Purification and molecular characterization of two inhibitors of yeast proteinase B

Genome-Wide Identification and Expression Analysis of the Protease Inhibitor Gene Families in Tomato

The protease inhibitors (PIs) in plants are involved primarily in defense against pathogens and pests and in response to abiotic stresses. However, information about the PI gene families in tomato (Solanumlycopersicum), one of the most important model plant for crop species, is limited. In this study, in silico analysis identified 55 PI genes and their conserved domains, phylogenetic relationships, and chromosome locations were characterized. According to genetic structure and evolutionary relationships, the PI gene families were divided into seven families. Genome-wide microarray transcription analysis indicated that the expression of SlPI genes can be induced by abiotic (heat, drought, and salt) and biotic (Botrytiscinerea and tomato spotted wilt virus (TSWV)) stresses. In addition, expression analysis using RNA-seq in various tissues and developmental stages revealed that some SlPI genes were highly or preferentially expressed, showing tissue- and developmental stage-specific expression profiles. The expressions of four representative SlPI genes in response to abscisic acid (ABA), salicylic acid (SA), ethylene (Eth), gibberellic acid (GA). and methyl viologen (MV) were determined. Our findings indicated that PI genes may mediate the response of tomato plants to environmental stresses to balance hormone signals. The data obtained here will improve the understanding of the potential function of PI gene and lay a foundation for tomato breeding and transgenic resistance to stresses.

A novel subtilase inhibitor in plants shows structural and functional similarities to protease propeptides

The propeptides of subtilisin-like serine proteinases (subtilases, SBTs) serve dual functions as intramolecular chaperones that are required for enzyme folding and as inhibitors of the mature proteases. SBT propeptides are homologous to the I9 family of protease inhibitors that have only been described in fungi. Here we report the identification and characterization of subtilisin propeptide-like inhibitor 1 (SPI-1) from Arabidopsis thaliana Sequence similarity and the shared β-α-β-β-α-β core structure identified SPI-1 as a member of the I9 inhibitor family and as the first independent I9 inhibitor in higher eukaryotes. SPI-1 was characterized as a high-affinity, tight-binding inhibitor of Arabidopsis subtilase SBT4.13 with K_d and K_i values in the picomolar range. SPI-1 acted as a stable inhibitor of SBT4.13 over the physiologically relevant range of pH, and its inhibitory profile included many other SBTs from plants but not bovine chymotrypsin or bacterial subtilisin A. Upon binding to SBT4.13, the C-terminal extension of SPI-1 was proteolytically cleaved. The last four amino acids at the newly formed C terminus of SPI-1 matched both the cleavage specificity of SBT4.13 and the consensus sequence of Arabidopsis SBTs at the junction of the propeptide with the catalytic domain. The data suggest that the C terminus of SPI-1 acts as a competitive inhibitor of target proteases as it remains bound to the active site in a product-like manner. SPI-1 thus resembles SBT propeptides with respect to its mode of protease inhibition. However, in contrast to SBT propeptides, SPI-1 could not substitute as a folding assistant for SBT4.13.

Some properties and possible biological role of peptidase inhibitors from the entomopathogenic fungus Tolypocladium cylindrosporum

The activities of secreted and mycelial inhibitors of proteolytic enzymes from fungi of the order Hypocreales have been investigated. Inhibitors of bromelain, papain, and trypsin of low molecular mass (about 1 kDa) and a subtilisin proteinaceous inhibitor with molecular mass of 45 kDa were revealed in the culture liquid of the fungus Tolypocladium cylindrosporum. The subtilisin inhibitor from T. cylindrosporum has antibiotic properties, significantly decreased the activity of purified bacterial enzymes, and prevented the growth of the bacterium Pseudomonas sp. Data suggesting the existence in fungi of the Hypocreales order of two pools of peptidase inhibitors have been obtained.

Fungal inhibitors of proteolytic enzymes: classification, properties, possible biological roles, and perspectives for practical use

Peptidase inhibitors are ubiquitous regulatory proteins controlling catalytic activity of proteolytic enzymes. Interest in these proteins increased substantially after it became clear that they can be used for therapy of various important diseases including cancer, malaria, and autoimmune and neurodegenerative diseases. In this review we summarize available data on peptidase inhibitors from fungi, emphasizing their properties, biological role, and possible practical applications of these proteins in the future. A number of fungal peptidase inhibitors with unique structure and specificity of action have no sequence homology with other classes of peptidase inhibitors, thus representing new and specific candidates for therapeutic use. The main classifications of inhibitors in current use are considered. Available data on structure, mechanisms and conditions of action, and diversity of functions of peptidase inhibitors of fungi are analyzed. It is mentioned that on one side the unique properties of some inhibitors can be used for selective inhibition of peptidases responsible for initiation and development of pathogenic processes. On the other side, general inhibitory activity of other inhibitors towards peptidases of various catalytic classes might be able to provide efficient defense of transgenic plants against insect pests by overcoming compensatory synthesis of new peptidases by these pests in response to introduction of a fungal inhibitor. Together, the data analyzed in this review reveal that fungal inhibitors extend the spectrum of known peptidase inhibitors potentially suitable for use in medicine and agriculture.

