Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus

Abstract

BackgroundNatural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is sparse. The clitellate annelid Lumbricus rubellus is a model organism for soil health testing, but genetic data have been lacking.ResultsWe generated a 17,000 sequence expressed sequence tag dataset, defining ~8,100 different putative genes, and built an 8,000-element transcriptome microarray for L. rubellus. Strikingly, less than half the putative genes (43%) were assigned annotations from the gene ontology (GO) system; this reflects the phylogenetic uniqueness of earthworms compared to the well-annotated model animals. The microarray was used to identify adult- and juvenile-specific transcript profiles in untreated animals and to determine dose-response transcription profiles following exposure to three xenobiotics from different chemical classes: inorganic (the metal cadmium), organic (the polycyclic aromatic hydrocarbon fluoranthene), and agrochemical (the herbicide atrazine). Analysis of these profiles revealed compound-specific fingerprints which identify the molecular responses of this annelid to each contaminant. The data and analyses are available in an integrated database, LumbriBASE.ConclusionL. rubellus has a complex response to contaminant exposure, but this can be efficiently analysed using molecular methods, revealing unique response profiles for different classes of effector. These profiles may assist in the development of novel monitoring or bioremediation protocols, as well as in understanding the ecosystem effects of exposure.

Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications

“…The DEG induced by Cu belongs to two different functions: protein metabolism (CadPk) and signal transduction (ficolin). Similar to what was observed in L. rubellus [44], down-regulation in calcium-binding proteins Development 30,2011suggests functional interactions between Ca 2þ and ions like Cu 2þ and Cd 2þ [45] that impair its original function. The ficolin protein family comprises three different molecules encoded by the FCN1, FCN2, and FCN3 genes, which play roles in innate immunity, providing organisms with defense mechanisms without requiring prior exposure.…”

The significance of genome-wide transcriptional regulation in the evolution of stress tolerance

“…To Evol Ecol (2010) 24:527-539 529 maximize survival and reproduction (i.e. Darwinian fitness), it is therefore of paramount importance to fine tune the timing, efficiency and specificity of targeted responses (Gasch et al 2000;Gracey et al 2001;Owen et al 2008). However, defining the precise boundaries of transcriptional norms is a major hurdle, mainly due to inter-and intraspecies genomic differences.…”

Inhibition of pyrene biotransformation by piperonyl butoxide and identification of two pyrene derivatives in Lumbriculus variegatus (Oligochaeta)

“…Based on a Blast search (J. Lemmetyinen, University of Eastern Finland, Joensuu, Finland, personal communication) carried out with Blast2GO software [36], the homology to some characterized CYP genes ranges from 45 to 64%. In addition, CYP genes have been isolated and purified in organisms belonging to the same class as L. variegatus: in Lumbricus terrestris (Oligochaeta) [37] and Lumbricus rubellus (Oligochaeta) [38].…”