y.-H.L.)
- Research Headquarters, Korea Brain Research Institute, 61 Cheomdan-ro, Dong-gu, Daegu 41068, Korea
- Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan;
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 6-3 Aramakiaza Aoba, Aoba-ku, Sendai 980-8578, Japan;
- Fusion Oriented Research for Disruptive Science and Technology, Japan Science Technology Agency, Chiyoda-ku, Tokyo 102-0075, Japan
- Correspondence: ; Tel.: +81-22-795-5764
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3
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Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation. Sci Rep 2021; 11:5655. [PMID: 33707747 PMCID: PMC7952739 DOI: 10.1038/s41598-021-85219-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/25/2021] [Indexed: 11/08/2022] Open
Abstract
Multi-domain proteins (MDPs) show a variety of domain conformations under physiological conditions, regulating their functions through such conformational changes. One of the typical MDPs, ER-60 which is a protein folding enzyme, has a U-shape with four domains and is thought to have different domain conformations in solution depending on the redox state at the active centres of the edge domains. In this work, an aggregation-free small-angle X-ray scattering revealed that the structures of oxidized and reduced ER-60 in solution are different from each other and are also different from those in the crystal. Furthermore, structural modelling with coarse-grained molecular dynamics simulation indicated that the distance between the two edge domains of oxidized ER-60 is longer than that of reduced ER-60. In addition, one of the edge domains has a more flexible conformation than the other.
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Abstract
ABSTRACT
For most of the proteins synthesized in the endoplasmic reticulum (ER), disulfide bond formation accompanies protein folding in a process called oxidative folding. Oxidative folding is catalyzed by a number of enzymes, including the family of protein disulfide isomerases (PDIs), as well as other proteins that supply oxidizing equivalents to PDI family proteins, like ER oxidoreductin 1 (Ero1). Oxidative protein folding in the ER is a basic vital function, and understanding its molecular mechanism is critical for the application of plants as protein production tools. Here, I review the recent research and progress related to the enzymes involved in oxidative folding in the plant ER. Firstly, nine groups of plant PDI family proteins are introduced. Next, the enzymatic properties of plant Ero1 are described. Finally, the cooperative folding by multiple PDI family proteins and Ero1 is described.
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Affiliation(s)
- Reiko Urade
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Osaka, Japan
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Fujikawa K, Seko A, Takeda Y, Ito Y. Approaches toward High-Mannose-Type Glycan Libraries. CHEM REC 2015; 16:35-46. [DOI: 10.1002/tcr.201500222] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Kohki Fujikawa
- Japan Science and Technology Agency (JST), ERATO Ito Glycotrilogy Project; 2-1 Hirosawa Wako Saitama 351-0198 Japan
- SUNTORY Bioorganic Research Institute; 8-1-1 Seikadai Seika-cho Soraku-gun Kyoto 619-0284 Japan
| | - Akira Seko
- Japan Science and Technology Agency (JST), ERATO Ito Glycotrilogy Project; 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Yoichi Takeda
- Japan Science and Technology Agency (JST), ERATO Ito Glycotrilogy Project; 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Department of Biotechnology, College of Life Sciences; Ritsumeikan University; 1-1-1 Noji-higashi Kusatsu Shiga 525-8577 Japan
| | - Yukishige Ito
- Japan Science and Technology Agency (JST), ERATO Ito Glycotrilogy Project; 2-1 Hirosawa Wako Saitama 351-0198 Japan
- Synthetic Cellular Chemistry Laboratory; RIKEN; 2-1 Hirosawa Wako Saitama 351-0198 Japan
