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Sánchez-Arroyo A, Plaza-Vinuesa L, Mancheño JM, de Las Rivas B, Muñoz R. Brevibacterium enzymes as biological tools for ochratoxin A detoxification in dairy foods. Int J Food Microbiol 2025; 428:110980. [PMID: 39580991 DOI: 10.1016/j.ijfoodmicro.2024.110980] [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: 06/26/2024] [Revised: 11/05/2024] [Accepted: 11/12/2024] [Indexed: 11/26/2024]
Abstract
The origin of ochratoxin A (OTA) in cheeses is mainly due to mould growth during the ripening process, and to a lesser extent, to the use of OTA-contaminated milk in cheese production. Bacterial smear-ripened cheeses developed a smear microbiota on their rind during ripening that greatly contributes to its typical aroma and texture. Bacteria from the Brevibacterium genus belong to the typical smear microbiota of cheeses. Type strains from Brevibacterium species frequently isolated from cheese and milk products were able to transform OTA into much less toxic ochratoxin α (OTα) and L-phenylalanine. Protein searches allowed the identification of a protein annotated as amidohydrolase in these OTA-degrader Brevibacterium strains. The OTA-hydrolytic activity of the identified amidohydrolase was demonstrated by the heterologous production of this protein from B. linens DSM 20425T (BlOTA). In vitro assays revealed that BlOTA transformed OTA into less toxic OTα, as well as ochratoxin B. When compared with other previously described OTA-degrading amidohydrolases, BlOTA exhibited optimal activity at a higher pH (8.0), while showing similar high temperature for optimal activity (55 °C) and thermostability; in addition, a clear preference for substrates with Phe, Tyr or Leu amino acid residues at the C-terminal position was clearly observed. BlOTA efficiently detoxifies OTA-contaminated bovine milk, without provoking changes on its free amino acid composition. Moreover, in silico predictions revealed that BlOTA is a non-allergenic, non-antigenic, and poorly immunogenic protein. Therefore, the QPS status possessed by cheese-Brevibacterium species, as well as the characteristics exhibited by BlOTA, make them suitable tools for the biological detoxification of OTA in dairy and food products.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Instituto de Química-Física Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain
| | - Blanca de Las Rivas
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Rosario Muñoz
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain.
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2
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Wang J, Lu X, Zhuge B, Zong H. Enhancing the catalytic efficiency of M32 carboxypeptidase by semi-rational design and its applications in food taste improvement. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7375-7385. [PMID: 38666395 DOI: 10.1002/jsfa.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Carboxypeptidase is an exopeptidase that hydrolyzes amino acids at the C-terminal end of the peptide chain and has a wide range of applications in food. However, in industrial applications, the relatively low catalytic efficiency of carboxypeptidases is one of the main limiting factors for industrialization. RESULTS The study has enhanced the catalytic efficiency of Bacillus megaterium M32 carboxypeptidase (BmeCPM32) through semi-rational design. Firstly, the specific activity of the optimal mutant, BmeCPM32-M2, obtained through single-site mutagenesis and combinatorial mutagenesis, was 2.2-fold higher than that of the wild type (187.9 versus 417.8 U mg-1), and the catalytic efficiency was 2.9-fold higher (110.14 versus 325.75 s-1 mmol-1). Secondly, compared to the wild type, BmeCPM32-M2 exhibited a 1.8-fold increase in half-life at 60 °C, with no significant changes in its enzymatic properties (optimal pH, optimal temperature). Finally, BmeCPM32-M2 significantly increased the umami intensity of soy protein isolate hydrolysate by 55% and reduced bitterness by 83%, indicating its potential in developing tasty protein components. CONCLUSION Our research has revealed that the strategy based on protein sequence evolution and computational residue mutation energy led to an improved catalytic efficiency of BmeCPM32. Molecular dynamics simulations have revealed that a smaller substrate binding pocket and increased enzyme-substrate affinity are the reasons for the enhanced catalytic efficiency. Furthermore the number of hydrogen bonds and solvent and surface area may contribute to the improvement of thermostability. Finally, the de-bittering effect of BmeCPM32-M2 in soy protein isolate hydrolysate suggests its potential in developing palatable protein components. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jinjiang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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3
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Singh Rajkumar M, Ibanez-Carrasco F, Avila CA, Mandadi KK. Insights into Bactericera cockerelli and Candidatus Liberibacter solanacearum interaction: a tissue-specific transcriptomic approach. FRONTIERS IN PLANT SCIENCE 2024; 15:1393994. [PMID: 39280947 PMCID: PMC11392735 DOI: 10.3389/fpls.2024.1393994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 08/14/2024] [Indexed: 09/18/2024]
Abstract
The tomato-potato psyllid, Bactericera cockerelli (Šulc), belonging to the Hemiptera order, is an insect pest of solanaceous crops and vectors a fastidious bacterium, Candidatus Liberibacter solanacearum (CLso), the presumptive causal agent of zebra chip and vein greening diseases in potatoes and tomatoes, respectively. The genome of B. cockerelli has been sequenced recently, providing new avenues to elucidate mechanistic insights into pathogenesis in vegetable crops. In this study, we performed RNA-sequencing of the critical psyllid organs (salivary glands and ovaries) involved in CLso pathology and transmission to host plants. Transcriptome analysis revealed differentially expressed genes and organ-specific enrichment of gene ontology (GO) terms related to metabolic processes, response to stress/stimulus, phagocytosis, proteolysis, endocytosis, and provided candidate genes encoding transcription factors (TFs). To examine gene regulatory networks across the psyllid organs under CLso(-) and CLso(+) conditions, we performed weighted gene co-expression network analysis (WGCNA), and unique modules differentiating the psyllid organs were identified. A comparative GO analysis of the unique gene modules revealed functional terms enriched in response to stress, gene regulation, and cell division processes in the ovaries. In contrast, respiration, transport, and neuronal transmission-related GO terms were enriched in the salivary glands. Altogether, this study reveals new insights into tissue-specific expression of the psyllid organs in the absence or presence of CLso bacterium. This knowledge can be leveraged to develop new pest and disease management strategies by delineating the regulatory networks involved in the psyllid-CLso interaction.
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Affiliation(s)
| | - Freddy Ibanez-Carrasco
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Carlos A Avila
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, United States
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, United States
- Institute for Advancing Health Through Agriculture, Texas A&M AgriLife, College Station, TX, United States
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4
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Sánchez-Arroyo A, Plaza-Vinuesa L, de las Rivas B, Mancheño JM, Muñoz R. Aspergillus niger Ochratoxinase Is a Highly Specific, Metal-Dependent Amidohydrolase Suitable for OTA Biodetoxification in Food and Feed. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:18658-18669. [PMID: 39110482 PMCID: PMC11342369 DOI: 10.1021/acs.jafc.4c02944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 07/10/2024] [Accepted: 07/29/2024] [Indexed: 08/22/2024]
Abstract
Microbial enzymes can be used as processing aids or additives in food and feed industries. Enzymatic detoxification of ochratoxin A (OTA) is a promising method to reduce OTA content. Here, we characterize the full-length enzyme ochratoxinase (AnOTA), an amidohydrolase from Aspergillus niger. AnOTA hydrolyzes OTA and ochratoxin B (OTB) mycotoxins efficiently and also other substrates containing phenylalanine, alanine, or leucine residues at their C-terminal position, revealing a narrow specificity profile. AnOTA lacks endopeptidase or aminoacylase activities. The structural basis of the molecular recognition by AnOTA of OTA, OTB, and a wide array of model substrates has been investigated by molecular docking simulation. AnOTA shows maximal hydrolytic activity at neutral pH and high temperature (65 °C) and retained high activity after prolonged incubation at 45 °C. The reduction of OTA levels in food products by AnOTA has been investigated using several commercial plant-based beverages. The results showed complete degradation of OTA with no detectable modification of beverage proteins. Therefore, the addition of AnOTA seems to be a useful procedure to eliminate OTA in plant-based beverages. Moreover, computational predictions of in vivo characteristics indicated that AnOTA is neither an allergenic nor antigenic protein. All characteristics found for AnOTA supported the suitability of its use for OTA detoxification in food and feed.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Bacterial
Biotechnology, Institute of Food Science,
Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Bacterial
Biotechnology, Institute of Food Science,
Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Blanca de las Rivas
- Bacterial
Biotechnology, Institute of Food Science,
Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Department
of Crystallography and Structural Biology, Institute of Physical Chemistry Blas Cabrera (IQF), CSIC, Serrano 119, 28006 Madrid, Spain
| | - Rosario Muñoz
- Bacterial
Biotechnology, Institute of Food Science,
Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
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5
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Lyons PJ. Inactive metallopeptidase homologs: the secret lives of pseudopeptidases. Front Mol Biosci 2024; 11:1436917. [PMID: 39050735 PMCID: PMC11266112 DOI: 10.3389/fmolb.2024.1436917] [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: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. Other metallopeptidase families contain pseudopeptidases involved in protein synthesis at the ribosome and protein import into organelles, sometimes using their pseudo-active sites for these interactions. Although the functions of these pseudopeptidases have been challenging to study, ongoing work is teasing out the secret lives of these proteins.
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Affiliation(s)
- Peter J. Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, United States
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6
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Chen J, Zehr EA, Gruschus JM, Szyk A, Liu Y, Tanner ME, Tjandra N, Roll-Mecak A. Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Nature 2024; 631:905-912. [PMID: 39020174 DOI: 10.1038/s41586-024-07699-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/11/2024] [Indexed: 07/19/2024]
Abstract
Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes1. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification2. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family1. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function3-9, and mutations in CCPs lead to human disease10-13. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax.
