The chemistry and enzymology of the type I signal peptidases

The discovery that proteins exported from the cytoplasm are typically synthesized as larger precursors with cleavable signal peptides has focused interest on the peptidases that remove the signal peptides. Here, we review the membrane-bound peptidases dedicated to the processing of protein precursors that are found in the plasma membrane of prokaryotes and the endoplasmic reticulum, the mitochondrial inner membrane, and the chloroplast thylakoidal membrane of eukaryotes. These peptidases are termed type I signal (or leader) peptidases. They share the unusual feature of being resistant to the general inhibitors of the four well-characterized peptidase classes. The eukaryotic and prokaryotic signal peptidases appear to belong to a single peptidase family. This review emphasizes the evolutionary concepts, current knowledge of the catalytic mechanism, and substrate specificity requirements of the signal peptidases.     

Peptidases in the kidney and urine of rats after castration

Summary The localization of various peptidases in the renal section of the rat was investigated histochemically, and their activities were determined fluorometrically in renal homogenate. The membrane-bound peptidases aminopeptidase A (APA), aminopeptidase M (APM), -glutamyl-transferase (-GT), dipeptidylpeptidase IV (DAP IV), and the lysosomal dipeptidyl peptidases I (DAP I) and II (DAP II) were investigated in male and female (estrus) rats both before and 30 days after castration. In addition, protein excretion and APA, APM, DAP I and DAP IV activities were measured in the urine of these animals. Histochemically, the membrane-bound peptidases are demonstrable mainly in the brush borders of the proximal tubules. In addition, APA and DAP IV are found in the glomeruli, -GT and DAP IV in the thin descending limbs of the loops of Henle, and -GT in the basal labyrinth of the S₂ and S₃ segments. The lysosomal peptidases are most concentrated in the S₁ and S₂ segments of the proximal tubule, in the distal tubule, and in certain cells of the connecting tubule and collecting duct, where they are contained in lysosomes of varying size. Sex differences and castration effects are demonstrable both histochemically and biochemically for the investigated peptidases. Histochemically these effects are most pronounced in the S₃ segments for the membrane-bound peptidases, and in the lysosomes of the proximal tubule for the lysosomal peptidases. Biochemical tests in controls show significantly higher lysosomal peptidase activities in the renal homogenate of females than of males. After castration the lysosomal peptidase activities in males increase, approaching those of females. This appears to have bearing on the sex-dependent proteinuria in rats, for lysosomal peptidases and proteinases are particularly important in the degradation of filtered proteins that are reabsorbed in the proximal tubule. In females high lysosomal peptidase activities correlate with a low proteinuria, while males demonstrate lower lysosomal peptidase activities and a significantly higher proteinuria than females. After castration, the lysosomal peptidase activities and proteinuria in males approach those in females. Renal peptidases are also excreted in the urine, again with sex differences, and so these excreted peptidases contribute to the proteinuria in rats.Supported by the Deutsche Forschungsgemeinschaft (SFB 105)     

An electrophoretic investigation of the cytosolic di- and tripeptidases of fish: Molecular weights,substrate specificities,and tissue and phylogenetic distributions

The cytosolic di- and tripeptidases of fish were studied in an electrophoretic phylogenetic survey that included elasmobranchs, a holostean, and teleosts. Antisera against four of the peptidases from tuna were raised in rabbits and used to establish homologies between the peptidases of tuna and other fish and between piscine PEP A, B, and S and corresponding enzymes of the higher vertebrates. Substrate specificities, tissue distributions, and electrophoretic mobilities were conserved during the evolution of the fish. The nomenclature for mammalian peptidases was extended to the piscine enzymes, but with reservations in the case of PEP C and E. Using this nomenclature, the six major, genetically independent peptidases are PEP A, B, C, D, E, and S. Within the fish substrate specificity was a reliable indicator of identity. The peptidases of vertebrates thus consist of a widely distributed group of enzymes with constant characteristics. Much of the confusion in the field is probably due to variable and poorly defined species-specific enzymes.     

