Structure and functions of bacterial proteinase precursors

The data on the precursors of bacterial proteases were generalized. The structure and special features of processing of the precursors of bacillary subtilisins, the alpha-lytic protease from Lysobacter enzymogenes and the related chymotrypsin-like proteases from Streptomyces griseus, and the metalloproteases from bacilli and Pseudomonas aeruginosa were discussed. The approaches to producing the precursors and the protease propeptides and to in vitro characterizing them were particularly analyzed. The following physiological functions of the propeptides within the protease precursors were considered probable: (a) inhibition of the proteases to protect the host cells from the proteolytic damage; (b) participation in the folding of the mature enzyme; and (c) providing for the protease interaction with the bacterial cell surveillance mechanisms, including protease translocation through the cell wall.     

Protease propeptide structures,mechanisms of activation,and functions

Abstract

Proteases are a diverse group of hydrolytic enzymes, ranging from single-domain catalytic molecules to sophisticated multi-functional macromolecules. Human proteases are divided into five mechanistic classes: aspartate, cysteine, metallo, serine and threonine proteases, based on the catalytic mechanism of hydrolysis. As a protective mechanism against uncontrolled proteolysis, proteases are often produced and secreted as inactive precursors, called zymogens, containing inhibitory N-terminal propeptides. Protease propeptide structures vary considerably in length, ranging from dipeptides and propeptides of about 10 amino acids to complex multifunctional prodomains with hundreds of residues. Interestingly, sequence analysis of the different protease domains has demonstrated that propeptide sequences present higher heterogeneity compared with their catalytic domains. Therefore, we suggest that protease inhibition targeting propeptides might be more specific and have less off-target effects than classical inhibitors. The roles of propeptides, besides keeping protease latency, include correct folding of proteases, compartmentalization, liganding, and functional modulation. Changes in the propeptide sequence, thus, have a tremendous impact on the cognate enzymes. Small modifications of the propeptide sequences modulate the activity of the enzymes, which may be useful as a therapeutic strategy. This review provides an overview of known human proteases, with a focus on the role of their propeptides. We review propeptide functions, activation mechanisms, and possible therapeutic applications.     

In vivo inhibition of glutamine synthetase induces sporulation in a protease deficient asporogenous mutant of Bacillus polymyxa

In vivo inhibition of glutamine synthetase (GS) by l-methionine sulfoximine induces sporulation in a protease deficient mutant of Bacillus polymyxa. This induction of sporulation is accompanied by derepression of EDTA insensitive proteases(s) which seems to be specific for differentiation. Some amino acid analogues derepress proteolytic activity without inducing sporulation, but these proteases are sensitive to metal chelators like those in the vegetative cells. When the proteolytic activity is restored, the mutant cells, which are smaller than the parental strain, regain their normal size.Abbreviations GS glutamine synthetase - GYS glucose-yeast extract-salts - MSO l-methionine sulfoximine - Pr protease deficient mutant - DON 6-diazo-5-oxo-l-norleucine - EDTA ethylene-diaminetetraacetic acid - EGTA ethylene glycol-bis (-aminoethyl ether) N,N,N,N-tetraacetic acid - Tris tris-(hydroxymethyl)-aminomethane     

Inhibition of Acid Proteases by a Pepsin Inhibitor (S-PI)

S–PI inhibited various acid proteases including pepsin, Rhodotorula glutinis acid protease and Cladosporium acid protease, but the rate of inhibition was different for each acid protease.

S–PI made an equimolar complex with these acid proteases. A part of the enzyme-S–PI complex dissociated in the reaction mixture and showed proteolytic activity. The specific activity of the enzyme-S–PI complex depended on the concentration of the complex in the reaction mixture. Compared with native (S–PI free) enzyme, each of the enzyme-S–PI complex showed 50% activity at the following concentrations, pepsin; 7.5×10^?10M, Rh. glutinis acid protease; 1.8×10^?7M, Cladosporium acid protease; 3.0×10^?6M.

These acid proteases were stabilized from heat or acid denaturation by making the enzyme-S–PI complex. S–PI protected the modification of these acid proteases by diazoacetyl-DL-norleucine methyl ester.