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Kimura S, Higashino Y, Kitao Y, Masuda T, Urade R. Expression and characterization of protein disulfide isomerase family proteins in bread wheat. BMC PLANT BIOLOGY 2015; 15:73. [PMID: 25849633 PMCID: PMC4355359 DOI: 10.1186/s12870-015-0460-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/13/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND The major wheat seed proteins are storage proteins that are synthesized in the rough endoplasmic reticulum (ER) of starchy endosperm cells. Many of these proteins have intra- and intermolecular disulfide bonds. In eukaryotes, the formation of most intramolecular disulfide bonds in the ER is thought to be catalyzed by protein disulfide isomerase (PDI) family proteins. The cDNAs that encode eight groups of bread wheat (Triticum aestivum L.) PDI family proteins have been cloned, and their expression levels in developing wheat grains have been determined. The purpose of the present study was to characterize the enzymatic properties of the wheat PDI family proteins and clarify their expression patterns in wheat caryopses. RESULTS PDI family cDNAs, which are categorized into group I (TaPDIL1Aα, TaPDIL1Aβ, TaPDIL1Aγ, TaPDIL1Aδ, and TaPDIL1B), group II (TaPDIL2), group III (TaPDIL3A), group IV (TaPDIL4D), and group V (TaPDIL5A), were cloned. The expression levels of recombinant TaPDIL1Aα, TaPDIL1B, TaPDIL2, TaPDIL3A, TaPDIL4D, and TaPDIL5A in Escherichia coli were established from the cloned cDNAs. All recombinant proteins were expressed in soluble forms and purified. Aside from TaPDIL3A, the recombinant proteins exhibited oxidative refolding activity on reduced and denatured ribonuclease A. Five groups of PDI family proteins were distributed throughout wheat caryopses, and expression levels of these proteins were higher during grain filling than in the late stage of maturing. Localization of these proteins in the ER was confirmed by fluorescent immunostaining of the immature caryopses. In mature grains, the five groups of PDI family proteins remained in the aleurone cells and the protein matrix of the starchy endosperm. CONCLUSIONS High expression of PDI family proteins during grain filling in the starchy endosperm suggest that these proteins play an important role in forming intramolecular disulfide bonds in seed storage proteins. In addition, these PDI family proteins that remain in the aleurone layers of mature grains likely assist in folding newly synthesized hydrolytic enzymes during germination.
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Affiliation(s)
- Shizuka Kimura
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Yuki Higashino
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Yuki Kitao
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Taro Masuda
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 Japan
| | - Reiko Urade
- Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011 Japan
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7
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Dar MA, Wahiduzzaman, Islam A, Hassan MI, Ahmad F. Purification and characterization of calreticulin: a Ca²⁺-binding chaperone from sheep kidney. Appl Biochem Biotechnol 2014; 174:1771-83. [PMID: 25149453 DOI: 10.1007/s12010-014-1150-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/14/2014] [Indexed: 01/02/2023]
Abstract
Calreticulin (CRT) is a molecular chaperone with a molecular mass of 46 kDa present in the endoplasmic reticulum (ER). This protein is primarily involved in the regulation of intracellular Ca(2+) homeostasis and Ca(2+) storage in the ER. CRT also plays a significant role in autoimmunity and cancer. This protein contains three distinct structural domains with specialized functions. Here, we are reporting a simple procedure for the purification of CRT from mammalian kidney. To isolate CRT, sheep kidney was crushed and kept for 12 h in the extraction buffer. The lysate was centrifuged, and supernatant was precipitated by ammonium sulphate. The precipitate of 90 % ammonium sulphate was extensively dialyzed and loaded on DEAE-Hi-Trap FF and Mono Q chromatography columns. The purity of CRT was confirmed by SDS-PAGE. Finally, the protein was identified by matrix-assisted laser desorption/ionization time of flight. The purified protein was further characterized for secondary structural elements using the far-UV circular dichroism measurements. Our purification procedure is fast and simple with high yield.