Membrane fusion catalyzed by a Rab, SNAREs, and SNARE chaperones is accompanied by enhanced permeability to small molecules and by lysis

The fusion of biological membranes entails a drastic rearrangement of the lipid bilayer. New assays that distinguish fusion from lysis were developed to study an in vitro reconstitution of the yeast vacuolar fusion machinery. These assays revealed that true fusion is accompanied by strongly enhanced membrane permeability to small molecules and by lysis.

The fusion of sealed biological membranes joins their enclosed aqueous compartments while mixing their membrane bilayers. Reconstituted fusion reactions are commonly assayed by lipid mixing, which can result from either true fusion or from lysis and its attendant reannealing of membranes. Fusion is also frequently assayed by the mixing of lumenal aqueous compartments, using probes of low molecular weight. With several probes (biotin, methylumbelliferyl-N-acetyl-α-d-neuraminic acid, and dithionite), we find that yeast vacuolar SNAREs (SNAP [Soluble NSF attachment protein] Receptors) increase the permeability of membranes to small molecules and that this permeabilization is enhanced by homotypic fusion and vacuole protein sorting complex (HOPS) and Sec17p/Sec18p, the vacuolar tethering and SNARE chaperone proteins. We now report the development of a novel assay that allows the parallel assessment of lipid mixing, the mixing of intact lumenal compartments, any lysis that occurs, and the membrane permeation of small molecules. Applying this assay to an all-purified reconstituted system consisting of vacuolar lipids, the four vacuolar SNAREs, the SNARE disassembly chaperones Sec17p and Sec18p, the Rab Ypt7p, and the Rab effector/SM protein complex HOPS, we show that true fusion is accompanied by strongly enhanced membrane permeability to small molecules and a measurable rate of lysis.

Peptidase inhibitors in the MEROPS database

The MEROPS website (http://merops.sanger.ac.uk) includes information on peptidase inhibitors as well as on peptidases and their substrates. Displays have been put in place to link peptidases and inhibitors together. The classification of protein peptidase inhibitors is continually being revised, and currently inhibitors are grouped into 67 families based on comparisons of protein sequences. These families can be further grouped into 38 clans based on comparisons of tertiary structure. Small molecule inhibitors are important reagents for peptidase characterization and, with the increasing importance of peptidases as drug targets, they are also important to the pharmaceutical industry. Small molecule inhibitors are now included in MEROPS and over 160 summaries have been written.

Excess vacuolar SNAREs drive lysis and Rab bypass fusion

Although concentrated soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) drive liposome fusion and lysis, the fusion of intracellular membranes also requires Rab GTPases, Rab effectors, SM proteins, and specific regulatory lipids and is accompanied by little or no lysis. To rationalize these findings, we generated yeast strains that overexpress all four vacuolar SNAREs (4SNARE(++)). Although vacuoles with physiological levels of Rab, Rab effector/SM complex, and SNAREs support rapid fusion without Rab- and SNARE-dependent lysis, vacuoles from 4SNARE(++) strains show extensive lysis and a reduced need for the Rab Ypt7p or regulatory lipids for fusion. SNARE overexpression and the addition of pure homotypic fusion and vacuole protein sorting complex (HOPS), which bears the vacuolar SM protein, enables ypt7Delta vacuoles to fuse, allowing direct comparison of Rab-dependent and Rab-independent fusion. Because 3- to 40-fold more of each of the five components that form the SNARE/HOPS fusion complex are required for vacuoles from ypt7Delta strains to fuse at the same rate as vacuoles from wild-type strains, the apparent forward rate constant of 4SNARE/HOPS complex assembly is enhanced many thousand-fold by Ypt7p. Rabs function in normal membrane fusion by concentrating SNAREs, other proteins (e.g., SM), and key lipids at a fusion site and activating them for fusion without lysis.

