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First published online April 20, 2007
Journal of Experimental Biology 210, 1593-1601 (2007)
Published by The Company of Biologists 2007
doi: 10.1242/jeb.000141

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Review Article

Functional genomics and proteomics of the cellular osmotic stress response in `non-model' organisms

Dietmar Kültz^1,*, Diego Fiol¹, Nelly Valkova¹, Silvia Gomez-Jimenez², Stephanie Y. Chan¹ and Jinoo Lee¹

¹ Physiological Genomics Group, Department of Animal Science, One Shields Avenue, University of California, Davis, CA 95616, USA
² Laboratorio de Fisiología de Invertebrados Marinos, CIAD, A.C. Carr. a la Victoria Km. 0.6, CP 83000, Hermosillo, Sonora, México

^* Author for correspondence (e-mail: dkueltz{at}ucdavis.edu)

Accepted 3 January 2007

All organisms are adapted to well-defined extracellular salinity ranges. Osmoregulatory mechanisms spanning all levels of biological organization, from molecules to behavior, are central to salinity adaptation. Functional genomics and proteomics approaches represent powerful tools for gaining insight into the molecular basis of salinity adaptation and euryhalinity in animals. In this review, we discuss our experience in applying such tools to so-called `non-model' species, including euryhaline animals that are well-suited for studies of salinity adaptation. Suppression subtractive hybridization, RACE-PCR and mass spectrometry-driven proteomics can be used to identify genes and proteins involved in salinity adaptation or other environmental stress responses in tilapia, sharks and sponges. For protein identification in non-model species, algorithms based on sequence homology searches such as MSBLASTP2 are most powerful. Subsequent gene ontology and pathway analysis can then utilize sets of identified genes and proteins for modeling molecular mechanisms of environmental adaptation. Current limitations for proteomics in non-model species can be overcome by improving sequence coverage, N- and C-terminal sequencing and analysis of intact proteins. Dependence on information about biochemical pathways and gene ontology databases for model species represents a more severe barrier for work with non-model species. To minimize such dependence, focusing on a single biological process (rather than attempting to describe the system as a whole) is key when applying `omics' approaches to non-model organisms.

Key words: salinity adaptation, osmotic stress, systems biology, euryhaline fish, proteomics

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