Binding between these acid proteases and S–PI dissociated at around neutral pH. S–PI was separated from enzyme-S–PI complex by dialysis at pH 7.5. In this case, pepsin underwent denaturation, while denaturations of Rh. glutinis acid protease and Cladosporium acid protease were slight. Rh. glutinis acid protease and Cladosporium acid protease were recovered from enzyme-S–PI complex by DEAE cellulose column chromatography as a native form.     

Synthesis and release of proteases byBacteroides fragilis

Protease production byBacteroides fragilis ATCC 25285 was determined in batch and continuous cultures. During exponential growth in batch culture, the majority of proteolysis was cell associated. However, as the bacteria reached stationary phase, most of the intracellular proteases were released into the culture medium. Measurements of alkaline phosphatase and -galactosidase, which are respectively periplasmic and cytoplasmic marker enzymes inB. fragilis, showed that secretion of proteases in the stationary phase was a discrete event and was not associated with a general release of cytoplasmic contents. When the bacterium was grown in continuous culture, cell-associated protease activity increased concomitantly with dilution rate (D=0.03–0.23/h). The ratio of intracellular to whole cell protease activity also increased with growth rate (11 at D=0.03/h; 11.7 at D=0.23/h). Extracellular protease activity was detected only in trace amounts in continuous cultures at the lowest dilution rate. Determinations of the distribution of extracellular protease activity in batch culture after 48 h incubation showed that the majority of proteolysis (ca. 90%) was soluble. Nevertheless, a proportion was associated with particulate fractions, which had high specific activities.     

Bradykinin Generation Triggered by Pseudomonas Proteases Facilitates Invasion of the Systemic Circulation by Pseudomonas aeruginosa

To elucidate the mechanism of bacterial exoprotease in promotion of the intravascular dissemination of Pseudomonas aeruginosa, we examined the possible involvement of bradykinin (whose generation is induced by pseudomonal proteases in septic foci) in the invasion by bacteria, and in access of bacterial toxins to systemic blood circulation. P. aeruginosa 621 (PA 621), which produces very little protease, was injected intraperitoneally into mice together with pseudomonal exoproteases (elastase/alkaline protease). Dissemination of bacteria from the peritoneal septic foci to the blood was assessed by counting viable bacteria in the blood and spleen by use of the colony-forming assay. The results showed that pseudomonal proteases markedly enhanced (10- to 100-fold) intravascular dissemination of bacteria in mice. This enhancement was induced not only by pseudomonal proteases but also by bradykinin. More importantly, the increased spread of PA 621 induced by pseudomonal protease and bradykinin was significantly augmented by the addition of kininase inhibitors, indicating the direct involvement of bradykinin in bacterial dissemination. Similarly, bradykinin caused effective dissemination of pseudomonal toxins such as endotoxin (lipopolysaccharide) and exotoxin A when the toxins were injected into the peritoneal cavity with bradykinin. Furthermore, the lethality of the infection with PA 621 was strongly enhanced by pseudomonal proteases given i.p. simultaneously with PA 621. On the basis of these results, it is strongly suggested that pseudomonal proteases as well as bradykinin generated in infectious foci are involved in facilitation of bacterial dissemination in vivo.     

Activation of a CPP32-like protease during L1210 cell apoptosis induced by thiol deprivation

Reduced thiols (e.g., cysteine) are important in the maintenance of lymphocyte cell viability and growth. L1210 monocytic leukaemia cells were known to have a limited ability to uptake cystine, and they require cysteine for cell growth. L1210 cells underwent apoptosis when cultured without thiol-bearing and dithiol-cleaving compounds, adding thiols suppressed the apoptosis and promoted cell growth. A specific inhibitor of interleukin-1 -converting enzyme (ICE)-like and CPP32-like proteases could suppress L1210 cell apoptosis induced by thiol deprivation. The cell lysates of apoptotic L1210 cells exhibited protease activity that could cleave DEVD-AMC, but not YVAD-AMC, and so CPP32-like proteases, but not ICE-like proteases, were activated and participated in apoptosis. The addition of thiols could suppress CPP32-like protease activation. Although the cell death-suppressor bcl-2-family proteins (bcl-2 and bcl-XL) were recently found to suppress the activation of CPP32-like proteases, the expression levels of death-suppressor bcl-2-family proteins did not change when thiols were added. These results suggest that reduced thiols maintain L1210 cell survival by inhibiting the activation of CPP32-like proteases without changing the anti-apoptotic bcl-2-family protein expression.     

