Martin et al. BMC Genomics 2010, 11:418 http://www.biomedcentral.com/1471-2164/11/418 Table 1 Genes altered significantly in liver by starvation (Continued) Cell structure int_oss_T4C19_osl_sal_std_5p_11C int_oss_THA07_osl_sal_std_5p_11C CK885060 CN181319 int_rpk_78C22_osl_sgp_std_5p_11C CK885437 mus_snm_03C07_sti_tra_nrc_5p_11C EG649361 ova_oyr_04F11_gal_sal_std_5p_11S BM414013 Page 6 of 20 -2.15 -2.13 -2.76 -2.76 -3.96 Cd Cd Cd Cd Cd collagen a3(I) Oncorhynchus mykiss COL1A3 mRNA for collagen a3(I) complete cds (O00423) Echinoderm microtubule-associated protein-like 1 (EMAP-1) (O93484) Collagen alpha 2(I) chain precursor (P14105) Myosin-9 (Myosin heavy chain nonmuscle IIa) List of selected mRNAs found up and down regulated resulting from starvation and grouped according to functional classes (shown in bold). The selection was based on manual assignment of function and genes with greatest fold difference in expression are presented, the genes that are down regulated are denoted by (-) value. In this table the genes within each group are ordered by expression level following starvation (PSL). If the genes were significantly altered in the infection these values are also given. The genes shown were significant at P < 0.001 following correction for multiple tests and greater than 2 fold change. 1Indicates the unique code for the feature on the microarray, 2Accession number of the cDNA sequence, if “No Acc” the TRAITS web page. 3Fold change for genes increased in expression following Aeromonas salmonicida infection in fish fed a normal diet (AFLvsPFL). 4Fold change for genes increased in expression following A. salmonicida infection in fish starved prior to infection (ASLvsPSL). 5Fold change for genes increased expression following 28 days starvation. 6Identity of the cDNA as determined by BlastX and BlastN searches. 7This indicates if this gene is up regulated in one or more other experiments, Ad (AFL), Bd (ASL), Cd (PSL), ABd (AFL+ASL), ABCd (AFL+ASL+PSL). The complete list of genes can be found in Additional file Table S1. Transcription, protein and amino acid metabolism Following starvation there was a general decrease in expression of genes related to mRNA transcription, pro- tein synthesis and protein degradation suggesting a reduction in protein metabolism. Genes decreased and related to protein synthesis included ribosomal protein mRNAs, rRNA binding proteins and several key tran- scription initiation factors. For protein degradation, genes related to the ubiquitin proteasome pathway such as polyubiquitin and proteasome subunits were reduced as was the lysosomal enzyme, cathepsin D. However a calcium activated protease, calpain 1 mRNA was increased following the starvation indicating these path- ways of protein degradation are independently controlled. Although a general decrease in genes relating to protein turnover was observed in starved animals, an increase in genes encoding proteins related to amino acid catabolism was found after starvation. The increased amino acid cat- abolism may generate molecules that contribute to gluco- neogenesis and subsequent entry into the TCA cycle. Lipid and steroid metabolism Genes encoding proteins performing steroid biosynthesis and metabolism of fatty acids were up regulated following starvation suggesting a reallocation of lipid reserves and cholesterol metabolism. A number of genes encoding key proteins involved in cholesterol metabolism were found increased including hydroxymethyl-glutaryl-CoA synthetase (HMG-CoA), a rate limiting enzyme in cholesterol bio- synthesis, isopentenylpyrophosphate delta-isomerase (IPP), lathosterol, squalene monooxygenase and squalene synthe- tase, which together demonstrate the fish were attempting to compensate for the dramatic reduction in circulating cholesterol levels following starvation. A number of genes involved in fatty acid metabolism were decreased indicating a general decrease in lipid metabolism. Serum and oxygen transport Plasma and blood transport protein encoding genes were reduced, both a and b haemoglobins, serotransfer- rin and the calcium binding albumin protein parvalbu- min decreased in starved animals indicating a reduced requirement for transport of oxygen and ions in the blood, presumably reflecting reduced energy and oxygen demand from peripheral tissues. A member of the apoli- poprotein family, described as an antifreeze protein had reduced expression in starved fish. Two genes central to preventing oxidative damage that showed increased expression were glutathione peroxidase and superoxide dismutase, both implicated in the protection from reac- tive oxygen species that are often produced as a conse- quence of nitric oxide synthase activity. Thus these genes may have been up regulated to deal with toxic by products of amino acid catabolism. Immune and defence genes altered by starvation Interestingly, genes encoding a number of secreted immune related proteins were decreased in expression following starvation, including serum amyloid A, com- plement factor B and serotransferrin, suggesting a reduced level of production of these serum secreted proteins which were constitutively expressed at low levels in uninfected animals. During an infection these are major components of the acute phase response. A mRNA encoding precerebellin, a protein also related to the acute phase response was increased in the starved fish, indicating there is a requirement to maintain this plasma protein at higher levels even during starvation conditions. Two liver specific anti- microbial peptides were also down regulated by star- vation, hepcidin and LEAP 2, which could reflect a reduced ability of the starved fish to respond to bac- terial infection.