Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile

Abstract

We have performed a comprehensive characterization of global molecular changes for a model organism Pyrococcus furiosus using transcriptomic (DNA microarray), proteomic, and metabolomic analysis as it undergoes a cold adaptation response from its optimal 95 to 72 degrees C. Metabolic profiling on the same set of samples shows the down-regulation of many metabolites. However, some metabolites are found to be strongly up-regulated. An approach using accurate mass, isotopic pattern, database searching, and retention time is used to putatively identify several metabolites of interest. Many of the up-regulated metabolites are part of an alternative polyamine biosynthesis pathway previously established in a thermophilic bacterium Thermus thermophilus. Arginine, agmatine, spermidine, and branched polyamines N4-aminopropylspermidine and N4-( N-acetylaminopropyl)spermidine were unambiguously identified based on their accurate mass, isotopic pattern, and matching of MS/MS data acquired under identical conditions for the natural metabolite and a high purity standard. Both DNA microarray and semiquantitative proteomic analysis using a label-free spectral counting approach indicate the down-regulation of a large majority of genes with diverse predicted functions related to growth such as transcription, amino acid biosynthesis, and translation. Some genes are, however, found to be up-regulated through the measurement of their relative mRNA and protein levels. The complimentary information obtained by the various "omics" techniques is used to catalogue and correlate the overall molecular changes.

Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

“…E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations . In another study, Trauger et al (2008) studied the adaptation response of Pyrococcus furiosus when shifting from its optimal 95 u C to 72 u C using integrated transcriptomic, proteomic and metabolomic analysis. The complementary information obtained by the various 'omics' techniques was used to catalogue and correlate the overall molecular changes.…”

Dealing with the unknown: Metabolomics and Metabolite Atlases

“…However, in many cases it is not possible to separate sufficient quantities due to sample availability and/or complexity. In these cases, it is necessary to synthesize libraries of related hypothetical molecules and compare features (e.g., m/z, fragmentation masses, and method specific retention time) with the unknown metabolite [37,40].…”

System Response of Metabolic Networks in Chlamydomonas reinhardtii to Total Available Ammonium

“…Hence, the outcome of cellular regulation should encompass metabolite measurements to truly depict a systemic view of stress responses, called metabolomics. Metabolomics uses a range of platforms for surveying combinations of chemical compounds in biological systems (23)(24)(25)(26). Although measurements of proteins, especially enzymes, concomitant with their substrates, products and allosteric modifiers appear to be a logical choice of tools to study metabolic response to nutritional stress, there have been only a few investigations on metabolomics and proteomics data integration to enable a system level understanding of cellular metabolism.…”