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Vishwakarma MK, Bhati PK, Kumar U, Singh RP, Kumar S, Govindan V, Mavi GS, Thiyagarajan K, Dhar N, Joshi AK. Genetic dissection of value-added quality traits and agronomic parameters through genome-wide association mapping in bread wheat ( T. aestivum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1419227. [PMID: 39228836 PMCID: PMC11368860 DOI: 10.3389/fpls.2024.1419227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/12/2024] [Indexed: 09/05/2024]
Abstract
Bread wheat (T. aestivum) is one of the world's most widely consumed cereals. Since micronutrient deficiencies are becoming more common among people who primarily depend upon cereal-based diets, a need for better-quality wheat varieties has been felt. An association panel of 154 T. aestivum lines was evaluated for the following quality traits: grain appearance (GA) score, grain hardness (GH), phenol reaction (PR) score, protein percent, sodium dodecyl sulfate (SDS) sedimentation value, and test weight (TWt). In addition, the panel was also phenotyped for grain yield and related traits such as days to heading, days to maturity, plant height, and thousand kernel weight for the year 2017-18 at the Borlaug Institute for South Asia (BISA) Ludhiana and Jabalpur sites. We performed a genome-wide association analysis on this panel using 18,351 genotyping-by-sequencing (GBS) markers to find marker-trait associations for quality and grain yield-related traits. We detected 55 single nucleotide polymorphism (SNP) marker trait associations (MTAs) for quality-related traits on chromosomes 7B (10), 1A (9), 2A (8), 3B (6), 2B (5), 7A (4), and 1B (3), with 3A, 4A, and 6D, having two and the rest, 4B, 5A, 5B, and 1D, having one each. Additionally, 20 SNP MTAs were detected for yield-related traits based on a field experiment conducted in Ludhiana on 7D (4) and 4D (3) chromosomes, while 44 SNP MTAs were reported for Jabalpur on chromosomes 2D (6), 7A (5), 2A (4), and 4A (4). Utilizing these loci in marker-assisted selection will benefit from further validation studies for these loci to improve hexaploid wheat for better yield and grain quality.
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Affiliation(s)
| | | | - Uttam Kumar
- Astralyan Agro (OPC) Pvt. Ltd, Shamli, Uttar Pradesh, India
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Sundeep Kumar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Gurvinder Singh Mavi
- Department of Plant breeding and genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Narain Dhar
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Arun K. Joshi
- Borlaug Institute for South Asia (BISA), New Delhi, India
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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2
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Tesla R, Guhl C, Werthmann GC, Dixon D, Cenik B, Addepalli Y, Liang J, Fass DM, Rosenthal Z, Haggarty SJ, Williams NS, Posner BA, Ready JM, Herz J. Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency. Nat Commun 2024; 15:6125. [PMID: 39033178 PMCID: PMC11271458 DOI: 10.1038/s41467-024-50076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/01/2024] [Indexed: 07/23/2024] Open
Abstract
Heterozygous loss-of-function mutations in the GRN gene are a major cause of hereditary frontotemporal dementia. The mechanisms linking frontotemporal dementia pathogenesis to progranulin deficiency are not well understood, and there is currently no treatment. Our strategy to prevent the onset and progression of frontotemporal dementia in patients with GRN mutations is to utilize small molecule positive regulators of GRN expression to boost progranulin levels from the remaining functional GRN allele, thus restoring progranulin levels back to normal within the brain. This work describes a series of blood-brain-barrier-penetrant small molecules which significantly increase progranulin protein levels in human cellular models, correct progranulin protein deficiency in Grn+/- mouse brains, and reverse lysosomal proteome aberrations, a phenotypic hallmark of frontotemporal dementia, more efficiently than the previously described small molecule suberoylanilide hydroxamic acid. These molecules will allow further elucidation of the cellular functions of progranulin and its role in frontotemporal dementia and will also serve as lead structures for further drug development.
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Affiliation(s)
- Rachel Tesla
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, Dallas, TX, USA
| | - Charlotte Guhl
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Gordon C Werthmann
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, Dallas, TX, USA
| | - Danielle Dixon
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, Dallas, TX, USA
| | - Basar Cenik
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Translational Neurodegeneration Research, Dallas, TX, USA
| | - Yesu Addepalli
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jue Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel M Fass
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zachary Rosenthal
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Noelle S Williams
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bruce A Posner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph M Ready
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joachim Herz
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Translational Neurodegeneration Research, Dallas, TX, USA.
