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Hu B, Wang J, Li Y, Ge J, Pan J, Li G, He Y, Zhong H, Wang B, Huang Y, Han S, Xing Y, He H. Gut microbiota facilitates adaptation of the plateau zokor ( Myospalax baileyi) to the plateau living environment. Front Microbiol 2023; 14:1136845. [PMID: 36910168 PMCID: PMC9998695 DOI: 10.3389/fmicb.2023.1136845] [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: 01/03/2023] [Accepted: 02/06/2023] [Indexed: 03/14/2023] Open
Abstract
Gut microbiota not only helps the hosts to perform many key physiological functions such as food digestion, energy harvesting and immune regulation, but also influences host ecology and facilitates adaptation of the host to extreme environments. Plateau zokors epitomize successful physiological adaptation to their living environment in the face of the harsh environment characterized by low temperature, low pressure and hypoxia in the Tibetan plateau region and high concentrations of CO2 in their burrows. Therefore, here we used a metagenomic sequencing approach to explore how gut microbiota contributed to the adaptive evolution of the plateau zokor on the Qinghai-Tibet Plateau. Our metagenomic results show that the gut microbiota of plateau zokors on the Tibetan plateau is not only enriched in a large number of species related to energy metabolism and production of short-chain fatty acids (SCFAs), but also significantly enriched the KO terms that involve carbohydrate uptake pathways, which well address energy uptake in plateau zokors while also reducing inflammatory responses due to low pressure, hypoxia and high CO2 concentrations. There was also a significant enrichment of tripeptidyl-peptidase II (TPPII) associated with antigen processing, apoptosis, DNA damage repair and cell division, which may facilitate the immune response and tissue damage repair in plateau zokors under extreme conditions. These results suggest that these gut microbiota and their metabolites together contribute to the physiological adaptation of plateau zokors, providing new insights into the contribution of the microbiome to the evolution of mammalian adaptation.
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Affiliation(s)
- Bin Hu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jiamin Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Jin Ge
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jinchao Pan
- College of Animal Sciences, Anhui University of Science and Technology, Huainan, China
| | - Gaojian Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yongcai He
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Haishun Zhong
- Animal Husbandry and Veterinary Station of Xunhua, Xining, Qinghai, China
| | - Bo Wang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanyi Huang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shuyi Han
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Xing
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Hongxuan He
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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2
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Liao CL, Hu RC, Liao MS, Chen YJ, Chen YP, Hsieh HH, Tai CH, Chou TC, Chu CY, Chen YJ, Lo LC, Lin JJ. Unveiling a novel serpinB2/tripeptidyl peptidase II signaling axis during senescence. J Cell Sci 2022; 135:275508. [PMID: 35466366 DOI: 10.1242/jcs.259513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
Tripeptidyl peptidase II (TPPII) degrades N-terminal tripeptides from proteins and peptides. Studies in both human and mice have shown that TPPII deficiency is linked to cellular immune-senescence, lifespan regulation, and the aging process. However, the mechanism of how TPPII participates in these processes is less clear. In this study, we established a chemical probe-based assay and found that while the mRNA and protein levels of TPPII were not altered during senescence, its enzymatic activity was reduced in senescent human fibroblasts. We also showed that elevation of serine protease inhibitor serpinB2 reduced TPPII activity in senescent cells. Moreover, suppression of TPPII led to elevation of lysosomal contents as well as TPPI and -galactosidase activities, suggesting that the lysosome biogenesis is induced to compensate for the reduction of TPPII activity in senescent cells. Together this study discloses a critical role of the serpinB2/TPPII signaling pathway in proteostasis during senescence. Since serpinB2 level can be increased by a variety of cellular stresses, reduction of TPPII activity through activation of serpinB2 might represent a common pathway for cells to respond to different stress conditions.
