How to use the MEROPS database and website to help understand peptidase specificity

The MEROPS website ( https://www.ebi.ac.uk/merops ) and database was established in 1996 to present the classification and nomenclature of proteolytic enzymes. This was expanded to include a classification of protein inhibitors of proteolytic enzymes in 2004. Each peptidase or inhibitor is assigned to a distinct identifier, based on its biochemical and biological properties, and homologous sequences are assembled into a family. Families in which the proteins share similar tertiary structures are assembled into a clan. The MEROPS classification is thus a hierarchy with at least three levels (protein‐species, family, and clan) showing the evolutionary relationship. Several other data collections have been assembled, which are accessed from all levels in the hierarchy. These include, sequence homologs, selective bibliographies, substrate cleavage sites, peptidase–inhibitor interactions, alignments, and phylogenetic trees. The substrate cleavage collection has been assembled from the literature and includes physiological, pathological, and nonphysiological cleavages in proteins, peptides, and synthetic substrates. In this article, we make recommendations about how best to analyze these data and show analyses to indicate peptidase binding site preferences and exclusions. We also identify peptidases where co‐operative binding occurs between adjacent binding sites.     

MEROPS: the protease database

The MEROPS database (http://www.merops.ac.uk) has been redesigned to accommodate increased amounts of information still in pages of moderate size that load rapidly. The information on each PepCard, FamCard or ClanCard has been divided between several sub-pages that can be reached by use of navigation buttons in a frame at the top of the screen. Several important additions have also been made to the database. Amongst these are CGI searches that allow the user to find a peptidase by name, its MEROPS identifier or its human or mouse chromosome location. The user may also list all published tertiary structures for a peptidase clan or family, and search for peptidase specificity data by entering either a peptidase name, substrate or bond cleaved. The PepCards, FamCards and ClanCards now have literature pages listing about 10 000 key papers in total, mostly with links to MEDLINE. Many PepCards now include a protein sequence alignment and data table for matching human, mouse or rat expressed sequence tags. FamCards and ClanCards contain Structure pages showing diagrammatic representations of known secondary structures of member peptidases or family type examples, respectively. Many novel peptidases have been added to the database after being discovered in complete genomes, libraries of expressed sequence tags or data from high-throughput genomic sequencing, and we describe the methods by which these were found.     

Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics

Background

Peptidases are key proteins involved in essential plant physiological processes. Although protein peptidase inhibitors are essential molecules that modulate peptidase activity, their global presence in different plant species remains still unknown. Comparative genomic analyses are powerful tools to get advanced knowledge into the presence and evolution of both, peptidases and their inhibitors across the Viridiplantae kingdom.

Results

A genomic comparative analysis of peptidase inhibitors and several groups of peptidases in representative species of different plant taxonomic groups has been performed. The results point out: i) clade-specific presence is common to many families of peptidase inhibitors, being some families present in most land plants; ii) variability is a widespread feature for peptidase inhibitory families, with abundant species-specific (or clade-specific) gene family proliferations; iii) peptidases are more conserved in different plant clades, being C1A papain and S8 subtilisin families present in all species analyzed; and iv) a moderate correlation among peptidases and their inhibitors suggests that inhibitors proliferated to control both endogenous and exogenous peptidases.

Conclusions

Comparative genomics has provided valuable insights on plant peptidase inhibitor families and could explain the evolutionary reasons that lead to the current variable repertoire of peptidase inhibitors in specific plant clades.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-812) contains supplementary material, which is available to authorized users.     

