Abstract
The transcriptomes of model organisms have been defined under specific laboratory growth conditions. The standard protocol for Caenorhabditis elegans growth and maintenance is 20°C on an Escherichia coli diet. Temperatures ranging from 15°C to 25°C or feeding with other species of bacteria are considered physiological conditions, but the effect of these conditions on the worm transcriptome has not been well characterized. Here, we compare the global gene expression profile for the reference Caenorhabditis elegans strain (N2) grown at 15°C, 20°C, and 25°C on two different diets, Escherichia coli and Bacillus subtilis. When C. elegans were fed E. coli and the growth temperature was increased, we observed an enhancement of defense response pathways and down-regulation of genes associated with metabolic functions. However, when C. elegans were fed B. subtilis and the growth temperature was increased, the nematodes exhibited a decrease in defense response pathways and an enhancement of expression of genes associated with metabolic functions. Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiological range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome.
Highlights
The reproducibility of results obtained in studies using model organisms highly depends on uniformity of growing conditions
Our results show that C. elegans undergo significant metabolic and defense response changes when the maintenance temperature fluctuates within the physiological range and that the degree of pathogenicity of the bacterial diet can further alter the worm transcriptome
Raw sequence data generated in this study are available at the Gene Expression Omnibus (GEO) data repository (Accession number GSE101524). mRNA reads were aligned to the C. elegans N2 reference genome
Summary
The reproducibility of results obtained in studies using model organisms highly depends on uniformity of growing conditions. Temperatures outside this range are not considered physiological and have a harmful effect on the development and physiology of the worm (http:// www.wormbook.org). Using physiological temperatures above and below 20oC is a common practice when performing studies with C. elegans in the lab and it is especially important when analyzing thermosensitive mutants or when performing RNAi assays. At 25oC, laboratory maintained wild type C. elegans complete the life cycle in 2.5 days, whereas at 15oC worm development slows down and the life cycle extends up to 5 days. C. elegans studies performed at temperatures within the 15– 25oC physiological range may elicit different biological responses by the worm, yet results and conclusions from studies at different temperatures are often compared
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