Synthesis and physical characterization of a P1 arginine combinatorial library,and its application to the determination of the substrate specificity of serine peptidases

Serine peptidases are a large, well-studied, and medically important class of peptidases. Despite the attention these enzymes have received, details concerning the substrate specificity of even some of the best known enzymes in this class are lacking. One approach to rapidly characterizing substrate specificity for peptidases is the use of positional scanning combinatorial substrate libraries. We recently synthesized such a library for enzymes with a preference for arginine at P1 and demonstrated the use of this library with thrombin (Edwards et al. Bioorg. Med. Chem. Lett. 2000, 10, 2291). In the present work, we extend these studies by demonstrating good agreement between the theroretical and measured content of portions of this library and by showing that the library permits rapid characterization of the substrate specificity of additional SA clan serine peptidases including factor Xa, tryptase, and trypsin. These results were consistent both with cleavage sites in natural substrates and cleavage of commercially available synthetic substrates. We also demonstrate that pH or salt concentration have a quantitative effect on the rate of cleavage of the pooled library substrates but that correct prediction of optimal substrates for the enzymes studied appeared to be independent of these parameters. These studies provide new substrate specificity data on an important class of peptidases and are the first to provide physical characterization of a peptidase substrate library.     

Selective chromogenic and fluorogenic peptide substrates for the assay of cysteine peptidases in complex mixtures

This study describes the design, synthesis, and use of selective peptide substrates for cysteine peptidases of the C1 papain family, important in many biological processes. The structure of the newly synthesized substrates is Glp-Xaa-Ala-Y (where Glp = pyroglutamyl; Xaa = Phe or Val; and Y = pNA [p-nitroanilide], AMC [4-amino-7-methylcoumaride], or AFC [4-amino-7-trifluoromethyl-coumaride]). Substrates were synthesized enzymatically to guarantee selectivity of the reaction and optical purity of the target compounds, simplifying the scheme of synthesis and isolation of products. The hydrolysis of the synthesized substrates was evaluated by C1 cysteine peptidases from different organisms and with different functions, including plant enzymes papain, bromelain, ficin, and mammalian lysosomal cathepsins B and L. The new substrates were selective for C1 cysteine peptidases and were not hydrolyzed by serine, aspartic, or metallo peptidases. We demonstrated an application of the selectivity of the synthesized substrates during the chromatographic separation of a multicomponent set of digestive peptidases from a beetle, Tenebrio molitor. Used in combination with the cysteine peptidase inhibitor E-64, these substrates were able to differentiate cysteine peptidases from peptidases of other classes in midgut extracts from T. molitor larvae and larvae of the genus Tribolium; thus, they are useful in the analysis of complex mixtures containing peptidases from different classes.     

Peptidases A,B, C,D and S in the American mink: polymorphism and chromosome localization

Summary An electrophoretic analysis of peptidases was carried out in a population of American mink. Based on substrate and tissue specificities, as well as subunit composition, homologies were established between mink peptidases A, B, C, D and S and human peptidases. Polymorphism for peptidases B and D was demonstrated for minks of three coat colour types. Breeding data indicated that the peptidase variations are under the control of allele pairs at distinct autosomal loci designated as PEPB and PEPD, respectively. Using a panel of American mink-Chinese hamster hybrid clones, the gene for PEPB was assigned to mink chromosome 9.     

Enzymic inactivation of neurotensin by hypothalamic and brain extracts of the rat.

A sensitive and specific radioimmunoassay has been developed to study inactivation of neurotensin by hypothalamic and brain peptidases. Degrading activity of peptidases from both hypothalamus and brain seems to have similar activity. These peptidases are temperature- and time- dependent. Brain and hypothalamic enzymes of particulate fractions can be differentiated on the basis of the pH effects; brain peptidase(s) has (have) maximal activity at pH 7.4 and hypothalamic peptidase(s) displaying a maximal activity at pH 5.8. Kidneys and liver extracts contain enzyme(s) degrading neurotensin.     

