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Glover JNM, Kay CM, Lemieux J, Read RJ. Michael James (1940-2023). Acta Crystallogr D Struct Biol 2023; 79:953-955. [PMID: 37712437 PMCID: PMC10565731 DOI: 10.1107/s2059798323006976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023] Open
Abstract
Michael James is remembered.
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Affiliation(s)
- J. N. Mark Glover
- Department of Biochemistry, Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Cyril M. Kay
- Department of Biochemistry, Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Joanne Lemieux
- Department of Biochemistry, Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Hills Road, Cambridge CB2 0XY, United Kingdom
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2
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Pawar KS, Singh PN, Singh SK. Fungal alkaline proteases and their potential applications in different industries. Front Microbiol 2023; 14:1138401. [PMID: 37065163 PMCID: PMC10098022 DOI: 10.3389/fmicb.2023.1138401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/09/2023] [Indexed: 04/03/2023] Open
Abstract
The consumption of various enzymes in industrial applications around the world has increased immensely. Nowadays, industries are more focused on incorporating microbial enzymes in multiple processes to avoid the hazardous effects of chemicals. Among these commercially exploited enzymes, proteases are the most abundantly used enzymes in different industries. Numerous bacterial alkaline proteases have been studied widely and are commercially available; however, fungi exhibit a broader variety of proteases than bacteria. Additionally, since fungi are often recognized as generally regarded as safe (GRAS), using them as enzyme producers is safer than using bacteria. Fungal alkaline proteases are appealing models for industrial use because of their distinct spectrum of action and enormous diversity in terms of being active under alkaline range of pH. Unlike bacteria, fungi are less studied for alkaline protease production. Moreover, group of fungi growing at alkaline pH has remained unexplored for their capability for the production of commercially valuable products that are stable at alkaline pH. The current review focuses on the detailed classification of proteases, the production of alkaline proteases from different fungi by fermentation (submerged and solid–state), and their potential applications in detergent, leather, food, pharmaceutical industries along with their important role in silk degumming, waste management and silver recovery processes. Furthermore, the promising role of alkali–tolerant and alkaliphilic fungi in enzyme production has been discussed briefly. This will highlight the need for more research on fungi growing at alkaline pH and their biotechnological potential.
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Oda K, Wlodawer A. Overview of the Properties of Glutamic Peptidases That Are Present in Plant and Bacterial Pathogens and Play a Role in Celiac Disease and Cancer. Biochemistry 2023; 62:672-694. [PMID: 36705990 DOI: 10.1021/acs.biochem.2c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Seven peptidase (proteinase) families─aspartic, cysteine, metallo, serine, glutamic, threonine, and asparagine─are in the peptidase database MEROPS, version 12.4 (https://www.ebi.ac.uk/merops/). The glutamic peptidase family is assigned two clans, GA and GB, and comprises six subfamilies. This perspective summarizes the unique features of their representatives. (1) G1, scytalidoglutamic peptidase, has a β-sandwich structure containing catalytic residues glutamic acid (E) and glutamine (Q), thus the name eqolisin. Most family members are pepstatin-insensitive and act as plant pathogens. (2) G2, preneck appendage protein, originates in phages, is a transmembrane protein, and its catalytic residues consist of glutamic and aspartic acids. (3) G3, strawberry mottle virus glutamic peptidase, originates in viruses and has a β-sandwich structure with catalytic residues E and Q. Neprosin has propyl endopeptidase activity, is associated with celiac disease, has a β-sandwich structure, and contains catalytic residues E-E and Q-tryptophan. (4) G4, Tiki peptidase, of the erythromycin esterase family, is a transmembrane protein, and its catalytic residues are E-histidine pairs. (5) G5, RCE1 peptidase, is associated with cancer, is a transmembrane protein, and its catalytic residues are E-histidine and asparagine-histidine. Microcystinase, a bacterial toxin, is a transmembrane protein with catalytic residues E-histidine and asparagine-histidine. (6) G6, Ras/Rap1-specific peptidase, is a bacterial pathogen, a transmembrane protein, and its catalytic residues are E-histidine pairs. This family's common features are that their catalytic residues consist of a glutamic acid and another (variable) amino acid and that they exhibit a diversity of biological functions─plant and bacterial pathogens and involvement in celiac disease and cancer─that suggests they are viable drug targets.
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-Ku, Kyoto 606-8585, Japan
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy. Nat Commun 2022; 13:4446. [PMID: 35915115 PMCID: PMC9343461 DOI: 10.1038/s41467-022-32215-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022] Open
Abstract
The digestion of gluten generates toxic peptides, among which a highly immunogenic proline-rich 33-mer from wheat α-gliadin, that trigger coeliac disease. Neprosin from the pitcher plant is a reported prolyl endopeptidase. Here, we produce recombinant neprosin and its mutants, and find that full-length neprosin is a zymogen, which is self-activated at gastric pH by the release of an all-β pro-domain via a pH-switch mechanism featuring a lysine plug. The catalytic domain is an atypical 7+8-stranded β-sandwich with an extended active-site cleft containing an unprecedented pair of catalytic glutamates. Neprosin efficiently degrades both gliadin and the 33-mer in vitro under gastric conditions and is reversibly inactivated at pH > 5. Moreover, co-administration of gliadin and the neprosin zymogen at the ratio 500:1 reduces the abundance of the 33-mer in the small intestine of mice by up to 90%. Neprosin therefore founds a family of eukaryotic glutamate endopeptidases that fulfils requisites for a therapeutic glutenase. Celiac disease is characterized by intolerance to gluten, a cereal protein. Here, the authors show that neprosin, a glutamate peptidase from the pitcher plant, efficiently cleaves gluten components under physiological conditions in vitro and in the gut of mice.
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Oda K, Dunn BM, Wlodawer A. Serine-Carboxyl Peptidases, Sedolisins: From Discovery to Evolution. Biochemistry 2022; 61:1643-1664. [PMID: 35862020 DOI: 10.1021/acs.biochem.2c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sedolisin is a proteolytic enzyme, listed in the peptidase database MEROPS as a founding member of clan SB, family S53. This enzyme, although active at low pH, was originally shown not to be inhibited by an aspartic peptidase specific inhibitor, S-PI (pepstatin Ac). In this Perspective, the S53 family is described from the moment of original identification to evolution. The representative enzymes of the family are sedolisin, kumamolisin, and TPP-1. They exhibit the following unique features. (1) The fold of the molecule is similar to that of subtilisin, but the catalytic residues consist of a triad, Ser/Glu/Asp, that is unlike the Ser/His/Asp triad of subtilisin. (2) The molecule is expressed as a pro-form composed of the amino-terminal prosegment and the active domain. Additionally, some members of this family have an additional, carboxy-terminal prosegment. (3) Their optimum pH for activity is in the acidic region, not in the neutral to alkaline region where subtilisin is active. (4) Their distribution in nature is very broad across the three kingdoms of life. (5) Some of these enzymes from fungi and bacteria are pathogens to plants. (6) Some of them have significant potential applications for industry. (7) The lack of a TPP-1 gene in human brain is the cause of incurable juvenile neuronal ceroid lipofuscinosis (Batten's disease).
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Affiliation(s)
- Kohei Oda
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan
| | - Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, United States
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland 21702, United States
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Ting TY, Baharin A, Ramzi AB, Ng CL, Goh HH. Neprosin belongs to a new family of glutamic peptidase based on in silico evidence. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:23-35. [PMID: 35537348 DOI: 10.1016/j.plaphy.2022.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
Neprosin was first discovered in the insectivorous tropical pitcher plants of Nepenthes species as a novel protease with prolyl endopeptidase (PEP) activity. Neprosin has two uncharacterized domains of neprosin activation peptide and neprosin. A previous study has shown neprosin activity in hydrolyzing proline-rich gliadin, a gluten component that triggers celiac disease. In this study, we performed in silico structure-function analysis to investigate the catalytic mechanism of neprosin. Neprosin sequences lack the catalytic triad and motifs of PEP family S9. Protein structures of neprosins from Nepenthes × ventrata (NvNpr) and N. rafflesiana (NrNpr1) were generated by ab initio methods and comparatively assessed to obtain high-quality models. Structural alignment of models to experimental structures in the Protein Data Bank (PDB) found a high structural similarity to glutamic peptidases. Further investigations reveal other resemblances to the glutamic peptidases with low optimum pH that activates the enzyme via autoproteolysis for maturation. Two highly conserved glutamic acid residues, which are stable according to the molecular dynamics simulation, can be found at the active site of the substrate cleft. Protein docking demonstrated that mature neprosins bind well with potent antigen αI-gliadin at the putative active site. Taken together, neprosins represent a new glutamic peptidase family, with a putative catalytic dyad of two glutamic acids. This study illustrates a hypothetical enzymatic mechanism of the neprosin family and demonstrates the useful application of an accurate ab initio protein structure prediction in the structure-function study of a novel protein family.