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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3
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Pijning T, Vujičić‐Žagar A, van der Laan J, de Jong RM, Ramirez‐Palacios C, Vente A, Edens L, Dijkstra BW. Structural and time-resolved mechanistic investigations of protein hydrolysis by the acidic proline-specific endoprotease from Aspergillus niger. Protein Sci 2024; 33:e4856. [PMID: 38059672 PMCID: PMC10731622 DOI: 10.1002/pro.4856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/16/2023] [Accepted: 12/04/2023] [Indexed: 12/08/2023]
Abstract
Proline-specific endoproteases have been successfully used in, for example, the in-situ degradation of gluten, the hydrolysis of bitter peptides, the reduction of haze during beer production, and the generation of peptides for mass spectroscopy and proteomics applications. Here we present the crystal structure of the extracellular proline-specific endoprotease from Aspergillus niger (AnPEP), a member of the S28 peptidase family with rarely observed true proline-specific endoprotease activity. Family S28 proteases have a conventional Ser-Asp-His catalytic triad, but their oxyanion-stabilizing hole shows a glutamic acid, an amino acid not previously observed in this role. Since these enzymes have an acidic pH optimum, the presence of a glutamic acid in the oxyanion hole may confine their activity to an acidic pH. Yet, considering the presence of the conventional catalytic triad, it is remarkable that the A. niger enzyme remains active down to pH 1.5. The determination of the primary cleavage site of cytochrome c along with molecular dynamics-assisted docking studies indicate that the active site pocket of AnPEP can accommodate a reverse turn of approximately 12 amino acids with proline at the S1 specificity pocket. Comparison with the structures of two S28-proline-specific exopeptidases reveals not only a more spacious active site cavity but also the absence of any putative binding sites for amino- and carboxyl-terminal residues as observed in the exopeptidases, explaining AnPEP's observed endoprotease activity.
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Affiliation(s)
- Tjaard Pijning
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Andreja Vujičić‐Žagar
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | | | | | - Andre Vente
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Luppo Edens
- Taste, Texture and HealthDSM‐FirmenichDelftThe Netherlands
| | - Bauke W. Dijkstra
- Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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4
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Miyazono KI, Kubota K, Takahashi K, Tanokura M. Crystal structure and substrate recognition mechanism of the prolyl endoprotease PEP from Aspergillus niger. Biochem Biophys Res Commun 2022; 591:76-81. [PMID: 34999257 DOI: 10.1016/j.bbrc.2021.12.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 12/22/2021] [Accepted: 12/29/2021] [Indexed: 11/02/2022]
Abstract
Proteases are enzymes that are not only essential for life but also industrially important. Understanding the substrate recognition mechanisms of proteases is important to enhance the use of proteases. The fungus Aspergillus produces a wide variety of proteases, including PEP, which is a prolyl endoprotease from A. niger. Although PEP exhibits amino acid sequence similarity to the serine peptidase family S28 proteins (PRCP and DPP7) that recognize Pro-X bonds in the terminal regions of peptides, PEP recognizes Pro-X bonds not only in peptides but also in proteins. To reveal the structural basis of the prolyl endoprotease activity of PEP, we determined the structure of PEP by X-ray crystallography at a resolution of 1.75 Å. The PEP structure shows that PEP has a wide-open catalytic pocket compared to its homologs. The characteristic catalytic pocket structure of PEP is predicted to be important for the recognition of protein substrates.
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Affiliation(s)
- Ken-Ichi Miyazono
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Keiko Kubota
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan; Laboratory of Molecular Biochemistry, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi Hachioji, Tokyo, 192-0392, Japan
| | - Kenji Takahashi
- Laboratory of Molecular Biochemistry, School of Life Science, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi Hachioji, Tokyo, 192-0392, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo, 113-8657, Japan.
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5
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Qian XK, Zhang J, Li XD, Song PF, Zou LW. Research Progress on Dipeptidyl Peptidase Family: Structure, Function and Xenobiotic Metabolism. Curr Med Chem 2021; 29:2167-2188. [PMID: 34525910 DOI: 10.2174/0929867328666210915103431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/22/2022]
Abstract
Prolyl-specific peptidases or proteases, including Dipeptidyl Peptidase 2, 4, 6, 8, 9, 10, Fibroblast Activation Protein, prolyl endopeptidase and prolyl carboxypeptidase, belong to the dipeptidyl peptidase family. In human physiology and anatomy, they have homology amino acid sequences, similarities in structure, but play distinct functions and roles. Some of them also play important roles in the metabolism of drugs containing endogenous peptides, xenobiotics containing peptides, and exogenous peptides. The major functions of these peptidases in both the metabolism of human health and bioactive peptides are of significant importance in the development of effective inhibitors to control the metabolism of endogenous bioactive peptides. The structural characteristics, distribution of tissue, endogenous substrates, and biological functions were summarized in this review. Furthermore, the xenobiotics metabolism of the dipeptidyl peptidase family is illustrated. All the evidence and information summarized in this review would be very useful for researchers to extend the understanding of the proteins of these families and offer advice and assistance in physiology and pathology studies.