An Essential Signal Peptide Peptidase Identified in an RNAi Screen of Serine Peptidases of Trypanosoma brucei

The serine peptidases of Trypanosoma brucei have been viewed as potential drug targets. In particular, the S9 prolyl oligopeptidase subfamily is thought to be a good avenue for drug discovery. This is based on the finding that some S9 peptidases are secreted and active in the mammalian bloodstream, and that they are a class of enzyme against which drugs have successfully been developed. We collated a list of all serine peptidases in T. brucei, identifying 20 serine peptidase genes, of which nine are S9 peptidases. We screened all 20 serine peptidases by RNAi to determine which, if any, are essential for bloodstream form T. brucei survival. All S9 serine peptidases were dispensable for parasite survival in vitro, even when pairs of similar genes, coding for oligopeptidase B or prolyl oligopeptidase, were targeted simultaneously. We also found no effect on parasite survival in an animal host when the S9 peptidases oligopeptidase B, prolyl oligopeptidase or dipeptidyl peptidase 8 were targeted. The only serine peptidase to emerge from the RNAi screen as essential was a putative type-I signal peptide peptidase (SPP1). This gene was essential for parasite survival both in vitro and in vivo. The growth defect conferred by RNAi depletion of SPP1 was rescued by expression of a functional peptidase from an RNAi resistant SPP1 gene. However, expression of catalytically inactive SPP1 was unable to rescue cells from the SPP1 depleted phenotype, demonstrating that SPP1 serine peptidase activity is necessary for T. brucei survival.     

Aspartic peptidase inhibitors: implications in drug development

The last decade has witnessed an effervescence of research interest in the development of potent inhibitors of various aspartic peptidases. As an enzyme family, aspartic peptidases are relatively a small group that has received enormous interest because of their significant roles in human diseases like involvement of renin in hypertension, cathepsin D in metastasis of breast cancer, beta-Secretase in Alzheimer's Disease, plasmepsins in malaria, HIV-1 peptidase in acquired immune deficiency syndrome, and secreted aspartic peptidases in candidal infections. There have been developments on clinically active inhibitors of HIV-1 peptidase, which have been licensed for the treatment of AIDS. The inhibitors of plasmepsins and renin are considered a viable therapeutic strategy for the treatment of malaria and hypertension. Relatively few inhibitors of cathepsin D have been reported, partly because of its uncertain role as a viable target for therapeutic intervention. The beta-secretase inhibitors OM99-2 and OM003 were designed based on the substrate specificity information. The present article is a comprehensive state-of-the-art review describing the aspartic peptidase inhibitors illustrating the recent developments in the area. In addition, the homologies between the reported inhibitor sequences have been analyzed. The understanding of the structure-function relationships of aspartic peptidases and inhibitors will have a direct impact on the design of new inhibitor drugs.     

Prokaryote-derived protein inhibitors of peptidases: A sketchy occurrence and mostly unknown function

In metazoan organisms protein inhibitors of peptidases are important factors essential for regulation of proteolytic activity. In vertebrates genes encoding peptidase inhibitors constitute up to 1% of genes reflecting a need for tight and specific control of proteolysis especially in extracellular body fluids. In stark contrast unicellular organisms, both prokaryotic and eukaryotic consistently contain only few, if any, genes coding for putative peptidase inhibitors. This may seem perplexing in the light of the fact that these organisms produce large numbers of proteases of different catalytic classes with the genes constituting up to 6% of the total gene count with the average being about 3%. Apparently, however, a unicellular life-style is fully compatible with other mechanisms of regulation of proteolysis and does not require protein inhibitors to control their intracellular and extracellular proteolytic activity. So in prokaryotes occurrence of genes encoding different types of peptidase inhibitors is infrequent and often scattered among phylogenetically distinct orders or even phyla of microbiota. Genes encoding proteins homologous to alpha-2-macroglobulin (family I39), serine carboxypeptidase Y inhibitor (family I51), alpha-1-peptidase inhibitor (family I4) and ecotin (family I11) are the most frequently represented in Bacteria. Although several of these gene products were shown to possess inhibitory activity, with an exception of ecotin and staphostatins, the biological function of microbial inhibitors is unclear. In this review we present distribution of protein inhibitors from different families among prokaryotes, describe their mode of action and hypothesize on their role in microbial physiology and interactions with hosts and environment.     