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Affiliation(s)
- Tiew-Yik Ting
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Anis Baharin
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Chyan-Leong Ng
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600, UKM, Bangi, Selangor, Malaysia.
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Dong Z, Yang S, Lee BH. Bioinformatic mapping of a more precise Aspergillus niger degradome. Sci Rep 2021; 11:693. [PMID: 33436802 PMCID: PMC7804941 DOI: 10.1038/s41598-020-80028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
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Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid-Line of South-To-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Shuangshuang Yang
- College of Physical Education, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Byong H Lee
- Department of Microbiology/Immunology, McGill University, Montreal, QC, Canada
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Shin S, Hong JH, Na Y, Lee M, Qian WJ, Kim VN, Kim JS. Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster. Anal Chem 2020; 92:4926-4934. [DOI: 10.1021/acs.analchem.9b05035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ji Hye Hong
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - V. Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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Rawlings ND. Twenty-five years of nomenclature and classification of proteolytic enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140345. [PMID: 31838087 DOI: 10.1016/j.bbapap.2019.140345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
Proteolytic enzymes and their homologues have been classified into clans by comparing the tertiary structures of the peptidase domains, into families by comparing the protein sequences of the peptidase domains, and into protein-species by comparing various attributes including domain architecture, substrate preference, inhibitor interactions, subcellular location, and phylogeny. The results are compared with the earlier classification (Rawlings and Barrett, 1993 [1]). The numbers of sequences, protein-species, families, clans and even catalytic type have substantially increased during the intervening 26 years. The alternative classifications by catalytic type and/or activity are shown not to reflect evolutionary relationships.
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Affiliation(s)
- Neil D Rawlings
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
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Paschkowsky S, Hsiao JM, Young JC, Munter LM. The discovery of proteases and intramembrane proteolysis. Biochem Cell Biol 2019; 97:265-269. [DOI: 10.1139/bcb-2018-0186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Sandra Paschkowsky
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
| | - Jacqueline Melissa Hsiao
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Jason C. Young
- Department of Biochemistry, McGill University, McIntyre Building, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada
| | - Lisa Marie Munter
- Department of Pharmacology & Therapeutics, McGill University, Bellini Life Sciences Complex, 3649 Promenade Sir William Osler, Montreal, QC H3G 0B1, Canada
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Mann KS, Chisholm J, Sanfaçon H. Strawberry Mottle Virus (Family Secoviridae, Order Picornavirales) Encodes a Novel Glutamic Protease To Process the RNA2 Polyprotein at Two Cleavage Sites. J Virol 2019; 93:e01679-18. [PMID: 30541838 PMCID: PMC6384087 DOI: 10.1128/jvi.01679-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/19/2018] [Indexed: 01/29/2023] Open
Abstract
Strawberry mottle virus (SMoV) belongs to the family Secoviridae (order Picornavirales) and has a bipartite genome with each RNA encoding one polyprotein. All characterized secovirids encode a single protease related to the picornavirus 3C protease. The SMoV 3C-like protease was previously shown to cut the RNA2 polyprotein (P2) at a single site between the predicted movement protein and coat protein (CP) domains. However, the SMoV P2 polyprotein includes an extended C-terminal region with a coding capacity of up to 70 kDa downstream of the presumed CP domain, an unusual characteristic for this family. In this study, we identified a novel cleavage event at a P↓AFP sequence immediately downstream of the CP domain. Following deletion of the PAFP sequence, the polyprotein was processed at or near a related PKFP sequence 40 kDa further downstream, defining two protein domains in the C-terminal region of the P2 polyprotein. Both processing events were dependent on a novel protease domain located between the two cleavage sites. Mutagenesis of amino acids that are conserved among isolates of SMoV and of the related Black raspberry necrosis virus did not identify essential cysteine, serine, or histidine residues, suggesting that the RNA2-encoded SMoV protease is not related to serine or cysteine proteases of other picorna-like viruses. Rather, two highly conserved glutamic acid residues spaced by 82 residues were found to be strictly required for protease activity. We conclude that the processing of SMoV polyproteins requires two viral proteases, the RNA1-encoded 3C-like protease and a novel glutamic protease encoded by RNA2.IMPORTANCE Many viruses encode proteases to release mature proteins and intermediate polyproteins from viral polyproteins. Polyprotein processing allows regulation of the accumulation and activity of viral proteins. Many viral proteases also cleave host factors to facilitate virus infection. Thus, viral proteases are key virulence factors. To date, viruses with a positive-strand RNA genome are only known to encode cysteine or serine proteases, most of which are related to the cellular papain, trypsin, or chymotrypsin proteases. Here, we characterize the first glutamic protease encoded by a plant virus or by a positive-strand RNA virus. The novel glutamic protease is unique to a few members of the family Secoviridae, suggesting that it is a recent acquisition in the evolution of this family. The protease does not resemble known cellular proteases. Rather, it is predicted to share structural similarities with a family of fungal and bacterial glutamic proteases that adopt a lectin fold.
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Affiliation(s)
- Krin S Mann
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
| | - Joan Chisholm
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
| | - Hélène Sanfaçon
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia, Canada
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Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group-A Model for yet Unknown Peptidases? Molecules 2019; 24:molecules24030572. [PMID: 30764512 PMCID: PMC6384577 DOI: 10.3390/molecules24030572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/13/2022] Open
Abstract
Unconstrained amides that undergo fast hydrolysis under mild conditions are valuable sources of information about how amide bonds may be activated in enzymatic transformations. We report a compound possessing an unconstrained amide bond surrounded by an amino and a carboxyl group, each mounted in close proximity on a bicyclic scaffold. Fast amide hydrolysis of this model compound was found to depend on the presence of both the amino and carboxyl functions, and to involve a proton transfer in the rate-limiting step. Possible mechanisms for the hydrolytic cleavage and their relevance to peptide bond cleavage catalyzed by natural enzymes are discussed. Experimental observations suggest that the most probable mechanisms of the model compound hydrolysis might include a twisted amide intermediate and a rate-determining proton transfer.
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Mann KS, Sanfaçon H. Expanding Repertoire of Plant Positive-Strand RNA Virus Proteases. Viruses 2019; 11:v11010066. [PMID: 30650571 PMCID: PMC6357015 DOI: 10.3390/v11010066] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/13/2022] Open
Abstract
Many plant viruses express their proteins through a polyprotein strategy, requiring the acquisition of protease domains to regulate the release of functional mature proteins and/or intermediate polyproteins. Positive-strand RNA viruses constitute the vast majority of plant viruses and they are diverse in their genomic organization and protein expression strategies. Until recently, proteases encoded by positive-strand RNA viruses were described as belonging to two categories: (1) chymotrypsin-like cysteine and serine proteases and (2) papain-like cysteine protease. However, the functional characterization of plant virus cysteine and serine proteases has highlighted their diversity in terms of biological activities, cleavage site specificities, regulatory mechanisms, and three-dimensional structures. The recent discovery of a plant picorna-like virus glutamic protease with possible structural similarities with fungal and bacterial glutamic proteases also revealed new unexpected sources of protease domains. We discuss the variety of plant positive-strand RNA virus protease domains. We also highlight possible evolution scenarios of these viral proteases, including evidence for the exchange of protease domains amongst unrelated viruses.
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Affiliation(s)
- Krin S Mann
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
| | - Hélène Sanfaçon
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC V0H 1Z0, Canada.
