Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity

2013 ◽  
Vol 457 (2) ◽  
pp. 335-346 ◽  
Author(s):  
Giada Marino ◽  
Pitter F. Huesgen ◽  
Ulrich Eckhard ◽  
Christopher M. Overall ◽  
Wolfgang P. Schröder ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Cleavage Site ◽  
Biochemical Properties ◽  
Site Specificity ◽  
Sequence Specificity ◽  
Cleavage Sites ◽  
Protease Cleavage ◽  
Protease Cleavage Sites ◽  
Proteomic Identification

The five recombinant MMP-like proteins of Arabidopsis thaliana have specific biochemical properties. Detailed analysis of their sequence specificity using proteomic identification of protease cleavage sites revealed cleavage profiles similar to human MMPs.

scholarly journals Proteolytic Cleavage of Bovine Adenovirus 3-Encoded pVIII

2017 ◽  
Vol 91 (10) ◽  
Author(s):  
Amit Gaba ◽  
Lisanework Ayalew ◽  
Niraj Makadiya ◽  
Suresh Tikoo
Keyword(s):  
Cleavage Site ◽  
Virus Assembly ◽  
Proteolytic Cleavage ◽  
Efficient Production ◽  
Cleavage Sites ◽  
Bovine Adenovirus ◽  
Protease Cleavage Site ◽  
Protease Cleavage ◽  
Protease Cleavage Sites ◽  
Single Protease

ABSTRACT Proteolytic maturation involving cleavage of one nonstructural and six structural precursor proteins including pVIII by adenovirus protease is an important aspect of the adenovirus life cycle. The pVIII encoded by bovine adenovirus 3 (BAdV-3) is a protein of 216 amino acids and contains two potential protease cleavage sites. Here, we report that BAdV-3 pVIII is cleaved by adenovirus protease at both potential consensus protease cleavage sites. Usage of at least one cleavage site appears essential for the production of progeny BAdV-3 virions as glycine-to-alanine mutation of both protease cleavage sites appears lethal for the production of progeny virions. However, mutation of a single protease cleavage site of BAdV-3 pVIII significantly affects the efficient production of infectious progeny virions. Further analysis revealed no significant defect in endosome escape, genome replication, capsid formation, and virus assembly. Interestingly, cleavage of pVIII at both potential cleavage sites appears essential for the production of stable BAdV-3 virions as BAdV-3 expressing pVIII containing a glycine-to-alanine mutation of either of the potential cleavage sites is thermolabile, and this mutation leads to the production of noninfectious virions. IMPORTANCE Here, we demonstrated that the BAdV-3 adenovirus protease cleaves BAdV-3 pVIII at both potential protease cleavage sites. Although cleavage of pVIII at one of the two adenoviral protease cleavage sites is required for the production of progeny virions, the mutation of a single cleavage site of pVIII affects the efficient production of infectious progeny virions. Further analysis indicated that the mutation of a single protease cleavage site (glycine to alanine) of pVIII produces thermolabile virions, which leads to the production of noninfectious virions with disrupted capsids. We thus provide evidence about the requirement of proteolytic cleavage of pVIII for production of infectious progeny virions. We feel that our study has significantly advanced the understanding of the requirement of adenovirus protease cleavage of pVIII.

scholarly journals Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites

2011 ◽  
Vol 392 (11) ◽  
Author(s):  
Oliver Schilling ◽  
Ulrich auf dem Keller ◽  
Christopher M. Overall
Keyword(s):  
Factor Xa ◽  
Site Specificity ◽  
Cleavage Sites ◽  
Web Based ◽  
Protease Cleavage ◽  
Proteomic Approach ◽  
Site Selectivity ◽  
User Access ◽  
Proteomic Identification ◽  
Subsite Mapping

Abstract Proteomic identification of protease cleavage site specificity (PICS) is a recent proteomic approach for the easy mapping of protease subsite preferences that determines both the prime- and non-prime side specificity concurrently. Here we greatly facilitate user access by providing an automated and simple web-based data-analysis resource termed WebPics (http://clipserve.clip.ubc.ca/pics/). We demonstrate the utility of WebPics analysis of PICS data by determining the substrate specificity of factor Xa from P6-P6’, an important blood coagulation protease that proteolytically generates thrombin from prothrombin. PICS confirms existing data on non-prime site specificity and refines our knowledge of factor Xa prime-site selectivity.

scholarly journals Human Immunodeficiency Virus Type 1 Protease Cleavage Site Mutations Associated with Protease Inhibitor Cross-Resistance Selected by Indinavir, Ritonavir, and/or Saquinavir

2001 ◽  
Vol 75 (2) ◽  
pp. 589-594 ◽  
Author(s):  
Hélène C. F. Côté ◽  
Zabrina L. Brumme ◽  
P. Richard Harrigan
Keyword(s):  
Human Immunodeficiency Virus ◽  
Protease Inhibitor ◽  
Cleavage Site ◽  
Cross Resistance ◽  
Cleavage Sites ◽  
Protease Cleavage ◽  
Immunodeficiency Virus ◽  
Before And After ◽  
Protease Cleavage Sites

ABSTRACT We examined the prevalence of cleavage site mutations, both within and outside the gag region, in 28 protease inhibitor (PI) cross-resistant patients treated with indinavir, ritonavir, and/or saquinavir compared to control patients treated with reverse transcriptase inhibitors. Three human immunodeficiency virus protease cleavage sites within gag (p2/NC, NC/p1, and NC/TFP) showed considerable in vivo evolution before and after therapy with indinavir, ritonavir, and/or saquinavir. Another gag cleavage site (p1/p6 gag ) showed a trend compared to matched controls. The other eight recognized cleavage sites showed relatively little difference between PI-resistant cases and controls. An A→V substitution at the P2 position of the NC/p1 and NC/TFP cleavage sites was the most common (29%) change selected by the PIs used in this study.

