Changing the protease specificity for activation of a flavivirus, tick-borne encephalitis virus

The infectivity of flavivirus particles depends on a maturation process that is triggered by the proteolytic cleavage of the precursor of the M protein (prM). This activation cleavage is naturally performed by ubiquitous cellular proteases of the furin family, which typically recognize the multibasic sequence motif R-X-R/K-R. Previously, we demonstrated that a tick-borne encephalitis virus (TBEV) mutant with an altered cleavage motif, R-X-R, produced immature, noninfectious particles that could be activated by exogenous trypsin, which cleaves after single basic residues. Here, we report the adaptation of this mutant to chymotrypsin, a protease specific for large, hydrophobic amino acid residues. Using selection pressure in cell culture, two different mutations conferring a chymotrypsin-dependent phenotype were identified. Surprisingly, one of these mutations (Ser85Phe) occurred three positions upstream of the natural cleavage site. The other mutation (Arg89His) arose at the natural cleavage position but involved a His residue, which is not a typical chymotrypsin cleavage site. Efficient cleavage of protein prM and activation by the heterologous protease were confirmed using various recombinant TBEV mutants. Mutants with only the originally selected mutations exhibited unimpaired export kinetics and were genotypically stable during at least six cell culture passages. However, in contrast to the wild-type virus or trypsin-dependent mutants, chymotrypsin-dependent mutants were not neurovirulent in suckling mice. Our results demonstrate that flaviviruses with altered protease specificities can be generated and suggest that this approach can be used for the construction of viral mutants or vectors that can be activated on demand and have restricted tissue tropism and virulence.     

Polyribosome degradation as a sensitive assay for endolytic messenger-ribonuclease activity

A method is described whereby picogram amounts of pancreatic RNase can be accurately measured using polyribosomes as substrate. The method involves incubating isolated polysomes in RNase, separating them on gradients, and calculating the number of interribosomal bonds for each profile. The decrease in number of interribosomal bonds is proportional to the amount of enzyme added from 20 to 200 pg of pancreatic RNase per assay when conducted at 2°C for 20 min. Sensitivity can be increased by increasing the temperature or the duration of the incubation.Since the method of analysis of the reaction product is unaffected by exonuclease activity, the assay is specific for endonucleases. It can, therefore be used to assay for the presence of endonucleases as contaminants in preparations of exonucleases and to determine the mode of action of nucleases. The method has been used to measure the amount of soluble and polysome-associated RNase in pea stem tissue.     

A rapid and sensitive assay for quantification of siRNA efficiency and specificity

RNA Interference has rapidly emerged as an efficient procedure for knocking down gene expression in model systems. However, cross-reactivity, whereby multiple genes may be simultaneously targeted by a single short interfering RNA (siRNA), can potentially jeopardize correct interpretation of gene function. As such, it is essential to test the specificity of a siRNA prior to a full phenotypic analysis. To this end, we have adapted a reporter-based assay harnessing the sensitivity of luciferase activity to provide a quantitative readout of relative RNAi efficacy and specificity. We have tested different siRNAs directed against Thymosin β4 (Tβ4); determined their effectiveness at silencing Tβ4 and have both excluded off-target silencing of the Tβ4 homologue Thymosin β10 (Tβ10) and demonstrated partial knockdown of Tβ10 despite significant (12/23; 52%) sequence mismatch. This assay system is applicable to any RNAi study where there is a risk of targeting homologous genes and to the monitoring of off-target effects at the genome level following microarray expression profiling.     

Inhibition of hepatic enzyme induction as a sensitive assay for endotoxin

Bacterial endotoxins in mice reduced the induction by cortisone of two hepatic enzymes, tryptophan oxygenase, and phosphoenolpyruvate carboxykinase, they prevented the glyconeogenesis in liver induced by the same hormone, and they induced in intact animals the liver enzyme tyrosine-alpha-ketoglutarate transaminase, all in proportion to their ld(50). When cortisone was given in the least amount (100 mug), it resulted in near maximal induction of tryptophan oxygenase; a smaller amount of endotoxin reduced significantly the level of enzyme than that required when 5 mg of hormone was injected. The smallest amount of endotoxin that prevented tryptophan oxygenase induction was given intravenously to adrenalectomized mice in which 25 mug of cortisone was administered. The amount (0.01 mug) is 1/40,000th of the ld(50). The other metabolic processes subject to alteration by endotoxin required at least 100 to 400 times as much. This property of endotoxin can serve as a sensitive bioassay, although the dose-response curve is steep.     