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Stocchi N, Revuelta MV, Castronuovo PAL, Vera DMA, Ten Have A. Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins. BMC Bioinformatics 2018; 19:338. [PMID: 30249179 PMCID: PMC6154417 DOI: 10.1186/s12859-018-2348-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/29/2018] [Indexed: 11/30/2022] Open
Abstract
Background Eqolisins are rare acid proteases found in archaea, bacteria and fungi. Certain fungi secrete acids as part of their lifestyle and interestingly these also have many eqolisin paralogs, up to nine paralogs have been recorded. This suggests a process of functional redundancy and diversification has occurred, which was the subject of the research we performed and describe here. Results We identified eqolisin homologs by means of iterative HMMER analysis of the NR database. The identified sequences were scrutinized for which new hallmarks were identified by molecular dynamics simulations of mutants in highly conserved positions, using the structure of an eqolisin that was crystallized in the presence of a transition state inhibitor. Four conserved glycines were shown to be important for functionality. A substitution of W67F is shown to be accompanied by the L105W substitution. Molecular dynamics shows that the W67 binds to the substrate via a π-π stacking and a salt bridge, the latter being stronger in a virtual W67F/L105W double mutant of the resolved structure of Scytalido-carboxyl peptidase-B (PDB ID: 2IFW). Additional problematic mutations are discussed. Upon sequence scrutiny we obtained a set of 233 sequences that was used to reconstruct a Bayesian phylogenetic tree. We identified 14 putative specificity determining positions (SDPs) of which four are explained by mere structural explanations and nine seem to correspond to functional diversification related with substrate binding and specificity. A first sub-network of SDPs is related to substrate specificity whereas the second sub-network seems to affect the dynamics of three loops that are involved in substrate binding. Conclusion The eqolisins form a small superfamily of acid proteases with nevertheless many paralogs in acidic fungi. Functional redundancy has resulted in diversification related to substrate specificity and substrate binding. Electronic supplementary material The online version of this article (10.1186/s12859-018-2348-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolás Stocchi
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina
| | - María Victoria Revuelta
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina.,Pressent address: Department of Medicine, Hematology and Oncology Division, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Priscila Ailín Lanza Castronuovo
- QUIAMM-INBIOTEC-CONICET, Department of Chemistry - Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Argentina
| | - D Mariano A Vera
- QUIAMM-INBIOTEC-CONICET, Department of Chemistry - Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3350, 7600, Mar del Plata, Argentina
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600, Mar del Plata, Argentina.
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Abstract
Ras converting enzyme 1 (Rce1) is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins, whose members play important roles in cell signaling processes. Examples include the Ras family of small GTPases, the γ-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. CaaX proteins, especially Ras, have been implicated in cancer, and understanding the post-translational modifications of CaaX proteins would provide insight into their biological function and regulation. Many proteolytic mechanisms have been proposed for Rce1, but sequence alignment, mutational studies, topology, and recent crystallographic data point to a novel mechanism involving a glutamate-activated water and an oxyanion hole. Studies using in vivo and in vitro reporters of Rce1 activity have revealed that the enzyme cleaves only prenylated substrates and the identity of the a2 amino residue in the Ca1a2X sequence is most critical for recognition, preferring Ile, Leu, or Val. Substrate mimetics can be somewhat effective inhibitors of Rce1 in vitro. Small-molecule inhibitor discovery is currently limited by the lack of structural information on a eukaryotic enzyme, but a set of 8-hydroxyquinoline derivatives has demonstrated an ability to mislocalize all three mammalian Ras isoforms, giving optimism that potent, selective inhibitors might be developed. Much remains to be discovered regarding cleavage specificity, the impact of chemical inhibition, and the potential of Rce1 as a therapeutic target, not only for cancer, but also for other diseases.
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Affiliation(s)
| | - Timothy M Dore
- a New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.,b Department of Chemistry , University of Georgia , Athens , GA , USA
| | - Walter K Schmidt
- c Department of Biochemistry & Molecular Biology , University of Georgia , Athens , GA , USA
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16
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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: 123] [Impact Index Per Article: 17.6] [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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17
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Abaskharon RM, Brown SP, Zhang W, Chen J, Smith AB, Gai F. Isotope-Labeled Aspartate Sidechain as a Non-Perturbing Infrared Probe: Application to Investigate the Dynamics of a Carboxylate Buried Inside a Protein. Chem Phys Lett 2017; 683:193-198. [PMID: 29033461 DOI: 10.1016/j.cplett.2017.03.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Because of their negatively charged carboxylates, aspartate and glutamate are frequently found at the active or binding site of proteins. However, studying a specific carboxylate in proteins that contain multiple aspartates and/or glutamates via infrared spectroscopy is difficult due to spectral overlap. We show, herein, that isotopic-labeling of the aspartate sidechain can overcome this limitation as the resultant 13C=O asymmetric stretching vibration resides in a transparent region of the protein IR spectrum. Applicability of this site-specific vibrational probe is demonstrated by using it to assess the dynamics of an aspartate ion buried inside a small protein via two-dimensional infrared spectroscopy.
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Affiliation(s)
- Rachel M Abaskharon
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Stephen P Brown
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Wenkai Zhang
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Jianxin Chen
- Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA.,Ultrafast Optical Processes Laboratory, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104, USA
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18
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Yamada O, Machida M, Hosoyama A, Goto M, Takahashi T, Futagami T, Yamagata Y, Takeuchi M, Kobayashi T, Koike H, Abe K, Asai K, Arita M, Fujita N, Fukuda K, Higa KI, Horikawa H, Ishikawa T, Jinno K, Kato Y, Kirimura K, Mizutani O, Nakasone K, Sano M, Shiraishi Y, Tsukahara M, Gomi K. Genome sequence of Aspergillus luchuensis NBRC 4314. DNA Res 2016; 23:507-515. [PMID: 27651094 PMCID: PMC5144674 DOI: 10.1093/dnares/dsw032] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/02/2016] [Indexed: 12/03/2022] Open
Abstract
Awamori is a traditional distilled beverage made from steamed Thai-Indica rice in Okinawa, Japan. For brewing the liquor, two microbes, local kuro (black) koji mold Aspergillus luchuensis and awamori yeast Saccharomyces cerevisiae are involved. In contrast, that yeasts are used for ethanol fermentation throughout the world, a characteristic of Japanese fermentation industries is the use of Aspergillus molds as a source of enzymes for the maceration and saccharification of raw materials. Here we report the draft genome of a kuro (black) koji mold, A. luchuensis NBRC 4314 (RIB 2604). The total length of nonredundant sequences was nearly 34.7 Mb, comprising approximately 2,300 contigs with 16 telomere-like sequences. In total, 11,691 genes were predicted to encode proteins. Most of the housekeeping genes, such as transcription factors and N-and O-glycosylation system, were conserved with respect to Aspergillus niger and Aspergillus oryzae An alternative oxidase and acid-stable α-amylase regarding citric acid production and fermentation at a low pH as well as a unique glutamic peptidase were also found in the genome. Furthermore, key biosynthetic gene clusters of ochratoxin A and fumonisin B were absent when compared with A. niger genome, showing the safety of A. luchuensis for food and beverage production. This genome information will facilitate not only comparative genomics with industrial kuro-koji molds, but also molecular breeding of the molds in improvements of awamori fermentation.
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Affiliation(s)
- Osamu Yamada
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Masayuki Machida
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba, Ibaraki 305-8566, Japan
| | - Akira Hosoyama
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Masatoshi Goto
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Toru Takahashi
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Taiki Futagami
- Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Youhei Yamagata
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-0054, Japan
| | - Michio Takeuchi
- Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-0054, Japan
| | | | - Hideaki Koike
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, AIST, Tsukuba, Ibaraki 305-8566, Japan
| | - Keietsu Abe
- Tohoku University, Aoba-ku, Sendai 981-8555, Japan
| | - Kiyoshi Asai
- Computational Biology Research Center, AIST, Koto-ku, Tokyo 135-0064, Japan
| | - Masanori Arita
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Nobuyuki Fujita
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Kazuro Fukuda
- Asahi Breweries, LTD, Sumida-ku, Tokyo 130-8602, Japan
| | - Ken-Ichi Higa
- Industrial Technology Center, Okinawa Prefectural Government, Uruma, Okinawa 904-2234, Japan
| | - Hiroshi Horikawa
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | | | - Koji Jinno
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Yumiko Kato
- National Institute of Technology and Evaluation, Shibuya-ku, Tokyo 151-0066, Japan
| | - Kohtaro Kirimura
- Department of Applied Chemistry, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Osamu Mizutani
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Kaoru Nakasone
- Kinki University Faculty of Engineering, Higashi-hiroshima, Hiroshima 739-2116, Japan
| | - Motoaki Sano
- Kanazawa Institute of Technology, Nonoichi, Ishikawa 921-8501, Japan
| | - Yohei Shiraishi
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | | | - Katsuya Gomi
- Tohoku University, Aoba-ku, Sendai 981-8555, Japan
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19
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Arutyunova E, Smithers CC, Corradi V, Espiritu AC, Young HS, Tieleman DP, Lemieux MJ. Probing catalytic rate enhancement during intramembrane proteolysis. Biol Chem 2016; 397:907-19. [DOI: 10.1515/hsz-2016-0124] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Rhomboids are ubiquitous intramembrane serine proteases involved in various signaling pathways. While the high-resolution structures of the Escherichia coli rhomboid GlpG with various inhibitors revealed an active site comprised of a serine-histidine dyad and an extensive oxyanion hole, the molecular details of rhomboid catalysis were unclear because substrates are unknown for most of the family members. Here we used the only known physiological pair of AarA rhomboid with its psTatA substrate to decipher the contribution of catalytically important residues to the reaction rate enhancement. An MD-refined homology model of AarA was used to identify residues important for catalysis. We demonstrated that the AarA active site geometry is strict and intolerant to alterations. We probed the roles of H83 and N87 oxyanion hole residues and determined that substitution of H83 either abolished AarA activity or reduced the transition state stabilization energy (ΔΔG‡) by 3.1 kcal/mol; substitution of N87 decreased ΔΔG‡ by 1.6–3.9 kcal/mol. Substitution M154, a residue conserved in most rhomboids that stabilizes the catalytic general base, to tyrosine, provided insight into the mechanism of nucleophile generation for the catalytic dyad. This study provides a quantitative evaluation of the role of several residues important for hydrolytic efficiency and oxyanion stabilization during intramembrane proteolysis.