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Affiliation(s)
- Chia-Li Liao
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 100, Taiwan
| | - Rong-Chi Hu
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 100, Taiwan
| | - Min-Shiang Liao
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Ya-Ping Chen
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Hsi-Hsien Hsieh
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, 112, Taiwan
| | - Chih-Hsuan Tai
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Tzyy-Chao Chou
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Chi-Yuan Chu
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Lee-Chiang Lo
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Jing-Jer Lin
- Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, 100, Taiwan
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3
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Liaño-Pons J, Arsenian-Henriksson M, León J. The Multiple Faces of MNT and Its Role as a MYC Modulator. Cancers (Basel) 2021; 13:4682. [PMID: 34572909 PMCID: PMC8465425 DOI: 10.3390/cancers13184682] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/29/2022] Open
Abstract
MNT is a crucial modulator of MYC, controls several cellular functions, and is activated in most human cancers. It is the largest, most divergent, and most ubiquitously expressed protein of the MXD family. MNT was first described as a MYC antagonist and tumor suppressor. Indeed, 10% of human tumors present deletions of one MNT allele. However, some reports show that MNT functions in cooperation with MYC by maintaining cell proliferation, promoting tumor cell survival, and supporting MYC-driven tumorigenesis in cellular and animal models. Although MAX was originally considered MNT's obligate partner, our recent findings demonstrate that MNT also works independently. MNT forms homodimers and interacts with proteins both outside and inside of the proximal MYC network. These complexes are involved in a wide array of cellular processes, from transcriptional repression via SIN3 to the modulation of metabolism through MLX as well as immunity and apoptosis via REL. In this review, we discuss the present knowledge of MNT with a special focus on its interactome, which sheds light on the complex and essential role of MNT in cell biology.
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Affiliation(s)
- Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden;
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 65 Stockholm, Sweden;
| | - Javier León
- Departmento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, 39011 Santander, Spain;
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4
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Covarrubias-Zambrano O, Yu J, Bossmann SH. Nano-Inspired Technologies for Peptide Delivery. Curr Protein Pept Sci 2019; 21:379-400. [PMID: 31793426 DOI: 10.2174/1389203720666191202112429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/26/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
Nano-inspired technologies offer unique opportunities to treat numerous diseases by using therapeutic peptides. Therapeutic peptides have attractive pharmacological profiles and can be manufactured at relatively low costs. The major advantages of using a nanodelivery approach comprises significantly lower required dosages compared to systemic delivery, and thus reduced toxicity and immunogenicity. The combination of therapeutic peptides with delivery peptides and nanoparticles or small molecule drugs offers systemic treatment approaches, instead of aiming for single biological targets or pathways. This review article discusses exemplary state-of-the-art nanosized delivery systems for therapeutic peptides and antibodies, as well as their biochemical and biophysical foundations and emphasizes still remaining challenges. The competition between using different nanoplatforms, such as liposome-, hydrogel-, polymer-, silica nanosphere-, or nanosponge-based delivery systems is still "on" and no clear frontrunner has emerged to date.
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Affiliation(s)
| | - Jing Yu
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States.,Johns Hopkins University, Department of Radiology, Baltimore, MD, United States
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, 419 CBC Building, Manhattan, KS 66506-0401, United States
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5
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Tomkinson B. Tripeptidyl-peptidase II: Update on an oldie that still counts. Biochimie 2019; 166:27-37. [DOI: 10.1016/j.biochi.2019.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/14/2019] [Indexed: 12/30/2022]
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6
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Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K. Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Cell Rep 2019; 29:1351-1368.e5. [PMID: 31665645 PMCID: PMC6873818 DOI: 10.1016/j.celrep.2019.09.060] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/30/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022] Open
Abstract
RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% of known human protein complexes contain RNA. To explore the role of RNA in the assembly of each complex, we identify complexes that dissociate, change composition, or form stable protein-only complexes in the absence of RNA. We use our method to systematically identify cell-type-specific RNA-associated proteins in mouse embryonic stem cells and finally, distribute our resource, rna.MAP, in an easy-to-use online interface (rna.proteincomplexes.org). Our system thus provides a methodology for explorations across human tissues, disease states, and throughout all domains of life.
