title: Molecular characterization of the skate peripherin/rds gene: relationship to its orthologues and paralogues.
abstract: OBJECTIVE
  A great deal of information about functionally significant domains of a protein may be obtained by comparison of primary sequences of gene homologues over a broad phylogenetic base. This study was designed to identify evolutionarily conserved domains of the photoreceptor disc membrane protein peripherin/rds by analysis of the homologue in a primitive vertebrate, the skate.
  
  
  METHODS
  A skate retinal cDNA library was screened using a mouse peripherin/rds clone. The 5' and 3' untranslated regions of the skate peripherin/rds (srds) cDNA were isolated by the rapid amplification of cDNA ends (RACE) approach. The gene structure was characterized by PCR amplification and sequencing of genomic fragments. Northern and Western blot analyses were used to identify srds transcript and protein, respectively.
  
  
  RESULTS
  A new homologue of peripherin/rds was identified from the skate retinal cDNA library. SRDS is a glycoprotein with a predicted molecular mass of 40.2 kDa. The srds gene consists of two exons and one small intron and transcribes into a single 6-kb message. Phylogenetic analysis places SRDS at the base of peripherin/rds family and near the division of that group and the branch leading to rds-like and rom-1 genes. SRDS protein is 54.5% identical with peripherin/rds across species. Identity is significantly higher (73%) in the intradiscal domains. Sequence comparison revealed the conservation of all residues that have been shown, on mutation, to associate with retinitis pigmentosa and showed conservation of most residues associated with macular dystrophies. Comparison with ROM-1 and other rds-like proteins revealed the presence of a highly conserved domain in the large intradiscal loop.
  
  
  CONCLUSIONS
  Srds represents the skate orthologue of mammalian peripherin/rds genes. Conservation of most of the residues associated with human retinal diseases indicates that these residues serve important functional roles. The high degree of conservation of a short stretch within the large intradiscal loop also suggests an important function for this domain.
authors.affiliation: Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, College of Medicine, Chicago, Illinois, USA.
authors.forename: Chibo
authors.initials: C
authors.lastname: Li
authors.forename: Xi-Qin
authors.initials: XQ
authors.lastname: Ding
authors.forename: John
authors.initials: J
authors.lastname: O'Brien
authors.forename: Muayyad R
authors.initials: MR
authors.lastname: Al-Ubaidi
authors.forename: Muna I
authors.initials: MI
authors.lastname: Naash
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D015152:Blotting, Northern; D015153:Blotting, Western; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000302:isolation & purification; D005136:Eye Proteins / Q000235:genetics* / Q000302:isolation & purification; D007381:Intermediate Filament Proteins / Q000235:genetics* / Q000302:isolation & purification; D008562:Membrane Glycoproteins; D008969:Molecular Sequence Data; D008970:Molecular Weight; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000302:isolation & purification; D064531:Peripherins; D020419:Photoreceptor Cells, Vertebrate / Q000737:chemistry*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012860:Skates, Fish
chemical_list: D018076:DNA, Complementary; D005136:Eye Proteins; D007381:Intermediate Filament Proteins; D008562:Membrane Glycoproteins; D009419:Nerve Tissue Proteins; C578994:PRPH protein, human; C578997:PRPH2 protein, human; D064531:Peripherins; C578996:Prph2 protein, mouse