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20
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Characterization, biomedical and agricultural applications of protease inhibitors: A review. Int J Biol Macromol 2016; 91:1120-33. [PMID: 26955746 DOI: 10.1016/j.ijbiomac.2016.02.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 01/19/2023]
Abstract
This review describes Protease Inhibitors (PIs) which target or inhibit proteases, protein digesting enzymes. These proteases play a crucial task in many biological events including digestion, blood coagulation, apoptosis etc. Regardless of their crucial roles, they need to be checked regularly by PIs as their excess may possibly damage host organism. On basis of amino acid composition of PIs where Protease-PI enzymatic reactions occur i.e. serine, cysteine, and aspartic acid, they are classified. Nowadays, various PIs are being worked upon to fight various parasitic or viral diseases including malaria, schistosomiasis, colds, flu', dengue etc. They prevent an ongoing process begun by carcinogen exposure by keeping a check on metastasis. They also possess potential to reduce carcinogen-induced, increased levels of gene amplification to almost normal levels. Some PIs can principally be used for treatment of hypertension and congestive heart failure by blocking conversion of angiotensin I to angiotensin II for example Angiotensin-converting enzyme inhibitors (ACEIs). Also PIs target amyloid β-peptide (Aβ) level in brain which is prime responsible for development of Alzheimer's Disease (AD). Also, PIs inhibit enzymatic activity of HIV-1 Protease Receptor (PR) by preventing cleavage events in Gag and Gag-Pol that result in production of non-virulent virus particles.
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21
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Involvement of Kallikrein-Related Peptidases in Normal and Pathologic Processes. DISEASE MARKERS 2015; 2015:946572. [PMID: 26783378 PMCID: PMC4689925 DOI: 10.1155/2015/946572] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/16/2015] [Accepted: 10/29/2015] [Indexed: 12/31/2022]
Abstract
Human kallikrein-related peptidases (KLKs) are a subgroup of serine proteases that participate in proteolytic pathways and control protein levels in normal physiology as well as in several pathological conditions. Their complex network of stimulatory and inhibitory interactions may induce inflammatory and immune responses and contribute to the neoplastic phenotype through the regulation of several cellular processes, such as proliferation, survival, migration, and invasion. This family of proteases, which includes one of the most useful cancer biomarkers, kallikrein-related peptidase 3 or PSA, also has a protective effect against cancer promoting apoptosis or counteracting angiogenesis and cell proliferation. Therefore, they represent attractive therapeutic targets and may have important applications in clinical oncology. Despite being intensively studied, many gaps in our knowledge on several molecular aspects of KLK functions still exist. This review aims to summarize recent data on their involvement in different processes related to health and disease, in particular those directly or indirectly linked to the neoplastic process.
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22
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Manolaridis I, Kulkarni K, Dodd RB, Ogasawara S, Zhang Z, Bineva G, Reilly NO, Hanrahan SJ, Thompson AJ, Cronin N, Iwata S, Barford D. Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1. Nature 2013; 504:301-5. [PMID: 24291792 PMCID: PMC3864837 DOI: 10.1038/nature12754] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/11/2013] [Indexed: 12/31/2022]
Abstract
CAAX proteins have essential roles in multiple signalling pathways, controlling processes such as proliferation, differentiation and carcinogenesis. The ∼120 mammalian CAAX proteins function at cellular membranes and include the Ras superfamily of small GTPases, nuclear lamins, the γ-subunit of heterotrimeric GTPases, and several protein kinases and phosphatases. The proper localization of CAAX proteins to cell membranes is orchestrated by a series of post-translational modifications of the carboxy-terminal CAAX motifs (where C is cysteine, A is an aliphatic amino acid and X is any amino acid). These reactions involve prenylation of the cysteine residue, cleavage at the AAX tripeptide and methylation of the carboxyl-prenylated cysteine residue. The major CAAX protease activity is mediated by Rce1 (Ras and a-factor converting enzyme 1), an intramembrane protease (IMP) of the endoplasmic reticulum. Information on the architecture and proteolytic mechanism of Rce1 has been lacking. Here we report the crystal structure of a Methanococcus maripaludis homologue of Rce1, whose endopeptidase specificity for farnesylated peptides mimics that of eukaryotic Rce1. Its structure, comprising eight transmembrane α-helices, and catalytic site are distinct from those of other IMPs. The catalytic residues are located ∼10 Å into the membrane and are exposed to the cytoplasm and membrane through a conical cavity that accommodates the prenylated CAAX substrate. We propose that the farnesyl lipid binds to a site at the opening of two transmembrane α-helices, which results in the scissile bond being positioned adjacent to a glutamate-activated nucleophilic water molecule. This study suggests that Rce1 is the founding member of a novel IMP family, the glutamate IMPs.
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Affiliation(s)
| | - Kiran Kulkarni
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Roger B Dodd
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Satoshi Ogasawara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- JST, Research Acceleration Program, Membrane Protein, Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Ziguo Zhang
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Ganka Bineva
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Nicola O' Reilly
- Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, WC2A 3LY, UK
| | - Sarah J Hanrahan
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | | | - Nora Cronin
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- JST, Research Acceleration Program, Membrane Protein, Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
- Division of Molecular Biosciences, Imperial College, London, SW7 2AZ, UK
| | - David Barford
- Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
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23
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Abstract
Thermopsin is a peptidase from Sulfolobus acidocaldarius that is active at low pH and high temperature. From reversible inhibition with pepstatin, thermopsin is thought to be an aspartic peptidase. It is a member of the only family of peptidases to be restricted entirely to the archaea, namely peptidase family A5. Evolution within this family has been mapped, using a taxonomic tree based on the known classification of archaea. Homologues are found only in archaeans that are both hyperthermophiles and acidophiles, and this implies lateral transfer of genes between archaea, because species with homologues are not necessarily closely related. Despite the remarkable stability and activity in extreme conditions, no tertiary structure has been solved for any member of the family, and the catalytic mechanism is unknown. Putative catalytic residues have been predicted here by examination of aligned sequences.
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Affiliation(s)
- Neil D. Rawlings
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
- * E-mail:
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24
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Takahashi K. Structure and function studies on enzymes with a catalytic carboxyl group(s): from ribonuclease T1 to carboxyl peptidases. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2013; 89:201-25. [PMID: 23759941 PMCID: PMC3749792 DOI: 10.2183/pjab.89.201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/04/2013] [Indexed: 06/02/2023]
Abstract
A group of enzymes, mostly hydrolases or certain transferases, utilize one or a few side-chain carboxyl groups of Asp and/or Glu as part of the catalytic machinery at their active sites. This review follows mainly the trail of studies performed by the author and his colleagues on the structure and function of such enzymes, starting from ribonuclease T1, then extending to three major types of carboxyl peptidases including aspartic peptidases, glutamic peptidases and serine-carboxyl peptidases.
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25
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Production of recombinant proteins by filamentous fungi. Biotechnol Adv 2012; 30:1119-39. [DOI: 10.1016/j.biotechadv.2011.09.012] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 08/30/2011] [Accepted: 09/15/2011] [Indexed: 11/17/2022]
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26
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Silva LL, Marcet-Houben M, Zerlotini A, Gabaldón T, Oliveira G, Nahum LA. Evolutionary histories of expanded peptidase families in Schistosoma mansoni. Mem Inst Oswaldo Cruz 2012; 106:864-77. [PMID: 22124560 DOI: 10.1590/s0074-02762011000700013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 08/09/2011] [Indexed: 11/22/2022] Open
Abstract
Schistosoma mansoni is one of the three main causative agents of human schistosomiasis, a major health problem with a vast socio-economic impact. Recent advances in the proteomic analysis of schistosomes have revealed that peptidases are the main virulence factors involved in the pathogenesis of this disease. In this context, evolutionary studies can be applied to identify peptidase families that have been expanded in genomes over time in response to different selection pressures. Using a phylogenomic approach, we searched for expanded endopeptidase families in the S. mansoni predicted proteome with the aim of contributing to the knowledge of such enzymes as potential therapeutic targets. We found three endopeptidase families that comprise leishmanolysins (metallopeptidase M8 family), cercarial elastases (serine peptidase S1 family) and cathepsin D proteins (aspartic peptidase A1 family). Our results suggest that the Schistosoma members of these families originated from successive gene duplication events in the parasite lineage after its diversification from other metazoans. Overall, critical residues are conserved among the duplicated genes/proteins. Furthermore, each protein family displays a distinct evolutionary history. Altogether, this work provides an evolutionary view of three S. mansoni peptidase families, which allows for a deeper understanding of the genomic complexity and lineage-specific adaptations potentially related to the parasitic lifestyle.