Involvement of the C-terminal region of yeast proteinase B inhibitor 2 in its inhibitory action

Yeast proteinase B inhibitor 2 (YIB2), which is composed of 74 amino acid residues, is an unusual serine protease inhibitor, since it lacks disulfide bonds. To identify its reactive site for proteases, we constructed an expression system for a synthetic YIB2 gene and then attempted to change the inhibitory properties of YIB2 by amino acid replacements. The purified wild-type YIB2 inhibited the activity of subtilisin BPN', a protein homologous to yeast proteinase B, although its binding ability was not strong, and a time-dependent decrease in its inhibitory activity was observed, demonstrating that wild-type YIB2 behaves as a temporary inhibitor when subtilisin BPN' is the target protease. Since YIB2 exhibits sequence homology to the propeptide of subtilisin, which inhibits a cognate protease using its C-terminal region, we replaced the six C-termi nal residues of YIB2 with those of the propeptide of subtilisin BPN' to make the mutant YIB2m1. This mutant exhibited markedly increased inhibitory activity toward subtilisin BPN' without a time-dependent decrease in its inhibitory activity. Replacement of only the C-terminal Asn of YIB2 by Tyr, or deletion of the C-terminal Tyr of YIB2m1, inhibited subtilisin, but the ability of these mutants to bind subtilisin and their resistance to proteolytic attack were weaker than those of YIB2m1, indicating that the C-terminal residue contributes to the interaction with the protease to a greater extent than the preceding five residues and that the resistance of YIB2 to proteolyic attack is closely related to its ability to bind a protease. These results demonstrate that YIB2 is a unique protease inhibitor that involves its C-terminal region in the interaction with the protease.

LMA1 binds to vacuoles at Sec18p (NSF), transfers upon ATP hydrolysis to a t-SNARE (Vam3p) complex, and is released during fusion

Vacuole fusion requires Sec18p (NSF), Sec17p (alpha-SNAP), Ypt7p (GTP binding protein), Vam3p (t-SNARE), Nyv1p (v-SNARE), and LMA1 (low Mr activity 1, a heterodimer of thioredoxin and I(B)2). LMA1 requires Sec18p for saturable, high-affinity binding to vacuoles, and Sec18p "priming" ATPase requires both Sec17p and LMA1. Either the sec18-1 mutation and deletion of I(B)2, or deletion of both I(B)2 and p13 (an I(B)2 homolog) causes a striking synthetic vacuole fragmentation phenotype. Upon Sec18p ATP hydrolysis, LMA1 transfers to (and stabilizes) a Vam3p complex. LMA1 is released from vacuoles in a phosphatase-regulated reaction. This LMA1 cycle explains how priming by Sec18p is coupled to t-SNARE stabilization and to fusion.

I2B is a small cytosolic protein that participates in vacuole fusion

Saccharomyces cerevisiae vacuole inheritance requires two low molecular weight activities, LMA1 and LMA2. LMA1 is a heterodimer of thioredoxin and protease B inhibitor 2 (I2B). Here we show that the second low molecular weight activity (LMA2) is monomeric I2B. Though LMA2/I2B was initially identified as a protease B inhibitor, this protease inhibitor activity is not related to its ability to promote vacuole fusion: (i) Low Mr protease B inhibitors cannot substitute for LMA1 or LMA 2, (ii) LMA1 and LMA2 promote the fusion of vacuoles from a strain that has no protease B, (iii) low concentrations of LMA2 that fully inhibit protease B do not promote vacuole fusion, and (iv) LMA1, in which I2B is complexed with thioredoxin, is far more active than LMA2/I2B in promoting vacuole fusion and far less active in inhibiting protease B. These studies establish a new function for I2B.

A heterodimer of thioredoxin and I(B)2 cooperates with Sec18p (NSF) to promote yeast vacuole inheritance

Early in S phase, the vacuole (lysosome) of Saccharomyces cerevisiae projects a stream of vesicles and membranous tubules into the bud where they fuse and establish the daughter vacuole. This inheritance reaction can be studied in vitro with isolated vacuoles. Rapid and efficient homotypic fusion between salt-washed vacuoles requires the addition of only two purified soluble proteins, Sec18p (NSF) and LMA1, a novel heterodimer with a thioredoxin subunit. We now report the identity of the second subunit of LMA1 as I(B)2, a previously identified cytosolic inhibitor of vacuolar proteinase B. Both subunits are needed for efficient vacuole inheritance in vivo and for the LMA1 activity in cell extracts. Each subunit acts via a novel mechanism, as the thioredoxin subunit is not acting through redox chemistry and LMA1 is still needed for the fusion of vacuoles which do not contain proteinase B. Both Sec18p and LMA1 act at an early stage of the in vitro reaction. Though LMA1 does not stimulate Sec18p-mediated Sec17p release, LMA1 cannot fulfill its function before Sec18p. Upon Sec17p/Sec18p action, vacuoles become labile but are rapidly stabilized by LMA1. The action of LMA1 and Sec18p is thus coupled and ordered. These data establish LMA1 as a novel factor in trafficking of yeast vacuoles.