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Affiliation(s)
- Mohammad Aasif Dar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
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9
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Takeda Y, Totani K, Matsuo I, Ito Y. Chemical approaches toward understanding glycan-mediated protein quality control. Curr Opin Chem Biol 2009; 13:582-91. [DOI: 10.1016/j.cbpa.2009.09.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 09/01/2009] [Accepted: 09/05/2009] [Indexed: 10/20/2022]
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10
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Alternative conformations of the x region of human protein disulphide-isomerase modulate exposure of the substrate binding b' domain. J Mol Biol 2008; 383:1144-55. [PMID: 18801374 DOI: 10.1016/j.jmb.2008.08.085] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 08/22/2008] [Accepted: 08/26/2008] [Indexed: 10/21/2022]
Abstract
Protein disulphide isomerase (PDI) is a key multi-domain protein folding catalyst in the endoplasmic reticulum. The b' domain of PDI is essential for the non-covalent binding of incompletely folded protein substrates. Earlier, we defined the substrate binding site in the b' domain of human PDI by modelling and mutagenesis studies. Here, we show by fluorescence and NMR that recombinant human PDI b'x (comprising the b' domain and the subsequent x linker region) can assume at least two different conformations in solution. We have screened mutants in the b'x region to identify mutations that favour one of these conformers in recombinant b'x, and isolated and characterised examples of both types. We have crystallised one mutant of b'x (I272A mutation) in which one conformer is stabilized, and determined its crystal structure to a resolution of 2.2 A. This structure shows that the b' domain has the typical thioredoxin fold and that the x region can interact with the b' domain by "capping" a hydrophobic site on the b' domain. This site is most likely the substrate binding site and hence such capping will inhibit substrate binding. All of the mutations we previously reported to inhibit substrate binding shift the equilibrium towards the capped conformer. Hence, these mutations act by altering the natural equilibrium and decreasing the accessibility of the substrate binding site. Furthermore, we have confirmed that the corresponding structural transition occurs in the wild type full-length PDI. A cross-comparison of our data with that for other PDI-family members, Pdi1p and ERp44, suggests that the x region of PDI can adopt alternative conformations during the functional cycle of PDI action and that these are linked to the ability of PDI to interact with folding substrates.
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11
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Pelletier G, Masson S, Wang YL, Wade MG, Mohottalage S, Kumarathasan P, Vincent R, Poon R, Chu I. Proteomic investigation of 1,6-dimethoxyhexane testicular toxicity. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2007; 24:129-133. [PMID: 21783800 DOI: 10.1016/j.etap.2007.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 04/04/2007] [Accepted: 04/09/2007] [Indexed: 05/31/2023]
Abstract
The aliphatic ether 1,6-dimethoxyhexane (DMH) was previously identified as a testicular toxicant. Testis protein extracts from control and DMH-treated rats were subjected to two-dimensional gel electrophoresis for comparison of protein expression profiles. MALDI-ToF peptide mass fingerprinting of differentially expressed proteins resulted in the conclusive identification of heat shock-related 70kDa protein 2 (HSP70.2), 60kDa heat shock protein, mitochondrial precursor (HSP60) and protein disulfide isomerase A3 precursor (ERp60). The potential involvement of these proteins in chemically induced perturbation of spermatogenesis and their utility as biomarkers of testicular toxicity are discussed in light of the knowledge currently available from the literature.
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Affiliation(s)
- Guillaume Pelletier
- Systemic Toxicology and Pharmacokinetics Section, Environmental and Occupational Toxicology Division, Environmental Health Sciences Bureau, Health Canada
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12
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Hagihara S, Goda K, Matsuo I, Ito Y. Analysis of ER-associated glycoprotein degradation using synthetic glycopeptide probes. Biochem Biophys Res Commun 2007; 360:357-62. [PMID: 17592722 DOI: 10.1016/j.bbrc.2007.06.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 06/08/2007] [Indexed: 11/22/2022]
Abstract
Quality control of proteins is an essential process for maintaining normal cell activity. It ensures that only correctly folded proteins are produced and terminally misfolded proteins are eliminated by degradation. ER-associated degradation (ERAD) of misfolded proteins is an important aspect of protein quality control system. Recent studies have revealed that glycoprotein glycans play significant roles in this process. It includes polyubiquitination, deglycosylation, and proteasomal degradation. In the present study, a systematic analysis of these steps was carried out using chemically synthesized glycopeptides. We revealed that N-linked glycopeptides are degraded by 20S proteasome, but with drastically reduced rate compared to non-glycosylated peptide. This result strongly suggests that deglycosylating activity of peptide:N-glycanase (PNGase) is important for the facile degradation of glycoproteins. Our study showed, for the first time, that PNGase cleaves truncated glycans as short as chitobiose from peptide. However, this cleavage required the presence of hydrophobic region nearby N-glycosylation site. Furthermore, analysis of interactions with F-box protein Fbs1 was conducted with fluorescent correlation spectroscopy (FCS). It was shown that the presence of Fbs1 perturb the activity of PNGase toward high-mannose-type glycopeptides.