A genomic survey of proteases in Aspergilli

Background

Proteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in this genus so far.

Results

We have performed a combined analysis of comparative genomics, proteomics and enzymology tests on seven Aspergillus species grown on wheat bran and sugar beet pulp. Putative proteases were identified by homology search and Pfam domains. These genes were then clusters based on orthology and extracellular proteases were identified by protein subcellular localization prediction. Proteomics was used to identify the secreted enzymes in the cultures, while protease essays with and without inhibitors were performed to determine the overall protease activity per protease class. All this data was then integrated to compare the protease productivities in Aspergilli.

Conclusions

Genomes of Aspergillus species contain a similar proportion of protease encoding genes. According to comparative genomics, proteomics and enzymatic experiments serine proteases make up the largest group in the protease spectrum across the species. In general wheat bran gives higher induction of proteases than sugar beet pulp. Interesting differences of protease activity, extracellular enzyme spectrum composition, protein occurrence and abundance were identified for species. By combining in silico and wet-lab experiments, we present the intriguing variety of protease productivity in Aspergilli.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-523) contains supplementary material, which is available to authorized users.     

Intramembrane Proteolysis by Signal Peptide Peptidases: A Comparative Discussion of GXGD-type Aspartyl Proteases

Intramembrane-cleaving proteases are required for reverse signaling and membrane protein degradation. A major class of these proteases is represented by the GXGD-type aspartyl proteases. GXGD describes a novel signature sequence that distinguishes these proteases from conventional aspartyl proteases. Members of the family of the GXGD-type aspartyl proteases are the Alzheimer disease-related γ-secretase, the signal peptide peptidases and their homologs, and the bacterial type IV prepilin peptidases. We will describe the major biochemical and functional properties of the signal peptide peptidases and their relatives. We then compare these properties with those of γ-secretase and discuss common mechanisms but also point out a number of substantial differences.During the last years, a number of intramembrane-cleaving proteases termed I-CLiPs³ have been identified (1). I-CLiPs are generally involved in regulated intramembrane proteolysis (2). Upon shedding of a large part of the ectodomain of membrane proteins, the remaining membrane-retained stub is cleaved by specialized proteases within the hydrophobic lipid membrane. Generally, this cleavage can have two predominant biological functions: first, signaling via the liberated ICD within the substrate-expressing cell (reverse signaling) (2); and second, degradation of membrane-retained stubs, which are not required for any further biological function (3). I-CLiPs of three protease classes, metalloproteases, serine proteases, and aspartyl proteases, have been discovered so far (see accompanying minireview by Wolfe (44)).Intramembrane-cleaving aspartyl proteases are represented by the class of the GXGD-type proteases (4). These are unconventional aspartyl proteases that, like the conventional aspartyl proteases, utilize two critical aspartyl residues for peptide bond cleavage. However, in contrast to the conventional proteases, the critical aspartyl residues are located within two TMDs (Fig. 1A). Moreover, these aspartyl residues are embedded in active-site motifs that are completely different from those of conventional aspartyl proteases. The class of GXGD-type aspartyl proteases is currently represented by three different protease families, the most prominent of which is the PS family, providing the catalytically active subunit of γ-secretase (Fig. 1A) (4). PS/γ-secretase is the I-CLiP that liberates amyloid β-peptide, the major component of senile plaques in Alzheimer disease patients (5). In addition, the bacterial type IV prepilin peptidases also belong to the class of the GXGD-type proteases (6). Besides these two protease families, two additional subfamilies of related proteases that also belong to the GXGD-type aspartyl protease family have been identified. These include SPP as well as the SPP homologs, the SPP-like (SPPL) proteases (Fig. 1A) (7, 8).Open in a separate windowFIGURE 1.A, schematic representation of SPPL2a/b, a member of the SPP/SPPL family, and PS, the catalytic core of theγ-secretase. Note the opposite topology of the active sites (indicated by arrows) of the two proteases and their substrates, APP for PS and TNFα for SPPL2a/b. B, proteolytic processing of APP and TNFα. Shedding releases the extracellular part of APP (APPs) and TNFα (TNFα soluble). In the case of APP, a C-terminal fragment (APP CTF), and in case of TNFα, an N-terminal fragment (TNFα NTF) are produced. These membrane-bound fragments are substrate to intramembrane cleavage by PS or SPPL2a/b, respectively, releasing small peptides to the extracellular space (Aβ and TNFα C-domain, respectively) and to the cytosol (APP intracellular domain (AICD) and TNFα ICD), respectively). TNFα FL, full-length TNFα.We will first describe the biochemical, functional, and structural properties of SPP family members. By comparison of these properties, we will then identify common mechanisms of intramembrane proteolysis by GXGD-type proteases but also point out some fundamental differences.     

