Genomic identification of a putative circadian system in the cladoceran crustacean Daphnia pulex

Abstract

Essentially nothing is known about the molecular underpinnings of crustacean circadian clocks. The genome of Daphnia pulex, the only crustacean genome available for public use, provides a unique resource for identifying putative circadian proteins in this species. Here, the Daphnia genome was mined for putative circadian protein genes using Drosophila melanogaster queries. The sequences of core clock (e.g. CLOCK, CYCLE, PERIOD, TIMELESS and CRYPTOCHROME 2), clock input (CRYPTOCHROME 1) and clock output (PIGMENT DISPERSING HORMONE RECEPTOR) proteins were deduced. Structural analyses and alignment of the Daphnia proteins with their Drosophila counterparts revealed extensive sequence conservation, particularly in functional domains. Comparisons of the Daphnia proteins with other sequences showed that they are, in most cases, more similar to homologs from other species, including vertebrates, than they are to those of Drosophila. The presence of both CRYPTOCHROME 1 and 2 in Daphnia suggests the organization of its clock may be more similar to that of the butterfly Danaus plexippus than to that of Drosophila (which possesses CRYPTOCHROME 1 but not CRYPTOCHROME 2). These data represent the first description of a putative circadian system from any crustacean, and provide a foundation for future molecular, anatomical and physiological investigations of circadian signaling in Daphnia.

From genes to behavior: investigations of neurochemical signaling come of age for the model crustacean Daphnia pulex

“…(B)Alignment of Drosophila melanogaster pigment dispersing factor receptor (Drome) (Adams et al, 2000) with D. pulex PDH receptor (Dappu) (Tilden et al, 2011). In each protein, hormone receptor and transmembrane domains are highlighted in black and gray, respectively.…”

“…In both A and B, asterisks indicate amino acids that are identically conserved, whereas single and double dots denote amino acids that are similar in structure (a single dot refers to a conservative substitution and a double dot to a highly conservative substitution). Data are modified from Gard et al (Gard et al, 2009), Christie et al and Tilden et al (Tilden et al, 2011). Daphnia pulex neurochemistry…”

“…In addition to the prediction of the peptidome of D. pulex, several putative neuropeptide receptors have been identified via genome mining (Table2). Specifically, the sequences of the receptors for insulin-like peptide (Boucher et al, 2010), oxytocin/vasopressinlike peptide (intocin) (Stafflinger et al, 2008) and pigment dispersing hormone (PDH) (Tilden et al, 2011; Fig.2B) have been deduced. Although unpublished, genes encoding the receptors for many of the other known Daphnia neuropeptides also appear within the D. pulex draft genome assembly (Table2).…”

“…Collectively, these data strongly suggest that PDH, and the medial lateral neurons that produce it, are key components of the circadian signaling system of Daphnia. Interestingly, the Daphnia circadian system itself has been a recent subject of genome mining (Tilden et al, 2011). Here, D. pulex homologs of all the major components necessary for the establishment of a Drosophila-like clock, e.g.…”

In silico characterization of the insect diapause-associated protein couch potato (CPO) in Calanus finmarchicus (Crustacea: Copepoda)

“…Moreover, on-line software programs available to search these data sets, translate nucleotide sequences, and predict the post-translational processing and structural domains present in the deduced proteins, make genome/transcriptome mining a rapid and readily accessible approach for protein discovery in crustaceans (e.g. Christie et al, 2008;Gard et al, 2009;Ma et al, 2009Ma et al, , 2010Christie et al, , 2011aMcCoole et al, 2011;Tilden et al, 2011;McCoole et al, 2012aMcCoole et al, , 2012b. Here, we have used both publicly-accessible expressed sequence tags (ESTs) and our own 454 pyrosequencing data to search for homologs of CPO in C. finmarchicus and other crustaceans.…”