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Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile

Academic Article
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Overview

authors

  • Trauger, S. A.
  • Kalisak, E.
  • Kalisiak, J.
  • Morita, H.
  • Weinberg, M. V.
  • Menon, A. L.
  • Poole, F. L.
  • Adams, M. W. W.
  • Siuzdak, Gary

publication date

  • March 2008

journal

  • Journal of Proteome Research  Journal

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.

subject areas

  • Adaptation, Physiological
  • Bacterial Proteins
  • Oligonucleotide Array Sequence Analysis
  • Peptides
  • Proteome
  • RNA, Messenger
  • Spectrometry, Mass, Electrospray Ionization
  • Thermus thermophilus
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Research

keywords

  • DNA microarray
  • Pyrococcus furiosus
  • hyperthermophile
  • mass spectrometry
  • metabolomics
  • polyamine
  • spermidine
  • tandem mass spectrometry
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Identity

International Standard Serial Number (ISSN)

  • 1535-3893

Digital Object Identifier (DOI)

  • 10.1021/pr700609j

PubMed ID

  • 18247545
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Additional Document Info

start page

  • 1027

end page

  • 1035

volume

  • 7

issue

  • 3

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