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Open Access Research article

From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Karin S Kassahn15*, Ross H Crozier1, Alister C Ward2, Glenn Stone3 and M Julian Caley4

Author Affiliations

1 School of Marine and Tropical Biology, James Cook University, Townsville, QLD 4811, Australia

2 School of Medicine, Deakin University, Geelong, VIC 3217, Australia

3 CSIRO Mathematical and Information Sciences, North Ryde, NSW 2113, Australia

4 Australian Institute of Marine Sciences, PMB No.3, Townsville, QLD 4810, Australia

5 ARC Centre of Excellence in Bioinformatics and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia

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BMC Genomics 2007, 8:358  doi:10.1186/1471-2164-8-358

Published: 5 October 2007

Abstract

Background

Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures.

Results

We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions.

Conclusion

This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat-responsive genes suggest that prolonged heat exposure leads to oxidative stress and protein damage, a challenge of the immune system, and the re-allocation of energy sources. This study hence offers insight into the effects of environmental stress on biological function and sheds light on the expected sensitivity of coral reef fishes to elevated temperatures in the future.