title: Classification of rice (Oryza sativa L. Japonica nipponbare) immunophilins (FKBPs, CYPs) and expression patterns under water stress.
abstract: BACKGROUND
  FK506 binding proteins (FKBPs) and cyclophilins (CYPs) are abundant and ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily, which regulate much of metabolism through a chaperone or an isomerization of proline residues during protein folding. They are collectively referred to as immunophilin (IMM), being present in almost all cellular organs. In particular, a number of IMMs relate to environmental stresses.
  
  
  RESULTS
  FKBP and CYP proteins in rice (Oryza sativa cv. Japonica) were identified and classified, and given the appropriate name for each IMM, considering the ortholog-relation with Arabidopsis and Chlamydomonas or molecular weight of the proteins. 29 FKBP and 27 CYP genes can putatively be identified in rice; among them, a number of genes can be putatively classified as orthologs of Arabidopsis IMMs. However, some genes were novel, did not match with those of Arabidopsis and Chlamydomonas, and several genes were paralogs by genetic duplication. Among 56 IMMs in rice, a significant number are regulated by salt and/or desiccation stress. In addition, their expression levels responding to the water-stress have been analyzed in different tissues, and some subcellular IMMs located by means of tagging with GFP protein.
  
  
  CONCLUSIONS
  Like other green photosynthetic organisms such as Arabidopsis (23 FKBPs and 29 CYPs) and Chlamydomonas (23 FKBs and 26 CYNs), rice has the highest number of IMM genes among organisms reported so far, suggesting that the numbers relate closely to photosynthesis. Classification of the putative FKBPs and CYPs in rice provides the information about their evolutional/functional significance when comparisons are drawn with the relatively well studied genera, Arabidopsis and Chlamydomonas. In addition, many of the genes upregulated by water stress offer the possibility of manipulating the stress responses in rice.
authors.affiliation: Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-506, Korea.
authors.forename: Jun Cheul
authors.initials: JC
authors.lastname: Ahn
authors.forename: Dae-Won
authors.initials: DW
authors.lastname: Kim
authors.forename: Young Nim
authors.initials: YN
authors.lastname: You
authors.forename: Min Sook
authors.initials: MS
authors.lastname: Seok
authors.forename: Jeong Mee
authors.initials: JM
authors.lastname: Park
authors.forename: Hyunsik
authors.initials: H
authors.lastname: Hwang
authors.forename: Beom-Gi
authors.initials: BG
authors.lastname: Kim
authors.forename: Sheng
authors.initials: S
authors.lastname: Luan
authors.forename: Hong-Seog
authors.initials: HS
authors.lastname: Park
authors.forename: Hye Sun
authors.initials: HS
authors.lastname: Cho
mesh_terms: D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000378:metabolism; D021983:Cyclophilins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D003593:Cytoplasm / Q000378:metabolism; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D049452:Green Fluorescent Proteins / Q000235:genetics / Q000378:metabolism; D020104:Immunophilins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D008856:Microscopy, Fluorescence; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D020033:Protein Isoforms / Q000145:classification / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012965:Sodium Chloride / Q000494:pharmacology; D022021:Tacrolimus Binding Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D014026:Nicotiana / Q000166:cytology; D014867:Water / Q000494:pharmacology
chemical_list: D020033:Protein Isoforms; D014867:Water; D049452:Green Fluorescent Proteins; D012965:Sodium Chloride; D021983:Cyclophilins; D022021:Tacrolimus Binding Proteins; D020104:Immunophilins