'Species' of peptidases

A good system for the naming and classification of peptidases can contribute much to the study of these enzymes. Having already described the building of families and clans in the MEROPS system, we here focus on the lowest level in the hierarchy, in which the huge number of individual peptidase proteins are assigned to a lesser number of what we term 'species' of peptidases. Just over 2000 peptidase species are recognised today, but we estimate that 25 000 will one day be known. Each species is built around a peptidase protein that has been adequately characterised. The cluster of peptidase proteins that represent the single species is then assembled primarily by analysis of a sequence 'tree' for the family. Each peptidase species is given a systematic identifier and a summary page of data regarding it is assembled. Because the characterisation of new peptidases lags far behind the sequencing, the majority of peptidase proteins are so far known only as amino acid sequences and cannot yet be assigned to species. We suggest that new forms of analysis of the sequences of the unassigned peptidases may give early indications of how they will cluster into the new species of the future.     

Inhibitory activity against papain, a CA1 cysteine peptidase, in Saccharomycetaceae

A search for new biological sources of cysteine peptidase inhibitors has not only an academic aspect but is of great importance in medicine and biotechnology. The activity of CA1 peptidases can be inhibited by proteins of nine structurally different families. Although these inhibitors are widespread in nature, there is little information on them in yeast and in the kingdom of fungi overall. To gain insight into the endogenous inhibitors of CA1 cysteine peptidases in unicellular fungi, we initiated a study of the extra- and intracellular antipapain activity in yeast. We report here, for the first time, an analysis of the inhibitory activity against papain in the culture medium and the cell-free extract of 16 yeast strains belonging to the Saccharomycetaceae family. The existence of the antipapain activity, likely from protein inhibitors, in all the tested yeast strains has been demonstrated.     

Further characterization of a neurotensin-degrading neutral metalloendopeptidase from rat brain

A peptidase inactivating neurotensin at the Pro¹⁰-Tyr¹¹ peptidyl bond, leading to the biologically inactive fragments neurotensin_1–10 and neurotensin_11–13 was purified from rat brain homogenate. The peptidase was characterized as a 70 kDa monomer and could be classified as a metaliopeptidase with respect to its sensitivity to o-phenanthroline, EDTA and divalent cations. The enzyme was also strongly inhibited by dithiothreitol but appeared totally insensitive to thiol-blocking agents, acidic and serine protease inhibitors. Experiments performed with a series of highly specific peptidase inhibitors clearly indicated that the peptidase was a novel enzyme distinct from previously purified cerebral peptidases. The enzyme displayed a rather high affinity for neurotensin (Km = 2.3 itM). Studies on its specificity indicated that: (i) neurotensin_9–13 was the shortest neurotensin fragment with full inhibitory potency of [³H]neurotensin degradation. Shortening the C-terminal end of the neurotensin molecule progressively led to inactive analogs; (ii) the peptidase exhibited a strong stereospecificity towards the residues in positions 8, 9 and 11. By contrast, neither introduction of a steric hindrance in position 11 nor amidation of the C-terminal end of the neurotensin molecule affected the ability of the corresponding analog to inhibit [³H]neurotensin degradation; (iii) Pro-Phe was the most potent dipeptide to compete for [³H]neurotensin degradation; (iv) the peptidase could not be described as an exclusive “neurotensinase” activity since, in addition to the neurotensin natural analogs (neuromedin N and xenopsin), non related natural peptides such as angiotensins I and II, dynorphins 1–8 and 1–13, atriopeptin III and bradykinin potently inhibited [³H]neurotensin degradation. Most of these peptides behaved as substrates for the enzyme.     

