title: Annotation and analysis of a large cuticular protein family with the R&R Consensus in Anopheles gambiae.
abstract: BACKGROUND
  The most abundant family of insect cuticular proteins, the CPR family, is recognized by the R&R Consensus, a domain of about 64 amino acids that binds to chitin and is present throughout arthropods. Several species have now been shown to have more than 100 CPR genes, inviting speculation as to the functional importance of this large number and diversity.
  
  
  RESULTS
  We have identified 156 genes in Anopheles gambiae that code for putative cuticular proteins in this CPR family, over 1% of the total number of predicted genes in this species. Annotation was verified using several criteria including identification of TATA boxes, INRs, and DPEs plus support from proteomic and gene expression analyses. Two previously recognized CPR classes, RR-1 and RR-2, form separate, well-supported clades with the exception of a small set of genes with long branches whose relationships are poorly resolved. Several of these outliers have clear orthologs in other species. Although both clades are under purifying selection, the RR-1 variant of the R&R Consensus is evolving at twice the rate of the RR-2 variant and is structurally more labile. In contrast, the regions flanking the R&R Consensus have diversified in amino-acid composition to a much greater extent in RR-2 genes compared with RR-1 genes. Many genes are found in compact tandem arrays that may include similar or dissimilar genes but always include just one of the two classes. Tandem arrays of RR-2 genes frequently contain subsets of genes coding for highly similar proteins (sequence clusters). Properties of the proteins indicated that each cluster may serve a distinct function in the cuticle.
  
  
  CONCLUSIONS
  The complete annotation of this large gene family provides insight on the mechanisms of gene family evolution and clues about the need for so many CPR genes. These data also should assist annotation of other Anopheles genes.
authors.affiliation: Department of Cellular Biology, University of Georgia, Athens, GA 30602 USA. scornman@uga.edu
authors.forename: R Scott
authors.initials: RS
authors.lastname: Cornman
authors.forename: Toru
authors.initials: T
authors.lastname: Togawa
authors.forename: W Augustine
authors.initials: WA
authors.lastname: Dunn
authors.forename: Ningjia
authors.initials: N
authors.lastname: He
authors.forename: Aaron C
authors.initials: AC
authors.lastname: Emmons
authors.forename: Judith H
authors.initials: JH
authors.lastname: Willis
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000852:Anopheles / Q000235:genetics*; D016384:Consensus Sequence / Q000235:genetics*; D030541:Databases, Genetic; D019143:Evolution, Molecular; D019476:Insect Proteins / Q000032:analysis* / Q000235:genetics*; D008954:Models, Biological; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D039104:RNA 3' Polyadenylation Signals / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D020506:Untranslated Regions / Q000032:analysis
chemical_list: D019476:Insect Proteins; D020506:Untranslated Regions; C047663:cuticle proteins, insects