Purification and characterization of the endogenous inhibitor for proteinase B from Schizosaccharomyces pombe

A rapid purification procedure for the endogenous inhibitor of proteinase yspB from Schizosaccharomyces pombe is described. Starting from a boiled extract, the purification procedure included an ionic exchange chromatography and two reverse phase chromatographies using a HPLC system. The molecular mass of the purified polypeptide was estimated to be 8,100 Da by gel filtration. The isoelectric point of the inhibitor was found to be 5.3 after electrofocusing of a purified preparation. The amino acid composition of the proteinase yspB inhibitor was analyzed after acid hydrolysis. The calculated number of residues was 67 and the corresponding molecular mass 7370 Da. There are several differences in the molecular characteristics between the inhibitor from Schizosaccharomyces pombe and the corresponding inhibitor previously purified from Saccharomyces cerevisiae which might reflect the evolutionary divergence between the two yeast genera.

Proteins released from stimulated neutrophils contain very high levels of oxidized methionine

In proteins released from quiescent human neutrophils during incubation, 21% of the methionine (Met) residues were found to be oxidized. However, the portion of oxidized Met in extracellular proteins increased to 66% after stimulating the cells with zymosan and to 75% after stimulation with phorbol myristate acetate (PMA). Generation of such high levels of oxidized Met in native proteins by activated neutrophils has, so far, not been observed. The presence of superoxide dismutase during incubation of PMA-stimulated cells produced a negligible effect on methionine oxidation, while the presence of catalase resulted in a methionine sulfoxide (Met(O)) content of only 28% in the released proteins. It is proposed that the conversion of Met to Met(O) in these proteins predominantly occurs by action of the myeloperoxidase/H2O2/Cl- system in the extracellular space.

Characterization of the proteolytic activity firmly attached to yeast phoshoenolpyruvate carboxykinase

Incubation of partially purified yeast phosphoenolpyruvate carboxykinase (ATP:oxaloacetate carboxy-lyase (transphosphorylating), EC 4.1.1.49) with 5% mercaptoethanol and 0.01% sodium dodecyl sulfate at 37 degrees C results in degradation of the enzyme. The degradation can be partially prevented by addition of proteinase B inhibitor 2 or phenylmethylsulfonyl fluoride, an inhibitor of proteinase B and carboxypeptidase Y. The degradation can be completely inhibited by addition of proteinase B inhibitor 2 together with pepstatin, and inhibitor of proteinase A. Thus it appears that proteolytic activities are firmly attached to phosphoenolpyruvate carboxykinase and are identical with the yeast proteinases A and B. The latter conclusion was supported by experiments using the pure yeast proteinases.

Localization and characterization of N-ethylmaleimide sensitive inhibitor(s) of thiol cathepsin activity from cultured nil and polyoma virus-transformed nil hamster cells

Exposure of cultured Nil (a stable line of fibroblast cells from Syrian hamsters) or polyoma virus-transformed (PyNil) hamster fibroblasts to 0.5 mM N-ethylmaleimide for 5 minutes resulted in striking increases in thiol cathepsin activity in unfractionated cell-free lysates. The paradoxical increase in activity of the normally N-ethylmaleimide-sensitive cathepsins apparently occurred as the result of the protective compartmentalization of the cathepsins in the lysosomes (20,000 X g sedimented fraction) and the unprotected localization of an inhibitor(s) in the soluble cytoplasm (175,000 X g supernatant fraction). Under continuous exposure of the cells to N-ethylmaleimide, a rapid increase in cathepsin activity (seen in the first 5 minutes) was followed by a steady decrease in activity (half inactivation time, 90 minutes). The relative difference in rates of N-ethylmaleimide inactivation of thiol cathepsins and thiol cathepsin inhibitors provides a means for estimating lysosomal cathepsin activity in whole cell extracts without the need for more time-consuming fractionation procedure. In reciprocal inhibition tests, it was found that, regardless of the source of cathepsins, the Nil and PyNil cathepsin inhibitor(s) inactivated the cathepsins to approximately the same extent. The inhibitors were heat stable (90-100 degrees C for 15 minutes) at pH 4, but were totally inactivated when boiled at pH 8.5. On a calibrated Sephadex G-100 column, the relative molecular weight (Mr) of the inhibitor(s) was 13,000 daltons. On the same column, the Mr of the cathepsins was 24,000 daltons. Compared with the cathepsin activity from Nil cells, there was about five times less cathepsin activity recoverable from the PyNil cells.