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Affiliation(s)
- Larissa Lopes Silva
- Grupo de Genômica e Biologia Computacional, Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais, Belo Horizonte, MG, Brasil
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27
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Sasaki H, Kubota K, Lee WC, Ohtsuka J, Kojima M, Iwata S, Nakagawa A, Takahashi K, Tanokura M. The crystal structure of an intermediate dimer of aspergilloglutamic peptidase that mimics the enzyme-activation product complex produced upon autoproteolysis. J Biochem 2012; 152:45-52. [PMID: 22569035 DOI: 10.1093/jb/mvs050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aspergilloglutamic peptidase from Aspergillus niger var. macrosporus (AGP) is one of the so-called pepstatin-insensitive acid endopeptidases, which are distinct from the well-studied aspartic peptidases. Among the known homologues of the glutamic peptidases, AGP is a unique two-chain enzyme with a light chain and a heavy chain bound non-covalently with each other, and thus is an interesting target for protein structure-function relationship studies. In this article, we report the crystal structure of a dimeric form of the enzyme at a resolution of 1.6 Å. This form has a unique structure in which the C-terminal region of the light chain of one of the molecules binds to the active site cleft of the other molecule like a part of a substrate. This form mimics the enzyme-activation product complex produced upon autoproteolysis, and provides a structural clue that could help to clarify the activation mechanism. This type of dimeric structure of a peptidase is here reported for the first time.
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Affiliation(s)
- Hiroshi Sasaki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo 113-0033, Japan
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28
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Arai R, Kobayashi N, Kimura A, Sato T, Matsuo K, Wang AF, Platt JM, Bradley LH, Hecht MH. Domain-Swapped Dimeric Structure of a Stable and Functional De Novo Four-Helix Bundle Protein, WA20. J Phys Chem B 2012; 116:6789-97. [DOI: 10.1021/jp212438h] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryoichi Arai
- International
Young Researchers
Empowerment Center, Shinshu University,
Ueda, Nagano 386-8567, Japan
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
- Department of Applied Biology, Faculty of Textile Science & Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Naoya Kobayashi
- Department of Applied Biology, Faculty of Textile Science & Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Akiho Kimura
- Department of Applied Biology, Faculty of Textile Science & Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Takaaki Sato
- International
Young Researchers
Empowerment Center, Shinshu University,
Ueda, Nagano 386-8567, Japan
| | - Kyoko Matsuo
- Department of Applied Biology, Faculty of Textile Science & Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Anna F. Wang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
| | - Jesse M. Platt
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
| | - Luke H. Bradley
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
- Departments of Anatomy & Neurobiology, Molecular & Cellular Biochemistry, Center of Structural Biology, University of Kentucky College of Medicine, Lexington, Kentucky 40536, United States
| | - Michael H. Hecht
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544,
United States
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29
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Aoki W, Kitahara N, Miura N, Morisaka H, Yamamoto Y, Kuroda K, Ueda M. Candida albicans possesses Sap7 as a pepstatin A-insensitive secreted aspartic protease. PLoS One 2012; 7:e32513. [PMID: 22384266 PMCID: PMC3287985 DOI: 10.1371/journal.pone.0032513] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 01/27/2012] [Indexed: 01/12/2023] Open
Abstract
Background Candida albicans, a commensal organism, is a part of the normal flora of healthy individuals. However, once the host immunity is compromised, C. albicans opportunistically causes recurrent superficial or fatal systemic candidiasis. Secreted aspartic proteases (Sap), encoded by 10 types of SAP genes, have been suggested to contribute to various virulence processes. Thus, it is important to elucidate their biochemical properties for better understanding of the molecular mechanisms that how Sap isozymes damage host tissues. Methodology/Principal Findings The SAP7 gene was cloned from C. albicans SC5314 and heterogeneously produced by Pichia pastoris. Measurement of Sap7 proteolytic activity using the FRETS-25Ala library showed that Sap7 was a pepstatin A-insensitive protease. To understand why Sap7 was insensitive to pepstatin A, alanine substitution mutants of Sap7 were constructed. We found that M242A and T467A mutants had normal proteolytic activity and sensitivity to pepstatin A. M242 and T467 were located in close proximity to the entrance to an active site, and alanine substitution at these positions widened the entrance. Our results suggest that this alteration might allow increased accessibility of pepstatin A to the active site. This inference was supported by the observation that the T467A mutant has stronger proteolytic activity than the wild type. Conclusions/Significance We found that Sap7 was a pepstatin A-insensitive protease, and that M242 and T467 restricted the accessibility of pepstatin A to the active site. This finding will lead to the development of a novel protease inhibitor beyond pepstatin A. Such a novel inhibitor will be an important research tool as well as pharmaceutical agent for patients suffering from candidiasis.
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Affiliation(s)
- Wataru Aoki
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Nao Kitahara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Natsuko Miura
- Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshihiro Yamamoto
- Industrial Technology Center, Kyoto Municipal Institute of Industrial Technology and Culture, Simogyo-ku, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail:
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Bai G, Pfaff SL. Protease regulation: the Yin and Yang of neural development and disease. Neuron 2011; 72:9-21. [PMID: 21982365 DOI: 10.1016/j.neuron.2011.09.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 01/08/2023]
Abstract
The formation, maintenance, and plasticity of neural circuits rely upon a complex interplay between progressive and regressive events. Increasingly, new functions are being identified for axon guidance molecules in the dynamic processes that occur within the embryonic and adult nervous system. The magnitude, duration, and spatial activity of axon guidance molecule signaling are precisely regulated by a variety of molecular mechanisms. Here we focus on recent progress in understanding the role of protease-mediated cleavage of guidance factors required for directional axon growth, with a particular emphasis on the role of metalloprotease and γ-secretase. Since axon guidance molecules have also been linked to neural degeneration and regeneration in adults, studies of guidance receptor proteolysis are beginning to define new relationships between neurodevelopment and neurodegeneration. These findings raise the possibility that the signaling checkpoints controlled by proteases could be useful targets to enhance regeneration.
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Affiliation(s)
- Ge Bai
- Howard Hughes Medical Institute and Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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Internally quenched fluorescent peptide libraries with randomized sequences designed to detect endopeptidases. Anal Biochem 2011; 421:299-307. [PMID: 22067978 DOI: 10.1016/j.ab.2011.10.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Revised: 09/20/2011] [Accepted: 10/14/2011] [Indexed: 11/23/2022]
Abstract
Identification of synthetic peptide substrates for novel peptidases is an essential step for their study. With this purpose we synthesized fluorescence resonance energy transfer (FRET) peptide libraries Abz (or MCA)-GXXXXXQ-EDDnp and Abz (or MCA)-GXXZXXQ-EDDnp, where X consists of an equimolar mixture of all amino acids, the Z position is fixed with one of the proteinogenic amino acids (cysteine was excluded), Abz (ortho-aminobenzoic acid) or MCA ([7-amino-4-methyl]coumarin) is the fluorescence donor and Q-EDDnp (glutamine-[N-(2,4-dinitrophenyl)-ethylenediamine]) is the fluorescence acceptor. The peptide libraries MCA-GXXX↓XXQ-EDDnp and MCA-GXXZ↓XXQ-EDDnp were cleaved as indicated (↓) by trypsin, chymotrypsin, cathepsin L, pepsin A, and Eqolisin as confirmed by Edman degradation of the products derived from the digestion of these libraries. The best hydrolyzed Abz-GXXZXXQ-EDDnp sublibraries by these proteases, including Dengue 2 virus NS2B-NS3 protease, contained amino acids at the Z position that are reported to be well accepted by their S(1) subsite. The pH profiles of the hydrolytic activities of these canonical proteases on the libraries were similar to those reported for typical substrates. The FRET peptide libraries provide an efficient and simple approach for detecting nanomolar concentrations of endopeptidases and are useful for initial specificity characterization as performed for two proteases secreted by a Bacillus subtilis.
