title: Protease gene families in Populus and Arabidopsis.
abstract: BACKGROUND
  Proteases play key roles in plants, maintaining strict protein quality control and degrading specific sets of proteins in response to diverse environmental and developmental stimuli. Similarities and differences between the proteases expressed in different species may give valuable insights into their physiological roles and evolution.
  
  
  RESULTS
  We have performed a comparative analysis of protease genes in the two sequenced dicot genomes, Arabidopsis thaliana and Populus trichocarpa by using genes coding for proteases in the MEROPS database 1 for Arabidopsis to identify homologous sequences in Populus. A multigene-based phylogenetic analysis was performed. Most protease families were found to be larger in Populus than in Arabidopsis, reflecting recent genome duplication. Detailed studies on e.g. the DegP, Clp, FtsH, Lon, rhomboid and papain-Like protease families showed the pattern of gene family expansion and gene loss was complex. We finally show that different Populus tissues express unique suites of protease genes and that the mRNA levels of different classes of proteases change along a developmental gradient.
  
  
  CONCLUSIONS
  Recent gene family expansion and contractions have made the Arabidopsis and Populus complements of proteases different and this, together with expression patterns, gives indications about the roles of the individual gene products or groups of proteases.
authors.affiliation: Umeå Plant Science Centre, Department of Biochemistry, Umeå University, S - 90187 Umeå, Sweden. maribel.garcia@chem.umu.se <maribel.garcia@chem.umu.se>
authors.forename: Maribel
authors.initials: M
authors.lastname: García-Lorenzo
authors.forename: Andreas
authors.initials: A
authors.lastname: Sjödin
authors.forename: Stefan
authors.initials: S
authors.lastname: Jansson
authors.forename: Christiane
authors.initials: C
authors.lastname: Funk
mesh_terms: D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D016000:Cluster Analysis; D030541:Databases, Genetic; D018745:Genome, Plant; D005810:Multigene Family; D010447:Peptide Hydrolases / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D032107:Populus / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D012333:RNA, Messenger / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid
chemical_list: D029681:Arabidopsis Proteins; D010940:Plant Proteins; D012333:RNA, Messenger; D010447:Peptide Hydrolases