Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile
| Autor: | Hirotoshi Morita, Michael V. Weinberg, Gary Siuzdak, Angeli Lal Menon, Michael W. W. Adams, Ewa Kalisak, Jaroslaw Kalisiak, Farris L. Poole, Sunia A. Trauger |
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| Rok vydání: | 2008 |
| Předmět: |
Spectrometry
Mass Electrospray Ionization Proteome Thermus thermophilus Metabolite General Chemistry Biology biology.organism_classification Adaptation Physiological Biochemistry Transcriptome chemistry.chemical_compound Metabolomics Bacterial Proteins chemistry Metabolome Pyrococcus furiosus RNA Messenger DNA microarray Peptides Oligonucleotide Array Sequence Analysis |
| Zdroj: | Journal of Proteome Research. 7:1027-1035 |
| ISSN: | 1535-3907 1535-3893 |
| DOI: | 10.1021/pr700609j |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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