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Oda K. New families of carboxyl peptidases: serine-carboxyl peptidases and glutamic peptidases. J Biochem 2011; 151:13-25. [PMID: 22016395 DOI: 10.1093/jb/mvr129] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Peptidases or proteinases are now classified into seven families based on the nature of the catalytic residues [MEROPS-the peptidase database (http://merops.sanger.ac.uk/)]. They are aspartic- (first described in 1993), cysteine- (1993), serine- (1993) metallo- (1993), threonine- (1997), glutamic- (2004) and asparagine-peptidase (2010). By using an S-PI (pepstatin Ac) as a probe, a new subfamily of serine peptidase, serine-carboxyl peptidase (sedolisin) was discovered in 2001. In addition, the sixth family of peptidase, glutamic peptidase (eqolisin) was also discovered in 2004. The former peptidase is widely distributed in nature from archea to mammals, including humans. One of these enzymes is related to a human fatal hereditable disease, Batten disease. In contrast, the distribution of the latter peptidases is limited, with most of them found in human or plant pathogenic fungi. One such enzyme was isolated from a fungal infection in an HIV-infected patient. In this review, the background of the findings, and crystal structures, catalytic mechanisms, substrates specificities and distribution of the new peptidase families are described.
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Affiliation(s)
- Kohei Oda
- Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.
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Rawlings ND, Barrett AJ, Bateman A. Asparagine peptide lyases: a seventh catalytic type of proteolytic enzymes. J Biol Chem 2011; 286:38321-38328. [PMID: 21832066 PMCID: PMC3207474 DOI: 10.1074/jbc.m111.260026] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The terms “proteolytic enzyme” and “peptidase” have been treated as synonymous, and all proteolytic enzymes have been considered to be hydrolases (EC 3.4). However, the recent discovery of proteins that cleave themselves at asparagine residues indicates that not all peptide bond cleavage occurs by hydrolysis. These self-cleaving proteins include the Tsh protein precursor of Escherichia coli, in which the large C-terminal propeptide acts as an autotransporter; certain viral coat proteins; and proteins containing inteins. Proteolysis is the action of an amidine lyase (EC 4.3.2). These proteolytic enzymes are also the first in which the nucleophile is an asparagine, defining the seventh proteolytic catalytic type and the first to be discovered since 2004. We have assembled ten families based on sequence similarity in which cleavage is thought to be catalyzed by an asparagine.
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Affiliation(s)
- Neil David Rawlings
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom.
| | - Alan John Barrett
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
| | - Alex Bateman
- Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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Purification and characterisation of a novel protease from Cordyceps sinensis and determination of the cleavage site motifs using oriented peptide library mixtures. Food Chem 2011. [DOI: 10.1016/j.foodchem.2010.10.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Madala PK, Tyndall JDA, Nall T, Fairlie DP. Update 1 of: Proteases Universally Recognize Beta Strands In Their Active Sites. Chem Rev 2011; 110:PR1-31. [DOI: 10.1021/cr900368a] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Praveen K. Madala
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - Tessa Nall
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
| | - David P. Fairlie
- Centre for Drug Design and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2005, 105 (3), 973−1000; Published (Web) Feb. 16, 2005. Updates to the text appear in red type
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Sriranganadane D, Reichard U, Salamin K, Fratti M, Jousson O, Waridel P, Quadroni M, Neuhaus JM, Monod M. Secreted glutamic protease rescues aspartic protease Pep deficiency in Aspergillus fumigatus during growth in acidic protein medium. MICROBIOLOGY-SGM 2011; 157:1541-1550. [PMID: 21349972 DOI: 10.1099/mic.0.048603-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In an acidic protein medium Aspergillus fumigatus secretes an aspartic endoprotease (Pep) as well as tripeptidyl-peptidases, a prolyl-peptidase and carboxypeptidases. In addition, LC-MS/MS revealed a novel glutamic protease, AfuGprA, homologous to Aspergillus niger aspergillopepsin II. The importance of AfuGprA in protein digestion was evaluated by deletion of its encoding gene in A. fumigatus wild-type D141 and in a pepΔ mutant. Either A. fumigatus Pep or AfuGprA was shown to be necessary for fungal growth in protein medium at low pH. Exoproteolytic activity is therefore not sufficient for complete protein hydrolysis and fungal growth in a medium containing proteins as the sole nitrogen source. Pep and AfuGprA constitute a pair of endoproteases active at low pH, in analogy to A. fumigatus alkaline protease (Alp) and metalloprotease I (Mep), where at least one of these enzymes is necessary for fungal growth in protein medium at neutral pH. Heterologous expression of AfuGprA in Pichia pastoris showed that the enzyme is synthesized as a preproprotein and that the propeptide is removed through an autoproteolytic reaction at low pH to generate the mature protease. In contrast to A. niger aspergillopepsin II, AfuGprA is a single-chain protein and is structurally more similar to G1 proteases characterized in other non-Aspergillus fungi.
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Affiliation(s)
- Dev Sriranganadane
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Utz Reichard
- Department of Medical Microbiology and National Reference Centre for Systemic Mycoses, University Hospital of Göttingen, Germany
| | - Karine Salamin
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Marina Fratti
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Olivier Jousson
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Patrice Waridel
- Protein Analysis Facility, Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Centre for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Marc Neuhaus
- Laboratory of Molecular and Cellular Biology, University of Neuchâtel, rue E-Argand 11, 2009 Neuchâtel, Switzerland
| | - Michel Monod
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
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Abstract
OBJECTIVES The role of proteases in the regulation of apoptosis is becoming increasingly apparent. Whilst many of these proteases are already characterised, some have yet to be identified. Traditionally caspases held the traditional role as the prime mediators of apoptosis; however, attention is now turning towards the contribution made by serine proteases. KEY FINDINGS As unregulated apoptosis is implicated in various disease states, the emergence of this proteolytic family as apoptotic regulators offers novel and alterative opportunities for therapeutic targets. SUMMARY This review presents a brief introduction and overview of proteases in general with particular attention given to those involved in apoptotic processing.
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Affiliation(s)
- Kelly L Moffitt
- Biomolecular Sciences Group, School of Pharmacy, Queen's University of Belfast, Belfast BT97BL, Northern Ireland, UK.
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39
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Jensen K, Østergaard PR, Wilting R, Lassen SF. Identification and characterization of a bacterial glutamic peptidase. BMC BIOCHEMISTRY 2010; 11:47. [PMID: 21122090 PMCID: PMC3009609 DOI: 10.1186/1471-2091-11-47] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 12/01/2010] [Indexed: 11/29/2022]
Abstract
Background Glutamic peptidases, from the MEROPS family G1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic pH and insensitivity towards the microbial derived protease inhibitor, pepstatin. Previously, only glutamic peptidases derived from filamentous fungi have been characterized. Results We report the first characterization of a bacterial glutamic peptidase (pepG1), derived from the thermoacidophilic bacteria Alicyclobacillus sp. DSM 15716. The amino acid sequence identity between pepG1 and known fungal glutamic peptidases is only 24-30% but homology modeling, the presence of the glutamate/glutamine catalytic dyad and a number of highly conserved motifs strongly support the inclusion of pepG1 as a glutamic peptidase. Phylogenetic analysis places pepG1 and other putative bacterial and archaeal glutamic peptidases in a cluster separate from the fungal glutamic peptidases, indicating a divergent and independent evolution of bacterial and fungal glutamic peptidases. Purification of pepG1, heterologously expressed in Bacillus subtilis, was performed using hydrophobic interaction chromatography and ion exchange chromatography. The purified peptidase was characterized with respect to its physical properties. Temperature and pH optimums were found to be 60°C and pH 3-4, in agreement with the values observed for the fungal members of family G1. In addition, pepG1 was found to be pepstatin-insensitive, a characteristic signature of glutamic peptidases. Conclusions Based on the obtained results, we suggest that pepG1 can be added to the MEROPS family G1 as the first characterized bacterial member.