CHO-recombinant human growth hormone as a protease sensitive reporter protein

Protein-free media are gaining more and more interest in mammalian cell culture technology. However, the range of commercially available protein-free media is wide, but lack of serum causes the lack of various substances (Keenan et al. in Cytotechnology, 50(1–3):49–56, 2006) which must be substituted case by case. Details on the composition of protein-free media are often unavailable or inaccessible in some cases, and as a consequence, there is an obvious need for testing procedures in order to evaluate the various commercialised products for their performance. Additionally, negative effects of tryptic meat digests on product quality have been reported in the literature (Gu et al. in Biotech Bioeng 56 (4):353–341, 1997). In the present studies of comparing various protein-free media for their suitability in propagation of recombinant CHO cells expressing human growth hormone (hGH), we have found somatotropin to be an excellent candidate for detection of protease activity. Somatotropin contains protease recognition sites for numerous proteases located around amino-acid residues 134–150. In this study, we demonstrate highly specific cleavage of recombinant hGH during batch cultivation. Analysis of the digested molecule was then performed by convergent methods like SDS-PAGE, HPLC and mass spectroscopy, and the results indicate hGH to be an ideal candidate for media and component screening in mammalian cell culture.     

A sensitive assay for proteolytic enzymes using bacterial luciferase as a substrate

A general assay for proteolytic enzymes using bacterial luciferase as a substrate is described. This luciferase is rapidly inactivated by unusually small amounts of different proteases having a wide spectrum of specificities. The activity is lost exponentially; the pseudo-first-order rate constant for inactivation is proportional to the amount of protease. Since luciferase activity can be measured by a very simple and rapid assay, it affords an accurate, sensitive, and convenient assay for proteolytic activity. This technique is capable of detecting as little as 20 ng of trypsin, requires no centrifugation, and is not hampered by the presence of contaminating pigments in the protease preparation. It is compared at pH 6, 7, and 8 to the phenol color assay and the azocoll assay using seven different proteases.     

Functional protease assay using liquid crystals as a signal reporter

We report a functional protease assay in which liquid crystals (LCs) are used as signal reporters to transduce the test results into optical signals. In this assay, an oligopeptide substrate (CLSELDDRADALQAGASQFESSAAKLKRKYWWKNLK) is used as a probe. This oligopeptide can be cleaved by α-chymotrypsin at multiple locations and become smaller fragments after the cleavage. When the original oligopeptide is immobilized on a solid surface, its long flexible oligopeptide chain is able to influence the orientation of a thin layer of LC supported on the surface, as is evident as a bright spot on the surface. In contrast, when the shorter oligopeptide fragments are immobilized on the same surface, their shorter, less flexible chains cannot disrupt the orientation of LC, and a dark spot is observed. On the basis of the dark or bright signal from LC, α-chymotrypsin in buffer solution or complex media such as chicken broth can be detected by using the naked eye. However, when the incubation time is 3h, the limit of detection (LOD) for α-chymotrypsin in buffer solution is 50 ng/mL, whereas that in chicken broth is only 500 ng/mL. Unlike traditional antibody-based assays which show little difference between active and inactive α-chymotrypsin, only active protease can be detected in this assay. This study shows the potential utility of LCs for detecting functional proteases with good specificity and sensitivity.     

Induced hepatocytes as a metabolic activation system for the mouse-lymphoma assay

We have developed methods for the coculture of hepatocytes and mouse lymphoma cells and have shown that this system can be used for evaluating promutagens from several chemical classes (Brock et al., 1987). In the present study we investigated the use of hepatocytes isolated from rats pretreated with a cytochrome P-450 inducer (PB) or a P-448 inducer (BNF). CP-induced mutagenicity was higher in the presence of PB-induced hepatocytes than in control hepatocytes. Control and BNF-induced hepatocytes were evaluated with B(a)P, B(l)A, and BA. A dose-related positive response was observed with B(a)P and B(l)A both in the presence of control or induced hepatocytes; however, somewhat higher mutant frequencies were obtained in the presence of BNF-induced hepatocytes. BA induced a very weak positive response (approx. 2 X b.g.) in the presence of control hepatocytes and was weakly positive in the presence of BNF-induced hepatocytes. Benzene was tested using control and both PB- and BNF-induced hepatocytes. Neither of these approaches were successful in activating benzene to a mutagenic metabolite. These studies indicate that for some chemicals the mutagenic response of mouse lymphoma cells can be increased by inducing hepatocytes prior to isolation and cocultivation, and expands the use of hepatocytes for research evaluating chemicals requiring metabolic activation.     