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Affiliation(s)
- Jiayi Chen
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - James M Gruschus
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Agnieszka Szyk
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Yanjie Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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7
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Nicot S, Gillard G, Impheng H, Joachimiak E, Urbach S, Mochizuki K, Wloga D, Juge F, Rogowski K. A family of carboxypeptidases catalyzing α- and β-tubulin tail processing and deglutamylation. SCIENCE ADVANCES 2023; 9:eadi7838. [PMID: 37703372 PMCID: PMC10499314 DOI: 10.1126/sciadv.adi7838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/10/2023] [Indexed: 09/15/2023]
Abstract
Tubulin posttranslational modifications represent an important mechanism involved in the regulation of microtubule functions. The most widespread among them are detyrosination, α∆2-tubulin, and polyglutamylation. Here, we describe a family of tubulin-modifying enzymes composed of two closely related proteins, KIAA0895L and KIAA0895, which have tubulin metallocarboxypeptidase activity and thus were termed TMCP1 and TMCP2, respectively. We show that TMCP1 (also known as MATCAP) acts as α-tubulin detyrosinase that also catalyzes α∆2-tubulin. In contrast, TMCP2 preferentially modifies βI-tubulin by removing three amino acids from its C terminus, generating previously unknown βI∆3 modification. We show that βI∆3-tubulin is mostly found on centrioles and mitotic spindles and in cilia. Moreover, we demonstrate that TMCPs also remove posttranslational polyglutamylation and thus act as tubulin deglutamylases. Together, our study describes the identification and comprehensive biochemical analysis of a previously unknown type of tubulin-modifying enzymes involved in the processing of α- and β-tubulin C-terminal tails and deglutamylation.
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Affiliation(s)
- Simon Nicot
- Tubulin Code team, Institute of Human Genetics, Université Montpellier, CNRS, Montpellier, France
| | - Ghislain Gillard
- Tubulin Code team, Institute of Human Genetics, Université Montpellier, CNRS, Montpellier, France
| | - Hathaichanok Impheng
- Department of Physiology, Faculty of Medical science, Naresuan University, Phitsanulok 65000, Thailand
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - Serge Urbach
- Functional Proteomics Platform (FPP), IGF, Université Montpellier, CNRS, INSERM, Montpellier, France
| | - Kazufumi Mochizuki
- Epigenetic Chromatin Regulation team, Institute of Human Genetics, Université Montpellier, CNRS, Montpellier, France
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland
| | - François Juge
- Tubulin Code team, Institute of Human Genetics, Université Montpellier, CNRS, Montpellier, France
| | - Krzysztof Rogowski
- Tubulin Code team, Institute of Human Genetics, Université Montpellier, CNRS, Montpellier, France
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8
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Rigo GV, Cardoso FG, Pereira MM, Devereux M, McCann M, Santos ALS, Tasca T. Peptidases Are Potential Targets of Copper(II)-1,10-Phenanthroline-5,6-dione Complex, a Promising and Potent New Drug against Trichomonas vaginalis. Pathogens 2023; 12:pathogens12050745. [PMID: 37242415 DOI: 10.3390/pathogens12050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Trichomonas vaginalis is responsible for 156 million new cases per year worldwide. When present asymptomatically, the parasite can lead to serious complications, such as development of cervical and prostate cancer. As infection increases the acquisition and transmission of HIV, the control of trichomoniasis represents an important niche for the discovery and development of new antiparasitic molecules. This urogenital parasite synthesizes several molecules that allow the establishment and pathogenesis of infection. Among them, peptidases occupy key roles as virulence factors, and the inhibition of these enzymes has become an important mechanism for modulating pathogenesis. Based on these premises, our group recently reported the potent anti-T. vaginalis action of the metal-based complex [Cu(phendione)3](ClO4)2.4H2O (Cu-phendione). In the present study, we evaluated the influence of Cu-phendione on the modulation of proteolytic activities produced by T. vaginalis by biochemical and molecular approaches. Cu-phendione showed strong inhibitory potential against T. vaginalis peptidases, especially cysteine- and metallo-type peptidases. The latter revealed a more prominent effect at both the post-transcriptional and post-translational levels. Molecular Docking analysis confirmed the interaction of Cu-phendione, with high binding energy (-9.7 and -10.7 kcal·mol-1, respectively) at the active site of both TvMP50 and TvGP63 metallopeptidases. In addition, Cu-phendione significantly reduced trophozoite-mediated cytolysis in human vaginal (HMVII) and monkey kidney (VERO) epithelial cell lineages. These results highlight the antiparasitic potential of Cu-phendione by interaction with important T. vaginalis virulence factors.
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Affiliation(s)
- Graziela Vargas Rigo
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
| | - Fernanda Gomes Cardoso
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
| | - Matheus Mendonça Pereira
- CIEPQPF, Department of Chemical Engineering, University of Coimbra, Rua Sílvio Lima, Pólo II-Pinhal de Marrocos, 3030-790 Coimbra, Portugal
| | - Michael Devereux
- The Inorganic Pharmaceutical and Biomimetic Research Centre, Focas Research Institute, Dublin Institute of Technology, D08 CKP1 Dublin, Ireland
| | - Malachy McCann
- Chemistry Department, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Ireland
| | - André L S Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil
| | - Tiana Tasca
- Faculdade de Farmácia and Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 90610-000, RS, Brazil
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9
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Naeemi SM, Aminzadeh S, Sari S, Nemati F, Naseroleslami M. In vitro and in silico characterization of a novel glutamate carboxypeptidase from Cohnella sp. A01. Biochimie 2023; 207:83-95. [PMID: 36493965 DOI: 10.1016/j.biochi.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 10/25/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Glutamate carboxypeptidase is a bacterial enzyme of metallopeptidase superfamily. This enzyme is an exo-peptidase that catalyzes the hydrolysis of glutamate residues at the C-terminus of folic acid. The rCP302 is a novel zinc ion-dependent recombinant glutamate carboxypeptidase derived from a thermophilic bacterium, Cohnella sp. A01 (PTCC No: 1921). By simulating the structure of rCP302, analyzing its activity in various environmental settings, and contrasting it with that of related enzymes, we wanted to evaluate the heterologous production, purification, and characterization of this enzyme. The bioinformatics study showed that rCP302 had maximum similarity to M20 family of metallopeptidases. The purified rCP302 molecular weight was about 41.6 kDa. The optimum temperature and pH for the catalytic activity of rCP302 were 50 °C and 7.2, respectively. Fluorescence spectroscopy data elucidated the secondary structure of rCP302 and determined conformational changes caused by alterations in ambient conditions. Using folate as a substrate, Km and specific activity values were calculated as 0.108 μM and 687 μmol/min/mg, respectively. The enzyme activity was strongly inhibited when EDTA sequestered zinc ions. The half-life of this enzyme at 30 °C was 2012 min. Regarding the ability of rCP302 to degrade folic acid, and its long half-life at 37 °C, the normal temperature of many mammals, this enzyme can be introduced for further study for use in the pharmaceutical industry.
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Affiliation(s)
- Seyed Mahdi Naeemi
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Soyar Sari
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fahimeh Nemati
- Department of Biotechnoligy, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Naseroleslami
- Department of Molecular and Cellular Sciences, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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10
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Sánchez-Arroyo A, Plaza-Vinuesa L, Rivas BDL, Mancheño JM, Muñoz R. The salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans DSM 6986T is a bifunctional enzyme that inactivates the mycotoxin ochratoxin A by a novel amidohydrolase activity. Int J Biol Macromol 2023; 237:124230. [PMID: 36990411 DOI: 10.1016/j.ijbiomac.2023.124230] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/14/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023]
Abstract
The salicylate 1,2-dioxygenase from the bacterium Pseudaminobacter salicylatoxidans DSM 6986T (PsSDO) is a versatile metalloenzyme that participates in the aerobic biodegradation of aromatic compounds, such as gentisates and salicylates. Surprisingly, and unrelated to this metabolic role, it has been reported that PsSDO may transform the mycotoxin ochratoxin A (OTA), a molecule that appears in numerous food products that results in serious biotechnological concern. In this work, we show that PsSDO, together with its dioxygenase activity, behaves as an amidohydrolase with a marked specificity for substrates containing a C-terminal phenylalanine residue, similar to OTA, although its presence is not an absolute requirement. This side chain would establish aromatic stacking interactions with the indole ring of Trp104. PsSDO hydrolysed the amide bond of OTA rendering the much less toxic ochratoxin α and L-β-phenylalanine. The binding mode of OTA and of a diverse set of synthetic carboxypeptidase substrates these substrates have been characterized by molecular docking simulations, which has permitted us to propose a catalytic mechanism of hydrolysis by PsSDO that, similarly to metallocarboxypeptidases, assumes a water-induced pathway following a general acid/base mechanism in which the side chain of Glu82 would provide the solvent nucleophilicity required for the enzymatic reaction. Since the PsSDO chromosomal region, absent in other Pseudaminobacter strains, contained a set of genes present in conjugative plasmids, it could have been acquired by horizontal gene transfer, probably from a Celeribacter strain.
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Affiliation(s)
- Ana Sánchez-Arroyo
- Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Laura Plaza-Vinuesa
- Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - Blanca de Las Rivas
- Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain
| | - José Miguel Mancheño
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain.
| | - Rosario Muñoz
- Institute of Food Science, Technology and Nutrition (ICTAN), CSIC, José Antonio Novais 6, 28040 Madrid, Spain.
