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Chen L, Kashina A. Post-translational Modifications of the Protein Termini. Front Cell Dev Biol 2021; 9:719590. [PMID: 34395449 PMCID: PMC8358657 DOI: 10.3389/fcell.2021.719590] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis. These modifications greatly increase biological complexity and are responsible for orders of magnitude change between the variety of proteins encoded in the genome and the variety of their biological functions. Many of these modifications occur at the protein termini, which contain reactive amino- and carboxy-groups of the polypeptide chain and often are pre-primed through the actions of cellular machinery to expose highly reactive residues. Such modifications have been known for decades, but only a few of them have been functionally characterized. The vast majority of eukaryotic proteins are N- and C-terminally modified by acetylation, arginylation, tyrosination, lipidation, and many others. Post-translational modifications of the protein termini have been linked to different normal and disease-related processes and constitute a rapidly emerging area of biological regulation. Here we highlight recent progress in our understanding of post-translational modifications of the protein termini and outline the role that these modifications play in vivo.
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Affiliation(s)
| | - Anna Kashina
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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2
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Soybean (Glycine max) Protein Hydrolysates as Sources of Peptide Bitter-Tasting Indicators: An Analysis Based on Hybrid and Fragmentomic Approaches. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The aim of this study was to analyze soybean proteins as sources of peptides likely to be bitter using fragmentomic and hybrid approaches involving in silico and in vitro studies. The bitterness of peptides (called parent peptides) was theoretically estimated based on the presence of bitter-tasting motifs, particularly those defined as bitter-tasting indicators. They were selected based on previously published multilinear stepwise regression results. Bioinformatic-assisted analyses covered the hydrolysis of five major soybean-originating protein sequences using bromelain, ficin, papain, and proteinase K. Verification of the results in experimental conditions included soy protein concentrate (SPC) hydrolysis, RP-HPLC (for monitoring the proteolysis), and identification of peptides using RP-HPLC-MS/MS. Discrepancies between in silico and in vitro results were observed when identifying parent peptide SPC hydrolysate samples. However, both analyses revealed that conglycinins were the most abundant sources of parent peptides likely to taste bitter. The compatibility percentage of the in silico and in vitro results was 3%. Nine parent peptides with the following sequences were identified in SPC hydrolysates: LSVISPK, DVLVIPLG, LIVILNG, NPFLFG, ISSTIV, PQMIIV, PFPSIL, DDFFL, and FFEITPEK (indicators are in bold). The fragmentomic idea of research might provide a supportive method for predicting the bitterness of hydrolysates. However, this statement needs to be confirmed experimentally.
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Iwaniak A, Minkiewicz P, Hrynkiewicz M, Bucholska J, Darewicz M. Hybrid Approach in the Analysis of Bovine Milk Protein Hydrolysates as a Source of Peptides Containing Di- and Tripeptide Bitterness Indicators. POL J FOOD NUTR SCI 2020. [DOI: 10.31883/pjfns/113532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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4
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Gingimaps: Protein Localization in the Oral Pathogen Porphyromonas gingivalis. Microbiol Mol Biol Rev 2020; 84:84/1/e00032-19. [PMID: 31896547 DOI: 10.1128/mmbr.00032-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Porphyromonas gingivalis is an oral pathogen involved in the widespread disease periodontitis. In recent years, however, this bacterium has been implicated in the etiology of another common disorder, the autoimmune disease rheumatoid arthritis. Periodontitis and rheumatoid arthritis were known to correlate for decades, but only recently a possible molecular connection underlying this association has been unveiled. P. gingivalis possesses an enzyme that citrullinates certain host proteins and, potentially, elicits autoimmune antibodies against such citrullinated proteins. These autoantibodies are highly specific for rheumatoid arthritis and have been purported both as a symptom and a potential cause of the disease. The citrullinating enzyme and other major virulence factors of P. gingivalis, including some that were implicated in the etiology of rheumatoid arthritis, are targeted to the host tissue as secreted or outer-membrane-bound proteins. These targeting events play pivotal roles in the interactions between the pathogen and its human host. Accordingly, the overall protein sorting and secretion events in P. gingivalis are of prime relevance for understanding its full disease-causing potential and for developing preventive and therapeutic approaches. The aim of this review is therefore to offer a comprehensive overview of the subcellular and extracellular localization of all proteins in three reference strains and four clinical isolates of P. gingivalis, as well as the mechanisms employed to reach these destinations.
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Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res 2019; 46:D624-D632. [PMID: 29145643 PMCID: PMC5753285 DOI: 10.1093/nar/gkx1134] [Citation(s) in RCA: 973] [Impact Index Per Article: 194.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022] Open
Abstract
The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources. Because of the increasing size of the MEROPS sequence collection, in future only sequences of characterized proteins, and from completely sequenced genomes of organisms of evolutionary, medical or commercial significance will be added. As an example, peptidase homologues in four proteomes from the Asgard superphylum of Archaea have been identified and compared to other archaean, bacterial and eukaryote proteomes. This has given insights into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in Asgard archaeotes and as organisms increase in complexity. Novel structures for proteasome complexes in archaea are postulated.
