Modulation of gene expression in heart and liver of hibernating black bears (Ursus americanus)

Abstract

Background: Hibernation is an adaptive strategy to survive in highly seasonal or unpredictable environments. The molecular and genetic basis of hibernation physiology in mammals has only recently been studied using large scale genomic approaches. We analyzed gene expression in the American black bear, Ursus americanus, using a custom 12,800 cDNA probe microarray to detect differences in expression that occur in heart and liver during winter hibernation in comparison to summer active animals.

Results: We identified 245 genes in heart and 319 genes in liver that were differentially expressed between winter and summer. The expression of 24 genes was significantly elevated during hibernation in both heart and liver. These genes are mostly involved in lipid catabolism and protein biosynthesis and include RNA binding protein motif 3 (Rbm3), which enhances protein synthesis at mildly hypothermic temperatures. Elevated expression of protein biosynthesis genes suggests induction of translation that may be related to adaptive mechanisms reducing cardiac and muscle atrophies over extended periods of low metabolism and immobility during hibernation in bears. Coordinated reduction of transcription of genes involved in amino acid catabolism suggests redirection of amino acids from catabolic pathways to protein biosynthesis. We identify common for black bears and small mammalian hibernators transcriptional changes in the liver that include induction of genes responsible for fatty acid β oxidation and carbohydrate synthesis and depression of genes involved in lipid biosynthesis, carbohydrate catabolism, cellular respiration and detoxification pathways.

Conclusions: Our findings show that modulation of gene expression during winter hibernation represents molecular mechanism of adaptation to extreme environments.

Figure 1

Selection of genes differentially expressed during hibernation in heart (A) and liver (B) tissue in black bears. Expression values are normalized to the mean in summer active animals. Solid bars show expression values obtained in real-time PCR, open bars in microarray experiments, error bars are SDs.

Figure 2

Gene set enrichment analysis results for the translation category. The translation category is enriched by up regulated genes in heart (A, false discovery rate (FDR) of <0.001) and liver (B, FDR = 0.046) of hibernating black bears. An expression data set sorted by correlation with hibernating phenotype and the corresponding heat map with red for up regulated and blue for down regulated genes during hibernation are shown on the left. Dates on the top indicate time of tissue sampling from each bear. Plot of the running sum for enrichment score (ES) in the data set (top) and location of genes (hits) from each GO category in the list ranked according to expression differences (middle) and the ranked list metric (bottom) are shown on the right.

Figure 3

Gene set enrichment analysis results for the fatty acid β oxidation and amino acid catabolism categories. The fatty acid β oxidation category (A) is enriched by up regulated genes (FDR = 0.043) and amino acid catabolism (B) is enriched by down regulated genes (FDR = 0.015) in liver of hibernating black bears. The figure legend is explained in the text of Figure 2.