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Affiliation(s)
- Xing-Kai Qian
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai. China
| | - Jing Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai. China
| | - Xiao-Dong Li
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai. China
| | - Pei-Fang Song
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai. China
| | - Li-Wei Zou
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai. China
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6
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Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7. Sci Rep 2021; 11:7929. [PMID: 33846449 PMCID: PMC8041751 DOI: 10.1038/s41598-021-86965-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The emergence of drug-resistant bacteria has become a major problem worldwide. Bacterial dipeptidyl peptidases 7 and 11 (DPP7s and DPP11s), belonging to the family-S46 peptidases, are important enzymes for bacterial growth and are not present in mammals. Therefore, specific inhibitors for these peptidases are promising as potential antibiotics. While the molecular mechanisms underlining strict specificity at the S1 subsite of S46 peptidases have been well studied, those of relatively broad preference at the S2 subsite of these peptidases are unknown. In this study, we performed structural and biochemical analyses on DPP7 from Stenotrophomonas maltophilia (SmDPP7). SmDPP7 showed preference for the accommodation of hydrophobic amino acids at the S2 subsite in general, but as an exception, also for asparagine, a hydrophilic amino acid. Structural analyses of SmDPP7 revealed that this exceptional preference to asparagine is caused by a hydrogen bonding network at the bottom of the S2 subsite. The residues in the S2 subsite are well conserved among S46 peptidases as compared with those in the S1 subsite. We expect that our findings will contribute toward the development of a universal inhibitor of S46 peptidases.
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7
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Nemoto TK, Ohara Nemoto Y. Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:145-156. [PMID: 33006264 PMCID: PMC8048996 DOI: 10.1111/omi.12317] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023]
Abstract
Porphyromonas gingivalis, a pathogen of chronic periodontitis, is an asaccharolytic microorganism that solely utilizes nutritional amino acids as its energy source and cellular constituents. The bacterium is considered to incorporate proteinaceous nutrients mainly as dipeptides, thus exopeptidases that produce dipeptides from polypeptides are critical for survival and proliferation. We present here an overview of dipeptide production by P. gingivalis mediated by dipeptidyl-peptidases (DPPs), e.g., DPP4, DPP5, DPP7, and DPP11, serine exopeptidases localized in periplasm, which release dipeptides from the N-terminus of polypeptides. Additionally, two other exopeptidases, acylpeptidyl-oligopeptidase (AOP) and prolyl tripeptidyl-peptidase A (PTP-A), which liberate N-terminal acylated di-/tri-peptides and tripeptides with Pro at the third position, respectively, provide polypeptides in an acceptable form for DPPs. Hence, a large fraction of dipeptides is produced from nutritional polypeptides by DPPs with differential specificities in combination with AOP and PTP-A. The resultant dipeptides are then incorporated across the inner membrane mainly via a proton-dependent oligopeptide transporter (POT), a member of the major facilitator superfamily. Recent studies also indicate that DPP4 and DPP7 directly link between periodontal and systemic diseases, such as type 2 diabetes mellitus and coagulation abnormality, respectively. Therefore, these dipeptide-producing and incorporation molecules are considered to be potent targets for prevention and treatment of periodontal and related systemic diseases.
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Affiliation(s)
- Takayuki K Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuko Ohara Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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8
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Dunaevsky YE, Tereshchenkova VF, Oppert B, Belozersky MA, Filippova IY, Elpidina EN. Human proline specific peptidases: A comprehensive analysis. Biochim Biophys Acta Gen Subj 2020; 1864:129636. [DOI: 10.1016/j.bbagen.2020.129636] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
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9
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Guerder S, Hassel C, Carrier A. Thymus-specific serine protease, a protease that shapes the CD4 T cell repertoire. Immunogenetics 2018; 71:223-232. [PMID: 30225612 DOI: 10.1007/s00251-018-1078-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022]
Abstract
The lifespan of T cells is determined by continuous interactions of their T cell receptors (TCR) with self-peptide-MHC (self-pMHC) complexes presented by different subsets of antigen-presenting cells (APC). In the thymus, developing thymocytes are positively selected through recognition of self-pMHC presented by cortical thymic epithelial cells (cTEC). They are subsequently negatively selected by medullary thymic epithelial cells (mTEC) or thymic dendritic cells (DC) presenting self-pMHC complexes. In the periphery, the homeostasis of mature T cells is likewise controlled by the interaction of their TCR with self-pMHC complexes presented by lymph node stromal cells while they may be tolerized by DC presenting tissue-derived self-antigens. To perform these tasks, the different subsets of APC are equipped with distinct combination of antigen processing enzymes and consequently present specific repertoire of self-peptides. Here, we discuss one such antigen processing enzyme, the thymus-specific serine protease (TSSP), which is predominantly expressed by thymic stromal cells. In thymic DC and TEC, TSSP edits the repertoire of peptide presented by class II molecules and thus shapes the CD4 T cell repertoire.