Cysteine digestive peptidases function as post-glutamine cleaving enzymes in tenebrionid stored-product pests

The major storage proteins in cereals, prolamins, have an abundance of the amino acids glutamine and proline. Storage pests need specific digestive enzymes to efficiently hydrolyze these storage proteins. Therefore, post-glutamine cleaving peptidases (PGP) were isolated from the midgut of the stored-product pest, Tenebrio molitor (yellow mealworm). Three distinct PGP activities were found in the anterior and posterior midgut using the highly-specific chromogenic peptide substrate N-benzyloxycarbonyl-L-Ala-L-Ala-L-Gln p-nitroanilide. PGP peptidases were characterized according to gel elution times, activity profiles in buffers of different pH, electrophoretic mobility under native conditions, and inhibitor sensitivity. The results indicate that PGP activity is due to cysteine and not serine chymotrypsin-like peptidases from the T. molitor larvae midgut. We propose that the evolutionary conservation of cysteine peptidases in the complement of digestive peptidases of tenebrionid stored-product beetles is due not only to the adaptation of insects to plants rich in serine peptidase inhibitors, but also to accommodate the need to efficiently cleave major dietary proteins rich in glutamine.     

Gene expression and activity analysis of the first thermophilic U32 peptidase

Peptidase family U32 is one of the few whose catalytic type and structure has not yet been described. It is generally accepted that U32 peptidases represent putative collagenases and contribute to the pathogenicity of some bacteria. Meanwhile, U32 peptidases are also found in nonpathogenic bacteria including thermophiles and hyperthermophiles. Here we report cloning of the U32.002 peptidase gene from thermophilic Geobacillus thermoleovorans DSM 15325 and demonstrate expression and characterization of the recombinant protein. It has been determined that U32.002 peptidase is constitutively expressed in the cells of thermophilic G. thermoleovorans DSM 15325. The recombinant oligomeric enzyme showed its activity only against heat-treated collagen. It was unable to degrade albumin, casein, elastin, gelatine and keratin. In contrast to this, the monomeric recombinant protein showed no activity at all. This paper is the first report about the thermophilic U32 peptidase. As the thermophilic bacteria are non-pathogenic, the role of constitutively expressed extracellular collagenolytic U32 peptidase in these bacteria is unclear.     

Cholinesterases Display Genuine Arylacylamidase Activity but Are Totally Devoid of Intrinsic Peptidase Activities

Abstract: The purpose of this article was to evaluate the intrinsic character of arylacylamidase and peptidase activities that are often detected along with cholinesterase activities. Various pools of commercial or affinity-purified acetylcholinesterases (AChEs) were examined. Affinity-purified AChE displays esterase- and amidase-specific activities that are similarly enriched when compared with commercial AChE. By contrast, commercial AChE exhibits much higher tryptic-like and carboxypeptidase-specific activities than the affinity-purified enzyme. The parallel enrichment in esterase and arylacylamidase suggests that these two activities are copurified, whereas peptidases do not seem to behave similarly. We show that trypsinolysis or spontaneous degradation of affinity-purified AChE leads to the conversion of the 75-kDa monomer protein into two fragments of 50 and 25 kDa after sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. However, these modifications are without effect on the esterase, arylacylamidase, and peptidase activities. This clearly shows that AChE does not behave as a zymogen of peptidases that would have been activated on autolysis of AChE. Immunoprecipitation of AChEs with a purified monoclonal antibody directed toward electric eel AChE totally separated the esterase and arylacylamidase activities (pellet) from peptidase activities (supernatant). The immunoprecipitated AChEs could be dissociated from the interaction with IgGs. These resolubilized AChE preparations have kept the same percentage of initial esterase and arylacylamidase activities but were totally devoid of peptidase activities. These data clearly indicate that commercial and affinity-purified AChEs from Electrophorus electricus bear an intrinsic arylacylamidase activity but that the peptidase activity detected in these preparations is not an integral property of the AChE molecule and most probably represents a contaminating activity. It appears therefore unlikely that AChE may participate to the processing of the β-amyloid protein precursor (β-APP) leading to the secretion of protease nexin II and therefore acts as an APP secretase, as was recently suggested. By a similar approach, we established that human butyrylcholinesterase recovered after immunoprecipitation retained its esterase activity but was no longer able to act as a peptidase.     

