title: Cross genome comparisons of serine proteases in Arabidopsis and rice.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  Despite 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.
  
  
  CONCLUSIONS
  The 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.
authors.affiliation: National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560 065, India. lokesh@ncbs.res.in
authors.forename: Lokesh P
authors.initials: LP
authors.lastname: Tripathi
authors.forename: R
authors.initials: R
authors.lastname: Sowdhamini
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D002268:Carboxypeptidases / Q000235:genetics; D029721:Drosophila Proteins / Q000235:genetics; D049071:Endopeptidase Clp / Q000235:genetics; D010450:Endopeptidases / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D006360:Heat-Shock Proteins / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D028861:Nuclear Pore Complex Proteins / Q000378:metabolism; D012275:Oryza / Q000235:genetics*; D010447:Peptide Hydrolases / Q000235:genetics; D033903:Periplasmic Proteins / Q000235:genetics; D010802:Phylogeny; D000085822:Prolyl Oligopeptidases; D049070:Protease La / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000235:genetics*; D013381:Subtilisins / Q000235:genetics; D001618:beta-Lactamases / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D029721:Drosophila Proteins; D006360:Heat-Shock Proteins; D008565:Membrane Proteins; D028861:Nuclear Pore Complex Proteins; D033903:Periplasmic Proteins; C081481:Rho protein, Drosophila; D002268:Carboxypeptidases; D010450:Endopeptidases; D010447:Peptide Hydrolases; C022448:lysosomal Pro-X carboxypeptidase; C022633:serine carboxypeptidase; C061682:DegP protease; C436319:SPPA protein, Arabidopsis; D012697:Serine Endopeptidases; D013381:Subtilisins; C072135:C-terminal processing peptidase; D000085822:Prolyl Oligopeptidases; D049070:Protease La; C026515:type I signal peptidase; D049071:Endopeptidase Clp; C030732:protease IV; D001618:beta-Lactamases