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Affiliation(s)
- Anna L Mallam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Wisath Sae-Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey M Schaub
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fan Tu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Anna Battenhouse
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Jin Jang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Kevin Drew
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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7
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Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs). Sci Rep 2019; 9:12485. [PMID: 31462749 PMCID: PMC6713707 DOI: 10.1038/s41598-019-48664-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/09/2019] [Indexed: 12/31/2022] Open
Abstract
Plant subtilases (SBTs) are a widely distributed family of serine proteases which participates in plant developmental processes and immune responses. Although SBTs are divided into seven subgroups in plants, their origin and evolution, particularly in green algae remain elusive. Here, we present a comprehensive large-scale evolutionary analysis of all subtilases. The plant subtilases SBT1-5 were found to be monophyletic, nested within a larger radiation of bacteria suggesting that they originated from bacteria by a single horizontal gene transfer (HGT) event. A group of bacterial subtilases comprising representatives from four phyla was identified as a sister group to SBT1-5. The phylogenetic analyses, based on evaluation of novel streptophyte algal genomes, suggested that the recipient of the HGT of bacterial subtilases was the common ancestor of Coleochaetophyceae, Zygnematophyceae and embryophytes. Following the HGT, the subtilase gene duplicated in the common ancestor and the two genes diversified into SBT2 and SBT1, 3–5 respectively. Comparative structural analysis of homology-modeled SBT2 proteins also showed their conservation from bacteria to embryophytes. Our study provides the first molecular evidence about the evolution of plant subtilases via HGT followed by a first gene duplication in the common ancestor of Coleochaetophyceae, Zygnematophyceae, and embryophytes, and subsequent expansion in embryophytes.
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8
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Tibúrcio R, Nunes S, Nunes I, Rosa Ampuero M, Silva IB, Lima R, Machado Tavares N, Brodskyn C. Molecular Aspects of Dendritic Cell Activation in Leishmaniasis: An Immunobiological View. Front Immunol 2019; 10:227. [PMID: 30873156 PMCID: PMC6401646 DOI: 10.3389/fimmu.2019.00227] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/28/2019] [Indexed: 12/11/2022] Open
Abstract
Dendritic cells (DC) are a diverse group of leukocytes responsible for bridging innate and adaptive immunity. Despite their functional versatility, DCs exist primarily in two basic functional states: immature and mature. A large body of evidence suggests that upon interactions with pathogens, DCs undergo intricate cellular processes that culminate in their activation, which is paramount to the orchestration of effective immune responses against Leishmania parasites. Herein we offer a concise review of the emerging hallmarks of DCs activation in leishmaniasis as well as a comprehensive discussion of the following underlying molecular events: DC-Leishmania interaction, antigen uptake, costimulatory molecule expression, parasite ability to affect DC migration, antigen presentation, metabolic reprogramming, and epigenetic alterations.
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Affiliation(s)
- Rafael Tibúrcio
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Sara Nunes
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Ivanéia Nunes
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Mariana Rosa Ampuero
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Icaro Bonyek Silva
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Reinan Lima
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil
| | - Natalia Machado Tavares
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil.,Instituto Nacional de Ciência e Tecnologia (INCT) iii Instituto de Investigação em Imunologia, São Paulo, Brazil
| | - Cláudia Brodskyn
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil.,Federal University of Bahia, Salvador, Brazil.,Instituto Nacional de Ciência e Tecnologia (INCT) iii Instituto de Investigação em Imunologia, São Paulo, Brazil
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9
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Wagner J, Schaffer M, Fernández-Busnadiego R. Cryo-electron tomography-the cell biology that came in from the cold. FEBS Lett 2017; 591:2520-2533. [PMID: 28726246 DOI: 10.1002/1873-3468.12757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/26/2017] [Accepted: 07/14/2017] [Indexed: 12/27/2022]
Abstract
Cryo-electron tomography (cryo-ET) provides high-resolution 3D views into cells pristinely preserved by vitrification. Recent technical advances such as direct electron detectors, the Volta phase plate and cryo-focused ion beam milling have dramatically pushed image quality and expanded the range of cryo-ET applications. Cryo-ET not only allows mapping the positions and interactions of macromolecules within their intact cellular context, but can also reveal their in situ structure at increasing resolution. Here, we review how recent work using cutting-edge cryo-ET technologies is starting to provide fresh views into different aspects of cellular biology at an unprecedented level of detail. We anticipate that these developments will soon make cryo-ET a fundamental technique in cell biology.