Screening and genetic identification of acidic and neutral protease-producing yeasts strains by 26S rRNA gene sequencing

Protease enzymes (proteases), particularly those produced by microorganisms, play very important roles in industry, due to their diverse applications. Considering the richness of microbial diversity in nature, a good chance always exists that proteases more suitable, with better properties for commercial application, may be discovered while screening novel microorganisms from local environments. In this study, 94 yeasts were isolated from different natural sources collected from the Abha region, Kingdom of Saudi Arabia, to determine extracellular protease production and activity. Among them, 23 isolates (24.46%) showed protease activity using a casein hydrolysis test. Of these, five isolates (21.74%) were selected and identified as the best protease producers by exhibiting the largest clearance zones around colonies. A 26S rRNA gene D1/D2 domain sequence alignment, comparison, and phylogenetic analysis of our study yeasts to published D1/D2 domain rRNA gene sequences from GenBank, identifies the isolates as Rhodotorula mucilaginosa KKU-M12c, Cryptococcus albidus KKU-M13c, Pichia membranifaciens KKU-M18c, Hanseniaspora uvarum KKU-M19c, and Candida californica KKU-M20c. The influence of varying pH (4.0–9.0) on the yield and activity of the proteases was investigated using 0.5% (w/v) casein as a substrate, to detect optimum pH values for yeast extracellular protease production. Enzyme activity was measured using qualitative and quantitative assays. Results show all of the study yeasts secreting protease enzyme at all tested pH levels, with the exception of pH 9.0. This indicates that none of the five yeasts are alkaline protease producers. Maximum protease activity (187 U/mL) was observed in strain H. uvarum KKU-M19c at pH 6.0 (only), indicating that strain KKU-M19c only produces neutral protease. The other four yeast isolates, R. mucilaginosa KKU-M12c, C. albidus KKU-M13c, P. membranifaciens KKU-M18c, and C. californica KKU-M20c, produced both acidic (at pH 4.0) and neutral (at pH 6.0 and 7.0) proteases. Strain C. californica KKU-M20c was found to be the best acidic and neutral protease producer (138 U/mL at pH 4.0, and 185 U/mL at pH 7.0). This is the first report of the discovery and isolation of local, powerful yeasts producing acidic and neutral protease enzymes from the Abha region, Kingdom of Saudi Arabia.     

Intracellular proteolytic activity in developing myxospores of Myxococcus xanthus

1. Cell-free extracts from vegetative cells and developing myxospores of Myxococcus xanthus were found to contain similar amounts of proteolytic activity, approximately 80% of which was due to one or more neutral metal proteases.
2. Sixty per cent of the proteolytic activity was particulate.
3. The specific activity of the proteases was high throughout all stages of myxospore formation and displayed small increases in activity at two stages of development: (1) during cell shortening and (2) immediately following the conversion to spheres. The first peak in activity was apparent in assays conducted at pH 8 or 10 whereas the second peak was obvious only at pH 6.
4. A mutant which develops into myxospores only after a lag of approximately 7–8 h possessed levels of proteases similar to the wild type and displayed a peak in proteolytic activity after a delay of 7–8 h.
5. Low levels of serine protease activity were occasionally detected in both vegetative cells and myxospores; no sulfhydryl proteases were detectable in either cell type.
6. Extracellular proteases accumulated in the medium throughout myxospore development but differed from the intracellular proteases in pH optima and sensitivity to inhibitors.