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Fajardo D, Saint Jean R, Lyons PJ. Acquisition of new function through gene duplication in the metallocarboxypeptidase family. Sci Rep 2023; 13:2512. [PMID: 36781897 PMCID: PMC9925722 DOI: 10.1038/s41598-023-29800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Gene duplication is a key first step in the process of expanding the functionality of a multigene family. In order to better understand the process of gene duplication and its role in the formation of new enzymes, we investigated recent duplication events in the M14 family of proteolytic enzymes. Within vertebrates, four of 23 M14 genes were frequently found in duplicate form. While AEBP1, CPXM1, and CPZ genes were duplicated once through a large-scale, likely whole-genome duplication event, the CPO gene underwent many duplication events within fish and Xenopus lineages. Bioinformatic analyses of enzyme specificity and conservation suggested a greater amount of neofunctionalization and purifying selection in CPO paralogs compared with other CPA/B enzymes. To examine the functional consequences of evolutionary changes on CPO paralogs, the four CPO paralogs from Xenopus tropicalis were expressed in Sf9 and HEK293T cells. Immunocytochemistry showed subcellular distribution of Xenopus CPO paralogs to be similar to that of human CPO. Upon activation with trypsin, the enzymes demonstrated differential activity against three substrates, suggesting an acquisition of new function following duplication and subsequent mutagenesis. Characteristics such as gene size and enzyme activation mechanisms are possible contributors to the evolutionary capacity of the CPO gene.
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Affiliation(s)
- Daniel Fajardo
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA
| | - Ritchie Saint Jean
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA
| | - Peter J Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, 49104, USA.
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12
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Sarkar T, Reaux CR, Li J, Raghavan VV, Xu W. The specific applications of the TSR-based method in identifying Zn 2+ binding sites of proteases and ACE/ACE2. Data Brief 2022; 45:108629. [PMID: 36426009 PMCID: PMC9679521 DOI: 10.1016/j.dib.2022.108629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/27/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022] Open
Abstract
We have developed an alignment-free TSR (Triangular Spatial Relationship)-based computational method for protein structural comparison and motif identification and discovery. To demonstrate the potential applications of the method, we have generated two datasets. One dataset contains five classes: Actin/Hsp70, serine protease (chymotrypsin/trypsin/elastase), ArsC/Prdx2, PKA/PKB/PKC, and AChE/BChE at the hierarchical level 1 and twelve groups at the level 2. The other dataset includes representative proteases and ACE/ACE2. The x,y, z coordinates of the structures were obtained from PDB. We calculated the keys (or features) that represent each structure using the TSR-based method. The dataset and data presented here include additional information that help the readers become aware of specific applications of the TSR-based method in protein clustering, identification and discovery of metal ion binding sites as well as to understand the effect of amino acid grouping on protein 3D structural relationships at both global and local levels.
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Affiliation(s)
- Titli Sarkar
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
- Department of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USA
| | - Camille R. Reaux
- Department of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USA
| | - Jianxiong Li
- High Performance Computing, Frey Computing Services Center, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vijay V. Raghavan
- The Center for Advanced Computer Studies, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, PO Box 44370, Lafayette, LA 70504, USA
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13
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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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14
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McDonald RC, Schott MJ, Idowu TA, Lyons PJ. Biochemical and genetic analysis of Ecm14, a conserved fungal pseudopeptidase. BMC Mol Cell Biol 2020; 21:86. [PMID: 33256608 PMCID: PMC7706225 DOI: 10.1186/s12860-020-00330-w] [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: 08/14/2020] [Accepted: 11/18/2020] [Indexed: 01/28/2023] Open
Abstract
Background Like most major enzyme families, the M14 family of metallocarboxypeptidases (MCPs) contains a number of pseudoenzymes predicted to lack enzyme activity and with poorly characterized molecular function. The genome of the yeast Saccharomyces cerevisiae encodes one member of the M14 MCP family, a pseudoenzyme named Ecm14 proposed to function in the extracellular matrix. In order to better understand the function of such pseudoenzymes, we studied the structure and function of Ecm14 in S. cerevisiae. Results A phylogenetic analysis of Ecm14 in fungi found it to be conserved throughout the ascomycete phylum, with a group of related pseudoenzymes found in basidiomycetes. To investigate the structure and function of this conserved protein, His6-tagged Ecm14 was overexpressed in Sf9 cells and purified. The prodomain of Ecm14 was cleaved in vivo and in vitro by endopeptidases, suggesting an activation mechanism; however, no activity was detectable using standard carboxypeptidase substrates. In order to determine the function of Ecm14 using an unbiased screen, we undertook a synthetic lethal assay. Upon screening approximately 27,000 yeast colonies, twenty-two putative synthetic lethal clones were identified. Further analysis showed many to be synthetic lethal with auxotrophic marker genes and requiring multiple mutations, suggesting that there are few, if any, single S. cerevisiae genes that present synthetic lethal interactions with ecm14Δ. Conclusions We show in this study that Ecm14, although lacking detectable enzyme activity, is a conserved carboxypeptidase-like protein that is secreted from cells and is processed to a mature form by the action of an endopeptidase. Our study and datasets from other recent large-scale screens suggest a role for Ecm14 in processes such as vesicle-mediated transport and aggregate invasion, a fungal process that has been selected against in modern laboratory strains of S. cerevisiae. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-020-00330-w.
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Affiliation(s)
| | - Matthew J Schott
- Department of Biology, Andrews University, Berrien Springs, MI, USA
| | - Temitope A Idowu
- Department of Biology, Andrews University, Berrien Springs, MI, USA
| | - Peter J Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, USA.
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15
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Sharma RK, Stevens BR, Obukhov AG, Grant MB, Oudit GY, Li Q, Richards EM, Pepine CJ, Raizada MK. ACE2 (Angiotensin-Converting Enzyme 2) in Cardiopulmonary Diseases: Ramifications for the Control of SARS-CoV-2. Hypertension 2020; 76:651-661. [PMID: 32783758 DOI: 10.1161/hypertensionaha.120.15595] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Discovery of ACE2 (angiotensin-converting enzyme 2) revealed that the renin-angiotensin system has 2 counterbalancing arms. ACE2 is a major player in the protective arm, highly expressed in lungs and gut with the ability to mitigate cardiopulmonary diseases such as inflammatory lung disease. ACE2 also exhibits activities involving gut microbiome, nutrition, and as a chaperone stabilizing the neutral amino acid transporter, B0AT1, in gut. But the current interest in ACE2 arises because it is the cell surface receptor for the novel coronavirus, severe acute respiratory syndrome coronavirus-2, to infect host cells, similar to severe acute respiratory syndrome coronavirus-2. This suggests that ACE2 be considered harmful, however, because of its important other roles, it is paradoxically a potential therapeutic target for cardiopulmonary diseases, including coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2. This review describes the discovery of ACE2, its physiological functions, and its place in the renin-angiotensin system. It illustrates new analyses of the structure of ACE2 that provides better understanding of its actions particularly in lung and gut, shedding of ACE2 by ADAM17 (a disintegrin and metallopeptidase domain 17 protein), and role of TMPRSS2 (transmembrane serine proteases 2) in severe acute respiratory syndrome coronavirus-2 entry into host cells. Cardiopulmonary diseases are associated with decreased ACE2 activity and the mitigation by increasing ACE2 activity along with its therapeutic relevance are addressed. Finally, the potential use of ACE2 as a treatment target in COVID-19, despite its role to allow viral entry into host cells, is suggested.
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Affiliation(s)
- Ravindra K Sharma
- From the Division of Nephrology, Hypertension and Renal Transplantation, Department of Medicine (R.K.S.), University of Florida College of Medicine, Gainesville
| | - Bruce R Stevens
- Department of Physiology and Functional Genomics (B.R.S., E.M.R., M.K.R.), University of Florida College of Medicine, Gainesville
| | - Alexander G Obukhov
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis (A.G.O.)
| | - Maria B Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama College of Medicine, Birmingham (M.B.G.)
| | - Gavin Y Oudit
- Department of Medicine, University of Alberta College of Medicine, Edmonton, Canada (G.Y.O.)
| | - Qiuhong Li
- Department of Ophthalmology (Q.L.), University of Florida College of Medicine, Gainesville
| | - Elaine M Richards
- Department of Physiology and Functional Genomics (B.R.S., E.M.R., M.K.R.), University of Florida College of Medicine, Gainesville
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine (C.J.P.), University of Florida College of Medicine, Gainesville
| | - Mohan K Raizada
- Department of Physiology and Functional Genomics (B.R.S., E.M.R., M.K.R.), University of Florida College of Medicine, Gainesville
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16
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Hayashi K, Longenecker KL, Koenig P, Prashar A, Hampl J, Stoll V, Vivona S. Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity. J Struct Biol 2020; 211:107512. [DOI: 10.1016/j.jsb.2020.107512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 01/30/2023]
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17
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Guevara T, Rodriguez-Banqueri A, Ksiazek M, Potempa J, Gomis-Rüth FX. Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases. IUCRJ 2020; 7:18-29. [PMID: 31949901 PMCID: PMC6949598 DOI: 10.1107/s2052252519013848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/10/2019] [Indexed: 05/23/2023]
Abstract
Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54-Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 Å revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine-glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 Å structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.