The MEROPS database as a protease information system

Peptidases (often termed proteases) are of great relevance to biology, medicine, and biotechnology. This practical importance creates a need for an integrated source of information about peptidases. In the MEROPS database (www.merops.ac.uk), peptidases are classified by structural similarities in the parts of the molecules responsible for their enzymatic activity. They are grouped into families on the basis of amino acid sequence homology, and the families are assembled into clans in light of evidence that they share common ancestry. The evidence for clan-level relationships usually comes from similarities in tertiary structure, but we suggest that secondary structure profiles may also be useful in the future. The classification forms a framework around which a wealth of supplementary information about the peptidases is organized. This includes images of three-dimensional structures, alignments of matching human and mouse ESTs, comments on biomedical relevance, human and other gene symbols, and literature references linked to PubMed. For each family, there is an amino acid sequence alignment and a dendrogram. There is a list of all peptidases known from each of over 1000 species, together with summary data for the distributions of the families and clans throughout the major groups of organisms. A set of online searches provides access to information about the location of peptidases on human chromosomes and peptidase substrate specificity.     

Evolution of the Thermopsin Peptidase Family (A5)

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.     

Cysteine peptidases in the tomato trypanosomatid Phytomonas serpens: influence of growth conditions, similarities with cruzipain and secretion to the extracellular environment

We have characterized the cysteine peptidase production by Phytomonas serpens, a tomato trypanosomatid. The parasites were cultivated in four distinct media, since growth conditions could modulate the synthesis of bioactive molecules. The proteolytic profile has not changed qualitatively regardless the media, showing two peptidases of 38 and 40 kDa; however, few quantitative changes were observed including a drastic reduction (around 70%) on the 40 and 38 kDa peptidase activities when parasites were grown in yeast extract and liver infusion trypticase medium, respectively, in comparison with parasites cultured in Warren medium. The time-span of growth did not significantly alter the protein and peptidase expression. The proteolytic activities were blocked by classical cysteine peptidase inhibitors (E-64, leupeptin, and cystatin), being more active at pH 5.0 and showing complete dependence to reducing agents (dithiothreitol and l-cysteine) for full activity. The cysteine peptidases were able to hydrolyze several proteinaceous substrates, including salivary gland proteins from Oncopeltus fasciatus, suggesting broad substrate utilization. By means of agglutination, fluorescence microscopy, flow cytometry and Western blotting analyses we showed that both cysteine peptidases produced by P. serpens share common epitopes with cruzipain, the major cysteine peptidase of Trypanosoma cruzi. Moreover, our data suggest that the 40 kDa cysteine peptidase was located at the P. serpens cell surface, attached to membrane domains via a glycosylphosphatidylinositol anchor. The 40 kDa peptidase was also detected in the cell-free culture supernatant, in an active form, which suggests secretion of this peptidase to the extracellular environment.     

Dissection of key determinants of cleavage activity in signal peptidase III (SPaseIII) PibD

In Archaea, type IV prepilins and prearchaellins are processed by designated signal peptidase III (SPaseIII) prior to their incorporation into pili and the archaellum, respectively. These peptidases belong to the family of integral membrane aspartic acid proteases that contain two essential aspartate residues of which the second aspartate is located in a conserved GxGD motif. To this group also bacterial type IV prepilin peptidases, Alzheimer disease-related secretases, signal peptide peptidases and signal peptide peptidase-like proteases in humans belong. Here we have performed detailed in vivo analyses to understand the cleavage activity of PibD, SPaseIII from the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. Using an already established in vivo heterologous system cleavage assay, we could successfully identify the key amino acid residues essential for catalysis of PibD. Furthermore, in trans complementation of a pibD S. acidocaldarius deletion mutant with PibD variants having substituted key amino acids has consolidated our observations of the importance of these residues in catalysis. Based on our data, we propose to re-define class III peptidases/type IV prepilin/prearchaellin peptidases as GxHyD group (rather than GxGD) of proteases [Hy-hydrophobic amino acid].