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40
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Unal EB, Gursoy A, Erman B. VitAL: Viterbi algorithm for de novo peptide design. PLoS One 2010; 5:e10926. [PMID: 20532195 PMCID: PMC2880006 DOI: 10.1371/journal.pone.0010926] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 05/07/2010] [Indexed: 01/18/2023] Open
Abstract
Background Drug design against proteins to cure various diseases has been studied for several years. Numerous design techniques were discovered for small organic molecules for specific protein targets. The specificity, toxicity and selectivity of small molecules are hard problems to solve. The use of peptide drugs enables a partial solution to the toxicity problem. There has been a wide interest in peptide design, but the design techniques of a specific and selective peptide inhibitor against a protein target have not yet been established. Methodology/Principal Findings A novel de novo peptide design approach is developed to block activities of disease related protein targets. No prior training, based on known peptides, is necessary. The method sequentially generates the peptide by docking its residues pair by pair along a chosen path on a protein. The binding site on the protein is determined via the coarse grained Gaussian Network Model. A binding path is determined. The best fitting peptide is constructed by generating all possible peptide pairs at each point along the path and determining the binding energies between these pairs and the specific location on the protein using AutoDock. The Markov based partition function for all possible choices of the peptides along the path is generated by a matrix multiplication scheme. The best fitting peptide for the given surface is obtained by a Hidden Markov model using Viterbi decoding. The suitability of the conformations of the peptides that result upon binding on the surface are included in the algorithm by considering the intrinsic Ramachandran potentials. Conclusions/Significance The model is tested on known protein-peptide inhibitor complexes. The present algorithm predicts peptides that have better binding energies than those of the existing ones. Finally, a heptapeptide is designed for a protein that has excellent binding affinity according to AutoDock results.
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Affiliation(s)
- E. Besray Unal
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Attila Gursoy
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
| | - Burak Erman
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
- * E-mail:
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41
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Kondo MY, Okamoto DN, Santos JAN, Juliano MA, Oda K, Pillai B, James MNG, Juliano L, Gouvea IE. Studies on the catalytic mechanism of a glutamic peptidase. J Biol Chem 2010; 285:21437-45. [PMID: 20442413 DOI: 10.1074/jbc.m110.122432] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Scytalidoglutamic peptidase (SGP) is the prototype of fungal glutamic peptidases that are characteristically pepstatin insensitive. These enzymes have a unique catalytic dyad comprised of Gln(53) and Glu(136) that activate a bound water molecule for nucleophilic attack on the carbonyl carbon atom of the scissile peptide bond. The hydrolysis by SGP at peptide bonds with proline in the P(1)' position is a rare event among peptidases that we investigated using the series of fluorescence resonance energy transfer peptides, Abz-KLXPSKQ-EDDnp, compared with the series Abz-KLXSSKQ-EDDnp. The preference observed in these two series for Phe and His over Leu, Ile, Val, Arg, and Lys, seems to be related to the structure of the S(1) subsite of SGP. These results and the pH profiles of SGP activity showed that its S(1) subsite can accommodate the benzyl group of Phe at pH 4 as well as the positively charged imidazolium group of His. In the pH range 2 to 7, SGP maintains its structure and activity, but at pH 8 or higher it is irreversibly denatured. The intrinsic fluorescence of the Trp residues of SGP were sensitive to the titration of carboxyl groups having low pK values; this can be attributed to the buried Asp(57) and/or Asp(43) as described in SGP three-dimensional structure. The solvent kinetic isotope effects and the proton inventory experiments support a mechanism for the glutamic peptidase SGP that involves the nucleophilic attack of the general base (Glu(136)) activated water, and establish a fundamental role of the S(1) subsite interactions in promoting catalysis.
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Affiliation(s)
- Márcia Y Kondo
- Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, Rua Três de Maio 100, 04044-20 São Paulo, Brazil
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42
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Philominathan STL, Koide T, Hamada K, Yasui H, Seifert S, Matsushita O, Sakon J. Unidirectional binding of clostridial collagenase to triple helical substrates. J Biol Chem 2009; 284:10868-76. [PMID: 19208618 DOI: 10.1074/jbc.m807684200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Histotoxic clostridia produce collagenases responsible for extensive tissue destruction in gas gangrene. The C-terminal collagen-binding domain (CBD) of these enzymes is the minimal segment required to bind to collagen fibril. Collagen binding efficiency of CBD is more pronounced in the presence of Ca(2+). We have shown that CBD can be functional to anchor growth factors in local tissue. A (1)H-(15)N HSQC NMR titration study with three different tropocollagen analogues ((POG)(10))(3), ((GPOG)(7)PRG)(3), and (GPRG(POG)(7)C-carbamidomethyl)(3), mapped a saddle-like binding cleft on CBD. NMR titrations with three nitroxide spin-labeled analogues of collagenous peptide, (PROXYL-G(POG)(7)PRG)(3), (PROXYL-G(POG)(7))(3), and (GPRG(POG)(7)C-PROXYL)(3) (where PROXYL represents 2,2,5,5-tetramethyl-l-pyrrolidinyloxy), unambiguously demonstrated unidirectional binding of CBD to the tropocollagen analogues. Small angle x-ray scattering data revealed that CBD binds closer to a terminus for each of the five different tropocollagen analogues, which in conjunction with NMR titration studies, implies a binding mode where CBD binds to the C terminus of the triple helix.
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43
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Abstract
Proteolytic enzymes play an essential role in many biological and pathological processes. Taking advantage of the recent availability of several mammalian genome sequences and by using a set of computational approaches, we have annotated and compared the degradome or complete repertoire of proteases of different mammalian species including human, mouse, rat, and chimpanzee. These studies have allowed us to expand our knowledge about the complexity, evolution, and diversity of proteolytic systems, which represent about 2% of the studied genomes. In this chapter, we review the genomic and computational methodologies used in this degradomic analysis and summarize the main findings derived from comparison of mammalian degradomes.
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Affiliation(s)
- Gonzalo R Ordóñez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
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44
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O'Donoghue AJ, Mahon CS, Goetz DH, O'Malley JM, Gallagher DM, Zhou M, Murray PG, Craik CS, Tuohy MG. Inhibition of a secreted glutamic peptidase prevents growth of the fungus Talaromyces emersonii. J Biol Chem 2008; 283:29186-95. [PMID: 18687686 DOI: 10.1074/jbc.m802366200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The thermophilic filamentous fungus Talaromyces emersonii secretes a variety of hydrolytic enzymes that are of interest for processing of biomass into fuel. Many carbohydrases have been isolated and characterized from this fungus, but no studies had been performed on peptidases. In this study, two acid-acting endopeptidases were isolated and characterized from the culture filtrate of T. emersonii. One of these enzymes was identified as a member of the recently classified glutamic peptidase family and was subsequently named T. emersonii glutamic peptidase 1 (TGP1). The second enzyme was identified as an aspartyl peptidase (PEP1). TGP1 was cloned and sequenced and shown to exhibit 64 and 47% protein identity to peptidases from Aspergillus niger and Scytalidium lignocolum, respectively. Substrate profiling of 16 peptides determined that TGP1 has broad specificity with a preference for large residues in the P1 site, particularly Met, Gln, Phe, Lys, Glu, and small amino acids at P1' such as Ala, Gly, Ser, or Thr. This enzyme efficiently cleaves an internally quenched fluorescent substrate containing the zymogen activation sequence (k(cat)/K(m)=2 x 10(5) m(-1) s(-1)). Maximum hydrolysis occurs at pH 3.4 and 50 degrees C. The reaction is strongly inhibited by a transition state peptide analog, TA1 (K(i)=1.5 nM), as well as a portion of the propeptide sequence, PT1 (K(i)=32 nM). Ex vivo studies show that hyphal extension of T. emersonii in complex media is unaffected by the aspartyl peptidase inhibitor pepstatin but is inhibited by TA1 and PT1. This study provides insight into the functional role of the glutamic peptidase TGP1 for growth of T. emersonii.
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Affiliation(s)
- Anthony J O'Donoghue
- Department of Biochemistry, National University of Ireland, University Road, Galway, Ireland
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45
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Rawlings ND, Morton FR. The MEROPS batch BLAST: a tool to detect peptidases and their non-peptidase homologues in a genome. Biochimie 2007; 90:243-59. [PMID: 17980477 DOI: 10.1016/j.biochi.2007.09.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Accepted: 09/21/2007] [Indexed: 11/29/2022]
Abstract
Many of the 181 families of peptidases contain homologues that are known to have functions other than peptide bond hydrolysis. Distinguishing an active peptidase from a homologue that is not a peptidase requires specialist knowledge of the important active site residues, because replacement or lack of one of these catalytic residues is an important clue that the homologue in question is unlikely to hydrolyse peptide bonds. Now that the rate at which proteins are characterized is outstripped by the rate that genome sequences are determined, many genes are being incorrectly annotated because only sequence similarity is taken into consideration. We present a tool called the MEROPS batch BLAST which not only performs a comparison against the MEROPS sequence collection, but also does a pair-wise alignment with the closest homologue detected and calculates the position of the active site residues. A non-peptidase homologue can be distinguished by the absence or unacceptable replacement of any of these residues. An analysis of peptidase homologues in the genome of the bacterium Erythrobacter litoralis is presented as an example.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.