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Affiliation(s)
- Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Arturo Rodriguez-Banqueri
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - Jan Potempa
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, 501 South Preston Street, Louisville, KY 40202, USA
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, Kraków 30-387, Poland
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/ Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
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18
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Moss S, Subramanian V, Acharya KR. Crystal structure of peptide-bound neprilysin reveals key binding interactions. FEBS Lett 2019; 594:327-336. [PMID: 31514225 DOI: 10.1002/1873-3468.13602] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 11/09/2022]
Abstract
Neprilysin (NEP) is a promiscuous zinc metalloprotease with broad substrate specificity and cleaves a remarkable diversity of substrates through endopeptidase action. Two of these - amyloid-β and natriuretic peptides - implicate the enzyme in both Alzheimer's disease and cardiovascular disease, respectively. Here, we report the creation of a catalytically inactive NEP (E584D) to determine the first peptide-bound crystal structure at 2.6 Å resolution. The structure reveals key interactions involved in substrate binding which we have identified to be conserved in other known zinc metalloproteases. In addition, the structure provides evidence for a potential exosite within the central cavity that may play a critical role in substrate positioning. Together, these results contribute to our understanding of the molecular function of NEP.
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Affiliation(s)
- Stephen Moss
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, Claverton Down, University of Bath, UK
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19
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Niu G, Yang Y, Ren J, Song T, Hu Z, Chen L, Hong R, Xia J, Ke C, Wang X. Overexpression of CPXM2 predicts an unfavorable prognosis and promotes the proliferation and migration of gastric cancer. Oncol Rep 2019; 42:1283-1294. [PMID: 31364750 PMCID: PMC6718098 DOI: 10.3892/or.2019.7254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/24/2019] [Indexed: 12/24/2022] Open
Abstract
Carboxypeptidase X, M14 family member 2 (CPXM2), has been associated with several human disorders such as developmental diseases. However, whether CPXM2 is involved in oncogenesis or tumor progression remains unclear. In the present study, we used clinical samples from gastric cancer (GC) patients to investigate potential roles of CPXM2 in GC. We also analyzed datasets from the Oncomine database, The Cancer Genome Atlas (TCGA), and the Kaplan‑Meier Plotter to validate these results. We found that CPXM2 was overexpressed in GC and that the overexpression was associated with an unfavorable prognosis, regardless of the Lauren classification and tumor node metastasis staging. In addition, knockdown of CPXM2 in cultured GC cells significantly impeded cell proliferation and migration, as indicated by the cholecystokinin octapeptide, colony formation assay, scratch wound healing assay, and Transwell® migration assay. Furthermore, gene set enrichment analysis using RNA‑seq data from TCGA indicated that high CPXM2 expression in GC patients was positively correlated with the HALLMARK_APICAL_JUNCTION and HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION gene sets. Finally, western blotting results revealed that several key molecules involved in the epithelial mesenchymal transition were regulated by CPXM2. Taken together, these results imply an active role for CPXM2 in promoting tumor aggressiveness via epithelial to mesenchymal transition (EMT) modulation in GCs.
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Affiliation(s)
- Gengming Niu
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Yazhe Yang
- Queen Mary College of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jun Ren
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Tao Song
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Zhiqing Hu
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Liang Chen
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Runqi Hong
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Jie Xia
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Chongwei Ke
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
| | - Xin Wang
- Department of General Surgery, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, P.R. China
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20
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Cuppari A, Körschgen H, Fahrenkamp D, Schmitz C, Guevara T, Karmilin K, Kuske M, Olf M, Dietzel E, Yiallouros I, de Sanctis D, Goulas T, Weiskirchen R, Jahnen-Dechent W, Floehr J, Stoecker W, Jovine L, Gomis-Rüth FX. Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition. IUCRJ 2019; 6:317-330. [PMID: 30867929 PMCID: PMC6400186 DOI: 10.1107/s2052252519001568] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWVXGP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWVXGP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.
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Affiliation(s)
- Anna Cuppari
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Hagen Körschgen
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Carlo Schmitz
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Konstantin Karmilin
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Michael Kuske
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Mario Olf
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Eileen Dietzel
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Daniele de Sanctis
- ESRF – The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France
| | - Theodoros Goulas
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Willi Jahnen-Dechent
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Julia Floehr
- Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany
| | - Walter Stoecker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany
| | - Luca Jovine
- Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden
| | - F. Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain
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21
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Burke LC, Ezeribe HO, Kwon AY, Dockery D, Lyons PJ. Carboxypeptidase O is a lipid droplet-associated enzyme able to cleave both acidic and polar C-terminal amino acids. PLoS One 2018; 13:e0206824. [PMID: 30388170 PMCID: PMC6214572 DOI: 10.1371/journal.pone.0206824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 10/19/2018] [Indexed: 11/18/2022] Open
Abstract
Carboxypeptidase O (CPO) is a member of the M14 family of metallocarboxypeptidases with a preference for the cleavage of C-terminal acidic amino acids. CPO is largely expressed in the small intestine, although it has been detected in other tissues such as the brain and ovaries. CPO does not contain a prodomain, nor is it strongly regulated by pH, and hence appears to exist as a constitutively active enzyme. The goal of this study was to investigate the intracellular distribution and activity of CPO in order to predict physiological substrates and function. The distribution of CPO, when expressed in MDCK cells, was analyzed by immunofluorescence microscopy. Soon after addition of nutrient-rich media, CPO was found to associate with lipid droplets, causing an increase in lipid droplet quantity. As media became depleted, CPO moved to a broader ER distribution, no longer impacting lipid droplet numbers. Membrane cholesterol levels played a role in the distribution and in vitro enzymatic activity of CPO, with cholesterol enrichment leading to decreased lipid droplet association and enzymatic activity. The ability of CPO to cleave C-terminal amino acids within the early secretory pathway (in vivo) was examined using Gaussia luciferase as a substrate, C-terminally tagged with variants of an ER retention signal. While no effect of cholesterol was observed, these data show that CPO does function as an active enzyme within the ER where it removes C-terminal glutamates and aspartates, as well as a number of polar amino acids.
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Affiliation(s)
- Linnea C. Burke
- Department of Biology, Andrews University, Berrien Springs, Michigan, United States of America
| | - Hazel O. Ezeribe
- Department of Biology, Andrews University, Berrien Springs, Michigan, United States of America
| | - Anna Y. Kwon
- Department of Biology, Andrews University, Berrien Springs, Michigan, United States of America
| | - Donnel Dockery
- Department of Biology, Andrews University, Berrien Springs, Michigan, United States of America
| | - Peter J. Lyons
- Department of Biology, Andrews University, Berrien Springs, Michigan, United States of America
- * E-mail:
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22
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Characterization of a Glycyl-Specific TET Aminopeptidase Complex from Pyrococcus horikoshii. J Bacteriol 2018; 200:JB.00059-18. [PMID: 29866801 DOI: 10.1128/jb.00059-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/29/2018] [Indexed: 01/03/2023] Open
Abstract
The TET peptidases are large self-compartmentalized complexes that form dodecameric particles. These metallopeptidases, members of the M42 family, are widely distributed in prokaryotes. Three different versions of TET complexes, with different substrate specificities, were found to coexist in the cytosol of the hyperthermophilic archaeon Pyrococcus horikoshii In the present work, we identified a novel type of TET complex that we named PhTET4. The recombinant PhTET4 enzyme was found to self-assemble as a tetrahedral edifice similar to other TET complexes. We determined PhTET4 substrate specificity using a broad range of monoacyl chromogenic and fluorogenic compounds. High-performance liquid chromatographic peptide degradation assays were also performed. These experiments demonstrated that PhTET4 is a strict glycyl aminopeptidase, devoid of amidolytic activity toward other types of amino acids. The catalytic efficiency of PhTET4 was studied under various conditions. The protein was found to be a hyperthermophilic alkaline aminopeptidase. Interestingly, unlike other peptidases from the same family, it was activated only by nickel ions.IMPORTANCE We describe here the first known peptidase displaying exclusive activity toward N-terminal glycine residues. This work indicates a specific role for intracellular glycyl peptidases in deep sea hyperthermophilic archaeal metabolism. These observations also provide critical evidence for the use of these archaeal extremozymes for biotechnological applications.