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Affiliation(s)
- Neil D Rawlings
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Alan J Barrett
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Paul D Thomas
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, 1450 Biggy St, NRT 2502, Los Angeles, CA 90033, USA
| | - Xiaosong Huang
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, 1450 Biggy St, NRT 2502, Los Angeles, CA 90033, USA
| | - Alex Bateman
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Robert D Finn
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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6
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Tucker RP. Teneurins: Domain Architecture, Evolutionary Origins, and Patterns of Expression. Front Neurosci 2018; 12:938. [PMID: 30618567 PMCID: PMC6297184 DOI: 10.3389/fnins.2018.00938] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022] Open
Abstract
Disruption of teneurin expression results in abnormal neural networks, but just how teneurins support the development of the central nervous system remains an area of active research. This review summarizes some of what we know about the functions of the various domains of teneurins, the possible evolution of teneurins from a bacterial toxin, and the intriguing patterns of teneurin expression. Teneurins are a family of type-2 transmembrane proteins. The N-terminal intracellular domain can be processed and localized to the nucleus, but the significance of this nuclear localization is unknown. The extracellular domain of teneurins is largely composed of tyrosine-aspartic acid repeats that fold into a hollow barrel, and the C-terminal domains of teneurins are stuffed, and least partly, into the barrel. A 6-bladed beta-propeller is found at the other end of the barrel. The same arrangement-6-bladed beta-propeller, tyrosine-aspartic acid repeat barrel, and the C-terminal domain inside the barrel-is seen in toxic proteins from bacteria, and there is evidence that teneurins may have evolved from a gene encoding a prokaryotic toxin via horizontal gene transfer into an ancestral choanoflagellate. Patterns of teneurin expression are often, but not always, complementary. In the central nervous system, where teneurins are best studied, interconnected populations of neurons often express the same teneurin. For example, in the chicken embryo neurons forming the tectofugal pathway express teneurin-1, whereas neurons forming the thalamofugal pathway express teneurin-2. In Drosophila melanogaster, Caenorhabditis elegans, zebrafish and mice, misexpression or knocking out teneurin expression leads to abnormal connections in the neural networks that normally express the relevant teneurin. Teneurins are also expressed in non-neuronal tissue during development, and in at least some regions the patterns of non-neuronal expression are also complementary. The function of teneurins outside the nervous system remains unclear.
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Affiliation(s)
- Richard P. Tucker
- Department of Cell Biology and Human Anatomy, University of California at Davis, Davis, CA, United States
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7
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Arreola R, Villalpando JL, Puente-Rivera J, Morales-Montor J, Rudiño-Piñera E, Alvarez-Sánchez ME. Trichomonas vaginalis metalloproteinase TvMP50 is a monomeric Aminopeptidase P-like enzyme. Mol Biotechnol 2018; 60:563-575. [PMID: 29936696 DOI: 10.1007/s12033-018-0097-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Previously, metalloproteinase was isolated and identified from Trichomonas vaginalis, belonging to the aminopeptidase P-like metalloproteinase subfamily A/B, family M24 of clan MG, named TvMP50. The native and recombinant TvMP50 showed proteolytic activity, determined by gelatin zymogram, and a 50 kDa band, suggesting that TvMP50 is a monomeric active enzyme. This was an unexpected finding since other Xaa-Pro aminopeptidases/prolidases are active as a biological unit formed by dimers/tetramers. In this study, the evolutionary history of TvMP50 and the preliminary crystal structure of the recombinant enzyme determined at 3.4 Å resolution is reported. TvMP50 was shown to be a type of putative, eukaryotic, monomeric aminopeptidase P, and the crystallographic coordinates showed a monomer on a "pseudo-homodimer" array on the asymmetric unit that resembles the quaternary structure of the M24B dimeric family and suggests a homodimeric aminopeptidase P-like enzyme as a likely ancestor. Interestingly, TvMP50 had a modified N-terminal region compared with other Xaa-Pro aminopeptidases/prolidases with three-dimensional structures; however, the formation of the standard dimer is structurally unstable in aqueous solution, and a comparably reduced number of hydrogen bridges and lack of saline bridges were found between subunits A/B, which could explain why TvMP50 portrays monomeric functionality. Additionally, we found that the Parabasalia group contains two protein lineages with a "pita bread" fold; the ancestral monomeric group 1 was probably derived from an ancestral dimeric aminopeptidase P-type enzyme, and group 2 has a probable dimeric kind of ancestral eukaryotic prolidase lineage. The implications of such hypotheses are also presented.
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Affiliation(s)
- Rodrigo Arreola
- Psychiatric Genetics Department, Clinical Research Branch, National Institute of Psychiatry, Ramón de la Fuente, Calzada México-Xochimilco 101, Colonia San Lorenzo Huipulco, Tlalpan, 14370, Mexico City, DF, Mexico
| | - José Luis Villalpando
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), San Lorenzo # 290, Colonia Del Valle, CP 0310, Mexico City, Mexico
| | - Jonathan Puente-Rivera
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), San Lorenzo # 290, Colonia Del Valle, CP 0310, Mexico City, Mexico
| | - Jorge Morales-Montor
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ap 70228, CP 04510, Mexico City, Mexico
| | - Enrique Rudiño-Piñera
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, 62210, Cuernavaca, MOR, Mexico
| | - María Elizbeth Alvarez-Sánchez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), San Lorenzo # 290, Colonia Del Valle, CP 0310, Mexico City, Mexico.
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Le T, Lee HJ, Jin HJ. Recognition Site Generated by Natural Changes in Erm Proteins Leads to Unexpectedly High Susceptibility to Chymotrypsin. ACS OMEGA 2017; 2:8129-8140. [PMID: 30023575 PMCID: PMC6045372 DOI: 10.1021/acsomega.7b00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/10/2017] [Indexed: 06/08/2023]
Abstract
Erms are proteins that methylate the adenine (A2058) in Escherichia coli 23S rRNA, which results in resistance to macrolide, lincosamide, and streptogramin B antibiotics. In a previous report, ErmN appeared to be more susceptible to contaminating proteases in DNase I. To determine the underlying mechanism, cleavage with chymotrypsin over time was investigated. ErmN possesses unusually high-susceptibility recognition site (F45) as evidenced by a band (band 1) that represented greater than 80% of the total band intensity at 30 s. The exposure rate of the hydrophobic core was more than 67-fold and 104-fold faster in ErmN than those in ErmS and ErmE, respectively. After cleavage at F45, some of the hydrophobic interactions were disrupted. Further digestion of band 1 occurred through the exposed F163 with a half-life of 3.18 min. After 30 min, less than 1% of ErmN remained. On the basis of the structure of ErmC', the location of F45 was presumed to be in an α helix at the bottom of a cavity. Both substitution of most common amino acids such as isoleucine, valine, or leucine with phenylalanine (ErmH, ErmI, ErmN, and ErmZ out of the 37 known Erms) and the apparent added flexibility, which could result from the additional loop region attached to phenylalanine that is four to nine amino acids longer (ErmI, ErmN, and ErmZ, which form one cluster in the phylogenetic tree), could cause unusually high susceptibility. The unexpectedly high susceptibility among the homologous proteins could indicate that caution should be taken not to misinterpret the observations when conducting any procedure in which protease or protease contamination is involved.