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10
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Zhao F, Gao LH, Li SS, Wei ZY, Fu WZ, He JW, Liu YJ, Hu YQ, Dong J, Zhang ZL. Association between SNPs and haplotypes in the METTL21C gene and peak bone mineral density and body composition in Chinese male nuclear families. J Bone Miner Metab 2017; 35:437-447. [PMID: 27628047 DOI: 10.1007/s00774-016-0774-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/30/2016] [Indexed: 10/21/2022]
Abstract
The methyltransferase-like 21C gene (METTL21C), which is mainly expressed in muscle, can promote the differentiation of myoblasts to myotubes and reduce glucocorticoid-induced apoptosis of osteocytes. The purpose of this study was to explore the association between single nucleotide polymorphisms of METTL21C and peak bone mineral density (BMD), body mass index, total fat mass (TFM), and total lean mass (TLM) in Chinese young men. Fifteen tagging single nucleotide polymorphisms were genotyped, and haplotype blocks were derived in 400 Chinese male nuclear families. The peak BMD of the lumbar and hip, TFM, and TLM were measured by dual-energy X-ray absorptiometry. The association analyses were performed by a quantitative transmission disequilibrium test. Both TLM and TFM had a significant positive effect on peak BMD, but the positive regulation of TLM was stronger than that of TFM. After 1000 permutations, significant within-family associations were found between rs9585961 and lumbar spine BMD and femoral neck BMD, rs9518810 and femoral neck BMD, and rs599976 and body mass index, TFM, and percentage fat mass (all P < 0.05). The association analyses with haplotypes showed that haplotype AG in block 1 was significantly associated with TFM (P = 0.031) and haplotype CAG in block 2 was significantly associated with lumbar spine BMD (P = 0.020). Our study, for the first time, demonstrates that the polymorphisms and haplotypes of METTL21C contribute to the peak BMD and TFM in Chinese males, which suggests that as a quantitative trait locus with potential pleiotropy it may have an influence on osteoporosis and obesity.
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Affiliation(s)
- Fei Zhao
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
- Department of Endocrinology, Shanxi Medical University Affiliated First Hospital, Taiyuan, 030001, China
| | - Li-Hong Gao
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Shan-Shan Li
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Zhan-Ying Wei
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Wen-Zhen Fu
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Jin-Wei He
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Yu-Juan Liu
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Yun-Qiu Hu
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China
| | - Jing Dong
- Department of Endocrinology, Shanxi Medical University Affiliated First Hospital, Taiyuan, 030001, China
| | - Zhen-Lin Zhang
- Division of Osteoporosis and Bone Disease, Metabolic Bone Disease and Genetic Research Unit, Department of Endocrinology and Metabolism, Shanghai Jiao Tong University Affiliated Six People's Hospital, Shanghai, 200233, China.
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11
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In situ structural studies of tripeptidyl peptidase II (TPPII) reveal spatial association with proteasomes. Proc Natl Acad Sci U S A 2017; 114:4412-4417. [PMID: 28396430 DOI: 10.1073/pnas.1701367114] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tripeptidyl peptidase II (TPPII) is a eukaryotic protease acting downstream of the 26S proteasome; it removes tripeptides from the degradation products released by the proteasome. Structural studies in vitro have revealed the basic architecture of TPPII, a two-stranded linear polymer that assembles to form a spindle-shaped complex of ∼6 MDa. Dependent on protein concentration, TPPII has a distinct tendency for polymorphism. Therefore, its structure in vivo has remained unclear. To resolve this issue, we have scrutinized cryo-electron tomograms of rat hippocampal neurons for the occurrence and spatial distribution of TPPII by template matching. The quality of the tomograms recorded with the Volta phase plate enabled a detailed structural analysis of TPPII despite its low abundance. Two different assembly states (36-mers and 32-mers) coexist as well as occasional extended forms with longer strands. A distance analysis of the relative locations of TPPII and 26S proteasomes confirmed the visual impression that these two complexes spatially associate in agreement with TPPII's role in postproteasomal degradation.