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Affiliation(s)
- Sylvie Guerder
- INSERM, U1043, 31300, Toulouse, France. .,CNRS, UMR5282, 31300, Toulouse, France. .,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, 31300, Toulouse, France. .,INSERM UMR1043, Centre de Physiopathologie de Toulouse Purpan, CHU Purpan, BP 3028, 31024, Toulouse CEDEX 3, France.
| | - Chervin Hassel
- INSERM, U1043, 31300, Toulouse, France.,CNRS, UMR5282, 31300, Toulouse, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, 31300, Toulouse, France
| | - Alice Carrier
- Aix-Marseille University, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France
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10
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Serre L, Girard M, Ramadan A, Menut P, Rouquié N, Lucca LE, Mahiddine K, Leobon B, Mars LT, Guerder S. Thymic-Specific Serine Protease Limits Central Tolerance and Exacerbates Experimental Autoimmune Encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2017; 199:3748-3756. [PMID: 29061767 DOI: 10.4049/jimmunol.1700667] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
The genetic predisposition to multiple sclerosis (MS) is most strongly conveyed by MHC class II haplotypes, possibly by shaping the autoimmune CD4 T cell repertoire. Whether Ag-processing enzymes contribute to MS susceptibility by editing the peptide repertoire presented by these MHC haplotypes is unclear. Thymus-specific serine protease (TSSP) is expressed by thymic epithelial cells and thymic dendritic cells (DCs) and, in these two stromal compartments, TSSP edits the peptide repertoire presented by class II molecules. We show in this article that TSSP increases experimental autoimmune encephalomyelitis severity by limiting central tolerance to myelin oligodendrocyte glycoprotein. The effect on experimental autoimmune encephalomyelitis severity was MHC class II allele dependent, because the lack of TSSP expression conferred protection in NOD mice but not in C57BL/6 mice. Importantly, although human thymic DCs express TSSP, individuals segregate into two groups having a high or 10-fold lower level of expression. Therefore, the level of TSSP expression by thymic DCs may modify the risk factors for MS conferred by some MHC class II haplotypes.
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Affiliation(s)
- Laurent Serre
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Maeva Girard
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Abdoulraouf Ramadan
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Paul Menut
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Nelly Rouquié
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Liliana E Lucca
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Karim Mahiddine
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
| | - Bertrand Leobon
- Department of Pediatric Cardiology and Cardiovascular Surgery, Children's Hospital of Toulouse, Toulouse F-31300, France
| | - Lennart T Mars
- INSERM, U1043, Toulouse F-31300, France.,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France.,INSERM UMR995, Lille Inflammation Research International Center, F-59000 Lille, France; and.,Centre d'Excellence LICEND and FHU IMMINeNT, Université Lille, F-59000 Lille, France
| | - Sylvie Guerder
- INSERM, U1043, Toulouse F-31300, France; .,CNRS, UMR5282, Toulouse F-31300, France.,Centre de Physiopathologie de Toulouse Purpan, Université Toulouse III Paul-Sabatier, Toulouse F-31300, France
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11
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Nemoto TK, Ohara-Nemoto Y, Bezerra GA, Shimoyama Y, Kimura S. A Porphyromonas gingivalis Periplasmic Novel Exopeptidase, Acylpeptidyl Oligopeptidase, Releases N-Acylated Di- and Tripeptides from Oligopeptides. J Biol Chem 2016; 291:5913-5925. [PMID: 26733202 PMCID: PMC4786725 DOI: 10.1074/jbc.m115.687566] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 12/06/2015] [Indexed: 01/01/2023] Open
Abstract
Exopeptidases, including dipeptidyl- and tripeptidylpeptidase, are crucial for the growth of Porphyromonas gingivalis, a periodontopathic asaccharolytic bacterium that incorporates amino acids mainly as di- and tripeptides. In this study, we identified a novel exopeptidase, designated acylpeptidyl oligopeptidase (AOP), composed of 759 amino acid residues with active Ser(615) and encoded by PGN_1349 in P. gingivalis ATCC 33277. AOP is currently listed as an unassigned S9 family peptidase or prolyl oligopeptidase. Recombinant AOP did not hydrolyze a Pro-Xaa bond. In addition, although sequence similarities to human and archaea-type acylaminoacyl peptidase sequences were observed, its enzymatic properties were apparently distinct from those, because AOP scarcely released an N-acyl-amino acid as compared with di- and tripeptides, especially with N-terminal modification. The kcat/Km value against benzyloxycarbonyl-Val-Lys-Met-4-methycoumaryl-7-amide, the most potent substrate, was 123.3 ± 17.3 μm(-1) s(-1), optimal pH was 7-8.5, and the activity was decreased with increased NaCl concentrations. AOP existed predominantly in the periplasmic fraction as a monomer, whereas equilibrium between monomers and oligomers was observed with a recombinant molecule, suggesting a tendency of oligomerization mediated by the N-terminal region (Met(16)-Glu(101)). Three-dimensional modeling revealed the three domain structures (residues Met(16)-Ala(126), which has no similar homologue with known structure; residues Leu(127)-Met(495) (β-propeller domain); and residues Ala(496)-Phe(736) (α/β-hydrolase domain)) and further indicated the hydrophobic S1 site of AOP in accord with its hydrophobic P1 preference. AOP orthologues are widely distributed in bacteria, archaea, and eukaryotes, suggesting its importance for processing of nutritional and/or bioactive oligopeptides.
