title: The family of Deg/HtrA proteases in plants.
abstract: BACKGROUND
  The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.
  
  
  RESULTS
  Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell.
  
  
  CONCLUSIONS
  In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.
authors.affiliation: Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr, 10, 78457, Konstanz, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Schuhmann
authors.forename: Pitter F
authors.initials: PF
authors.lastname: Huesgen
authors.forename: Iwona
authors.initials: I
authors.lastname: Adamska
mesh_terms: D000595:Amino Acid Sequence; D020134:Catalytic Domain; D030562:Databases, Protein; D020440:Gene Duplication; D017343:Genes, Plant; D006360:Heat-Shock Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D054731:PDZ Domains; D033903:Periplasmic Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D010944:Plants / Q000201:enzymology* / Q000235:genetics; D016415:Sequence Alignment; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000145:classification / Q000235:genetics
chemical_list: D006360:Heat-Shock Proteins; D033903:Periplasmic Proteins; D010940:Plant Proteins; C061682:DegP protease; D012697:Serine Endopeptidases