Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile
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- 作者：Sunia A. Trauger ; Ewa Kalisak ; Jaroslaw Kalisiak ; Hirotoshi Morita ; Michael V. Weinberg ; Angeli Lal Menon ; Farris L. Poole II ; Michael W. W. Adams ; Gary Siuzdak
- 刊名：Journal of Proteome Research
- 出版年：2008
- 出版时间：March 2008
- 年：2008
- 卷：7
- 期：3
- 页码：1027 - 1035
- 全文大小：1054K
- 年卷期：v.7,no.3(March 2008)
- ISSN：1535-3907
文摘
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 °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.