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Affiliation(s)
- Shinya Hagihara
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Hagihara S, Miyazaki A, Matsuo I, Tatami A, Suzuki T, Ito Y. Fluorescently labeled inhibitor for profiling cytoplasmic peptide:N-glycanase. Glycobiology 2007; 17:1070-6. [PMID: 17640972 DOI: 10.1093/glycob/cwm079] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cytoplasmic peptide:N-glycanase (PNGase) is an enzyme that removes N-glycans from misfolded glycoproteins. The function of cytoplasmic PNGase plays a significant role in the degradation of misfolded glycoproteins, which is critical for cell viability. Recently, we reported that haloacetoamidyl derivatives of high-mannose-type oligosaccharides selectively modify the catalytic cysteine of cytoplasmic PNGase and serve as its specific inhibitor. Interestingly, a drastically simplified chloroacetamidyl chitobiose derivative [(GlcNAc)(2)-ClAc] was also reactive to PNGase. In our work, it was conjugated to a hydrophobic fluorophore in order to render (GlcNAc)(2)-ClAc cells permeable. We demonstrated that this compound [BODIPY-(GlcNAc)(2)-ClAc] specifically binds to cytoplasmic PNGase from budding yeast (Png1). To date, only Z-VAD-fmk is known as an inhibitor of PNGase. BODIPY-(GlcNAc)(2)-ClAc and Z-VAD-fmk share the same binding site on Png1, while BODIPY-(GlcNAc)(2)-ClAc has markedly stronger inhibitory activity. The functional analysis of PNGase using Z-VAD-fmk should be carefully interpreted because of its intrinsic property as a caspase inhibitor. In sharp contrast, chloroacetamidyl chitobiose was not reactive to caspase. In addition, BODIPY-(GlcNAc)(2)-ClAc did not bind either chitobiose-binding lectins or PNGase from other sources. Moreover, fluorescent microscopy clearly showed that BODIPY-(GlcNAc)(2)-ClAc was efficiently introduced into cells. These results suggest that this compound could be an in vivo inhibitor of cytoplasmic PNGase.
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Affiliation(s)
- Shinya Hagihara
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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14
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Wadahama H, Kamauchi S, Ishimoto M, Kawada T, Urade R. Protein disulfide isomerase family proteins involved in soybean protein biogenesis. FEBS J 2007; 274:687-703. [PMID: 17181539 DOI: 10.1111/j.1742-4658.2006.05613.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein disulfide isomerase family proteins are known to play important roles in the folding of nascent polypeptides and the formation of disulfide bonds in the endoplasmic reticulum. In this study, we cloned two similar protein disulfide isomerase family genes from soybean leaf (Glycine max L. Merrill cv. Jack) mRNA by RT-PCR using forward and reverse primers designed from the expressed sequence tag clone sequences. The cDNA encodes a protein of either 364 or 362 amino acids, named GmPDIS-1 or GmPDIS-2, respectively. The nucleotide and amino acid sequence identities of GmPDIS-1 and GmPDIS-2 were 68% and 74%, respectively. Both proteins lack the C-terminal, endoplasmic reticulum-retrieval signal, KDEL. Recombinant proteins of both GmPDIS-1 and GmPDIS-2 were expressed in Escherichia coli as soluble folded proteins that showed both an oxidative refolding activity of denatured ribonuclease A and a chaperone activity. Their domain structures were identified as containing two thioredoxin-like domains, a and a', and an ERp29c domain by peptide mapping with either trypsin or V8 protease. In cotyledon cells, both proteins were shown to distribute to the endoplasmic reticulum and protein storage vacuoles by confocal microscopy. Data from coimmunoprecipitation and crosslinking experiments suggested that GmPDIS-1 associates with proglycinin, a precursor of the seed storage protein glycinin, in the cotyledon. Levels of GmPDIS-1, but not of GmPDIS-2, were increased in cotyledons, where glycinin accumulates during seed development. GmPDIS-1, but not GmPDIS-2, was induced under endoplasmic reticulum-stress conditions.