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Arolas JL, Goulas T, Cuppari A, Gomis-Rüth FX. Multiple Architectures and Mechanisms of Latency in Metallopeptidase Zymogens. Chem Rev 2018; 118:5581-5597. [PMID: 29775286 DOI: 10.1021/acs.chemrev.8b00030] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metallopeptidases cleave polypeptides bound in the active-site cleft of catalytic domains through a general base/acid mechanism. This involves a solvent molecule bound to a catalytic zinc and general regulation of the mechanism through zymogen-based latency. Sixty reported structures from 11 metallopeptidase families reveal that prosegments, mostly N-terminal of the catalytic domain, block the cleft regardless of their size. Prosegments may be peptides (5-14 residues), which are only structured within the zymogens, or large moieties (<227 residues) of one or two folded domains. While some prosegments globally shield the catalytic domain through a few contacts, others specifically run across the cleft in the same or opposite direction as a substrate, making numerous interactions. Some prosegments block the zinc by replacing the solvent with particular side chains, while others use terminal α-amino or carboxylate groups. Overall, metallopeptidase zymogens employ disparate mechanisms that diverge even within families, which supports that latency is less conserved than catalysis.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Theodoros Goulas
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - Anna Cuppari
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Structural Biology Unit ("María-de-Maeztu" Unit of Excellence) , Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas , Barcelona Science Park, c/Baldiri Reixac 15-21 , 08028 Barcelona , Catalonia , Spain
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Klein T, Eckhard U, Dufour A, Solis N, Overall CM. Proteolytic Cleavage-Mechanisms, Function, and "Omic" Approaches for a Near-Ubiquitous Posttranslational Modification. Chem Rev 2017; 118:1137-1168. [PMID: 29265812 DOI: 10.1021/acs.chemrev.7b00120] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteases enzymatically hydrolyze peptide bonds in substrate proteins, resulting in a widespread, irreversible posttranslational modification of the protein's structure and biological function. Often regarded as a mere degradative mechanism in destruction of proteins or turnover in maintaining physiological homeostasis, recent research in the field of degradomics has led to the recognition of two main yet unexpected concepts. First, that targeted, limited proteolytic cleavage events by a wide repertoire of proteases are pivotal regulators of most, if not all, physiological and pathological processes. Second, an unexpected in vivo abundance of stable cleaved proteins revealed pervasive, functionally relevant protein processing in normal and diseased tissue-from 40 to 70% of proteins also occur in vivo as distinct stable proteoforms with undocumented N- or C-termini, meaning these proteoforms are stable functional cleavage products, most with unknown functional implications. In this Review, we discuss the structural biology aspects and mechanisms of catalysis by different protease classes. We also provide an overview of biological pathways that utilize specific proteolytic cleavage as a precision control mechanism in protein quality control, stability, localization, and maturation, as well as proteolytic cleavage as a mediator in signaling pathways. Lastly, we provide a comprehensive overview of analytical methods and approaches to study activity and substrates of proteolytic enzymes in relevant biological models, both historical and focusing on state of the art proteomics techniques in the field of degradomics research.
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Affiliation(s)
- Theo Klein
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Ulrich Eckhard
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Antoine Dufour
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Nestor Solis
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
| | - Christopher M Overall
- Life Sciences Institute, Department of Oral Biological and Medical Sciences, and ‡Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z4, Canada
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25
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Garcia-Pardo J, Tanco S, Díaz L, Dasgupta S, Fernandez-Recio J, Lorenzo J, Aviles FX, Fricker LD. Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains. PLoS One 2017; 12:e0187778. [PMID: 29131831 PMCID: PMC5683605 DOI: 10.1371/journal.pone.0187778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 11/18/2022] Open
Abstract
Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5–7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell.
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Affiliation(s)
- Javier Garcia-Pardo
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Sebastian Tanco
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lucía Díaz
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona, Spain
| | - Sayani Dasgupta
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona, Spain
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francesc X. Aviles
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- * E-mail: (LDF); (FXA)
| | - Lloyd D. Fricker
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail: (LDF); (FXA)
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26
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Puente-Rivera J, Villalpando JL, Villalobos-Osnaya A, Vázquez-Carrillo LI, León-Ávila G, Ponce-Regalado MD, López-Camarillo C, Elizalde-Contreras JM, Ruiz-May E, Arroyo R, Alvarez-Sánchez ME. The 50 kDa metalloproteinase TvMP50 is a zinc-mediated Trichomonas vaginalis virulence factor. Mol Biochem Parasitol 2017; 217:32-41. [DOI: 10.1016/j.molbiopara.2017.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/28/2017] [Accepted: 09/01/2017] [Indexed: 12/18/2022]
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27
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Pomowski A, Usón I, Nowakowska Z, Veillard F, Sztukowska MN, Guevara T, Goulas T, Mizgalska D, Nowak M, Potempa B, Huntington JA, Potempa J, Gomis-Rüth FX. Structural insights unravel the zymogenic mechanism of the virulence factor gingipain K from Porphyromonas gingivalis, a causative agent of gum disease from the human oral microbiome. J Biol Chem 2017; 292:5724-5735. [PMID: 28196869 DOI: 10.1074/jbc.m117.776724] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/06/2017] [Indexed: 01/11/2023] Open
Abstract
Skewing of the human oral microbiome causes dysbiosis and preponderance of bacteria such as Porphyromonas gingivalis, the main etiological agent of periodontitis. P. gingivalis secretes proteolytic gingipains (Kgp and RgpA/B) as zymogens inhibited by a pro-domain that is removed during extracellular activation. Unraveling the molecular mechanism of Kgp zymogenicity is essential to design inhibitors blocking its activity. Here, we found that the isolated 209-residue Kgp pro-domain is a boomerang-shaped all-β protein similar to the RgpB pro-domain. Using composite structural information of Kgp and RgpB, we derived a plausible homology model and mechanism of Kgp-regulating zymogenicity. Accordingly, the pro-domain would laterally attach to the catalytic moiety in Kgp and block the active site through an exposed inhibitory loop. This loop features a lysine (Lys129) likely occupying the S1 specificity pocket and exerting latency. Lys129 mutation to glutamate or arginine led to misfolded protein that was degraded in vivo Mutation to alanine gave milder effects but still strongly diminished proteolytic activity, without affecting the subcellular location of the enzyme. Accordingly, the interactions of Lys129 within the S1 pocket are also essential for correct folding. Uniquely for gingipains, the isolated Kgp pro-domain dimerized through an interface, which partially overlapped with that between the catalytic moiety and the pro-domain within the zymogen, i.e. both complexes are mutually exclusive. Thus, pro-domain dimerization, together with partial rearrangement of the active site upon activation, explains the lack of inhibition of the pro-domain in trans. Our results reveal that the specific latency mechanism of Kgp differs from those of Rgps.
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Affiliation(s)
- Anja Pomowski
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Isabel Usón
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain.,the Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Catalonia, Spain
| | - Zuzanna Nowakowska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Florian Veillard
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Maryta N Sztukowska
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - Tibisay Guevara
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Theodoros Goulas
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain
| | - Danuta Mizgalska
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Magdalena Nowak
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and
| | - Barbara Potempa
- the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - James A Huntington
- From the Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Kraków, Poland, and .,the Department of Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202
| | - F Xavier Gomis-Rüth
- the Proteolysis Lab and Crystallographic Methods Lab, Structural Biology Unit, "María de Maeztu" Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Catalonia, Spain,
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28
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Chandrasekaran M, Chandrasekar R, Chun SC, Sathiyabama M. Isolation, characterization and molecular three-dimensional structural predictions of metalloprotease from a phytopathogenic fungus, Alternaria solani (Ell. and Mart.) Sor. J Biosci Bioeng 2016; 122:131-9. [DOI: 10.1016/j.jbiosc.2015.12.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/14/2015] [Accepted: 12/31/2015] [Indexed: 02/09/2023]
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29
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Plug T, Meijers JCM. Structure-function relationships in thrombin-activatable fibrinolysis inhibitor. J Thromb Haemost 2016; 14:633-44. [PMID: 26786060 DOI: 10.1111/jth.13261] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 11/30/2022]
Abstract
Thrombin-activatable fibrinolysis inhibitor (TAFI) is an important regulator in the balance of coagulation and fibrinolysis. TAFI is a metallocarboxypeptidase that circulates in plasma as zymogen. Activated TAFI (TAFIa) cleaves C-terminal lysine or arginine residues from peptide substrates. The removal of C-terminal lysine residues from partially degraded fibrin leads to reduced plasmin formation and thus attenuation of fibrinolysis. TAFI also plays a role in inflammatory processes via the removal of C-terminal arginine or lysine residues from bradykinin, thrombin-cleaved osteopontin, C3a, C5a and chemerin. TAFI has been studied extensively over the past three decades and recent publications provide a wealth of information, including crystal structures, mutants and structural data obtained with antibodies and peptides. In this review, we combined and compared available data on structure/function relationships of TAFI.
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Affiliation(s)
- T Plug
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - J C M Meijers
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Plasma Proteins, Sanquin Research, Amsterdam, the Netherlands
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30
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Reddy S, Akgul A, Karsi A, Abdelhamed H, Wills RW, Lawrence ML. The role of Listeria monocytogenes cell wall surface anchor protein LapB in virulence, adherence, and intracellular replication. Microb Pathog 2016; 92:19-25. [DOI: 10.1016/j.micpath.2015.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/19/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
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31
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Zhang X, MacDonald BT, Gao H, Shamashkin M, Coyle AJ, Martinez RV, He X. Characterization of Tiki, a New Family of Wnt-specific Metalloproteases. J Biol Chem 2015; 291:2435-43. [PMID: 26631728 DOI: 10.1074/jbc.m115.677807] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 11/06/2022] Open
Abstract
The Wnt family of secreted glycolipoproteins plays pivotal roles in development and human diseases. Tiki family proteins were identified as novel Wnt inhibitors that act by cleaving the Wnt amino-terminal region to inactivate specific Wnt ligands. Tiki represents a new metalloprotease family that is dependent on Mn(2+)/Co(2+) but lacks known metalloprotease motifs. The Tiki extracellular domain shares homology with bacterial TraB/PrgY proteins, known for their roles in the inhibition of mating pheromones. The TIKI/TraB fold is predicted to be distantly related to structures of additional bacterial proteins and may use a core β-sheet within an α+β-fold to coordinate conserved residues for catalysis. In this study, using assays for Wnt3a cleavage and signaling inhibition, we performed mutagenesis analyses of human TIKI2 to examine the structural prediction and identify the active site residues. We also established an in vitro assay for TIKI2 protease activity using FRET peptide substrates derived from the cleavage motifs of Wnt3a and Xenopus wnt8 (Xwnt8). We further identified two pairs of potential disulfide bonds that reside outside the β-sheet catalytic core but likely assist the folding of the TIKI domain. Finally, we systematically analyzed TIKI2 cleavage of the 19 human WNT proteins, of which we identified 10 as potential TIKI2 substrates, revealing the hydrophobic nature of Tiki cleavage sites. Our study provides insights into the Tiki family of proteases and its Wnt substrates.
