Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish

Abstract

Coral reef fishes are expected to experience rising sea surface temperatures due to climate change. How well tropical reef fishes will respond to these increased temperatures and which genes are important in the response to elevated temperatures is not known. Microarray technology provides a powerful tool for gene discovery studies, but the development of microarrays for individual species can be expensive and time-consuming. In this study, we tested the suitability of a Danio rerio oligonucleotide microarray for application in a species with few genomic resources, the coral reef fish Pomacentrus moluccensis. Results from a comparative genomic hybridization experiment and direct sequence comparisons indicate that for most genes there is considerable sequence similarity between the two species, suggesting that the D. rerio array is useful for genomic studies of P. moluccensis. We employed this heterologous microarray approach to characterize the early transcriptional response to heat stress in P. moluccensis. A total of 111 gene loci, many of which are involved in protein processing, transcription, and cell growth, showed significant changes in transcript abundance following exposure to elevated temperatures. Changes in transcript abundance were validated for a selection of candidate genes using quantitative real-time polymerase chain reaction. This study demonstrates that heterologous microarrays can be successfully employed to study species for which specific microarrays have not yet been developed, and so have the potential to greatly enhance the utility of microarray technology to the field of environmental and functional genomics.

Strict thermal threshold identified by quantitative PCR in the sponge Rhopaloeides odorabile

“…In order to predict the ability of reef organisms to adapt to changing environmental conditions, we need to enhance our understanding of their responses to stress, particularly at the molecular level. To date, research on thermal-stress responses in reef organisms has focused on corals and their symbiotic zooxanthellae, and only a few studies have assessed this response in other phyla (Kassahn et al 2007, López-Legentil et al 2008. This constitutes an important gap in coral reef biology, as other keystone reef organisms, especially invertebrates, remain largely under-studied (Przeslawski et al 2008).…”

“…The reef fish Pomacentrus moluccensis reacted to heat stress with a suppression of cell growth, repression of transcriptional activity and an increase of protein breakdown (Kassahn et al 2007). The reported gene-expression profiles obtained in response to stressors, the present study included, are consistent with an interpretation of metabolic re-organisation following the onset of stress, which would precede the induction of genes and de novo synthesis of proteins, which may ultimately allow the organism to cope with prolonged exposure to stress (Kassahn et al 2007). …”

Variation in the heat shock response and its implication for predicting the effect of global climate change on species' biogeographical distribution ranges and metabolic costs

“…However, some intertidal Antarctic invertebrates do show an inducible response at temperatures 10-12°C above those they inhabit, although they will probably never experience these temperatures under natural conditions (Clark et al, 2008b). Another interesting example is a recent study on the HSR of a warm stenothermal coral reef fish (Kassahn et al, 2007). A survey of heat-induced mRNA, using a non-species specific microarray, showed no induction of any of the typical inducible Hsps, e.g.…”

A microarray-based transcriptomic time-course of hyper- and hypo-osmotic stress signaling events in the euryhaline fishGillichthys mirabilis:osmosensors to effectors

“…A Tukey's post hoc test was subsequently employed to isolate genes whose expression differed significantly at each time point during hyper-and hypo-osmotic stress. Importantly, we did not impose an arbitrary minimal foldchange threshold on our data set as is common practice in microarray-based studies (Gracey et al, 2001;Podrabsky and Somero, 2004;Buckley et al, 2006;Aluru and Vijayan, 2007;Kassahn et al, 2007). Therefore, all genes deemed significant using the methodology described above were considered in subsequent analyses (see Table S2 in supplementary material).…”