     

Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance

The HIV protease plays a major role in the life cycle of the virus and has long been a target in antiviral therapy. Resistance of HIV protease to protease inhibitors (PIs) is problematic for the effective treatment of HIV infection. The South African HIV-1 subtype C protease (C-SA PR), which contains eight polymorphisms relative to the consensus HIV-1 subtype B protease, was expressed in Escherichia coli, purified, and crystallized. The crystal structure of the C-SA PR was resolved at 2.7?Å, which is the first crystal structure of a HIV-1 subtype C protease that predominates in Africa. Structural analyses of the C-SA PR in comparison to HIV-1 subtype B proteases indicated that polymorphisms at position 36 of the homodimeric HIV-1 protease may impact on the stability of the hinge region of the protease, and hence the dynamics of the flap region. Molecular dynamics simulations showed that the flap region of the C-SA PR displays a wider range of movements over time as compared to the subtype B proteases. Reduced stability in the hinge region resulting from the absent E35-R57 salt bridge in the C-SA PR, most likely contributes to the increased flexibility of the flaps which may be associated with reduced susceptibility to PIs.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:36     

A continuous culture study of the bioenergetic aspects of growth and production of exocellular protease in Bacillus licheniformis

Summary Bacillus licheniformis S 1684 is able to produce an alkaline serine protease exocellularly. In glucose-limited chemostat cultures the specific rate of protease production was maximal at a -value of 0.22. Above this growth rate protease production was repressed. Dependent on 10–20% of the glucose input was used for exocellular product formation. The degree of reduction of exocellular products was 4.1.Maximum molar growth yields were high and indicate a high efficiency of growth. The values of Y _glu ^max and YO ₂ ^max were 83.8 and 53.3, respectively. When Y _glu ^max was corrected for the amount of glucose used for product formation a value of 100.3 was obtained. These high maximum molar growth yields are most probably caused by a high Y _ATP ^max . Anaerobic batch experiments showed a Y _ATP of 14.6.Sometimes the used strain was instable in cell morphology and protease production. Non-protease producing cells most probably develop from producing cells by mutation in the rel-gene. Producing cells most probably are relaxed (rel ^-) and non-producing cells stringent (rel ⁺).Glossary specific growth rate (h^-1) - Y _sub growth yield permol substrate (g biomass/mol) - Y ^max maximum molar growth yield, corrected for maintenance requirements (g biomass/mol) - Y ^max(corr) Y ^max corrected for product formation (g biomass/mol) - m _sub maintenance requirements (mol/g biomass·h) - m _sub(corr) maintenance requirements corrected for product formation (mol/g biomass·h) - Y _c fraction of organic substrate converted in biomass - z fraction of organic substrate converted in exocellular products - d fraction of organic substrate converted in CO₂ (g mol/g atom C) - Crec% carbon recovery % - average degree of reduction of exocellular products - P/O amount of ATP produced during electron-transport of 2 electrons to oxygen     

Cloning and characterization of a novel NK cell-specific serine protease gene and its functional 5′-flanking sequences

Rat natural killer cell Met-ase-1 (RNK-Met-1) is a 30 000 M _r serine protease (granzyme) found in the cytolytic granules of CD3- large granular lymphocytes (LGL) with natural killer (NK) activity. To characterize the genomic sequences responsible for the CD3- LGL-restricted expression of this gene, we screened a rat genomic library with RNK-Met-1 cDNA, and obtained bacteriophage clones that contained the RNK-Met-1 gene. The RNK-Met-1 gene comprises 5 exons and spans approximately 5.2 kilobases (kb), exhibiting a similar structural organization to a class of CTL-serine proteases with protease catalytic residues encoded near the borders of exons 2, 3, and 5. The 5-flanking region of the RNK-Met-1 gene contains a number of putative promoter and enhancer regulatory elements and shares several regions of homology with the 5-flanking region of the mouse perforin gene. We have prepared nested deletions from approximately 3.3 kb of the 5-flanking region of the RNK-Met-1 gene, and inserted these upstream of the chloramphenicol acetyltransferase (CAT) reporter gene. These 5-flanking RNK-Met-1-CAT constructs were transiently transfected into rat LGL leukemia, T-lymphoma, and basophilic leukemia cell lines.The nucleotide sequence data reported in this Papershave been submitted to the EMBL/GenBank nucleotide sequence database and have been assigned the accession number L38482.     

