Prediction of the protein components of a putative Calanus finmarchicus (Crustacea, Copepoda) circadian signaling system using a de novo assembled transcriptome

Abstract

Diel vertical migration and seasonal diapause are critical life history events for the copepod Calanus finmarchicus. While much is known about these behaviors phenomenologically, little is known about their molecular underpinnings. Recent studies in insects suggest that some circadian genes/proteins also contribute to the establishment of seasonal diapause. Thus, it is possible that in Calanus these distinct timing regimes share some genetic components. To begin to address this possibility, we used the well-established Drosophila melanogaster circadian system as a reference for mining clock transcripts from a 200,000+ sequence Calanus transcriptome; the proteins encoded by the identified transcripts were also deduced and characterized. Sequences encoding homologs of the Drosophila core clock proteins CLOCK, CYCLE, PERIOD and TIMELESS were identified, as was one encoding CRYPTOCHROME 2, a core clock protein in ancestral insect systems, but absent in Drosophila. Calanus transcripts encoding proteins known to modulate the Drosophila core clock were also identified and characterized, e.g. CLOCKWORK ORANGE, DOUBLETIME, SHAGGY and VRILLE. Alignment and structural analyses of the deduced Calanus proteins with their Drosophila counterparts revealed extensive sequence conservation, particularly in functional domains. Interestingly, reverse BLAST analyses of these sequences against all arthropod proteins typically revealed non-Drosophila isoforms to be most similar to the Calanus queries. This, in combination with the presence of both CRYPTOCHROME 1 (a clock input pathway protein) and CRYPTOCHROME 2 in Calanus, suggests that the organization of the copepod circadian system is an ancestral one, more similar to that of insects like Danaus plexippus than to that of Drosophila.

Differential expression of circadian clock genes in two strains of beetles reveals candidates related to photoperiodic induction of summer diapause

“…Many of the deduced amino acid sequences of protein domains were highly conserved among different species, especially dbt, sgg and vri. It has been reported that the dbt, sgg and vri genes of the copepod Calanus finmarchicus show extensive sequence conservation with the corresponding genes in D. melanogaster, especially in functional domains (Christie et al, 2013). Many studies also suggest a high degree of evolutionary conservation between D. melanogaster dbt and sgg genes and those of vertebrates (Ruel et al, 1993;Fan et al, 2009).…”

Identification and developmental expression of the enzymes responsible for dopamine, histamine, octopamine and serotonin biosynthesis in the copepod crustacean Calanus finmarchicus

“…Searches of the transcriptome assembly produced by Trinity were conducted using the DeCypher Tera-BLASTP algorithm on the Mount Desert Island Biological Laboratory’s TimeLogic DeCypher server (MDIBL, Salisbury Cove, ME, USA; http://decypher.mdibl.org/decypher/algo-tera-blast/tera-tblastn_an.shtml) as described in several recent publications (Christie et al, 2013a, 2013b). For all searches, the DeCypher program database was set to the combined Trinity assembly and a known fruit fly Drosophila melanogaster protein was used as the query sequence.…”

“…Analyses of protein conservation and structure were conducted using a workflow described in Christie et al (2013a, 2013b). To identify the proteins most similar to each of the C. finmarchicus amine biosynthetic enzymes identified in this study, the deduced Calanus sequence was used to query the annotated protein dataset present in FlyBase (version FB2013_01), as well as the non-redundant arthropod protein dataset (taxid:6656) curated in GenBank (excluding C. finmarchicus proteins, obvious partial proteins, synthetic constructs, and provisional/unannotated hypothetical protein sequences); for both searches the blastp algorithm was used (Altschul et al, 1997).…”

“…As part of an ongoing effort to identify and characterize the neurochemical signaling systems of the copepod crustacean Calanus finmarchicus (Christie et al, 2013a, 2013b), the biomass dominant zooplankton for much of the North Atlantic Ocean (Dale et al, 2001; Marshall and Orr, 1955; Meise and O’Reilly, 1996), we have mined a de novo assembled transcriptome for sequences encoding the enzymes responsible for the generation of dopamine, histamine, octopamine and serotonin. This study complements and augments an earlier report describing transcripts/proteins that contribute to peptidergic signaling in this ecologically important species (Christie et al, 2013a).…”

In silico characterization of the neuropeptidome of the Western black widow spider Latrodectus hesperus

“…Here, more limited starting material can often be used for the development of the transcriptome, and once produced, the resource provides a stable platform for the identification of essentially any protein of interest (e.g. Christie et al, 2013bChristie et al, , 2014aLenz et al, 2014), including neuropeptide precursors (e.g. Christie 2008aChristie ,b, 2014aChristie et al, 2008Christie et al, , 2010aChristie et al, , 2011aChristie et al, ,b, 2013aGard et al, 2009;Ma et al, 2009Ma et al, , 2010Toullec et al, 2013;Yan et al, 2012).…”