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Affiliation(s)
- Tien Le
- Department
of Bioscience and Biotechnology, The University
of Suwon, Hwaseong City, Gyeonggi-Do 18323, Republic of Korea
| | - Hak Jin Lee
- Department
of Life Science, Korea University Graduate
School, Seoul 02841, Republic of Korea
| | - Hyung Jong Jin
- Department
of Bioscience and Biotechnology, The University
of Suwon, Hwaseong City, Gyeonggi-Do 18323, Republic of Korea
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Rawlings ND. Using the MEROPS Database for Investigation of Lysosomal Peptidases, Their Inhibitors, and Substrates. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1594:213-226. [PMID: 28456986 DOI: 10.1007/978-1-4939-6934-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter describes how to retrieve data on lysosomal peptidases from the MEROPS database for proteolytic enzymes, their substrates and inhibitors ( http://merops.sanger.ac.uk ). Features described in this chapter include the summary page, pages for structure, interactions with inhibitors, substrates, literature and involvement in physiological pathways, and how to download data from the MEROPS FTP site. The lysosomal peptidase legumain is used as an example.
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Affiliation(s)
- Neil D Rawlings
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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10
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Chen Q, Zobel J, Verspoor K. Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:baw163. [PMID: 28077566 PMCID: PMC5225397 DOI: 10.1093/database/baw163] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/22/2023]
Abstract
GenBank, the EMBL European Nucleotide Archive and the DNA DataBank of Japan, known collectively as the International Nucleotide Sequence Database Collaboration or INSDC, are the three most significant nucleotide sequence databases. Their records are derived from laboratory work undertaken by different individuals, by different teams, with a range of technologies and assumptions and over a period of decades. As a consequence, they contain a great many duplicates, redundancies and inconsistencies, but neither the prevalence nor the characteristics of various types of duplicates have been rigorously assessed. Existing duplicate detection methods in bioinformatics only address specific duplicate types, with inconsistent assumptions; and the impact of duplicates in bioinformatics databases has not been carefully assessed, making it difficult to judge the value of such methods. Our goal is to assess the scale, kinds and impact of duplicates in bioinformatics databases, through a retrospective analysis of merged groups in INSDC databases. Our outcomes are threefold: (1) We analyse a benchmark dataset consisting of duplicates manually identified in INSDC—a dataset of 67 888 merged groups with 111 823 duplicate pairs across 21 organisms from INSDC databases – in terms of the prevalence, types and impacts of duplicates. (2) We categorize duplicates at both sequence and annotation level, with supporting quantitative statistics, showing that different organisms have different prevalence of distinct kinds of duplicate. (3) We show that the presence of duplicates has practical impact via a simple case study on duplicates, in terms of GC content and melting temperature. We demonstrate that duplicates not only introduce redundancy, but can lead to inconsistent results for certain tasks. Our findings lead to a better understanding of the problem of duplication in biological databases. Database URL: the merged records are available at https://cloudstor.aarnet.edu.au/plus/index.php/s/Xef2fvsebBEAv9w
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Affiliation(s)
- Qingyu Chen
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Zobel
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karin Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Parkville, VIC, 3010, Australia
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Fuchs JE, Schilling O, Liedl KR. Determinants of Macromolecular Specificity from Proteomics-Derived Peptide Substrate Data. Curr Protein Pept Sci 2017; 18:905-913. [PMID: 27455965 PMCID: PMC5898033 DOI: 10.2174/1389203717666160724211231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/30/2017] [Accepted: 04/15/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in proteomics methodologies allow for high throughput profiling of proteolytic cleavage events. The resulting substrate peptide distributions provide deep insights in the underlying macromolecular recognition events, as determinants of biomolecular specificity identified by proteomics approaches may be compared to structure-based analysis of corresponding protein-protein interfaces. METHOD Here, we present an overview of experimental and computational methodologies and tools applied in the area and provide an outlook beyond the protein class of proteases. RESULTS AND CONCLUSION We discuss here future potential, synergies and needs of the emerging overlap disciplines of proteomics and structure-based modelling.
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Affiliation(s)
- Julian E. Fuchs
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, United Kingdom
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Str. 17, D-79104 Freiburg, Germany and BIOSS Centre for Biological Signaling Studies, University of Freiburg, D-79104Freiburg, Germany
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, A-6020Innsbruck, Austria
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12
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Interspecies comparison of peptide substrate reporter metabolism using compartment-based modeling. Anal Bioanal Chem 2016; 409:1173-1183. [PMID: 27900431 DOI: 10.1007/s00216-016-0085-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/07/2016] [Indexed: 01/03/2023]
Abstract
Peptide substrate reporters are fluorescently labeled peptides that can be acted upon by one or more enzymes of interest. Peptide substrates are readily synthesized and more easily separated than full-length protein substrates; however, they are often more rapidly degraded by peptidases. As a result, peptide reporters must be made resistant to proteolysis in order to study enzymes in intact cells and lysates. This is typically achieved by optimizing the reporter sequence in a single cell type or model organism, but studies of reporter stability in a variety of organisms are needed to establish the robustness and broader utility of these molecular tools. We measured peptidase activity toward a peptide substrate reporter for protein kinase B (Akt) in E. coli, D. discoideum, and S. cerevisiae using capillary electrophoresis with laser-induced fluorescence (CE-LIF). Using compartment-based modeling, we determined individual rate constants for all potential peptidase reactions and explored how these rate constants differed between species. We found the reporter to be stable in D. discoideum (t 1/2 = 82-103 min) and S. cerevisiae (t 1/2 = 279-314 min), but less stable in E. coli (t 1/2 = 21-44 min). These data suggest that the reporter is sufficiently stable to be used for kinase assays in eukaryotic cell types while also demonstrating the potential utility of compartment-based models in peptide substrate reporter design. Graphical abstract Cell lysates from several evolutionarily divergent species were incubated with a peptide substrate reporter, and compartment-based modeling was used to determine key steps in the metabolism of the reporter in each cell type.