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Affiliation(s)
- Takayuki K Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Yuko Ohara-Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588, Japan
| | - Gustavo Arruda Bezerra
- the Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria, and.
| | - Yu Shimoyama
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan
| | - Shigenobu Kimura
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, Japan
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Wagner L, Klemann C, Stephan M, von Hörsten S. Unravelling the immunological roles of dipeptidyl peptidase 4 (DPP4) activity and/or structure homologue (DASH) proteins. Clin Exp Immunol 2016; 184:265-83. [PMID: 26671446 DOI: 10.1111/cei.12757] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/01/2015] [Accepted: 12/14/2015] [Indexed: 12/31/2022] Open
Abstract
Dipeptidyl peptidase (DPP) 4 (CD26, DPP4) is a multi-functional protein involved in T cell activation by co-stimulation via its association with adenosine deaminase (ADA), caveolin-1, CARMA-1, CD45, mannose-6-phosphate/insulin growth factor-II receptor (M6P/IGFII-R) and C-X-C motif receptor 4 (CXC-R4). The proline-specific dipeptidyl peptidase also modulates the bioactivity of several chemokines. However, a number of enzymes displaying either DPP4-like activities or representing structural homologues have been discovered in the past two decades and are referred to as DPP4 activity and/or structure homologue (DASH) proteins. Apart from DPP4, DASH proteins include fibroblast activation protein alpha (FAP), DPP8, DPP9, DPP4-like protein 1 (DPL1, DPP6, DPPX L, DPPX S), DPP4-like protein 2 (DPL2, DPP10) from the DPP4-gene family S9b and structurally unrelated enzyme DPP2, displaying DPP4-like activity. In contrast, DPP6 and DPP10 lack enzymatic DPP4-like activity. These DASH proteins play important roles in the immune system involving quiescence (DPP2), proliferation (DPP8/DPP9), antigen-presenting (DPP9), co-stimulation (DPP4), T cell activation (DPP4), signal transduction (DPP4, DPP8 and DPP9), differentiation (DPP4, DPP8) and tissue remodelling (DPP4, FAP). Thus, they are involved in many pathophysiological processes and have therefore been proposed for potential biomarkers or even drug targets in various cancers (DPP4 and FAP) and inflammatory diseases (DPP4, DPP8/DPP9). However, they also pose the challenge of drug selectivity concerning other DASH members for better efficacy and/or avoidance of unwanted side effects. Therefore, this review unravels the complex roles of DASH proteins in immunology.
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Affiliation(s)
- L Wagner
- Deutschsprachige Selbsthilfegruppe für Alkaptonurie (DSAKU) e.V, Stuttgart.,Department for Experimental Therapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - C Klemann
- Centre of Paediatric Surgery.,Centre for Paediatrics and Adolescent Medicine
| | - M Stephan
- Clinic for Psychosomatics and Psychotherapy, Hannover Medical School, Hannover
| | - S von Hörsten
- Department for Experimental Therapy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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13
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Nemoto TK, Ohara-Nemoto Y. Exopeptidases and gingipains in Porphyromonas gingivalis as prerequisites for its amino acid metabolism. JAPANESE DENTAL SCIENCE REVIEW 2016; 52:22-29. [PMID: 28408952 PMCID: PMC5382784 DOI: 10.1016/j.jdsr.2015.08.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/20/2015] [Accepted: 08/20/2015] [Indexed: 01/22/2023] Open
Abstract
Porphyromonas gingivalis, an asaccharolytic bacterium, utilizes amino acids as energy and carbon sources. Since amino acids are incorporated into the bacterial cells mainly as di- and tri-peptides, exopeptidases including dipeptidyl-peptidase (DPP) and tripeptidyl-peptidase are considered to be prerequisite components for their metabolism. We recently discovered DPP11, DPP5, and acylpeptidyl oligopeptidase in addition to previously reported DPP4, DPP7, and prolyl tripeptidyl peptidase A. DPP11 is a novel enzyme specific for acidic P1 residues (Asp and Glu) and distributed ubiquitously in eubacteria, while DPP5 is preferential for the hydrophobic P1 residue and the first entity identified in prokaryotes. Recently, acylpeptidyl oligopeptidase with a preference for hydrophobic P1 residues was found to release N-terminally blocked di- and tri-peptides. Furthermore, we also demonstrated that gingipains R and K contribute to P1-basic dipeptide production. These observations implicate that most, if not all, combinations of di- and tri-peptides are produced from extracellular oligopeptides even with an N-terminal modification. Here, we review P. gingivalis exopeptidases mainly in regard to their enzymatic characteristics. These exopeptidases with various substrate specificities benefit P. gingivalis for obtaining energy and carbon sources from the nutritionally limited subgingival environment.