Prediction of peptidase category based on functional domain composition

Peptidases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, aging, and death of all organisms. These regulatory roles include activation, synthesis and turnover of proteins. In the proteomics era, computational methods to identify peptidases and catalog the peptidases into six different major classes-aspartic peptidases, cysteine peptidases, glutamic peptidases, metallo peptidases, serine peptidases and threonine peptidases can give an instant glance at the biological functions of a newly identified protein. In this contribution, by combining the nearest neighbor algorithm and the functional domain composition, we introduce both an automatic peptidase identifier and an automatic peptidase classier. The successful identification and classification rates are 93.7% and 96.5% for our peptidase identifier and peptidase classifier, respectively. Free online peptidase identifier and peptidase classifier are provided on our Web page http://pcal.biosino.org/protease_classification.html.     

Trypsin-like proteins of the fungi as possible markers of pathogenicity

Sequences of peptidases with conserved motifs around the active site residues that are characteristic of trypsins (similar to trypsin peptidases, STP) were obtained from publicly-available fungal genomes and related databases. Among the 75 fungal genomes, 29 species of parasitic Ascomycota contained genes encoding STP and their homologs. Searches of non-redundant protein sequences, patented protein sequences, and expressed sequence tags resulted in another 18 STP sequences in 10 fungal species from Ascomycota, Basidiomycota, and Zygomycota. A comparison of fungi species containing STP sequences revealed that almost all are pathogens of plants, animals or fungi. A comparison of the primary structure of homologous proteins, including the residues responsible for substrate binding and specificity of the enzyme, revealed three groups of homologous sequences, all presumably from S1 family: trypsin-like peptidases, chymotrypsin-like peptidases and serine peptidases with unknown substrate specificity. Homologs that are presumably functionally inactive were predicted in all groups. The results in general support the hypothesis that the expression of trypsin-like peptidases in fungi represents a marker of fungal phytopathogenicity. A phylogenetic tree was constructed using peptidase and homolog amino acid sequences, demonstrating that all have noticeable differences and almost immediately deviate from the common root. Therefore, we conclude that the changes that occurred in STP of pathogenic fungi in the course of evolution represent specific adaptations to proteins of their respective hosts, and mutations in peptidase genes are important components of life-style changes and taxonomic divergence.     

Identification and characterization of a dense cluster of placenta-specific cysteine peptidase genes and related genes on mouse chromosome 13

Genes encoding novel murine cysteine peptidases of the papain family C1A and related genes were cloned and mapped to mouse chromosome 13, colocalizing with the previously assigned cathepsin J gene. We constructed a <460-kb phage artificial chromosome (PAC) contig and characterized a dense cluster comprising eight C1A cysteine peptidase genes, cathepsins J, M, Q, R, -1, -2, -3, and -6; three pseudogenes of cathepsins M, -1, and -2; and four genes encoding putative cysteine peptidase inhibitors related to the proregion of C1A peptidases (trophoblast-specific proteins alpha and beta and cytotoxic T-lymphocyte-associated proteins 2alpha and -beta). Because of sequence homologies of 61.9-72.0% between cathepsin J and the other seven putative cysteine peptidases of the cluster, these peptidases are classified as "cathepsin J-like". The absence of cathepsin J-like peptidases and related genes from the human genome suggests that the cathepsin J cluster arose by partial and complete gene duplication events after the divergence of primate and rodent lineages. The expression of cathepsin J-like peptidases and related genes in the cluster is restricted to the placenta only. Clustered genes are induced at specific time points, and their expression increases toward the end of gestation. The specific expression pattern and high expression level suggest an essential role of cathepsin J-like peptidases and related genes in formation and development of the murine placenta.     

Extracellular peptidases of insect-associated fungi and their possible use in biological control programs and as pathogenicity markers

This review deals with characteristics of peptidases of fungi whose life cycles are associated with insects to varying degrees. The review examines the characteristic features of the extracellular peptidases of entomopathogenic fungi, the dependence of the specificity of these peptidases on the ecological characteristics of the fungi, and the role of peptidases in the development of the pathogenesis. Data on the properties and physiological role of hydrolytic enzymes of symbiotic fungi in “fungal gardens” are also considered in detail. For the development of representations about mechanisms of control over populations of insect pests, special attention is given to analysis of possibilities of genetic engineering for the creation of entomopathogens with enhanced virulence. Clarification of the role of fungi and their secreted enzymes and careful environmental studies are still required to explain their significance in the composition of the biota and to ensure widespread adoption of these organisms as effective biological control agents. The systematization and comparative analysis of the existing data on extracellular peptidases of insect-associated fungi will help in the planning of further work and the search for markers of pathogenesis and symbiosis.     