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15
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Abstract
Secretory and transmembrane proteins are synthesized in the endoplasmic reticulum (ER) in eukaryotic cells. Nascent polypeptide chains, which are translated on the rough ER, are translocated to the ER lumen and folded into their native conformation. When protein folding is inhibited because of mutations or unbalanced ratios of subunits of hetero-oligomeric proteins, unfolded or misfolded proteins accumulate in the ER in an event called ER stress. As ER stress often disturbs normal cellular functions, signal-transduction pathways are activated in an attempt to maintain the homeostasis of the ER. These pathways are collectively referred to as the unfolded protein response (UPR). There have been great advances in our understanding of the molecular mechanisms underlying the UPR in yeast and mammals over the past two decades. In plants, a UPR analogous to those in yeast and mammals has been recognized and has recently attracted considerable attention. This review will summarize recent advances in the plant UPR and highlight the remaining questions that have yet to be addressed.
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Affiliation(s)
- Reiko Urade
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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16
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Görlach A, Klappa P, Kietzmann T. The endoplasmic reticulum: folding, calcium homeostasis, signaling, and redox control. Antioxid Redox Signal 2006; 8:1391-418. [PMID: 16986999 DOI: 10.1089/ars.2006.8.1391] [Citation(s) in RCA: 500] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The endoplasmic reticulum (ER) plays a major role in regulating synthesis, folding, and orderly transport of proteins. It is also essentially involved in various cellular signaling processes, primarily by its function as a dynamic Ca(2+) store. Compared to the cytosol, oxidizing conditions are found in the ER that allow oxidation of cysteine residues in nascent polypeptide chains to form intramolecular disulfide bonds. However, compounds and enzymes such as PDI that catalyze disulfide bonds become reduced and have to be reoxidized for further catalytic cycles. A number of enzymes, among them products of the ERO1 gene, appear to provide oxidizing equivalents, and oxygen appears to be the final oxidant in aerobic living organisms. Thus, protein oxidation in the ER is connected with generation of reactive oxygen species (ROS). Changes in the redox state and the presence of ROS also affect the Ca(2+) homeostasis by modulating the functionality of ER-based channels and buffering chaperones. In addition, a close relationship exists between oxidative stress and ER stress, which both may activate signaling events leading to a rebalance of folding capacity and folding demand or to cell death. Thus, redox homeostasis appears to be a prerequisite for proper functioning of the ER.
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Affiliation(s)
- Agnes Görlach
- Experimental Pediatric Cardiology, Department of Pediatric Cardiology and Congenital Heart Disease, German Heart Center Munich at the Technical University Munich, Munich, Germany
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17
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Okudo H, Kato H, Arakaki Y, Urade R. Cooperation of ER-60 and BiP in the Oxidative Refolding of Denatured Proteins In Vitro. ACTA ACUST UNITED AC 2005; 138:773-80. [PMID: 16428306 DOI: 10.1093/jb/mvi166] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
ER-60 is a PDI family protein that has protein thiol-disulfide oxidoreductase activity. It has been shown to associate with BiP in the endoplasmic reticulum. Here, we analyzed the cooperation of ER-60 and BiP in the oxidative refolding of denatured proteins in vitro. ER-60 facilitated the refolding of 20 or 30% of denatured alpha-lactalbumin or ribonuclease B during incubation for 80 min, and these levels of nearly doubled on the addition of BiP to the reaction mixture. BiP alone could not refold denatured ribonuclease B, but could refold denatured alpha-lactalbumin a little. Enhancement of oxidative refolding of alpha-lactalbumin by ER-60 could be detected only when ER-60 was present from the start of refolding. On surface plasmon resonance analysis, ER-60 was shown to associate with BiP. The association was not influenced by ATP or ADP. Domains a and/or b' of ER-60 were implicated in the association with BiP.