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Affiliation(s)
- Xinjun Zhang
- From the F. M. Kirby Neurobiology Center, Boston Children's Hospital, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115 and
| | - Bryan T MacDonald
- From the F. M. Kirby Neurobiology Center, Boston Children's Hospital, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115 and
| | - Huilan Gao
- the Centers for Therapeutic Innovation, Pfizer, Boston, Massachusetts 02115
| | - Michael Shamashkin
- the Centers for Therapeutic Innovation, Pfizer, Boston, Massachusetts 02115
| | - Anthony J Coyle
- the Centers for Therapeutic Innovation, Pfizer, Boston, Massachusetts 02115
| | - Robert V Martinez
- the Centers for Therapeutic Innovation, Pfizer, Boston, Massachusetts 02115
| | - Xi He
- From the F. M. Kirby Neurobiology Center, Boston Children's Hospital, Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115 and
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32
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Sapio MR, Vessaz M, Thomas P, Genton P, Fricker LD, Salzmann A. Novel carboxypeptidase A6 (CPA6) mutations identified in patients with juvenile myoclonic and generalized epilepsy. PLoS One 2015; 10:e0123180. [PMID: 25875328 PMCID: PMC4395397 DOI: 10.1371/journal.pone.0123180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 02/17/2015] [Indexed: 01/12/2023] Open
Abstract
Carboxypeptidase A6 (CPA6) is a peptidase that removes C-terminal hydrophobic amino acids from peptides and proteins. The CPA6 gene is expressed in the brains of humans and animals, with high levels of expression during development. It is translated with a prodomain (as proCPA6), which is removed before secretion. The active form of CPA6 binds tightly to the extracellular matrix (ECM) where it is thought to function in the processing of peptides and proteins. Mutations in the CPA6 gene have been identified in patients with temporal lobe epilepsy and febrile seizures. In the present study, we screened for CPA6 mutations in patients with juvenile myoclonic epilepsy and identified two novel missense mutations: Arg36His and Asn271Ser. Patients harboring these mutations also presented with generalized epilepsy. Neither of the novel mutations was found in a control population. Asn271 is highly conserved in CPA6 and other related metallocarboxypeptidases. Arg36 is present in the prodomain and is not highly conserved. To assess structural consequences of the amino acid substitutions, both mutants were modeled within the predicted structure of the enzyme. To examine the effects of these mutations on enzyme expression and activity, we expressed the mutated enzymes in human embryonic kidney 293T cells. These analyses revealed that Asn271Ser abolished enzymatic activity, while Arg36His led to a ~50% reduction in CPA6 levels in the ECM. Pulse-chase using radio-labeled amino acids was performed to follow secretion. Newly-synthesized CPA6 appeared in the ECM with peak levels between 2-8 hours. There was no major difference in time course between wild-type and mutant forms, although the amount of radiolabeled CPA6 in the ECM was lower for the mutants. Our experiments demonstrate that these mutations in CPA6 are deleterious and provide further evidence for the involvement of CPA6 mutations in the predisposition for several types of epilepsy.
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Affiliation(s)
- Matthew R. Sapio
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Monique Vessaz
- Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, Geneva, Switzerland
| | - Pierre Thomas
- Department of Neurology, University Hospital, Nice, France
| | - Pierre Genton
- Centre Saint Paul, Hôpital Henri Gastaut, Marseille, France
| | - Lloyd D. Fricker
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, United States of America
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States of America
- * E-mail: (LDF); (AS)
| | - Annick Salzmann
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
- * E-mail: (LDF); (AS)
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33
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López-Pelegrín M, Ksiazek M, Karim AY, Guevara T, Arolas JL, Potempa J, Gomis-Rüth FX. A novel mechanism of latency in matrix metalloproteinases. J Biol Chem 2015; 290:4728-4740. [PMID: 25555916 DOI: 10.1074/jbc.m114.605956] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The matrix metalloproteinases (MMPs) are a family of secreted soluble or membrane-anchored multimodular peptidases regularly found in several paralogous copies in animals and plants, where they have multiple functions. The minimal consensus domain architecture comprises a signal peptide, a 60-90-residue globular prodomain with a conserved sequence motif including a cysteine engaged in "cysteine-switch" or "Velcro" mediated latency, and a catalytic domain. Karilysin, from the human periodontopathogen Tannerella forsythia, is the only bacterial MMP to have been characterized biochemically to date. It shares with eukaryotic forms the catalytic domain but none of the flanking domains. Instead of the consensus MMP prodomain, it features a 14-residue propeptide, the shortest reported for a metallopeptidase, which lacks cysteines. Here we determined the structure of a prokarilysin fragment encompassing the propeptide and the catalytic domain, and found that the former runs across the cleft in the opposite direction to a bound substrate and inhibits the latter through an "aspartate-switch" mechanism. This finding is reminiscent of latency maintenance in the otherwise unrelated astacin and fragilysin metallopeptidase families. In addition, in vivo and biochemical assays showed that the propeptide contributes to protein folding and stability. Our analysis of prokarilysin reveals a novel mechanism of latency and activation in MMPs. Finally, our findings support the view that the karilysin catalytic domain was co-opted by competent bacteria through horizontal gene transfer from a eukaryotic source, and later evolved in a specific bacterial environment.
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Affiliation(s)
- Mar López-Pelegrín
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Miroslaw Ksiazek
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Abdulkarim Y Karim
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and
| | - Tibisay Guevara
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain
| | - Joan L Arolas
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
| | - Jan Potempa
- the Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Ul. Gronostajowa 7, 30-387 Kraków, Poland, and; the Oral Immunology and Infectious Disease, University of Louisville School of Dentistry, Louisville, Kentucky 40202.
| | - F Xavier Gomis-Rüth
- From the Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, c/Baldiri Reixac, 15-21, 08028 Barcelona, Catalonia, Spain,.
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34
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Jalkute CB, Barage SH, Sonawane KD. Insight into molecular interactions of Aβ peptide and gelatinase from Enterococcus faecalis: a molecular modeling approach. RSC Adv 2015. [DOI: 10.1039/c4ra09354b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease is characterized by the presence of extracellular deposition of amyloid beta (Aβ) peptides.
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Affiliation(s)
| | - Sagar H. Barage
- Department of Biotechnology
- Shivaji University
- Kolhapur 416004
- India
| | - Kailas D. Sonawane
- Department of Microbiology
- Shivaji University
- Kolhapur 416004
- India
- Structural Bioinformatics Unit
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35
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Chan ACK, Blair KM, Liu Y, Frirdich E, Gaynor EC, Tanner ME, Salama NR, Murphy MEP. Helical shape of Helicobacter pylori requires an atypical glutamine as a zinc ligand in the carboxypeptidase Csd4. J Biol Chem 2014; 290:3622-38. [PMID: 25505267 DOI: 10.1074/jbc.m114.624734] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peptidoglycan modifying carboxypeptidases (CPs) are important determinants of bacterial cell shape. Here, we report crystal structures of Csd4, a three-domain protein from the human gastric pathogen Helicobacter pylori. The catalytic zinc in Csd4 is coordinated by a rare His-Glu-Gln configuration that is conserved among most Csd4 homologs, which form a distinct subfamily of CPs. Substitution of the glutamine to histidine, the residue found in prototypical zinc carboxypeptidases, resulted in decreased enzyme activity and inhibition by phosphate. Expression of the histidine variant at the native locus in a H. pylori csd4 deletion strain did not restore the wild-type helical morphology. Biochemical assays show that Csd4 can cleave a tripeptide peptidoglycan substrate analog to release m-DAP. Structures of Csd4 with this substrate analog or product bound at the active site reveal determinants of peptidoglycan specificity and the mechanism to cleave an isopeptide bond to release m-DAP. Our data suggest that Csd4 is the archetype of a new CP subfamily with a domain scheme that differs from this large family of peptide-cleaving enzymes.
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Affiliation(s)
- Anson C K Chan
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kris M Blair
- the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, the Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, and
| | - Yanjie Liu
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Emilisa Frirdich
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Erin C Gaynor
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Martin E Tanner
- the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Nina R Salama
- the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, the Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, and
| | - Michael E P Murphy
- From the Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada,
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36
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Huesgen PF, Lange PF, Rogers LD, Solis N, Eckhard U, Kleifeld O, Goulas T, Gomis-Rüth FX, Overall CM. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nat Methods 2014; 12:55-8. [DOI: 10.1038/nmeth.3177] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/07/2014] [Indexed: 12/25/2022]
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37
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Cerdà-Costa N, Gomis-Rüth FX. Architecture and function of metallopeptidase catalytic domains. Protein Sci 2014; 23:123-44. [PMID: 24596965 DOI: 10.1002/pro.2400] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The cleavage of peptide bonds by metallopeptidases (MPs) is essential for life. These ubiquitous enzymes participate in all major physiological processes, and so their deregulation leads to diseases ranging from cancer and metastasis, inflammation, and microbial infection to neurological insults and cardiovascular disorders. MPs cleave their substrates without a covalent intermediate in a single-step reaction involving a solvent molecule, a general base/acid, and a mono- or dinuclear catalytic metal site. Most monometallic MPs comprise a short metal-binding motif (HEXXH), which includes two metal-binding histidines and a general base/acid glutamate, and they are grouped into the zincin tribe of MPs. The latter divides mainly into the gluzincin and metzincin clans. Metzincins consist of globular ∼ 130-270-residue catalytic domains, which are usually preceded by N-terminal pro-segments, typically required for folding and latency maintenance. The catalytic domains are often followed by C-terminal domains for substrate recognition and other protein-protein interactions, anchoring to membranes, oligomerization, and compartmentalization. Metzincin catalytic domains consist of a structurally conserved N-terminal subdomain spanning a five-stranded β-sheet, a backing helix, and an active-site helix. The latter contains most of the metal-binding motif, which is here characteristically extended to HEXXHXXGXX(H,D). Downstream C-terminal subdomains are generally shorter, differ more among metzincins, and mainly share a conserved loop--the Met-turn--and a C-terminal helix. The accumulated structural data from more than 300 deposited structures of the 12 currently characterized metzincin families reviewed here provide detailed knowledge of the molecular features of their catalytic domains, help in our understanding of their working mechanisms, and form the basis for the design of novel drugs.