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46
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Porter SB, Hildebrandt ER, Breevoort SR, Mokry DZ, Dore TM, Schmidt WK. Inhibition of the CaaX proteases Rce1p and Ste24p by peptidyl (acyloxy)methyl ketones. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:853-62. [PMID: 17467817 PMCID: PMC1976251 DOI: 10.1016/j.bbamcr.2007.03.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/16/2007] [Accepted: 03/01/2007] [Indexed: 11/16/2022]
Abstract
The CaaX proteases Rce1p and Ste24p can independently promote a proteolytic step required for the maturation of certain isoprenylated proteins. Although functionally related, Rce1p and Ste24p are unrelated in primary sequence. They have distinct enzymatic properties, which are reflected in part by their distinct inhibitor profiles. Moreover, Rce1p has an undefined catalytic mechanism, whereas Ste24p is an established zinc-dependent metalloprotease. This study demonstrates that both enzymes are inhibited by peptidyl (acyloxy)methyl ketones (AOMKs), making these compounds the first documented dual specificity inhibitors of the CaaX proteases. Further investigation of AOMK-mediated inhibition reveals that varying the peptidyl moiety can significantly alter the inhibitory properties of AOMKs toward Rce1p and Ste24p and that these enzymes display subtle differences in sensitivity to AOMKs. This observation suggests that this compound class could potentially be engineered to be selective for either of the CaaX proteases. We also demonstrate that the reported sensitivity of Rce1p to TPCK is substrate-dependent, which significantly alters the interpretation of certain reports having used TPCK sensitivity for mechanistic classification of Rce1p. Finally, we show that an AOMK inhibits the isoprenylcysteine carboxyl methyltransferase Ste14p. In sum, our observations raise important considerations regarding the specificity of agents targeting enzymes involved in the maturation of isoprenylated proteins, some of which are being developed as anti-cancer therapeutic agents.
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Affiliation(s)
- Stephen B Porter
- Department of Biochemistry and Molecular Biology, The University of Georgia, 120 Green Street, Athens, GA 30602, USA
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47
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Huang XP, Yabuki Y, Kojima M, Inoue H, Takahashi K. Activation profiles of the zymogen of aspergilloglutamic peptidase. Biol Chem 2007; 388:129-33. [PMID: 17214557 DOI: 10.1515/bc.2007.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Aspergilloglutamic peptidase produced by Aspergillus niger var. macrosporus belongs to the novel glutamic peptidase family. Its zymogen is autocatalytically activated under acidic conditions to the mature enzyme with a two-chain structure. Analyses by SDS-PAGE and mass spectrometry of the activation products of the recombinant zymogen showed that the major pathway of activation includes initial fast cleavage at Glu12-Ala13, followed by stepwise cleavages in the N-terminal and intervening propeptide regions. Essentially the same activation profile was obtained with the recombinant zymogen lacking the N-terminal 12-aa sequence. The missing region includes the most prominent cluster of basic residues of the propeptide, indicating low importance of this cluster for activation and refolding of the zymogen.
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Affiliation(s)
- Xiang-Ping Huang
- Laboratory of Molecular Biochemistry, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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48
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Moon JL, Shaw LN, Mayo JA, Potempa J, Travis J. Isolation and properties of extracellular proteinases of Penicillium marneffei. Biol Chem 2006; 387:985-93. [PMID: 16913848 DOI: 10.1515/bc.2006.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Penicillium marneffei is a dimorphic fungus native to Southeast Asia. Disease caused by this organism, until recently a very rare condition, has increased dramatically in parallel with the increase in the number of individuals in the region immunocompromised by AIDS and other conditions. While much research has been performed on the control of dimorphic switching in P. marneffei, there is a relative dearth of information regarding the proteinases secreted by this pathogen. Our laboratory has purified and characterized two proteinases produced by this organism in liquid culture and cloned the gene of a third. Both the recombinant enzyme expressed from the cloned gene and one of those purified from culture supernatants have been identified as members of the eqolisin family, a group of pepstatin-insensitive acid proteinases. The other enzyme purified from a culture supernatant is a serine proteinase with activity in the neutral pH range. These enzymes appear to be differentially expressed, depending on culture conditions.
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Affiliation(s)
- Jonathan L Moon
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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49
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Pillai B, Cherney MM, Hiraga K, Takada K, Oda K, James MNG. Crystal structure of scytalidoglutamic peptidase with its first potent inhibitor provides insights into substrate specificity and catalysis. J Mol Biol 2006; 365:343-61. [PMID: 17069854 DOI: 10.1016/j.jmb.2006.09.058] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 09/20/2006] [Accepted: 09/22/2006] [Indexed: 11/21/2022]
Abstract
Scytalidoglutamic peptidase (SGP) from Scytalidium lignicolum is the founding member of the newly discovered\ family of peptidases, G1, so far found exclusively in fungi. The crystal structure of SGP revealed a previously undescribed fold for peptidases and a unique catalytic dyad of residues Gln53 and Glu136. Surprisingly, the beta-sandwich structure of SGP is strikingly similar to members of the carbohydrate-binding concanavalin A-like lectins/glucanases superfamily. By analogy with the active sites of aspartic peptidases, a mechanism employing nucleophillic attack by a water molecule activated by the general base functionality of Glu136 has been proposed. Here, we report the first crystal structures of SGP in complex with two transition state peptide analogs designed to mimic the tetrahedral intermediate of the proteolytic reaction. Of these two analogs, the one containing a central S-hydroxyl group is a potent sub-nanomolar inhibitor of SGP. The inhibitor binds non-covalently to the concave surface of the upper beta-sheet and enables delineation of the S4 to S3' substrate specificity pockets of the enzyme. Structural differences in these pockets account for the unique substrate preferences of SGP among peptidases having an acidic pH optimum. Inhibitor binding is accompanied by a structuring of the region comprising residues Tyr71-Gly80 from being mostly disordered in the apoenzyme and leading to positioning of crucial active site residues for establishing enzyme-inhibitor contacts. In addition, conformational rearrangements are seen in a disulfide bridged surface loop (Cys141-Cys148), which moves inwards, partially closing the open substrate binding cleft of the native enzyme. The non-hydrolysable scissile bond analog of the inhibitor is located in the active site forming close contacts with Gln53 and Glu136. The nucleophilic water molecule is displaced and a unique mode of binding is observed with the S-OH of the inhibitor occupying the oxyanion binding site of the proposed tetrahedral intermediate. Details of the enzyme-inhibitor interactions and mechanistic interpretations are discussed.
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Affiliation(s)
- B Pillai
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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50
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Plummer LJ, Hildebrandt ER, Porter SB, Rogers VA, McCracken J, Schmidt WK. Mutational analysis of the ras converting enzyme reveals a requirement for glutamate and histidine residues. J Biol Chem 2006; 281:4596-605. [PMID: 16361710 PMCID: PMC2937830 DOI: 10.1074/jbc.m506284200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ras converting enzyme (RCE) promotes a proteolytic activity that is required for the maturation of Ras, the yeast a-factor mating pheromone, and certain other proteins whose precursors bear a C-terminal CAAX tetrapeptide motif. Despite the physiological importance of RCE, the enzymatic mechanism of this protease remains undefined. In this study, we have evaluated the substrate specificity of RCE orthologs from yeast (Rce1p), worm, plant, and human and have determined the importance of conserved residues toward enzymatic activity. Our findings indicate that RCE orthologs have conserved substrate specificity, cleaving CVIA, CTLM, and certain other CAAX motifs, but not the CASQ motif, when these motifs are placed in the context of the yeast a-factor precursor. Our mutational studies of residues conserved between the orthologs indicate that an alanine substitution at His194 completely inactivates yeast Rce1p enzymatic activity, whereas a substitution at Glu156 or His248 results in marginal activity. We have also determined that residues Glu157, Tyr160, Phe190, and Asn252 impact the substrate selectivity of Rce1p. Computational methods predict that residues influencing Rce1p function are all near or within hydrophobic segments. Combined, our data indicate that yeast Rce1p function requires residues that are invariably conserved among an extended family of prokaryotic and eukaryotic enzymes and that these residues are likely to lie within or immediately adjacent to the transmembrane segments of this membrane-localized enzyme.
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Affiliation(s)
- Lisa J. Plummer
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
| | - Emily R. Hildebrandt
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
| | - Stephen B. Porter
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
| | - Victoria A. Rogers
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
| | - Jay McCracken
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
| | - Walter K. Schmidt
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, Georgia 30602
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