Depolarization after resonance energy transfer (DARET): a sensitive fluorescence-based assay for botulinum neurotoxin protease activity

The DARET (depolarization after resonance energy transfer) assay is a coupled Förster resonance energy transfer (FRET)–fluorescence polarization assay for botulinum neurotoxin type A or E (BoNT/A or BoNT/E) proteolytic activity that relies on a fully recombinant substrate. The substrate consists of blue fluorescent protein (BFP) and green fluorescent protein (GFP) flanking SNAP-25 (synaptosome-associated protein of 25 kDa) residues 134–206. In this assay, the substrate is excited with polarized light at 387 nm, which primarily excites the BFP, whereas emission from the GFP is monitored at 509 nm. Energy transfer from the BFP to the GFP in the intact substrate results in a substantial depolarization of the GFP emission. The energy transfer is eliminated when the fluorescent domains separate on cleavage by the endopeptidase, and emission from the directly excited GFP product fragment is then highly polarized, resulting in an overall increase in polarization. This increase in polarization can be monitored to assay the proteolytic activity of BoNT/A and BoNT/E in real time. It allows determination of the turnover rate of the substrate and the kinetic constants (V_max and k_cat) based on the concentration of cleaved substrate determined directly from the measurements using the additivity properties of polarization. The assay is amenable to high-throughput applications.     

Kosmotropic salt activation and substrate specificity of poliovirus protease 3C

Picornaviruses produce a large polyprotein, which is cleaved by virally encoded cysteine peptidases, picornain-2A and -3C. Picornain-3C has characteristics of both the serine peptidase chymotrypsin and the cysteine peptidase papain in that the 3D structure resembles chymotrypsin, but its nucleophile is a cysteine SH rather than a serine OH group. We investigated the specificity of poliovirus picornain-3C (PV3C) protease and the influence of kosmotropic salts on catalytic activity, using FRET peptides related to a cleavable segment of the virus polyprotein. The peptidase activity of PV3C was found to be 100-fold higher in the presence of 1.5 M sodium citrate. This activation was anion-dependent, following the Hofmeister series citrate(3-) > SO4(2-) > HPO4(2-) > acetate- > HCO3(-) > Cl-. The activation appeared to be independent of substrate sequence and arose primarily from an increase in kcat. A shift to higher pH was also observed for the pK1 of the enzyme pH-activity profile. Experiments with the fluorescent probe ANS (1-anilino-8-naphthalene sulfonate) showed that the protease bound the dye in the presence of 1 M sodium citrate but not in its absence or in the presence of 1 M NaCl. Structural changes in PV3C protease were detected using circular dichroism and the thermodynamic data indicated a more organized active site in the presence of sodium citrate. PV3C protease was also activated in D2O, which was added to the activation by citrate. These effects seem to be related to nonspecific interactions between the solvent and the protein. Our data show that the catalytic efficiency of PV3C protease is modulated by the composition of the environment and that this modulation may play a role in the optimal processing of polyprotein for the virus assembly that occurs inside specific vesicles formed in poliovirus-infected cells.     

A sensitive diffusion plate assay for screening inhibitors of protease activity in plant cell fractions

Proteolytic activity was detected, using a sensitive radial diffusion plate assay, in the plasma membrane fractions of corn (Zea mays L.) roots and from roots of several other plant species. The proteases could be effectively inhibited in corn with phenylmethane sulfonyl fluoride or chymostatin. Protease activity of oat roots, however, was not significantly reduced by these inhibitors. The results of diffusion plate assay were confirmed with the less sensitive azocasein assay using crude cell homogenates. Chymostatin and phenylmethane sulfonyl fluoride were effective in preventing protease degradation of polypeptides as revealed by electrophoresis. The diffusion plate assay uses a permanent support for a 0.75 millimeter thick agarose slab containing 200 micrograms per milliliter casein. By staining the fixed and dried gel with Coomassie blue R-250, proteolytic activity was visualized as a cleared area around the sample well with a detection limit of about 0.3 nanograms trypsin. The diffusion plate assay should prove useful for screening inhibitors of proteases where limited amounts of material are available, such as with plant cell fractions or highly purified proteins.     

