Gene expression profile of hepatopancreas from grass shrimp Palaemonetes pugio exposed to cyclic hypoxia

Estuarine organisms often experience periods of cyclic hypoxia characterized by hypoxia in the early morning and normoxia in the afternoon. Here we examine the genomic responses of grass shrimp, Palaemonetes pugio, exposed to cyclic hypoxia in the laboratory. Differentially expressed genes in the hepatopancreas were determined in cyclic hypoxic vs. normoxic control groups after 1, 2, 5 and 10 days of exposure to cyclic hypoxia using microarrays printed with 661 annotated transcripts obtained from multiple EST (expressed sequence tag) libraries. Sampling on each day was conducted at two different time series, one in the morning (representing low concentration of dissolved oxygen (DO), designated C-AM) and one in the afternoon (representing high DO concentration, designated C-PM). Distinct differences were observed between the number and identity of specific genes that were significantly down- or up-regulated in shrimp collected at the low DO and high DO points of the cyclic DO cycle. However, cluster analysis showed that the overall response patterns of high (C-PM) and low DO (C-AM) exposures were in the same cluster at 1, 2, and 5 days. In contrast, the response patterns on different days were in different clusters. Day 1 was characterized by up-regulation of 17 unknown genes in the morning and a transient down-regulation of several hemocyanin genes, which returned to normoxic control levels in the afternoon. Days 2 and 5 showed significant down-regulation of 10 (C-AM) and 15 (C-PM) unknown genes, respectively. On day 10 the high DO samples showed a dramatic increase in the number of up-regulated genes, including several distinct hemocyanin genes, and this profile did not cluster with any of the other treatment groups. Vitellogenin, cathepsin L, cytochrome c oxidase subunit III, and fatty acid binding protein 10 were the signature down-regulated genes at day 10 (C-AM). According to GO annotation, the most abundant group of genes for both cyclic low (C-AM) and high (C-PM) DO exposure was associated with transport, defense response, and metabolic process. The differentially expressed genes were mapped to KEGG metabolic and regulatory pathways according to the gene distribution in Drosophila pathway database. Cyclic high (C-PM) DO affected a broad range of pathways compared to cyclic low (C-AM) DO.