title: In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda).
abstract: Couch potato (CPO) is an RNA-binding protein involved in the regulation of nervous system development and adult diapause in insects. Within insects, this protein is highly conserved, yet it has not been identified in another large arthropod group, the Crustacea. Here, functional genomics was used to identify putative CPO homologs in the copepod Calanus finmarchicus, a planktonic crustacean that undergoes seasonal diapause. In silico mining of expressed sequence tag (EST) and 454 pyrosequencing data resulted in the identification of two full-length CPO proteins, each 205 amino acids long. The two C. finmarchicus CPOs (Calfi-CPO I and II) are identical in sequence with the exception of three amino acids, and are predicted to possess a single RNA recognition motif (RRM). Sequence comparison of the two Calfi-CPOs with those of insects shows high levels of amino acid conservation, particularly in their RRMs. Using the C. finmarchicus sequences as queries, ESTs encoding partial CPOs were identified from two other crustaceans, the parasitic copepod Lernaeocera branchialis and shrimp Penaeus monodon. Surprisingly, no convincing CPO-encoding transcripts were identified from crustacean species with very large (>100,000) EST datasets (e.g. Litopenaeus vannamei, Daphnia pulex and Lepeophtheirus salmonis), suggesting that CPO transcript/protein may be expressed at very low levels or absent in some crustaceans. RNA-Seq data suggested stage-specific expression of CPO in C. finmarchicus, with few transcripts present in eggs (which represent mixed embryonic stages) and adults, and high levels in nauplii and copepodites; stages exhibiting high CPO expression are consistent with a role for it in neuronal development.
authors.affiliation: Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, 96822, USA. crabman@pbrc.hawaii.edu
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Christie
authors.forename: Vittoria
authors.initials: V
authors.lastname: Roncalli
authors.forename: Paola Batta
authors.initials: PB
authors.lastname: Lona
authors.forename: Matthew D
authors.initials: MD
authors.lastname: McCoole
authors.forename: Benjamin L
authors.initials: BL
authors.lastname: King
authors.forename: Ann
authors.initials: A
authors.lastname: Bucklin
authors.forename: Daniel K
authors.initials: DK
authors.lastname: Hartline
authors.forename: Petra H
authors.initials: PH
authors.lastname: Lenz
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D060829:Arthropod Proteins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D003198:Computer Simulation; D033342:Copepoda / Q000737:chemistry / Q000235:genetics*; D003621:Daphnia; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005260:Female; D023281:Genomics; D008297:Male; D008969:Molecular Sequence Data; D012313:RNA / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*
chemical_list: D060829:Arthropod Proteins; D016601:RNA-Binding Proteins; D012313:RNA