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Characterizing Protease Specificity: How Many Substrates Do We Need? PLoS One 2015; 10:e0142658. [PMID: 26559682 PMCID: PMC4641643 DOI: 10.1371/journal.pone.0142658] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/26/2015] [Indexed: 12/26/2022] Open
Abstract
Calculation of cleavage entropies allows to quantify, map and compare protease substrate specificity by an information entropy based approach. The metric intrinsically depends on the number of experimentally determined substrates (data points). Thus a statistical analysis of its numerical stability is crucial to estimate the systematic error made by estimating specificity based on a limited number of substrates. In this contribution, we show the mathematical basis for estimating the uncertainty in cleavage entropies. Sets of cleavage entropies are calculated using experimental cleavage data and modeled extreme cases. By analyzing the underlying mathematics and applying statistical tools, a linear dependence of the metric in respect to 1/n was found. This allows us to extrapolate the values to an infinite number of samples and to estimate the errors. Analyzing the errors, a minimum number of 30 substrates was found to be necessary to characterize substrate specificity, in terms of amino acid variability, for a protease (S4-S4’) with an uncertainty of 5 percent. Therefore, we encourage experimental researchers in the protease field to record specificity profiles of novel proteases aiming to identify at least 30 peptide substrates of maximum sequence diversity. We expect a full characterization of protease specificity helpful to rationalize biological functions of proteases and to assist rational drug design.
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14
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Rawlings ND, Barrett AJ, Finn R. Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2015; 44:D343-50. [PMID: 26527717 PMCID: PMC4702814 DOI: 10.1093/nar/gkv1118] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/12/2015] [Indexed: 12/01/2022] Open
Abstract
The MEROPS database (http://merops.sanger.ac.uk) is an integrated source of information about peptidases, their substrates and inhibitors, which are of great relevance to biology, medicine and biotechnology. The hierarchical classification of the database is as follows: homologous sets of sequences are grouped into a protein species; protein species are grouped into a family; families are grouped into clans. There is a type example for each protein species (known as a ‘holotype’), family and clan, and each protein species, family and clan has its own unique identifier. Pages to show the involvement of peptidases and peptidase inhibitors in biological pathways have been created. Each page shows the peptidases and peptidase inhibitors involved in the pathway, along with the known substrate cleavages and peptidase-inhibitor interactions, and a link to the KEGG database of biological pathways. Links have also been established with the IUPHAR Guide to Pharmacology. A new service has been set up to allow the submission of identified substrate cleavages so that conservation of the cleavage site can be assessed. This should help establish whether or not a cleavage site is physiologically relevant on the basis that such a cleavage site is likely to be conserved.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK EMBO European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Alan J Barrett
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK EMBO European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Robert Finn
- EMBO European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
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15
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Yang J, Röwer C, Koy C, Ruß M, Rüger CP, Zimmermann R, von Fritschen U, Bredell M, Finke JC, Glocker MO. Mass spectrometric characterization of limited proteolysis activity in human plasma samples under mild acidic conditions. Methods 2015; 89:30-7. [PMID: 25726909 DOI: 10.1016/j.ymeth.2015.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/29/2015] [Accepted: 02/20/2015] [Indexed: 10/23/2022] Open
Abstract
We developed a limited proteolysis assay for estimating dynamics in plasma-borne protease activities using MALDI ToF MS analysis as readout. A highly specific limited proteolysis activity was elicited in human plasma by shifting the pH to 6. Mass spectrometry showed that two singly charged ion signals at m/z 2753.44 and m/z 2937.56 significantly increased in abundance under mild acidic conditions as a function of incubation time. For proving that a provoked proteolytic activity in mild acidic solution caused the appearance of the observed peptides, control measurements were performed (i) with pepstatin as protease inhibitor, (ii) with heat-denatured samples, (iii) at pH 1.7, and (iv) at pH 7.5. Mass spectrometric fragmentation analysis showed that the observed peptides encompass the amino acid sequences 1-24 and 1-26 from the N-terminus of human serum albumin. Investigations on peptidase specificities suggest that the two best candidates for the observed serum albumin cleavages are cathepsin D and E. Reproducibility, robustness, and sensitivity prove the potential of the developed limited proteolysis assay to become of clinical importance for estimating dynamics of plasma-borne proteases with respect to associated pathophysiological tissue conditions.
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Affiliation(s)
- Jingzhi Yang
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Manuela Ruß
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Christopher P Rüger
- Analytical Chemistry Department, Institute of Chemistry, University of Rostock, Rostock, Germany; Cooperation Group of Comprehensive Molecular Analytics, Helmholtz Zentrum München, Munich, Germany
| | - Ralf Zimmermann
- Analytical Chemistry Department, Institute of Chemistry, University of Rostock, Rostock, Germany; Cooperation Group of Comprehensive Molecular Analytics, Helmholtz Zentrum München, Munich, Germany
| | - Uwe von Fritschen
- Division of Plastic Surgery and Hand Surgery, HELIOS Clinic Emil von Behring, Berlin, Germany
| | - Marius Bredell
- Department of Cranio-Maxillofacial and Oral Surgery, University Hospital of Zürich, Zürich, Switzerland
| | - Juliane C Finke
- Division of Plastic Surgery and Hand Surgery, HELIOS Clinic Emil von Behring, Berlin, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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16
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Howes JM, Bihan D, Slatter DA, Hamaia SW, Packman LC, Knauper V, Visse R, Farndale RW. The recognition of collagen and triple-helical toolkit peptides by MMP-13: sequence specificity for binding and cleavage. J Biol Chem 2014; 289:24091-101. [PMID: 25008319 PMCID: PMC4148842 DOI: 10.1074/jbc.m114.583443] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Remodeling of collagen by matrix metalloproteinases (MMPs) is crucial to tissue homeostasis and repair. MMP-13 is a collagenase with a substrate preference for collagen II over collagens I and III. It recognizes a specific, well-known site in the tropocollagen molecule where its binding locally perturbs the triple helix, allowing the catalytic domain of the active enzyme to cleave the collagen α chains sequentially, at Gly775–Leu776 in collagen II. However, the specific residues upon which collagen recognition depends within and surrounding this locus have not been systematically mapped. Using our triple-helical peptide Collagen Toolkit libraries in solid-phase binding assays, we found that MMP-13 shows little affinity for Collagen Toolkit III, but binds selectively to two triple-helical peptides of Toolkit II. We have identified the residues required for the adhesion of both proMMP-13 and MMP-13 to one of these, Toolkit peptide II-44, which contains the canonical collagenase cleavage site. MMP-13 was unable to bind to a linear peptide of the same sequence as II-44. We also discovered a second binding site near the N terminus of collagen II (starting at helix residue 127) in Toolkit peptide II-8. The pattern of binding of the free hemopexin domain of MMP-13 was similar to that of the full-length enzyme, but the free catalytic subunit bound none of our peptides. The susceptibility of Toolkit peptides to proteolysis in solution was independent of the very specific recognition of immobilized peptides by MMP-13; the enzyme proved able to cleave a range of dissolved collagen peptides.