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12
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Gao X, Zeng J, Yi H, Zhang F, Tang B, Tang XF. Four Inserts within the Catalytic Domain Confer Extra Stability and Activity to Hyperthermostable Pyrolysin from Pyrococcus furiosus. Appl Environ Microbiol 2017; 83:e03228-16. [PMID: 28003199 PMCID: PMC5311392 DOI: 10.1128/aem.03228-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 12/17/2016] [Indexed: 11/20/2022] Open
Abstract
Pyrolysin from the hyperthermophilic archaeon Pyrococcus furiosus is the prototype of the pyrolysin family of the subtilisin-like serine protease superfamily (subtilases). It contains four inserts (IS147, IS29, IS27, and IS8) of unknown function in the catalytic domain. We performed domain deletions and showed that three inserts are either essential (IS147 and IS27) or important (IS8) for efficient maturation of pyrolysin at high temperatures, whereas IS29 is dispensable. The large insert IS147 contains Ca3 and Ca4, two calcium-binding Dx[DN]xDG motifs that are conserved in many pyrolysin-like proteases. Mutagenesis revealed that the Ca3 site contributes to enzyme thermostability and the Ca4 site is necessary for pyrolysin to fold into a maturation-competent conformation. Mature insert-deletion variants were characterized and showed that IS29 and IS8 contribute to enzyme activity and stability, respectively. In the presence of NaCl, pyrolysin undergoes autocleavage at two sites: one within IS29 and the other in IS27 Disrupting the ion pairs in IS27 and IS8 induces autocleavage in the absence of salts. Interestingly, autocleavage products combine noncovalently to form an active, nicked enzyme that is resistant to SDS and urea denaturation. Additionally, a single mutation in IS29 increases resistance to salt-induced autocleavage and further increases enzyme thermostability. Our results suggest that these extra structural elements play a crucial role in adapting pyrolysin to hyperthermal environments.IMPORTANCE Pyrolysin-like proteases belong to the subtilase superfamily and are characterized by large inserts and long C-terminal extensions; however, the role of the inserts in enzyme function is unclear. Our results demonstrate that four inserts in the catalytic domain of hyperthermostable pyrolysin contribute to the folding, maturation, stability, and activity of the enzyme at high temperatures. The modification of extra structural elements in pyrolysin-like proteases is a promising strategy for modulating global structure stability and enzymatic activity of this class of protease.
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Affiliation(s)
- Xiaowei Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jing Zeng
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huawei Yi
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Fang Zhang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Bing Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
| | - Xiao-Feng Tang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China
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13
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Tan Q, Ma S, Hu J, Chen X, Yu Y, Zang G, Tang Z. Role of tripeptidyl peptidase II in MHC class I antigen presentation: Biological characteristics, cellular crosstalk and signaling. Biomed Pharmacother 2016; 84:1954-1958. [PMID: 27829551 DOI: 10.1016/j.biopha.2016.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 01/29/2023] Open
Abstract
Tripeptidyl peptidase II (TPPII) is a multifunctional cytoplasmic serine protease. The main function of TPPII is to cleave proteasome-generated peptides into tripeptides, which can then be further degraded into free amino acids. Recent evidence suggests that TPPII plays an important role in epitope generation, but the mechanisms of TPPII in MHC class I antigen presentation remain unclear. Recent research has shed new light on the mechanisms and functions of TPPII in MHC class I antigen presentation. We therefore provide an updated review of the biological characteristics of TPPII and explore its role in MHC class I antigen presentation.
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Affiliation(s)
- Quanhui Tan
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Siyuan Ma
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Jianjun Hu
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Xiaohua Chen
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Yongsheng Yu
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Guoqing Zang
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Zhenghao Tang
- Department of Infectious Disease, Shanghai Jiao Tong University, Affiliated Sixth People's Hospital, Shanghai 200233, China.