Proteomic Identification of Protease Cleavage Sites Characterizes Prime and Non-prime Specificity of Cysteine Cathepsins B, L, and S

2011 ◽  
Vol 10 (12) ◽  
pp. 5363-5373 ◽  
Author(s):  
Martin L. Biniossek ◽  
Dorit K. Nägler ◽  
Christoph Becker-Pauly ◽  
Oliver Schilling
Keyword(s):  
Cleavage Sites ◽  
Protease Cleavage ◽  
Cysteine Cathepsins ◽  
Protease Cleavage Sites ◽  
Proteomic Identification

scholarly journals Variability at Human Immunodeficiency Virus Type 1 Subtype C Protease Cleavage Sites: an Indication of Viral Fitness?

2003 ◽  
Vol 77 (17) ◽  
pp. 9422-9430 ◽  
Author(s):  
Tulio de Oliveira ◽  
Susan Engelbrecht ◽  
Estrelita Janse van Rensburg ◽  
Michelle Gordon ◽  
Karen Bishop ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Cleavage Site ◽  
Cleavage Sites ◽  
Subtype C ◽  
Protease Cleavage ◽  
Immunodeficiency Virus ◽  
Protease Cleavage Sites ◽  
Hiv 1

ABSTRACT Naturally occurring polymorphisms in the protease of human immunodeficiency virus type 1 (HIV-1) subtype C would be expected to lead to adaptive (compensatory) changes in protease cleavage sites. To test this hypothesis, we examined the prevalences and patterns of cleavage site polymorphisms in the Gag, Gag-Pol, and Nef cleavage sites of C compared to those in non-C subtypes. Codon-based maximum-likelihood methods were used to assess the natural selection and evolutionary history of individual cleavage sites. Seven cleavage sites (p17/p24, p24/p2, NC/p1, NC/TFP, PR/RT, RT/p66, and p66/IN) were well conserved over time and in all HIV-1 subtypes. One site (p1/p6 gag ) exhibited moderate variation, and four sites (p2/NC, TFP/p6 pol , p6 pol /PR, and Nef) were highly variable, both within and between subtypes. Three of the variable sites are known to be major determinants of polyprotein processing and virion production. P2/NC controls the rate and order of cleavage, p6 gag is an important phosphoprotein required for virion release, and TFP/p6 pol , a novel cleavage site in the transframe domain, influences the specificity of Gag-Pol processing and the activation of protease. Overall, 58.3% of the 12 HIV-1 cleavage sites were significantly more diverse in C than in B viruses. When analyzed as a single concatenated fragment of 360 bp, 96.0% of group M cleavage site sequences fell into subtype-specific phylogenetic clusters, suggesting that they coevolved with the virus. Natural variation at C cleavage sites may play an important role, not only in regulation of the viral cycle but also in disease progression and response to therapy.

scholarly journals In Vivo Selection of Protease Cleavage Sites by Using Chimeric Sindbis Virus Libraries

2000 ◽  
Vol 74 (22) ◽  
pp. 10563-10570 ◽  
Author(s):  
Laura Pacini ◽  
Alessandra Vitelli ◽  
Gessica Filocamo ◽  
Linda Bartholomew ◽  
Mirko Brunetti ◽  
...  
Keyword(s):  
Sindbis Virus ◽  
Random Sequence ◽  
Biochemical Properties ◽  
Cleavage Sites ◽  
Viral Genomes ◽  
Protease Cleavage ◽  
Gene Coding ◽  
Protease Cleavage Sites

ABSTRACT Identifying protease cleavage sites contributes to our understanding of their specificity and biochemical properties and can help in designing specific inhibitors. One route to this end is the generation and screening of random libraries of cleavage sites. Both synthetic and phage-displayed libraries have been extensively used in vitro. We describe a novel system based on recombinant Sindbis virus which can be used to identify cleavage sites in vivo, thus eliminating the need for a purified enzyme and overcoming the problem of choosing the correct in vitro conditions. As a model we used the serine protease of the hepatitis C virus (HCV). We engineered the gene coding for this enzyme and two specific cleavage sites in the Sindbis virus structural gene and constructed libraries of viral genomes with a random sequence at either of the cleavage sites. The system was designed so that only viral genomes coding for sequences cleaved by the protease would produce viable viruses. With this system we selected viruses containing sequences mirroring those of the natural HCV protease substrates which were cleaved with comparable efficiencies.

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