Reversible oxidative modification as a mechanism for regulating retroviral protease dimerization and activation

Human immunodeficiency virus protease activity can be regulated by reversible oxidation of a sulfur-containing amino acid at the dimer interface. We show here that oxidation of this amino acid in human immunodeficiency virus type 1 protease prevents dimer formation. Moreover, we show that human T-cell leukemia virus type 1 protease can be similarly regulated through reversible glutathionylation of its two conserved cysteine residues. Based on the known three-dimensional structures and multiple sequence alignments of retroviral proteases, it is predicted that the majority of retroviral proteases have sulfur-containing amino acids at the dimer interface. The regulation of protease activity by the modification of a sulfur-containing amino acid at the dimer interface may be a conserved mechanism among the majority of retroviruses.     

Studies on aspartase VIII. Protease-mediated activation: comparative survey of protease specificity for activation and peptide cleavage

The active species of aspartase from Escherichia coli is further 3-5 fold activated upon limited proteolysis with trypsin releasing carboxy-terminal peptides as reported previously (N. Yumoto, M. Tokushige, and R. Hayashi. Biochim. Biophys. Acta, 616, 319 (1980) ). Survey of the protease specificity for the activation revealed that subtilisin BPN' and several other proteases having far broader substrate specificity than trypsin also activated the enzyme. The results of sequence analyses revealed that subtilisin BPN' cleaved mainly the serylarginine bond near the carboxy-terminal and released an octapeptide, while trypsin cleaved mainly the arginyltyrosine bond which is just next to the subtilisin cleavage site. These results suggest that the protease-mediated activation does not necessarily require a site-specific peptidyl cleavage, but the cleavage of any bond within a certain region centered at arginine, the eighth residue from the carboxy-terminal, is sufficient.     

Purification of a protease from Escherichia coli with specificity for oxidized glutamine synthetase

A soluble Escherichia coli protease has been identified and purified to homogeneity. The protease cleaves glutamine synthetase which has been modified by mixed function oxidation; native glutamine synthetase is not a substrate. Using [14C]glutamine synthetase as a substrate (prepared by growing E. coli on 14C-labeled amino acids), protease activity was assayed by determining the release of trichloroacetic acid-soluble material. The pure protease cleaves glutamine synthetase near the carboxyl terminus yielding 4,500 and 47,000 Mr products. The characteristics of this enzyme distinguish it from proteases previously purified from E. coli. These characteristics include a molecular weight of 75,000, alkaline pH optimum, lack of inhibition by serine protease inhibitors, and the ability to degrade insulin and casein. Oxidation of glutamine synthetase and other enzymes can be catalyzed by a variety of mixed function oxidase systems from bacterial and mammalian sources. Mixed function oxidation may be a "signal" or "marker" which consigns a protein for proteolytic degradation. Susceptibility to oxidation is subject to metabolic regulation, thereby providing control of proteolytic turnover. Isolation of a protease specific for modified glutamine synthetase provides the enzymatic basis for the specificity of this scheme.     

Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single-stranded DNA

Traditional methods to assay enzymatic cleavage of DNA are discontinuous and time consuming. In contrast, recently developed fluorescence methods are continuous and convenient. However, no fluorescence method has been developed for single-stranded DNA digestion. Here we introduce a novel method, based on molecular beacons, to assay single-stranded DNA cleavage by single strand-specific nucleases. A molecular beacon, a hairpin-shaped DNA probe labeled with a fluorophore and a quencher, is used as the substrate and enzymatic cleavage leads to fluorescence enhancement in the molecular beacon. This method permits real time detection of DNA cleavage and makes it easy to characterize the activity of DNA nucleases and to study the steady-state cleavage reaction kinetics. The excellent sensitivity, reproducibility and convenience will enable molecular beacons to be widely useful for the study of single-stranded DNA cleaving reactions.     