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14
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Wiemhoefer A, Stargardt A, van der Linden WA, Renner MC, van Kesteren RE, Stap J, Raspe MA, Tomkinson B, Kessels HW, Ovaa H, Overkleeft HS, Florea B, Reits EA. Tripeptidyl Peptidase II Mediates Levels of Nuclear Phosphorylated ERK1 and ERK2. Mol Cell Proteomics 2015; 14:2177-93. [PMID: 26041847 DOI: 10.1074/mcp.m114.043331] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Indexed: 12/22/2022] Open
Abstract
Tripeptidyl peptidase II (TPP2) is a serine peptidase involved in various biological processes, including antigen processing, cell growth, DNA repair, and neuropeptide mediated signaling. The underlying mechanisms of how a peptidase can influence this multitude of processes still remain unknown. We identified rapid proteomic changes in neuroblastoma cells following selective TPP2 inhibition using the known reversible inhibitor butabindide, as well as a new, more potent, and irreversible peptide phosphonate inhibitor. Our data show that TPP2 inhibition indirectly but rapidly decreases the levels of active, di-phosphorylated extracellular signal-regulated kinase 1 (ERK1) and ERK2 in the nucleus, thereby down-regulating signal transduction downstream of growth factors and mitogenic stimuli. We conclude that TPP2 mediates many important cellular functions by controlling ERK1 and ERK2 phosphorylation. For instance, we show that TPP2 inhibition of neurons in the hippocampus leads to an excessive strengthening of synapses, indicating that TPP2 activity is crucial for normal brain function.
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Affiliation(s)
- Anne Wiemhoefer
- From the ‡Department of Cell Biology and Histology, Academic Medical Centre- University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Anita Stargardt
- From the ‡Department of Cell Biology and Histology, Academic Medical Centre- University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Wouter A van der Linden
- §Department of Pathology, Stanford School of Medicine, 300 Pasteur Drive, Stanford, CA 94305-5324
| | - Maria C Renner
- ¶Netherlands Institute for Neuroscience, Meibergdreef 47, 1105BA Amsterdam, The Netherlands
| | - Ronald E van Kesteren
- ‖Center for Neurogenomics and Cognitive Research, VU University Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Jan Stap
- From the ‡Department of Cell Biology and Histology, Academic Medical Centre- University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands
| | - Marcel A Raspe
- **Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Birgitta Tomkinson
- ‡‡Department of Medical Biochemistry and Microbiology, University of Uppsala, Husargatan 3, 75123 Uppsala, Sweden
| | - Helmut W Kessels
- ¶Netherlands Institute for Neuroscience, Meibergdreef 47, 1105BA Amsterdam, The Netherlands
| | - Huib Ovaa
- **Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Herman S Overkleeft
- §§Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Bogdan Florea
- §§Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Eric A Reits
- From the ‡Department of Cell Biology and Histology, Academic Medical Centre- University of Amsterdam, Meibergdreef 15, 1105AZ Amsterdam, The Netherlands;
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15
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Early-onset Evans syndrome, immunodeficiency, and premature immunosenescence associated with tripeptidyl-peptidase II deficiency. Blood 2014; 125:753-61. [PMID: 25414442 DOI: 10.1182/blood-2014-08-593202] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Autoimmune cytopenia is a frequent manifestation of primary immunodeficiencies. Two siblings presented with Evans syndrome, viral infections, and progressive leukopenia. DNA available from one patient showed a homozygous frameshift mutation in tripeptidyl peptidase II (TPP2) abolishing protein expression. TPP2 is a serine exopeptidase involved in extralysosomal peptide degradation. Its deficiency in mice activates cell death programs and premature senescence. Similar to cells from naïve, uninfected TPP2-deficient mice, patient cells showed increased major histocompatibility complex I expression and most CD8(+) T-cells had a senescent CCR7-CD127(-)CD28(-)CD57(+) phenotype with poor proliferative responses and enhanced staurosporine-induced apoptosis. T-cells showed increased expression of the effector molecules perforin and interferon-γ with high expression of the transcription factor T-bet. Age-associated B-cells with a CD21(-) CD11c(+) phenotype expressing T-bet were increased in humans and mice, combined with antinuclear antibodies. Moreover, markers of senescence were also present in human and murine TPP2-deficient fibroblasts. Telomere lengths were normal in patient fibroblasts and granulocytes, and low normal in lymphocytes, which were compatible with activation of stress-induced rather than replicative senescence programs. TPP2 deficiency is the first primary immunodeficiency linking premature immunosenescence to severe autoimmunity. Determination of senescent lymphocytes should be part of the diagnostic evaluation of children with refractory multilineage cytopenias.