Genetically determined polymorphism of two peptidases in the Tuco-tuco (Ctenomys talarum talarum)

Six distinct peptidases have been found to occur in the erythrocytes of the Tuco-tuco. The substrate specificities suggest that these enzymes are homologous with the peptidases previously described in man and the mouse. Common polymorphisms of two of this group of enzymes are described.     

Cloning and sequence analysis of a signal peptidase I from the thermophilic cyanobacterium Phormidium laminosum

Type I signal peptidases are a widespread family of enzymes which remove the presequences from proteins translocated across cell membranes, including thylakoid and cytoplasmic membranes of cyanobacteria and thylakoid membranes of chloroplasts. We have cloned and sequenced a signal peptidase gene from the thermophilic cyanobacterium Phormidium laminosum which is believed to encode an enzyme common to both membrane systems. The deduced amino acid sequence is 203 residues long and although the overall similarity among signal peptidases is rather low there are a number of identifiable conserved regions present. The P. laminosum enzyme is predicted to have a single transmembrane domain, in contrast to other Gram-negative bacterial sequences, but similar to other type I signal peptidases.     

Regulatory role of membrane-bound peptidases in the progression of gynecologic malignancies

Membrane-bound peptidases play a key role in the control of growth, differentiation, and signal transduction of many cellular systems by degrading bioactive peptides. Thus, abnormal changes in their expression pattern and catalytic function result in altered peptide activation, which contributes to neoplastic transformation or progression. In this review, we describe our recent findings along with work from other groups on the expression and biological functions of membrane-bound peptidases in cancer, focusing on the regulatory roles of three peptidases, aminopeptidase A (APA), neutral endopeptidase (NEP) and placental leucine aminopeptidase (P-LAP), in the progression of gynecologic malignancies. APA, NEP and P-LAP are differentially expressed and localized in various gynecologic malignancies including cervical cancer, endometrial cancer, ovarian cancer and choriocarcinoma in a tumor-type specific pattern. The expression levels are up- or down-regulated depending on histological grade or disease progression. These peptidases play regulatory roles in tumor cell proliferation, invasion or angiogenesis via degradation/inactivation of target peptides such as angiotensin II, endothelin-1 and oxytocin, which act on cancer cells as stimulatory or inhibitory factors. Thus, membrane-bound peptidases may become not only a new diagnostic/prognostic marker, but also a novel molecular target for the treatment of gynecologic malignancies.     

Digestive proteolysis in the Colorado potato beetle,Leptinotarsa decemlineata: Activity-based profiling and imaging of a multipeptidase network

The Colorado potato beetle (CPB), Leptinotarsa decemlineata, is a major pest of potato plants, and its digestive system is a promising target for development of pest control strategies. This work focuses on functional proteomic analysis of the digestive proteolytic enzymes expressed in the CPB gut. We identified a set of peptidases using imaging with specific activity-based probes and activity profiling with selective substrates and inhibitors. The secreted luminal peptidases were classified as: (i) endopeptidases of cathepsin D, cathepsin L, and trypsin types and (ii) exopeptidases with aminopeptidase (cathepsin H), carboxypeptidase (serine carboxypeptidase, prolyl carboxypeptidase), and carboxydipeptidase (cathepsin B) activities. The proteolytic arsenal also includes non-luminal peptidases with prolyl oligopeptidase and metalloaminopeptidase activities. Our results indicate that the CPB gut employs a multienzyme network of peptidases with complementary specificities to efficiently degrade ingested proteins. This proteolytic system functions in both CPB larvae and adults and is controlled mainly by cysteine and aspartic peptidases and supported by serine and metallopeptidases. The component enzymes identified here are potential targets for inhibitors with tailored specificities that could be engineered into potato plants to confer resistance to CPB.     