A sensitive assay for allantoin

Allantoin is separated by thin-layer chromatography (TLC) and sprayed with an acidic solution ofp-dimethylaminobenzaldehyde. The yellow color produced is read in a densitometer and compared with that of a standard. The lower limit of quantitation is 0.1 μg per spot (0.5 mg/100 ml). The method can be utilized for the estimation of allantoin in serum, lymph, and urine.     

Altered specificity of a AAA+ protease

ClpXP, an ATP-dependent protease, degrades hundreds of different intracellular proteins. ClpX chooses substrates by binding peptide tags, typically displayed at the N or C terminus of the protein to be degraded. Here, we identify a ClpX mutant that displays a 300-fold change in substrate specificity, resulting in decreased degradation of ssrA-tagged substrates but improved degradation of proteins with other classes of degradation signals. The altered-specificity mutation occurs within "RKH" loops, which surround the entrance to the central pore of the ClpX hexamer and are highly conserved in the ClpX subfamily of AAA+ ATPases. These results support a major role for the RKH loops in substrate recognition and suggest that ClpX specificity represents an evolutionary compromise that has optimized degradation of multiple types of substrates rather than any single class.     

Selective inhibition of fibroblast activation protein protease based on dipeptide substrate specificity

Fibroblast activation protein (FAP) is a transmembrane serine peptidase that belongs to the prolyl peptidase family. FAP has been implicated in cancer; however, its specific role remains elusive because inhibitors that distinguish FAP from other prolyl peptidases like dipeptidyl peptidase-4 (DPP-4) have not been developed. To identify peptide motifs for FAP-selective inhibitor design, we used P(2)-Pro(1) and acetyl (Ac)-P(2)-Pro(1) dipeptide substrate libraries, where P(2) was varied and substrate hydrolysis occurs between Pro(1) and a fluorescent leaving group. With the P(2)-Pro(1) library, FAP preferred Ile, Pro, or Arg at the P(2) residue; however, DPP-4 showed broad reactivity against this library, precluding selectivity. By contrast, with the Ac-P(2)-Pro(1) library, FAP cleaved only Ac-Gly-Pro, whereas DPP-4 showed little reactivity with all substrates. FAP also cleaved formyl-, benzyloxycarbonyl-, biotinyl-, and peptidyl-Gly-Pro substrates, which DPP-4 cleaved poorly, suggesting an N-acyl-Gly-Pro motif for inhibitor design. Therefore, we synthesized and tested the compound Ac-Gly-prolineboronic acid, which inhibited FAP with a K(i) of 23 +/- 3 nm. This was approximately 9- to approximately 5400-fold lower than the K(i) values for other prolyl peptidases, including DPP-4, DPP-7, DPP-8, DPP-9, prolyl oligopeptidase, and acylpeptide hydrolase. These results identify Ac-Gly-BoroPro as a FAP-selective inhibitor and suggest that N-acyl-Gly-Pro-based inhibitors will allow testing of FAP as a therapeutic target.     

Characterization of a randomized FRET library for protease specificity determination

Protease specificity determination is an important first step when characterizing novel proteases. Given the large number of proteases that are known to exist from genomic sequencing efforts, we reason that sensitive, reliable, and high-throughput methods to determine protease specificity must be developed. This study describes the construction and initial characterization of a protein based FRET library using the fluorescent proteins GFP and DsRed for such a purpose. Using a DNA "cassette" that allowed for directional insertion of annealed oligonucleotides between the genes encoding the GFP and DsRed proteins, we constructed a library using a mixture of standard nucleotide bases at 27 positions in the center of the oligonucleotide cassette. This resulted in a randomized linker region between these fluorescent donor-acceptor pairs to produce substrates with varied amino acids located between the proteins. Kinetic assays were then performed and monitored using the increase in GFP fluorescence to arrive at relative reaction velocities for a set of enzymes. These results demonstrated the ability of the enzymes tested to discriminate between different substrates and the resistance of GFP and DsRed to proteolysis. Colony screening, using color development and restriction enzyme digests, were shown to help eliminate DNA samples in the library that contained stop codons and/or deletions and a flow plan for the efficient use of the library is presented.