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Affiliation(s)
- Takayuki K. Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Japan
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14
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Mortier A, Gouwy M, Van Damme J, Proost P, Struyf S. CD26/dipeptidylpeptidase IV-chemokine interactions: double-edged regulation of inflammation and tumor biology. J Leukoc Biol 2016; 99:955-69. [PMID: 26744452 PMCID: PMC7166560 DOI: 10.1189/jlb.3mr0915-401r] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/04/2015] [Indexed: 12/12/2022] Open
Abstract
Review of how chemokine processing by CD26/DPP IV regulates leukocyte trafficking. Post‐translational modification of chemokines is an essential regulatory mechanism to enhance or dampen the inflammatory response. CD26/dipeptidylpeptidase IV, ubiquitously expressed in tissues and blood, removes NH2‐terminal dipeptides from proteins with a penultimate Pro or Ala. A large number of human chemokines, including CXCL2, CXCL6, CXCL9, CXCL10, CXCL11, CXCL12, CCL3L1, CCL4, CCL5, CCL11, CCL14, and CCL22, are cleaved by CD26; however, the efficiency is clearly influenced by the amino acids surrounding the cleavage site and although not yet proven, potentially affected by the chemokine concentration and interactions with third molecules. NH2‐terminal cleavage of chemokines by CD26 has prominent effects on their receptor binding, signaling, and hence, in vitro and in vivo biologic activities. However, rather than having a similar result, the outcome of NH2‐terminal truncation is highly diverse. Either no difference in activity or drastic alterations in receptor recognition/specificity and hence, chemotactic activity are observed. Analogously, chemokine‐dependent inhibition of HIV infection is enhanced (for CCL3L1 and CCL5) or decreased (for CXCL12) by CD26 cleavage. The occurrence of CD26‐processed chemokine isoforms in plasma underscores the importance of the in vitro‐observed CD26 cleavages. Through modulation of chemokine activity, CD26 regulates leukocyte/tumor cell migration and progenitor cell release from the bone marrow, as shown by use of mice treated with CD26 inhibitors or CD26 knockout mice. As chemokine processing by CD26 has a significant impact on physiologic and pathologic processes, application of CD26 inhibitors to affect chemokine function is currently explored, e.g., as add‐on therapy in viral infection and cancer.
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Affiliation(s)
- Anneleen Mortier
- KU Leuven University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Leuven, Belgium
| | - Mieke Gouwy
- KU Leuven University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Leuven, Belgium
| | - Jo Van Damme
- KU Leuven University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Leuven, Belgium
| | - Paul Proost
- KU Leuven University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Leuven, Belgium
| | - Sofie Struyf
- KU Leuven University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Immunology, Leuven, Belgium
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15
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Khaket TP, Dhanda S, Jodha D, Singh J. Purification and biochemical characterization of dipeptidyl peptidase-II (DPP7) homologue from germinated Vigna radiata seeds. Bioorg Chem 2015; 63:132-41. [PMID: 26524724 DOI: 10.1016/j.bioorg.2015.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/06/2015] [Accepted: 10/12/2015] [Indexed: 11/25/2022]
Abstract
Dipeptidyl peptidases (DPPs) are potent exopeptidases, which possess central role in proteolysis. As compared to other members of DPP family, proline containing dipeptide hydrolysing activity of DPP-II (Dipeptidyl peptidase II) is unique as it hydrolyses imino group and plays a key role in protein metabolism. In present study, DPP-II was purified from germinated moong bean seeds using acid and ammonium sulphate precipitation followed by successive chromatographies on gel filtration (pH 7.4) and cation exchanger (pH 5.9). Native PAGE and in-situ gel assay confirmed the apparent homogeneity. Purified plant DPP-II is an oligomeric enzyme with molecular weight of 97.3kDa. Highest DPP-II activity was observed at pH 7.5 and 37°C, with stability in the range of neutral to alkaline pH. Substrate specificity showed consequent activity for proline containing dipeptide followed by Lys-Ala and other hydrophobic dipeptides, but none of the studied endopeptidase and monopeptidase substrate was hydrolysed. Catalytic characterization with modifier studies revealed the involvement of Ser and His residues in its catalytic mechanism. Its dipeptidyl peptidase activity for proline containing dipeptide supported its role in the bioactive peptide generation and food industry. Functional studies of DPP-II revealed the significant involvement of this glycoproteinous enzyme in protein mobilization during germination. Further studies on industrial applications exploring physiological role are in progress.