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Affiliation(s)
- Hirokazu Okudo
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011
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Ito Y, Hagihara S, Matsuo I, Totani K. Structural approaches to the study of oligosaccharides in glycoprotein quality control. Curr Opin Struct Biol 2005; 15:481-9. [PMID: 16154739 DOI: 10.1016/j.sbi.2005.08.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 06/08/2005] [Accepted: 08/31/2005] [Indexed: 11/23/2022]
Abstract
High-mannose-type oligosaccharides have been shown to play important roles in protein quality control. Several intracellular proteins, such as lectins, chaperones and glycan-processing enzymes, are involved in this process. These include calnexin/calreticulin, UDP-glucose:glycoprotein glucosyltransferase (UGGT), cargo receptors (such as VIP36 and ERGIC-53), mannosidase-like proteins (e.g. EDEM and Htm1p) and ubiquitin ligase (Fbs). They are thought to recognize high-mannose-type glycans with subtly different structures, although the precise specificities are yet to be clarified. In order to gain a clear understanding of these protein-carbohydrate interactions, comprehensive synthesis of high-mannose-type glycans was conducted. In addition, two approaches to the synthesis of artificial glycoproteins with homogeneous oligosaccharides were investigated. Furthermore, a novel substrate of UGGT was discovered.
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Affiliation(s)
- Yukishige Ito
- RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Ellgaard L, Ruddock LW. The human protein disulphide isomerase family: substrate interactions and functional properties. EMBO Rep 2005; 6:28-32. [PMID: 15643448 PMCID: PMC1299221 DOI: 10.1038/sj.embor.7400311] [Citation(s) in RCA: 578] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2004] [Accepted: 11/11/2004] [Indexed: 11/08/2022] Open
Abstract
The process of disulphide bond formation in the endoplasmic reticulum of eukaryotic cells was one of the first mechanisms of catalysed protein folding to be discovered. Protein disulphide isomerase (PDI) is now known to catalyse all of the reactions that are involved in native disulphide bond formation, but despite more than 40 years of study, its mechanism of action is still not fully understood. This review discusses recent advances in our understanding of the human PDI family of enzymes and focuses on their functional properties, substrate interactions and some recently identified family members.
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Affiliation(s)
- Lars Ellgaard
- Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Lloyd W. Ruddock
- Department of Biochemistry and Biocenter Oulu, PO Box 3000, University of Oulu, 90014 Oulu, Finland
- Tel: +358 8553 1683; Fax: +358 8553 1141;
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Kamauchi S, Nakatani H, Nakano C, Urade R. Gene expression in response to endoplasmic reticulum stress in Arabidopsis thaliana. FEBS J 2005; 272:3461-76. [PMID: 15978049 DOI: 10.1111/j.1742-4658.2005.04770.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Eukaryotic cells respond to the accumulation of unfolded proteins in the endoplasmic reticulum (ER). In this case, so-called unfolded protein response (UPR) genes are induced. We determined the transcriptional expression of Arabidopsis thaliana UPR genes by fluid microarray analysis of tunicamycin-treated plantlets. Two hundred and fifteen up-regulated genes and 17 down-regulated ones were identified. These genes were reanalyzed with functional DNA microarrays, using DNA fragments cloned through fluid microarray analysis. Finally, 36 up-regulated and two down-regulated genes were recognized as UPR genes. Among them, the up-regulation of genes related to protein degradation (HRD1, SEL-1L/HRD3 and DER1), regulation of translation (P58(IPK)), and apoptosis (BAX inhibitor-1) was reconfirmed by real-time reverse transcriptase-PCR. The induction of SEL-1L protein in an Arabidopsis membrane fraction on tunicamycin-treatment was demonstrated. Phosphorylation of initiation factor-2alpha, which was inhibited by P58(IPK), was decreased in tunicamycin-treated plantlets. However, regulatory changes in translation caused by ER stress were not detected in Arabidopsis. Plant cells appeared to have a strategy for overcoming ER stress through enhancement of protein folding activity, degradation of unfolded proteins, and regulation of apoptosis, but not regulation of translation.