Industrial applications of a cloned neutral protease gene in Bacillus subtilis

Summary Genes for the -amylase and neutral protease were cloned from an industrial Bacillus isolate, Bsl, onto two separate plasmids and introduced into a B. subtilis strain. Both plasmids were stably maintained in this strain. Analysis of the extracellular proteins showed that the plasmidcarrying strain produced predominantly the Bsl -amylase and neutral protease with few contaminating B. subtilis exoenzymes. The presence of high levels of protease enabled the strain to produce considerably more -amylase when grown on a complex industrial medium rich in protein.     

Production,isolation and characterization of extracellular protease of an alkaliphilic strain of Arthrobacter ramosus,MCM B-351 isolated from the alkaline lake of Lonar,India

An extracellular protease was produced by Arthrobacter ramosus isolated from the alkaline lake of Lonar, Buldhana District of Maharashtra, India when grown on a synthetic medium of pH 10 containing casein. The optimum conditions for production were 3.0% initial casein concentration, 2% inoculum of 1 × 10⁸ cells/ml, pH 9.0, temperature 30 °C and shaken culture conditions. The protease was purified by ammonium sulphate precipitation followed by Sephadex G-100 chromatography. Two proteases viz. Arthro I and Arthro II, having molecular weights 21 and 11.4 kDa respectively were isolated. The Arthro II fraction had K _m 395 g/ml and V _max 10.55 g/min for azocasein. The maximum activity of enzyme was at 55 °C and pH 8. It was thermostable (up to 80 °C), alkali stable (pH 12) and stable in commercial detergent. The enzyme may contain a thiol group at the active site.     

Linkage of sugar chains to a fragment peptide of FGF-5S by a chemoenzymatic strategy and changes in the rate of proteolytic hydrolysis

Various O-linked and N-linked sugar chains were linked enzymatically to a fragment peptide (Leu-Ser-Gln(or Asn)-Val-His-Arg) of FGF-5S. First, galactose was linked with -(13)-linkage to GalNAc-linked peptide by a transglycosylation using -galactosidase from Bacillus circulans (recombinant). Then sialic acid was linked with the aid of sialyltransferase from rat liver (recombinant) to give NeuAc-(23)-Gal-(13)-GalNAc-linked hexapeptide. Further, a sialylated 2-chain biantennary sugar chain was linked by a transglycosylation using endo N-acetyl--D-glucosaminidase from Mucor hiemalis (endo M, recombinant). The activity of DNA synthesis in a fibroblast cell line was increased by this glycosylation. The resistance of the obtained glycopeptides towards proteolytic hydrolysis by rat serum and by five proteases was compared with that of original peptide. The resistance was remarkably enhanced by the glycosylation.     

Overproduction and purification of Lon protease fromEscherichia coli using a maltose-binding protein fusion system

Lon protease, which plays a major role in degradation of abnormal proteins inEscherichia coli, was overproduced and efficiently purified using the maltose-binding protein (MBP) fusion vector. The MBP-Lon fusion protein was expressed in a soluble form inE. coli and purified to homogeneity by amylose resin in a single step. Lon protease was split from MBP by cleaving a fusion point between MBP and Lon with factor Xa and purified by amylose resin and subsequent gel filtration. In this simple method, Lon protease was purified to homogeneity. Purified MBP-Lon fusion protein and Lon protease showed similar breakdown activities with a peptide (succinyl-l-phenylalanyl-l-leucyl-phenylalanyl--d-methoxynaphthylamide) and protein (-casein) in the presence of ATP. Therefore, the gene-fusion approach described in this study is useful for the production of functional Lon protease. MBP-Lon fusion protein, which both binds to the amylose resin and has ATP-dependent protease activity, should be especially valuable for its application in the degradation of abnormal proteins by immobilized enzymes.