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Affiliation(s)
- Tejinder Pal Khaket
- Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India; Department of Biotechnology, Maharishi Markandeshwar University, Ambala, Haryana, India
| | - Suman Dhanda
- Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India
| | - Druksakshi Jodha
- Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India
| | - Jasbir Singh
- Department of Biochemistry, Kurukshetra University, Kurukshetra, Haryana, India.
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16
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Waumans Y, Baerts L, Kehoe K, Lambeir AM, De Meester I. The Dipeptidyl Peptidase Family, Prolyl Oligopeptidase, and Prolyl Carboxypeptidase in the Immune System and Inflammatory Disease, Including Atherosclerosis. Front Immunol 2015; 6:387. [PMID: 26300881 PMCID: PMC4528296 DOI: 10.3389/fimmu.2015.00387] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/13/2015] [Indexed: 12/19/2022] Open
Abstract
Research from over the past 20 years has implicated dipeptidyl peptidase (DPP) IV and its family members in many processes and different pathologies of the immune system. Most research has been focused on either DPPIV or just a few of its family members. It is, however, essential to consider the entire DPP family when discussing any one of its members. There is a substantial overlap between family members in their substrate specificity, inhibitors, and functions. In this review, we provide a comprehensive discussion on the role of prolyl-specific peptidases DPPIV, FAP, DPP8, DPP9, dipeptidyl peptidase II, prolyl carboxypeptidase, and prolyl oligopeptidase in the immune system and its diseases. We highlight possible therapeutic targets for the prevention and treatment of atherosclerosis, a condition that lies at the frontier between inflammation and cardiovascular disease.
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Affiliation(s)
- Yannick Waumans
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Lesley Baerts
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Kaat Kehoe
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp , Antwerp , Belgium
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Marie P, Labas V, Brionne A, Harichaux G, Hennequet-Antier C, Rodriguez-Navarro AB, Nys Y, Gautron J. Quantitative proteomics provides new insights into chicken eggshell matrix protein functions during the primary events of mineralisation and the active calcification phase. J Proteomics 2015; 126:140-54. [PMID: 26049031 DOI: 10.1016/j.jprot.2015.05.034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/11/2015] [Accepted: 05/29/2015] [Indexed: 01/04/2023]
Abstract
Eggshell is a bioceramic composed of 95% calcium carbonate mineral and 3.5% organic matrix. Its structural organisation is controlled by its organic matrix. We have used quantitative proteomics to study four key stages of shell mineralisation: 1) widespread deposition of amorphous calcium carbonate (ACC), 2) ACC transformation into crystalline calcite aggregates, 3) formation of larger calcite crystal units and 4) development of a columnar structure with preferential calcite crystal orientation. This approach explored the distribution of 216 shell matrix proteins found at the four stages. Variations in abundance according to these calcification events were observed for 175 proteins. A putative function related to the mineralisation process was predicted by bioinformatics for 77 of them and was further characterised. We confirmed the important role of lysozyme, ovotransferrin, ovocleidin-17 and ovocleidin-116 for shell calcification process, characterised major calcium binding proteins (EDIL3, ALB, MFGE8, NUCB2), and described novel proteoglycans core proteins (GPC4, HAPLN3). We suggest that OVAL and OC-17 play a role in the stabilisation of ACC. Finally, we report proteins involved in the regulation of proteins driving the mineralisation. They correspond to numerous molecular chaperones including CLU, PPIB and OCX21, protease and protease inhibitors including OVM and CST3, and regulators of phosphorylation.
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Affiliation(s)
- Pauline Marie
- INRA, UR83 Recherches avicoles, Fonction et Régulation des protéines de l'œuf, F-37380 Nouzilly, France
| | - Valérie Labas
- INRA, UMR INRA85, UMR CNRS 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | - Aurélien Brionne
- INRA, UR83 Recherches avicoles, Fonction et Régulation des protéines de l'œuf, F-37380 Nouzilly, France
| | - Grégoire Harichaux
- INRA, UMR INRA85, UMR CNRS 7247, Université de Tours, IFCE, Physiologie de la Reproduction et des Comportements, Plate-forme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, F-37380 Nouzilly, France
| | | | | | - Yves Nys
- INRA, UR83 Recherches avicoles, Fonction et Régulation des protéines de l'œuf, F-37380 Nouzilly, France
| | - Joël Gautron
- INRA, UR83 Recherches avicoles, Fonction et Régulation des protéines de l'œuf, F-37380 Nouzilly, France.
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18
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Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Gouda H, Nonaka T, Ogasawara W, Tanaka N. Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis. Acta Crystallogr F Struct Biol Commun 2015; 71:206-10. [PMID: 25664797 PMCID: PMC4321477 DOI: 10.1107/s2053230x15000424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 01/09/2015] [Indexed: 01/22/2023] Open
Abstract
Dipeptidyl peptidase 11 from Porphyromonas gingivalis (PgDPP11) preferentially cleaves substrate peptides with Asp and Glu at the P1 position [NH2-P2-P1(Asp/Glu)-P1'-P2'...]. For crystallographic studies, PgDPP11 was overproduced in Escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. X-ray diffraction data to 1.82 Å resolution were collected from an orthorhombic crystal form belonging to space group C2221, with unit-cell parameters a = 99.33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress.