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Affiliation(s)
- Shinya Kamauchi
- Graduate School of Agriculture, Kyoto University, Uji, Japan
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Kimura T, Imaishi K, Hagiwara Y, Horibe T, Hayano T, Takahashi N, Urade R, Kato K, Kikuchi M. ERp57 binds competitively to protein disulfide isomerase and calreticulin. Biochem Biophys Res Commun 2005; 331:224-30. [PMID: 15845382 DOI: 10.1016/j.bbrc.2005.03.147] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Indexed: 11/27/2022]
Abstract
In this study, we screened for protein disulfide isomerase (PDI)-binding proteins in bovine liver microsomes under strict salt concentrations, using affinity column chromatography. One main band observed using SDS-PAGE was identified as ERp57 (one of the PDI family proteins) by LC-MS/MS analysis. The K(D) value of PDI binding to ERp57 was calculated as 5.46x10(-6)M with the BIACORE system. The interactions between PDI and ERp57 occurred specifically at their a and b domains, respectively. Interestingly, low concentrations of ERp57 enhanced the chaperone activity of PDI, while high concentrations interfered with chaperone activity. On the other hand, ERp57 did not affect the isomerase activity of PDI. Additionally, following pre-incubation of ERp57 with calreticulin (CRT), decreased interactions were observed between ERp57 and PDI, and vice versa. Based on the data, we propose that once ERp57 binds to PDI or CRT, the resultant complex inhibits further interactions. Therefore, ERp57 selectively forms a protein-folding complex with PDI or CRT in ER.
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Affiliation(s)
- Taiji Kimura
- Department of Bioscience and Technology, Faculty of Science and Engineering, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
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Haugstetter J, Blicher T, Ellgaard L. Identification and Characterization of a Novel Thioredoxin-related Transmembrane Protein of the Endoplasmic Reticulum. J Biol Chem 2005; 280:8371-80. [PMID: 15623505 DOI: 10.1074/jbc.m413924200] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER) contains a number of thiol-disulfide oxidoreductases of the protein-disulfide isomerase (PDI) family that catalyze the formation of disulfide bonds in newly synthesized proteins. Here we describe the identification and characterization of a novel member of the human PDI family, TMX3 (thioredoxin-related transmembrane protein 3). The TMX3 gene encodes a protein of 454 amino acid residues that contains a predicted N-terminal signal sequence, a single domain with sequence similarity to thioredoxin and a CGHC active site sequence, a potential transmembrane domain, and a C-terminal KKKD tetrapeptide sequence that matches the classical KKXX-type consensus sequence for ER retrieval of type I transmembrane proteins. Endogenous TMX3 contains endoglycosidase H-sensitive glycans, localizes to the ER by immunofluorescence microscopy, and is present in the membrane fraction after alkaline extraction of the ER luminal content. The TMX3 transcript is found in a variety of tissues and is not up-regulated by the unfolded protein response. Circular dichroism spectroscopy of the recombinantly expressed luminal domain of TMX3 showed features typical of a properly folded protein of the alpha/beta type. The redox potential of recombinant luminal TMX3 was determined to -0.157 V, similar to the values previously found for PDI and ERp57. Interestingly, TMX3 showed oxidase activity, and in human tissue-culture cells the protein was found partially in the oxidized form, potentially suggesting a function of the protein as a dithiol oxidase.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Blotting, Northern
- Blotting, Western
- Catalysis
- Cell Line
- Cell Membrane/metabolism
- Cells, Cultured
- Chlorocebus aethiops
- Circular Dichroism
- Dose-Response Relationship, Drug
- Endoplasmic Reticulum/metabolism
- Exons
- Genetic Vectors
- Glutathione/chemistry
- Glycoside Hydrolases/chemistry
- Glycoside Hydrolases/metabolism
- HeLa Cells
- Humans
- Introns
- Kinetics
- Microscopy, Fluorescence
- Molecular Sequence Data
- Oxidation-Reduction
- Oxidoreductases/chemistry
- Oxidoreductases/metabolism
- Oxygen/metabolism
- Peptides/chemistry
- Plasmids/metabolism
- Protein Denaturation
- Protein Disulfide-Isomerases/biosynthesis
- Protein Disulfide-Isomerases/chemistry
- Protein Folding
- Protein Structure, Tertiary
- RNA, Messenger/metabolism
- Recombinant Proteins/chemistry
- Sequence Homology, Amino Acid
- Spectrometry, Fluorescence
- Spectrophotometry
- Subcellular Fractions
- Thioredoxins/chemistry
- Time Factors
- Tissue Distribution
- Transcription, Genetic
- Ultraviolet Rays
- Up-Regulation
- Vero Cells
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Abstract
The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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