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Affiliation(s)
- Joanna-Marie Howes
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
| | - Dominique Bihan
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
| | - David A Slatter
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
| | - Samir W Hamaia
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
| | - Len C Packman
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom
| | - Vera Knauper
- the Cardiff University Dental School, Dental Drive, Cardiff CF14 4XY, United Kingdom, and
| | - Robert Visse
- the Kennedy Institute of Rheumatology, Hammersmith, London W6 8LH, United Kingdom
| | - Richard W Farndale
- From the Department of Biochemistry, University of Cambridge, Downing Site, Cambridge CB2 1QW, United Kingdom,
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17
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Mangiola S, Young ND, Sternberg PW, Strube C, Korhonen PK, Mitreva M, Scheerlinck JP, Hofmann A, Jex AR, Gasser RB. Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. Int J Parasitol 2014; 44:251-61. [PMID: 24487001 DOI: 10.1016/j.ijpara.2013.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 12/11/2013] [Accepted: 12/18/2013] [Indexed: 01/09/2023]
Abstract
Parasitic nematodes cause diseases of major economic importance in animals. Key representatives are species of Dictyocaulus (=lungworms), which cause bronchitis (=dictyocaulosis, commonly known as "husk") and have a major adverse impact on the health of livestock. In spite of their economic importance, very little is known about the immunomolecular biology of these parasites. Here, we conducted a comprehensive investigation of the adult transcriptome of Dictyocaulus filaria of small ruminants and compared it with that of Dictyocaulus viviparus of bovids. We then identified a subset of highly transcribed molecules inferred to be linked to host-parasite interactions, including cathepsin B peptidases, fatty-acid and/or retinol-binding proteins, β-galactoside-binding galectins, secreted protein 6 precursors, macrophage migration inhibitory factors, glutathione peroxidases, a transthyretin-like protein and a type 2-like cystatin. We then studied homologues of D. filaria type 2-like cystatin encoded in D. viviparus and 24 other nematodes representing seven distinct taxonomic orders, with a particular focus on their proposed role in immunomodulation and/or metabolism. Taken together, the present study provides new insights into nematode-host interactions. The findings lay the foundation for future experimental studies and could have implications for designing new interventions against lungworms and other parasitic nematodes. The future characterisation of the genomes of Dictyocaulus spp. should underpin these endeavours.
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Affiliation(s)
- Stefano Mangiola
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia
| | - Neil D Young
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia.
| | - Paul W Sternberg
- HHMI, Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Christina Strube
- Institute for Parasitology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Pasi K Korhonen
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia
| | - Makedonka Mitreva
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Andreas Hofmann
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia; Eskitis Institute for Cell & Molecular Therapies, Griffith University, Brisbane, Australia
| | - Aaron R Jex
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia
| | - Robin B Gasser
- Faculty of Veterinary Science, The University of Melbourne, Victoria, Australia; Institute of Parasitology and Tropical Veterinary Medicine, Berlin, Germany.
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18
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Shahinian H, Tholen S, Schilling O. Proteomic identification of protease cleavage sites: cell-biological and biomedical applications. Expert Rev Proteomics 2014; 10:421-33. [DOI: 10.1586/14789450.2013.841547] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Wali N, Hosokawa K, Malik S, Saito H, Miyaguchi K, Imajoh-Ohmi S, Miki Y, Nakanishi A. Centrosomal BRCA2 is a target protein of membrane type-1 matrix metalloproteinase (MT1-MMP). Biochem Biophys Res Commun 2013; 443:1148-54. [PMID: 24384087 DOI: 10.1016/j.bbrc.2013.12.103] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/11/2013] [Indexed: 01/07/2023]
Abstract
BRCA2 localizes to centrosomes between G1 and prophase and is removed from the centrosomes during mitosis, but the underlying mechanism is not clear. Here we show that BRCA2 is cleaved into two fragments by membrane type-1 matrix metalloproteinase (MT1-MMP), and that knockdown of MT1-MMP prevents the removal of BRCA2 from centrosomes during metaphase. Mass spectrometry mapping revealed that the MT1-MMP cleavage site of human BRCA2 is between Asn-2135 and Leu-2136 ((2132)LSNN/LNVEGG(2141)), and the point mutation L2136D abrogated MT1-MMP cleavage. Our data demonstrate that MT1-MMP proteolysis of BRCA2 regulates the abundance of BRCA2 on centrosomes.