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Affiliation(s)
- Yasumitsu Sakamoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Yoshiyuki Suzuki
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Nigata 940-2188, Japan
| | - Ippei Iizuka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Chika Tateoka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Saori Roppongi
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Mayu Fujimoto
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Hiroaki Gouda
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
| | - Takamasa Nonaka
- School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Nigata 940-2188, Japan
| | - Nobutada Tanaka
- School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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S46 peptidases are the first exopeptidases to be members of clan PA. Sci Rep 2014; 4:4977. [PMID: 24827749 PMCID: PMC4021333 DOI: 10.1038/srep04977] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/24/2014] [Indexed: 01/09/2023] Open
Abstract
The dipeptidyl aminopeptidase BII (DAP BII) belongs to a serine peptidase family, S46. The amino acid sequence of the catalytic unit of DAP BII exhibits significant similarity to those of clan PA endopeptidases, such as chymotrypsin. However, the molecular mechanism of the exopeptidase activity of family S46 peptidase is unknown. Here, we report crystal structures of DAP BII. DAP BII contains a peptidase domain including a typical double β-barrel fold and previously unreported α-helical domain. The structures of peptide complexes revealed that the α-helical domain covers the active-site cleft and the side chain of Asn330 in the domain forms hydrogen bonds with the N-terminus of the bound peptide. These observations indicate that the α-helical domain regulates the exopeptidase activity of DAP BII. Because S46 peptidases are not found in mammals, we expect that our study will be useful for the design of specific inhibitors of S46 peptidases from pathogens.
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De Brabandere S, Mangelinckx S, Kadam ST, Nural Y, Augustyns K, Van der Veken P, Törnroos KW, De Kimpe N. Synthesis of γ,δ-Aziridino α-Amino Acid Derivatives and their Stereoselective Ring Transformation to 2-(Aminomethyl)-1-aminocyclopropanecarboxylic Acid Derivatives. European J Org Chem 2013. [DOI: 10.1002/ejoc.201301030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Rouf SMA, Ohara-Nemoto Y, Ono T, Shimoyama Y, Kimura S, Nemoto TK. Phenylalanine 664 of dipeptidyl peptidase (DPP) 7 and Phenylalanine 671 of DPP11 mediate preference for P2-position hydrophobic residues of a substrate. FEBS Open Bio 2013; 3:177-83. [PMID: 23772391 PMCID: PMC3668534 DOI: 10.1016/j.fob.2013.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/22/2013] [Accepted: 03/22/2013] [Indexed: 11/25/2022] Open
Abstract
Dipeptidyl peptidases (DPPs) are crucial for the energy metabolism in Porphyromonas gingivalis, a Gram-negative proteolytic and asaccharolytic anaerobic rod causing chronic periodontitis. Three DPPs, DPPIV specific for Pro, DPP7 for hydrophobic residues and DPP11 for Asp/Glu at the P1 position, are expressed in the bacterium. Like DPP7, DPP11 belongs to the S46 protease family, and they share 38.7% sequence identity. Although DPP11 is preferential for hydrophobic residues at the P2 position, it has been reported that DPP7 has no preference at the P2 position. In the present study, we defined the detailed P2 substrate preference of DPP7 and the amino acid residue responsible for the specificity. DPP7 most efficiently hydrolyzed Met-Leu-dipeptidyl-4-methylcoumaryl-7-amide (MCA) carrying hydrophobic residues at the P1 position with k cat/Km of 10.62 ± 2.51 μM(-1) s(-1), while it unexpectedly cleaved substrates with hydrophilic (Gln, Asn) or charged (Asp, Arg) residues. Examination with 21 dipeptidyl MCA demonstrated that DPP7-peptidase activity was dependent on hydrophobicity of the P2- as well as P1-position residue, thus it correlated best with the sum of the hydrophobicity index of P1- and P2-amino acid residues. Hydrophobicity of the P1 and P2 positions ensured efficient enzyme catalysis by increasing k cat and lowering Km values, respectively. Substitution of hydrophobic residues conserved in the S46 DPP7/DPP11 family to Ala revealed that Phe664 of DPP7 and Phe671 of DPP11 primarily afforded hydrophobic P2 preference. A modeling study suggested that Phe664 and Gly666 of DPP7 and Phe671 and Arg673 of DPP11 being associated with the P2- and P1-position residues, respectively, are located adjacent to the catalytic Ser648/Ser655. The present results expand the substrate repertoire of DPP7, which ensures efficient degradation of oligopeptides in asaccharolytic bacteria.
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Affiliation(s)
- Shakh M A Rouf
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
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