Dipeptidyl peptidases 8 and 9: specificity and molecular characterization compared with dipeptidyl peptidase IV

Dipeptidyl peptidases 8 and 9 have been identified as gene members of the S9b family of dipeptidyl peptidases. In the present paper, we report the characterization of recombinant dipeptidyl peptidases 8 and 9 using the baculovirus expression system. We have found that only the full-length variants of the two proteins can be expressed as active peptidases, which are 882 and 892 amino acids in length for dipeptidyl peptidase 8 and 9 respectively. We show further that the purified proteins are active dimers and that they show similar Michaelis-Menten kinetics and substrate specificity. Both cleave the peptide hormones glucagon-like peptide-1, glucagon-like peptide-2, neuropeptide Y and peptide YY with marked kinetic differences compared with dipeptidyl peptidase IV. Inhibition of dipeptidyl peptidases IV, 8 and 9 using the well-known dipeptidyl peptidase IV inhibitor valine pyrrolidide resulted in similar K(i) values, indicating that this inhibitor is non-selective for any of the three dipeptidyl peptidases.     

KLKs促进肿瘤增殖、迁移与侵袭的分子机制

组织激肽释放酶家族（kallikrein-related peptidases,KLKs）是一类具有胰蛋白酶或胰凝乳蛋白酶活性的分泌型丝氨酸蛋白酶,由15个成员（KLK1～15）组成。虽然发现较早,但关于其在肿瘤的发生与发展中所扮演的角色研究相对较少。KLKs作为肿瘤标志物在临床上的应用也有相应报道,如KLK3(PSA)作为前列腺特异性抗原用于前列腺癌的筛查。近年研究发现,KLKs家族在肿瘤进程中发挥重要作用,被认为是调节肿瘤细胞增殖、迁移和侵袭的关键因素。本文概述了在肿瘤进展过程中KLKs作用机制的最新进展,为其作为抗肿瘤治疗靶点的研究提供理论基础。     

Influence of various concentrations of phenol and its derivatives on the activity of fish intestinal peptidases

The effects of phenol and its derivatives (4-chlorophenol, 4-nirophenol and 2,4-dinitrophenol) on the activity of peptidases in five species of fish differing in feeding modes have been studied. The power of the effects depends on the fish species and localization of the enzyme (mucosa or chyme). As a rule, in the in vitro conditions the phenols in concentrations of 0.06?0.5 μM/L considerably decreases activities of the intestinal peptidases in bream; silver bream; and, especially, in pike. In some cases, phenol and its derivatives induce an inconsiderable increase in peptidase activities. In zander and perch, in fact, no changes in the enzymatic activity under impact of phenols are observed. It is suggested that the effect of phenol and its derivatives depends to a high extent on the species specificity of peptidases: in the fish of fam. Percidae, the enzymes are relatively tolerant; in fam. Cyprinidae and Esocidae, they are sensitive to the studied toxicants.     

Two thimet oligopeptidase-like Pz peptidases produced by a collagen-degrading thermophile, Geobacillus collagenovorans MO-1

A collagen-degrading thermophile, Geobacillus collagenovorans MO-1, was found to produce two metallopeptidases that hydrolyze the synthetic substrate 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (Pz-PLGPR), containing the collagen-specific sequence -Gly-Pro-X-. The peptidases, named Pz peptidases A and B, were purified to homogeneity and confirmed to hydrolyze collagen-derived oligopeptides but not collagen itself, indicating that Pz peptidases A and B contribute to collagen degradation in collaboration with a collagenolytic protease in G. collagenovorans MO-1. There were many similarities between Pz peptidases A and B in their catalytic properties; however, they had different molecular masses and shared no antigenic groups against the respective antibodies. Their primary structures clarified from the cloned genes showed lower identity (22%). From homology analysis for proteolytic enzymes in the database, the two Pz peptidases belong to the M3B family. In addition, Pz peptidases A and B shared high identities of over 70% with unassigned peptidases and oligopeptidase F-like peptidases of the M3B family, respectively. Those homologue proteins are putative in the genome database but form two distinct segments, including Pz peptidases A and B, in the phylogenic tree. Mammalian thimet oligopeptidases, which were previously thought to participate in collagen degradation and share catalytic identities with Pz peptidases, were found to have lower identities in the overall primary sequence with Pz peptidases A and B but a significant resemblance in the vicinity of the catalytic site.