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38
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Multiple Stable Conformations Account for Reversible Concentration-Dependent Oligomerization and Autoinhibition of a Metamorphic Metallopeptidase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Feld GK, El-Etr S, Corzett MH, Hunter MS, Belhocine K, Monack DM, Frank M, Segelke BW, Rasley A. Structure and function of REP34 implicates carboxypeptidase activity in Francisella tularensis host cell invasion. J Biol Chem 2014; 289:30668-30679. [PMID: 25231992 DOI: 10.1074/jbc.m114.599381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Francisella tularensis is the etiological agent of tularemia, or rabbit fever. Although F. tularensis is a recognized biothreat agent with broad and expanding geographical range, its mechanism of infection and environmental persistence remain poorly understood. Previously, we identified seven F. tularensis proteins that induce a rapid encystment phenotype (REP) in the free-living amoeba, Acanthamoeba castellanii. Encystment is essential to the pathogen's long term intracellular survival in the amoeba. Here, we characterize the cellular and molecular function of REP34, a REP protein with a mass of 34 kDa. A REP34 knock-out strain of F. tularensis has a reduced ability to both induce encystment in A. castellanii and invade human macrophages. We determined the crystal structure of REP34 to 2.05-Å resolution and demonstrate robust carboxypeptidase B-like activity for the enzyme. REP34 is a zinc-containing monomeric protein with close structural homology to the metallocarboxypeptidase family of peptidases. REP34 possesses a novel topology and substrate binding pocket that deviates from the canonical funnelin structure of carboxypeptidases, putatively resulting in a catalytic role for a conserved tyrosine and distinct S1' recognition site. Taken together, these results identify REP34 as an active carboxypeptidase, implicate the enzyme as a potential key F. tularensis effector protein, and may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells.
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Affiliation(s)
- Geoffrey K Feld
- Biosciences and Biotechnology and Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Sahar El-Etr
- Biosciences and Biotechnology and Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Michele H Corzett
- Biosciences and Biotechnology and Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Mark S Hunter
- Physics Divisions, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550 and
| | - Kamila Belhocine
- Stanford University School of Medicine, Stanford, California 94305
| | - Denise M Monack
- Stanford University School of Medicine, Stanford, California 94305
| | - Matthias Frank
- Physics Divisions, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550 and
| | - Brent W Segelke
- Biosciences and Biotechnology and Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Amy Rasley
- Biosciences and Biotechnology and Lawrence Livermore National Laboratory, Livermore, California 94550.
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40
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López-Pelegrín M, Cerdà-Costa N, Cintas-Pedrola A, Herranz-Trillo F, Bernadó P, Peinado JR, Arolas JL, Gomis-Rüth FX. Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase. Angew Chem Int Ed Engl 2014; 53:10624-30. [PMID: 25159620 DOI: 10.1002/anie.201405727] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 11/09/2022]
Abstract
Molecular plasticity controls enzymatic activity: the native fold of a protein in a given environment is normally unique and at a global free-energy minimum. Some proteins, however, spontaneously undergo substantial fold switching to reversibly transit between defined conformers, the "metamorphic" proteins. Here, we present a minimal metamorphic, selective, and specific caseinolytic metallopeptidase, selecase, which reversibly transits between several different states of defined three-dimensional structure, which are associated with loss of enzymatic activity due to autoinhibition. The latter is triggered by sequestering the competent conformation in incompetent but structured dimers, tetramers, and octamers. This system, which is compatible with a discrete multifunnel energy landscape, affords a switch that provides a reversible mechanism of control of catalytic activity unique in nature.
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Affiliation(s)
- Mar López-Pelegrín
- Proteolysis Lab, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park c/Baldiri Reixac, 15-21, 08028 Barcelona (Spain) http://www.ibmb.csic.es/home/xgomis
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41
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Brás NF, Fernandes PA, Ramos MJ. QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme. ACS Catal 2014. [DOI: 10.1021/cs500093h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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42
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Arolas JL, García-Castellanos R, Goulas T, Akiyama Y, Gomis-Rüth FX. Expression and purification of integral membrane metallopeptidase HtpX. Protein Expr Purif 2014; 99:113-8. [PMID: 24769134 DOI: 10.1016/j.pep.2014.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/24/2014] [Accepted: 04/16/2014] [Indexed: 11/29/2022]
Abstract
Little is known about the catalytic mechanism of integral membrane (IM) peptidases. HtpX is an IM metallopeptidase that plays a central role in protein quality control by preventing the accumulation of misfolded proteins in the membrane. Here we report the recombinant overexpression and purification of a catalytically ablated form of HtpX from Escherichia coli. Several E. coli strains, expression vectors, detergents, and purification strategies were tested to achieve maximum yields of pure and well-folded protein. HtpX was successfully overexpressed in E. coli BL21(DE3) cells using a pET-derived vector attaching a C-terminal His8-tag, extracted from the membranes using octyl-β-d-glucoside, and purified to homogeneity in the presence of this detergent in three consecutive steps: cobalt-affinity, anion-exchange, and size-exclusion chromatography. The production of HtpX in milligram amounts paves the way for structural studies, which will be essential to understand the catalytic mechanism of this IM peptidase and related family members.
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Affiliation(s)
- Joan L Arolas
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain.
| | - Raquel García-Castellanos
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain
| | - Theodoros Goulas
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain
| | - Yoshinori Akiyama
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - F Xavier Gomis-Rüth
- Proteolysis Lab, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, E-08028 Barcelona, Spain.
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43
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Sapio MR, Fricker LD. Carboxypeptidases in disease: insights from peptidomic studies. Proteomics Clin Appl 2014; 8:327-37. [PMID: 24470285 DOI: 10.1002/prca.201300090] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/10/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Abstract
Carboxypeptidases (CPs) perform many diverse physiological functions by removing C-terminal amino acids from proteins and peptides. Some CPs function in the degradation of proteins in the digestive tract while other enzymes play biosynthetic roles in the formation of neuropeptides and peptide hormones. Another set of CPs modify tubulin by removing amino acids from the C-terminus and from polyglutamyl side chains, thereby altering the properties of microtubules. This review focuses on three CPs: carboxypeptidase E, carboxypeptidase A6, and cytosolic carboxypeptidase 1. Naturally occurring mutations in all three of these enzymes are associated with disease phenotypes, ranging from obesity to epilepsy to neurodegeneration. Peptidomics is a useful tool to investigate the relationship between these mutations and alterations in peptide levels. This technique has also been used to define the function and characteristics of CPs. Results from peptidomics studies have helped to elucidate the function of CPs and clarify the biological underpinnings of pathologies by identifying peptides altered in disease states. This review describes the use of peptidomic techniques to gain insights into the normal function of CPs and the molecular defects caused by mutations in the enzymes.
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Affiliation(s)
- Matthew R Sapio
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
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44
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Rimsa V, Eadsforth TC, Joosten RP, Hunter WN. High-resolution structure of the M14-type cytosolic carboxypeptidase from Burkholderia cenocepacia refined exploiting PDB_REDO strategies. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:279-89. [PMID: 24531462 PMCID: PMC3940198 DOI: 10.1107/s1399004713026801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/30/2013] [Indexed: 01/01/2023]
Abstract
A potential cytosolic metallocarboxypeptidase from Burkholderia cenocepacia has been crystallized and a synchrotron-radiation microfocus beamline allowed the acquisition of diffraction data to 1.9 Å resolution. The asymmetric unit comprises a tetramer containing over 1500 amino acids, and the high-throughput automated protocols embedded in PDB_REDO were coupled with model-map inspections in refinement. This approach has highlighted the value of such protocols for efficient analyses. The subunit is constructed from two domains. The N-terminal domain has previously only been observed in cytosolic carboxypeptidase (CCP) proteins. The C-terminal domain, which carries the Zn2+-containing active site, serves to classify this protein as a member of the M14D subfamily of carboxypeptidases. Although eukaryotic CCPs possess deglutamylase activity and are implicated in processing modified tubulin, the function and substrates of the bacterial family members remain unknown. The B. cenocepacia protein did not display deglutamylase activity towards a furylacryloyl glutamate derivative, a potential substrate. Residues previously shown to coordinate the divalent cation and that contribute to peptide-bond cleavage in related enzymes such as bovine carboxypeptidase are conserved. The location of a conserved basic patch in the active site adjacent to the catalytic Zn2+, where an acetate ion is identified, suggests recognition of the carboxy-terminus in a similar fashion to other carboxypeptidases. However, there are significant differences that indicate the recognition of substrates with different properties. Of note is the presence of a lysine in the S1' recognition subsite that suggests specificity towards an acidic substrate.