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Affiliation(s)
- Nadila Wali
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan; Department of Obstetrics and Gynecology, Urumqi Friendship Hospital, Xinjiang, PR China
| | - Kana Hosokawa
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan
| | - Sadiya Malik
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan
| | - Hiroko Saito
- Department of Molecular Diagnosis, Cancer Institute, The Japanese Foundation of Cancer Research (JFCR), Japan
| | - Ken Miyaguchi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan
| | - Shinobu Imajoh-Ohmi
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan; Department of Molecular Diagnosis, Cancer Institute, The Japanese Foundation of Cancer Research (JFCR), Japan.
| | - Akira Nakanishi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Japan
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20
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Carroll IM, Maharshak N. Enteric bacterial proteases in inflammatory bowel disease- pathophysiology and clinical implications. World J Gastroenterol 2013; 19:7531-7543. [PMID: 24431894 PMCID: PMC3837251 DOI: 10.3748/wjg.v19.i43.7531] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/05/2013] [Accepted: 11/05/2013] [Indexed: 02/06/2023] Open
Abstract
Numerous reports have identified a dysbiosis in the intestinal microbiota in patients suffering from inflammatory bowel diseases (IBD), yet the mechanism(s) in which this complex microbial community initiates or perpetuates inflammation remains unclear. The purpose of this review is to present evidence for one such mechanism that implicates enteric microbial derived proteases in the pathogenesis of IBD. We highlight and discuss studies demonstrating that proteases and protease receptors are abundant in the digestive system. Additionally, we investigate studies demonstrating an association between increased luminal protease activity and activation of protease receptors, ultimately resulting in increased intestinal permeability and exacerbation of colitis in animal models as well as in human IBD. Proteases are essential for the normal functioning of bacteria and in some cases can serve as virulence factors for pathogenic bacteria. Although not classified as traditional virulence factors, proteases originating from commensal enteric bacteria also have a potential association with intestinal inflammation via increased enteric permeability. Reports of increased protease activity in stools from IBD patients support a possible mechanism for a dysbiotic enteric microbiota in IBD. A better understanding of these pathways and characterization of the enteric bacteria involved, their proteases, and protease receptors may pave the way for new therapeutic approaches for these diseases.
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21
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Fuchs JE, von Grafenstein S, Huber RG, Kramer C, Liedl KR. Substrate-driven mapping of the degradome by comparison of sequence logos. PLoS Comput Biol 2013; 9:e1003353. [PMID: 24244149 PMCID: PMC3828135 DOI: 10.1371/journal.pcbi.1003353] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/05/2013] [Indexed: 12/27/2022] Open
Abstract
Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available.
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Affiliation(s)
- Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Roland G. Huber
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Christian Kramer
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
- * E-mail:
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22
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Rawlings ND, Waller M, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2013; 42:D503-9. [PMID: 24157837 PMCID: PMC3964991 DOI: 10.1093/nar/gkt953] [Citation(s) in RCA: 658] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfill the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. Recent developments include the following. A community annotation project has been instigated in which acknowledged experts are invited to contribute summaries for peptidases. Software has been written to provide an Internet-based data entry form. Contributors are acknowledged on the relevant web page. A new display showing the intron/exon structures of eukaryote peptidase genes and the phasing of the junctions has been implemented. It is now possible to filter the list of peptidases from a completely sequenced bacterial genome for a particular strain of the organism. The MEROPS filing pipeline has been altered to circumvent the restrictions imposed on non-interactive blastp searches, and a HMMER search using specially generated alignments to maximize the distribution of organisms returned in the search results has been added.
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Affiliation(s)
- Neil D Rawlings
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK and Proteins and Protein Families, EMBO European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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23
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Rawlings ND. Identification and prioritization of novel uncharacterized peptidases for biochemical characterization. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat022. [PMID: 23584835 PMCID: PMC3625958 DOI: 10.1093/database/bat022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genome sequencing projects are generating enormous amounts of biological data that require analysis, which in turn identifies genes and proteins that require characterization. Enzymes that act on proteins are especially difficult to characterize because of the time required to distinguish one from another. This is particularly true of peptidases, the enzymes that activate, inactivate and degrade proteins. This article aims to identify clusters of sequences each of which represents the species variants of a single putative peptidase that is widely distributed and is thus merits biochemical characterization. The MEROPS database maintains large collections of sequences, references, substrate cleavage positions and inhibitor interactions of peptidases and their homologues. MEROPS also maintains a hierarchical classification of peptidase homologues, in which sequences are clustered as species variants of a single peptidase; homologous sequences are assembled into a family; and families are clustered into a clan. For each family, an alignment and a phylogenetic tree are generated. By assigning an identifier to a peptidase that has been biochemically characterized from a particular species (called a holotype), the identifier can be automatically extended to sequences from other species that cluster with the holotype. This permits transference of annotation from the holotype to other members of the cluster. By extending this concept to all peptidase homologues (including those of unknown function that have not been characterized) from model organisms representing all the major divisions of cellular life, clusters of sequences representing putative peptidases can also be identified. The 42 most widely distributed of these putative peptidases have been identified and discussed here and are prioritized as ideal candidates for biochemical characterization. Database URL:http://merops.sanger.ac.uk
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Affiliation(s)
- Neil D Rawlings
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
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24
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Cai H, Kuang R, Gu J, Wang Y. Proteases in malaria parasites - a phylogenomic perspective. Curr Genomics 2012; 12:417-27. [PMID: 22379395 PMCID: PMC3178910 DOI: 10.2174/138920211797248565] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 07/17/2011] [Accepted: 07/20/2011] [Indexed: 12/21/2022] Open
Abstract
Malaria continues to be one of the most devastating global health problems due to the high morbidity and mortality it causes in endemic regions. The search for new antimalarial targets is of high priority because of the increasing prevalence of drug resistance in malaria parasites. Malarial proteases constitute a class of promising therapeutic targets as they play important roles in the parasite life cycle and it is possible to design and screen for specific protease inhibitors. In this mini-review, we provide a phylogenomic overview of malarial proteases. An evolutionary perspective on the origin and divergence of these proteases will provide insights into the adaptive mechanisms of parasite growth, development, infection, and pathogenesis.B
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Affiliation(s)
- Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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25
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A novel virulence strategy for Pseudomonas aeruginosa mediated by an autotransporter with arginine-specific aminopeptidase activity. PLoS Pathog 2012; 8:e1002854. [PMID: 22927813 PMCID: PMC3426542 DOI: 10.1371/journal.ppat.1002854] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 06/26/2012] [Indexed: 12/22/2022] Open