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16
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Juenemann K, Schipper-Krom S, Wiemhoefer A, Kloss A, Sanz Sanz A, Reits EAJ. Expanded polyglutamine-containing N-terminal huntingtin fragments are entirely degraded by mammalian proteasomes. J Biol Chem 2013; 288:27068-27084. [PMID: 23908352 DOI: 10.1074/jbc.m113.486076] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Huntington disease is a neurodegenerative disorder caused by an expanded polyglutamine (polyQ) repeat within the protein huntingtin (Htt). N-terminal fragments of the mutant Htt (mHtt) proteins containing the polyQ repeat are aggregation-prone and form intracellular inclusion bodies. Improving the clearance of mHtt fragments by intracellular degradation pathways is relevant to obviate toxic mHtt species and subsequent neurodegeneration. Because the proteasomal degradation pathway has been the subject of controversy regarding the processing of expanded polyQ repeats, we examined whether the proteasome can efficiently degrade Htt-exon1 with an expanded polyQ stretch both in neuronal cells and in vitro. Upon targeting mHtt-exon1 to the proteasome, rapid and complete clearance of mHtt-exon1 was observed. Proteasomal degradation of mHtt-exon1 was devoid of polyQ peptides as partial cleavage products by incomplete proteolysis, indicating that mammalian proteasomes are capable of efficiently degrading expanded polyQ sequences without an inhibitory effect on the proteasomal activity.
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Affiliation(s)
- Katrin Juenemann
- Department of Cellbiology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
| | - Sabine Schipper-Krom
- Department of Cellbiology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Anne Wiemhoefer
- Department of Cellbiology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Alexander Kloss
- Institut für Biochemie/CCM, Charité-Universitätsmedizin Berlin, Monbijoustrasse 2, Berlin 10117, Germany
| | - Alicia Sanz Sanz
- Department of Cellbiology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Eric A J Reits
- Department of Cellbiology and Histology, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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17
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Withers-Martinez C, Suarez C, Fulle S, Kher S, Penzo M, Ebejer JP, Koussis K, Hackett F, Jirgensons A, Finn P, Blackman MJ. Plasmodium subtilisin-like protease 1 (SUB1): insights into the active-site structure, specificity and function of a pan-malaria drug target. Int J Parasitol 2012; 42:597-612. [PMID: 22543039 PMCID: PMC3378952 DOI: 10.1016/j.ijpara.2012.04.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 03/29/2012] [Accepted: 04/12/2012] [Indexed: 01/09/2023]
Abstract
Release of the malaria merozoite from its host erythrocyte (egress) and invasion of a fresh cell are crucial steps in the life cycle of the malaria pathogen. Subtilisin-like protease 1 (SUB1) is a parasite serine protease implicated in both processes. In the most dangerous human malarial species, Plasmodium falciparum, SUB1 has previously been shown to have several parasite-derived substrates, proteolytic cleavage of which is important both for egress and maturation of the merozoite surface to enable invasion. Here we have used molecular modelling, existing knowledge of SUB1 substrates, and recombinant expression and characterisation of additional Plasmodium SUB1 orthologues, to examine the active site architecture and substrate specificity of P. falciparum SUB1 and its orthologues from the two other major human malaria pathogens Plasmodium vivax and Plasmodium knowlesi, as well as from the rodent malaria species, Plasmodium berghei. Our results reveal a number of unusual features of the SUB1 substrate binding cleft, including a requirement to interact with both prime and non-prime side residues of the substrate recognition motif. Cleavage of conserved parasite substrates is mediated by SUB1 in all parasite species examined, and the importance of this is supported by evidence for species-specific co-evolution of protease and substrates. Two peptidyl alpha-ketoamides based on an authentic PfSUB1 substrate inhibit all SUB1 orthologues examined, with inhibitory potency enhanced by the presence of a carboxyl moiety designed to introduce prime side interactions with the protease. Our findings demonstrate that it should be possible to develop ‘pan-reactive’ drug-like compounds that inhibit SUB1 in all three major human malaria pathogens, enabling production of broad-spectrum antimalarial drugs targeting SUB1.
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18
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Schönegge AM, Villa E, Förster F, Hegerl R, Peters J, Baumeister W, Rockel B. The structure of human tripeptidyl peptidase II as determined by a hybrid approach. Structure 2012; 20:593-603. [PMID: 22483107 DOI: 10.1016/j.str.2012.01.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 10/28/2022]
Abstract
Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation.
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Affiliation(s)
- Anne-Marie Schönegge
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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