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Affiliation(s)
- Vadim Rimsa
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Robbie P. Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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45
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Li W, Liu Y, Sheng X, Yin P, Hu F, Liu Y, Chen C, Li Q, Yan C, Wang J. Structure and mechanism of a type III secretion protease, NleC. ACTA ACUST UNITED AC 2013; 70:40-7. [PMID: 24419377 DOI: 10.1107/s1399004713024619] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/03/2013] [Indexed: 11/10/2022]
Abstract
NleC is one of the virulence factors that is injected into infected host cells by enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC and EHEC) via a needle-like protein complex called the type III secretion system (T3SS). The cytosolic NleC specifically cleaves the p65 subunit of NF-κB in the p65-p50 heterodimeric complex just after the Cys38 site in its N-terminal domain. The degradation of the remainder of the p65 C-terminal domain by the proteasome disrupts the NF-κB signalling pathway, thus dampening the host inflammatory response. Here, the crystal structure of NleC is reported at 1.55 Å resolution. In conjunction with biochemical analyses, the structure reveals that NleC is a member of the zincin zinc protease family and that the configuration of the NleC active site resembles that of the metzincin clan of metallopeptidases but without the canonical Met turn of astacin. The extended zinc-binding motif of NleC (HEXXHXXTXXXD) includes three metal ligands. The fifth zinc ligand, a conserved tyrosine (a bound water molecule is the fourth ligand), lies 45 residues downstream of the zincin motif. Furthermore, the electrostatic potential complementarity between NleC and p65 also contributes to the cleavage activity of the protease. These results not only provide important insights into the mechanism of how NleC recognizes its substrates, but also shed light on the design of new antibiotics for the food-borne diseases arising from EPEC and EHEC.
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Affiliation(s)
- Wenqi Li
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yexing Liu
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Xinlei Sheng
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Ping Yin
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Feizhuo Hu
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Ying Liu
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Chen Chen
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Quanxiu Li
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Chuangye Yan
- Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
| | - Jiawei Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing 100084, People's Republic of China
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46
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Zhang X, Tan F, Skidgel RA. Carboxypeptidase M is a positive allosteric modulator of the kinin B1 receptor. J Biol Chem 2013; 288:33226-40. [PMID: 24108126 DOI: 10.1074/jbc.m113.520791] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ligand binding to extracellular domains of G protein-coupled receptors can result in novel and nuanced allosteric effects on receptor signaling. We previously showed that the protein-protein interaction of carboxypeptidase M (CPM) and kinin B1 receptor (B1R) enhances B1R signaling in two ways; 1) kinin binding to CPM causes a conformational activation of the B1R, and 2) CPM-generated des-Arg-kinin agonist is efficiently delivered to the B1R. Here, we show CPM is also a positive allosteric modulator of B1R signaling to its agonist, des-Arg(10)-kallidin (DAKD). In HEK cells stably transfected with B1R, co-expression of CPM enhanced DAKD-stimulated increases in intracellular Ca(2+) or phosphoinositide turnover by a leftward shift of the dose-response curve without changing the maximum. CPM increased B1R affinity for DAKD by ∼5-fold but had no effect on basal B1R-dependent phosphoinositide turnover. Soluble, recombinant CPM bound to HEK cells expressing B1Rs without stimulating receptor signaling. CPM positive allosteric action was independent of enzyme activity but depended on interaction of its C-terminal domain with the B1R extracellular loop 2. Disruption of the CPM/B1R interaction or knockdown of CPM in cytokine-treated primary human endothelial cells inhibited the allosteric enhancement of CPM on B1R DAKD binding or ERK1/2 activation. CPM also enhanced the DAKD-induced B1R conformational change as detected by increased intramolecular fluorescence or bioluminescence resonance energy transfer. Thus, CPM binding to extracellular loop 2 of the B1R results in positive allosteric modulation of B1R signaling, and disruption of this interaction could provide a novel therapeutic approach to reduce pathological B1R signaling.
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47
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Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. Proc Natl Acad Sci U S A 2013; 110:E3761-9. [PMID: 24043784 DOI: 10.1073/pnas.1307637110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both mitochondria and chloroplasts contain distinct proteolytic systems for precursor protein processing catalyzed by the mitochondrial and stromal processing peptidases and for the degradation of targeting peptides catalyzed by presequence protease. Here, we have identified and characterized a component of the organellar proteolytic systems in Arabidopsis thaliana, the organellar oligopeptidase, OOP (At5g65620). OOP belongs to the M3A family of peptide-degrading metalloproteases. Using two independent in vivo methods, we show that the protease is dually localized to mitochondria and chloroplasts. Furthermore, we localized the OPP homolog At5g10540 to the cytosol. Analysis of peptide degradation by OOP revealed substrate size restriction from 8 to 23 aa residues. Short mitochondrial targeting peptides (presequence of the ribosomal protein L29 and presequence of 1-aminocyclopropane-1-carboxylic acid deaminase 1) and N- and C-terminal fragments derived from the presequence of the ATPase beta subunit ranging in size from 11 to 20 aa could be degraded. MS analysis showed that OOP does not exhibit a strict cleavage pattern but shows a weak preference for hydrophobic residues (F/L) at the P1 position. The crystal structures of OOP, at 1.8-1.9 Å, exhibit an ellipsoidal shape consisting of two major domains enclosing the catalytic cavity of 3,000 Å(3). The structural and biochemical data suggest that the protein undergoes conformational changes to allow peptide binding and proteolysis. Our results demonstrate the complementary role of OOP in targeting-peptide degradation in mitochondria and chloroplasts.
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48
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Lyons PJ, Sapio MR, Fricker LD. Zebrafish cytosolic carboxypeptidases 1 and 5 are essential for embryonic development. J Biol Chem 2013; 288:30454-30462. [PMID: 24022483 DOI: 10.1074/jbc.m113.497933] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cytosolic carboxypeptidases (CCPs) are a subfamily of metalloenzymes within the larger M14 family of carboxypeptidases that have been implicated in the post-translational modification of tubulin. It has been suggested that at least four of the six mammalian CCPs function as tubulin deglutamylases. However, it is not yet clear whether these enzymes play redundant or unique roles within the cell. To address this question, genes encoding CCPs were identified in the zebrafish genome. Analysis by quantitative polymerase chain reaction indicated that CCP1, CCP2, CCP5, and CCP6 mRNAs were detectable between 2 h and 8 days postfertilization with highest levels 5-8 days postfertilization. CCP1, CCP2, and CCP5 mRNAs were predominantly expressed in tissues such as the brain, olfactory placodes, and pronephric ducts. Morpholino oligonucleotide-mediated knockdown of CCP1 and CCP5 mRNA resulted in a common phenotype including ventral body curvature and hydrocephalus. Confocal microscopy of morphant zebrafish revealed olfactory placodes with defective morphology as well as pronephric ducts with increased polyglutamylation. These data suggest that CCP1 and CCP5 play important roles in developmental processes, particularly the development and functioning of cilia. The robust and similar defects upon knockdown suggest that each CCP may have a function in microtubule modification and ciliary function and that other CCPs are not able to compensate for the loss of one.
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Affiliation(s)
| | - Matthew R Sapio
- Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
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49
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Stura EA, Visse R, Cuniasse P, Dive V, Nagase H. Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain. FASEB J 2013; 27:4395-405. [PMID: 23913860 DOI: 10.1096/fj.13-233601] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Matrix metalloproteinase (MMP)-13 is one of the mammalian collagenases that play key roles in tissue remodelling and repair and in progression of diseases such as cancer, arthritis, atherosclerosis, and aneurysm. For collagenase to cleave triple helical collagens, the triple helical structure has to be locally unwound before hydrolysis, but this process is not well understood. We report crystal structures of catalytically inactive full-length human MMP-13(E223A) in complex with peptides of 14-26 aa derived from the cleaved prodomain during activation. Peptides are bound to the active site of the enzyme by forming an extended β-strand with Glu(40) or Tyr(46) inserted into the S1' specificity pocket. The structure of the N-terminal part of the peptides is variable and interacts with different parts of the catalytic domain. Those areas are designated substrate-dependent exosites, in that they accommodate different peptide structures, whereas the precise positioning of the substrate backbone is maintained in the active site. These modes of peptide-MMP-13 interactions have led us to propose how triple helical collagen strands fit into the active site cleft of the collagenase.
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Affiliation(s)
- Enrico A Stura
- 2H.N., Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.
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50
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Rogers LD, Overall CM. Proteolytic post-translational modification of proteins: proteomic tools and methodology. Mol Cell Proteomics 2013; 12:3532-42. [PMID: 23887885 DOI: 10.1074/mcp.m113.031310] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteolytic processing is a ubiquitous and irreversible post-translational modification involving limited and highly specific hydrolysis of peptide and isopeptide bonds of a protein by a protease. Cleavage generates shorter protein chains displaying neo-N and -C termini, often with new or modified biological activities. Within the past decade, degradomics and terminomics have emerged as significant proteomics subfields dedicated to characterizing proteolysis products as well as natural protein N and C termini. Here we provide an overview of contemporary proteomics-based methods, including specific quantitation, data analysis, and curation considerations, and highlight exciting new and emerging applications within these fields enabling in vivo analysis of proteolytic events.
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Affiliation(s)
- Lindsay D Rogers
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Sciences, and Centre for Blood Research, University of British Columbia, 4.401 Life Sciences Institute, 2350 Health Sciences Mall, Vancouver, British Columbia, V6T 1Z3, Canada
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