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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+Show Affiliations

Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, 96822, USA. crabman@pbrc.hawaii.eduNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23262277

Citation

Christie, Andrew E., et al. "In Silico Characterization of the Insect Diapause-associated Protein Couch Potato (CPO) in Calanus Finmarchicus (Crustacea: Copepoda)." Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, vol. 8, no. 1, 2013, pp. 45-57.
Christie AE, Roncalli V, Lona PB, et al. In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). Comp Biochem Physiol Part D Genomics Proteomics. 2013;8(1):45-57.
Christie, A. E., Roncalli, V., Lona, P. B., McCoole, M. D., King, B. L., Bucklin, A., Hartline, D. K., & Lenz, P. H. (2013). In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, 8(1), 45-57. https://doi.org/10.1016/j.cbd.2012.11.002
Christie AE, et al. In Silico Characterization of the Insect Diapause-associated Protein Couch Potato (CPO) in Calanus Finmarchicus (Crustacea: Copepoda). Comp Biochem Physiol Part D Genomics Proteomics. 2013;8(1):45-57. PubMed PMID: 23262277.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda). AU - Christie,Andrew E, AU - Roncalli,Vittoria, AU - Lona,Paola Batta, AU - McCoole,Matthew D, AU - King,Benjamin L, AU - Bucklin,Ann, AU - Hartline,Daniel K, AU - Lenz,Petra H, Y1 - 2012/11/27/ PY - 2012/09/26/received PY - 2012/11/19/revised PY - 2012/11/19/accepted PY - 2012/12/25/entrez PY - 2012/12/25/pubmed PY - 2013/7/9/medline SP - 45 EP - 57 JF - Comparative biochemistry and physiology. Part D, Genomics & proteomics JO - Comp Biochem Physiol Part D Genomics Proteomics VL - 8 IS - 1 N2 - 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. SN - 1878-0407 UR - https://www.unboundmedicine.com/medline/citation/23262277/In_silico_characterization_of_the_insect_diapause_associated_protein_couch_potato__CPO__in_Calanus_finmarchicus__Crustacea:_Copepoda__ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1744-117X(12)00070-6 DB - PRIME DP - Unbound Medicine ER -