Abstract
The opportunistic human pathogen, Pseudomonas aeruginosa, is a major cause of infections in chronic wounds, burns and the lungs of cystic fibrosis patients. The P. aeruginosa genome encodes at least three proteins exhibiting the characteristic three domain structure of autotransporters, but much remains to be understood about the functions of these three proteins and their role in pathogenicity. Autotransporters are the largest family of secreted proteins in Gram-negative bacteria, and those characterised are virulence factors. Here, we demonstrate that the PA0328 autotransporter is a cell-surface tethered, arginine-specific aminopeptidase, and have defined its active site by site directed mutagenesis. Hence, we have assigned PA0328 with the name AaaA, for arginine-specific autotransporter of P. aeruginosa. We show that AaaA provides a fitness advantage in environments where the sole source of nitrogen is peptides with an aminoterminal arginine, and that this could be important for establishing an infection, as the lack of AaaA led to attenuation in a mouse chronic wound infection which correlated with lower levels of the cytokines TNFα, IL-1α, KC and COX-2. Consequently AaaA is an important virulence factor playing a significant role in the successful establishment of P. aeruginosa infections. We present a new Pseudomonas aeruginosa virulence factor that promotes chronic skin wound infections. We propose the name AaaA for this cell-surface tethered autotransporter. This arginine-specific aminopeptidase confers a growth advantage upon P. aeruginosa, providing a fitness advantage by creating a supply of arginine in chronic wounds where oxygen availability is limited and biofilm formation is involved. To our knowledge, this is the first mechanistic evidence linking the upregulation of genes involved in arginine metabolism with pathogenicity of P. aeruginosa, and we propose potential underlying mechanisms. The superbug P. aeruginosa is the leading cause of morbidity in cystic fibrosis patients. The ineffective host immune response to bacterial colonization is likely to play a critical role in the demise of these patients, making the possibility that AaaA could interface with the innate immune system, influencing the activity of iNOS and consequently the host's defence against invading pathogens. The surface localisation of AaaA makes it accessible to inhibitors that could reduce growth of P. aeruginosa during colonisation and alter biofilm formation, potentially improving the efficacy of current antimicrobials. Indeed, structurally related aminopeptidases play a central role in several disease states (stroke, diabetes, cancer, HIV and neuropsychiatric disorders), and inhibitors alleviate symptoms.
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26
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Dittwald P, Ostrowski J, Karczmarski J, Gambin A. Inferring serum proteolytic activity from LC-MS/MS data. BMC Bioinformatics 2012; 13 Suppl 5:S7. [PMID: 22537011 PMCID: PMC3358667 DOI: 10.1186/1471-2105-13-s5-s7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND In this paper we deal with modeling serum proteolysis process from tandem mass spectrometry data. The parameters of peptide degradation process inferred from LC-MS/MS data correspond directly to the activity of specific enzymes present in the serum samples of patients and healthy donors. Our approach integrate the existing knowledge about peptidases' activity stored in MEROPS database with the efficient procedure for estimation the model parameters. RESULTS Taking into account the inherent stochasticity of the process, the proteolytic activity is modeled with the use of Chemical Master Equation (CME). Assuming the stationarity of the Markov process we calculate the expected values of digested peptides in the model. The parameters are fitted to minimize the discrepancy between those expected values and the peptide activities observed in the MS data. Constrained optimization problem is solved by Levenberg-Marquadt algorithm. CONCLUSIONS Our results demonstrates the feasibility and potential of high-level analysis for LC-MS proteomic data. The estimated enzyme activities give insights into the molecular pathology of colorectal cancer. Moreover the developed framework is general and can be applied to study proteolytic activity in different systems.
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Affiliation(s)
- Piotr Dittwald
- Institute of Informatics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland.
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27
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Lilburn TG, Cai H, Zhou Z, Wang Y. Protease-associated cellular networks in malaria parasite Plasmodium falciparum. BMC Genomics 2011; 12 Suppl 5:S9. [PMID: 22369208 PMCID: PMC3287505 DOI: 10.1186/1471-2164-12-s5-s9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Malaria continues to be one of the most severe global infectious diseases, responsible for 1-2 million deaths yearly. The rapid evolution and spread of drug resistance in parasites has led to an urgent need for the development of novel antimalarial targets. Proteases are a group of enzymes that play essential roles in parasite growth and invasion. The possibility of designing specific inhibitors for proteases makes them promising drug targets. Previously, combining a comparative genomics approach and a machine learning approach, we identified the complement of proteases (degradome) in the malaria parasite Plasmodium falciparum and its sibling species [1-3], providing a catalog of targets for functional characterization and rational inhibitor design. Network analysis represents another route to revealing the role of proteins in the biology of parasites and we use this approach here to expand our understanding of the systems involving the proteases of P. falciparum. Results We investigated the roles of proteases in the parasite life cycle by constructing a network using protein-protein association data from the STRING database [4], and analyzing these data, in conjunction with the data from protein-protein interaction assays using the yeast 2-hybrid (Y2H) system [5], blood stage microarray experiments [6-8], proteomics [9-12], literature text mining, and sequence homology analysis. Seventy-seven (77) out of 124 predicted proteases were associated with at least one other protein, constituting 2,431 protein-protein interactions (PPIs). These proteases appear to play diverse roles in metabolism, cell cycle regulation, invasion and infection. Their degrees of connectivity (i.e., connections to other proteins), range from one to 143. The largest protease-associated sub-network is the ubiquitin-proteasome system which is crucial for protein recycling and stress response. Proteases are also implicated in heat shock response, signal peptide processing, cell cycle progression, transcriptional regulation, and signal transduction networks. Conclusions Our network analysis of proteases from P. falciparum uses a so-called guilt-by-association approach to extract sets of proteins from the proteome that are candidates for further study. Novel protease targets and previously unrecognized members of the protease-associated sub-systems provide new insights into the mechanisms underlying parasitism, pathogenesis and virulence.
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Affiliation(s)
- Timothy G Lilburn
- Department of Biology, University of Texas at San Antonio, San Antonio, TX 78249, USA
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28
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Rawlings ND, Barrett AJ, Bateman A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 2011; 40:D343-50. [PMID: 22086950 PMCID: PMC3245014 DOI: 10.1093/nar/gkr987] [Citation(s) in RCA: 661] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families, which are in turn grouped into clans. The database has been expanded to include proteolytic enzymes other than peptidases. Special identifiers for peptidases from a variety of model organisms have been established so that orthologues can be detected in other species. A table of predicted active-site residue and metal ligand positions and the residue ranges of the peptidase domains in orthologues has been added to each peptidase summary. New displays of tertiary structures, which can be rotated or have the surfaces displayed, have been added to the structure pages. New indexes for gene names and peptidase substrates have been made available. Among the enhancements to existing features are the inclusion of small-molecule inhibitors in the tables of peptidase–inhibitor interactions, a table of known cleavage sites for each protein substrate, and tables showing the substrate-binding preferences of peptidases derived from combinatorial peptide substrate libraries.
