Abstract
BackgroundSerine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. The availability of Arabidopsis thaliana and rice (Oryza sativa) genome sequences has permitted the identification and comparison of the repertoire of serine protease-like proteins in the two plant species.ResultsDespite the differences in genome sizes between Arabidopsis and rice, we identified a very similar number of serine protease-like proteins in the two plant species (206 and 222, respectively). Nearly 40% of the above sequences were identified as potential orthologues. Atypical members could be identified in the plant genomes for Deg, Clp, Lon, rhomboid proteases and species-specific members were observed for the highly populated subtilisin and serine carboxypeptidase families suggesting multiple lateral gene transfers. DegP proteases, prolyl oligopeptidases, Clp proteases and rhomboids share a significantly higher percentage orthology between the two genomes indicating substantial evolutionary divergence was set prior to speciation. Single domain architectures and paralogues for several putative subtilisins, serine carboxypeptidases and rhomboids suggest they may have been recruited for additional roles in secondary metabolism with spatial and temporal regulation. The analysis reveals some domain architectures unique to either or both of the plant species and some inactive proteases, like in rhomboids and Clp proteases, which could be involved in chaperone function.ConclusionThe systematic analysis of the serine protease-like proteins in the two plant species has provided some insight into the possible functional associations of previously uncharacterised serine protease-like proteins. Further investigation of these aspects may prove beneficial in our understanding of similar processes in commercially significant crop plant species.
Highlights
Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways
Such inactive-enzyme homologues are not restricted to serine proteases, but have been identified in diverse enzyme families, among proteins involved in signaling pathways and proteins that are apparently extracellular in function and are conserved across metazoan species
The current analysis provides an overview and a comparison of serine protease families of Arabidopsis and rice, the two plant species with completely sequenced genomes that constitute model plant systems for dicots and monocots, respectively
Summary
Serine proteases are one of the largest groups of proteolytic enzymes found across all kingdoms of life and are associated with several essential physiological pathways. Serine proteases are one of the largest groups of proteolytic enzymes involved in numerous regulatory processes They catalyse the hydrolysis of specific peptide bonds in their substrates and this activity depends (page number not for citation purposes). BMC Genomics 2006, 7:200 http://www.biomedcentral.com/1471-2164/7/200 on a set of amino acids in the active site of the enzyme, one of which is always a serine. They include both exopeptidases that act on the termini of polypeptide chains and endopeptidases that act in the interior of polypeptide chains and belong to many different protein families that are grouped into clans[3,4]. There are over 50 serine-protease families known as classified by MEROPS database[5], an information resource for peptidases and their inhibitors
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