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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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29
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Swedberg JE, Harris JM. Plasmin Substrate Binding Site Cooperativity Guides the Design of Potent Peptide Aldehyde Inhibitors. Biochemistry 2011; 50:8454-62. [DOI: 10.1021/bi201203y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Joakim E. Swedberg
- Institute of Health and
Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland
4059, Australia
| | - Jonathan M. Harris
- Institute of Health and
Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland
4059, Australia
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30
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Abstract
BACKGROUND Genome-wide prediction of protein subcellular localization is an important type of evidence used for inferring protein function. While a variety of computational tools have been developed for this purpose, errors in the gene models and use of protein sorting signals that are not recognized by the more commonly accepted tools can diminish the accuracy of their output. RESULTS As part of an effort to manually curate the annotations of 19 strains of Shewanella, numerous insights were gained regarding the use of computational tools and proteomics data to predict protein localization. Identification of the suite of secretion systems present in each strain at the start of the process made it possible to tailor-fit the subsequent localization prediction strategies to each strain for improved accuracy. Comparisons of the computational predictions among orthologous proteins revealed inconsistencies in the computational outputs, which could often be resolved by adjusting the gene models or ortholog group memberships. While proteomic data was useful for verifying start site predictions and post-translational proteolytic cleavage, care was needed to distinguish cellular versus sample processing-mediated cleavage events. Searches for lipoprotein signal peptides revealed that neither TatP nor LipoP are designed for identification of lipoprotein substrates of the twin arginine translocation system and that the +2 rule for lipoprotein sorting does not apply to this Genus. Analysis of the relationships between domain occurrence and protein localization prediction enabled identification of numerous location-informative domains which could then be used to refine or increase confidence in location predictions. This collective knowledge was used to develop a general strategy for predicting protein localization that could be adapted to other organisms. CONCLUSION Improved localization prediction accuracy is not simply a matter of developing better computational algorithms. It also entails gathering key knowledge regarding the host architecture and translocation machinery and associated substrate recognition via experimentation and integration of diverse computational analyses from many proteins and, where possible, that are derived from different species within the same genus.
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Affiliation(s)
- Margaret F Romine
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
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31
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GPS-CCD: a novel computational program for the prediction of calpain cleavage sites. PLoS One 2011; 6:e19001. [PMID: 21533053 PMCID: PMC3080405 DOI: 10.1371/journal.pone.0019001] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 03/21/2011] [Indexed: 11/19/2022] Open
Abstract
As one of the most essential post-translational modifications (PTMs) of proteins, proteolysis, especially calpain-mediated cleavage, plays an important role in many biological processes, including cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. Experimental identification of calpain targets with bona fide cleavage sites is fundamental for dissecting the molecular mechanisms and biological roles of calpain cleavage. In contrast to time-consuming and labor-intensive experimental approaches, computational prediction of calpain cleavage sites might more cheaply and readily provide useful information for further experimental investigation. In this work, we constructed a novel software package of GPS-CCD (Calpain Cleavage Detector) for the prediction of calpain cleavage sites, with an accuracy of 89.98%, sensitivity of 60.87% and specificity of 90.07%. With this software, we annotated potential calpain cleavage sites for hundreds of calpain substrates, for which the exact cleavage sites had not been previously determined. In this regard, GPS-CCD 1.0 is considered to be a useful tool for experimentalists. The online service and local packages of GPS-CCD 1.0 were implemented in JAVA and are freely available at: http://ccd.biocuckoo.org/.
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32
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Chichkova NV, Shaw J, Galiullina RA, Drury GE, Tuzhikov AI, Kim SH, Kalkum M, Hong TB, Gorshkova EN, Torrance L, Vartapetian AB, Taliansky M. Phytaspase, a relocalisable cell death promoting plant protease with caspase specificity. EMBO J 2010; 29:1149-61. [PMID: 20111004 PMCID: PMC2845272 DOI: 10.1038/emboj.2010.1] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 01/04/2010] [Indexed: 01/28/2023] Open
Abstract
Caspases are cysteine-dependent proteases and are important components of animal apoptosis. They introduce specific breaks after aspartate residues in a number of cellular proteins mediating programmed cell death (PCD). Plants encode only distant homologues of caspases, the metacaspases that are involved in PCD, but do not possess caspase-specific proteolytic activity. Nevertheless, plants do display caspase-like activities indicating that enzymes structurally distinct from classical caspases may operate as caspase-like proteases. Here, we report the identification and characterisation of a novel PCD-related subtilisin-like protease from tobacco and rice named phytaspase (plant aspartate-specific protease) that possesses caspase specificity distinct from that of other known caspase-like proteases. We provide evidence that phytaspase is synthesised as a proenzyme, which is autocatalytically processed to generate the mature enzyme. Overexpression and silencing of the phytaspase gene showed that phytaspase is essential for PCD-related responses to tobacco mosaic virus and abiotic stresses. Phytaspase is constitutively secreted into the apoplast before PCD, but unexpectedly is re-imported into the cell during PCD providing insights into how phytaspase operates.
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Affiliation(s)
- Nina V Chichkova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Jane Shaw
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
| | - Raisa A Galiullina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Georgina E Drury
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
| | - Alexander I Tuzhikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Sang Hyon Kim
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
- Division of Biosciences and Bioinformatics, Myongji University, Yongin, Kyeongki-do, Korea
| | - Markus Kalkum
- Department of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Teresa B Hong
- Department of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Elena N Gorshkova
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Lesley Torrance
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
| | - Andrey B Vartapetian
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Michael Taliansky
- Plant Pathology Programme, Scottish Crop Research Institute, Invergowrie, Dundee, UK
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