Publication

"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus

Zaparty, M., Esser, D., Gertig, S., Haferkamp, P., Kouril, T., Manica, A., Pham, T. K., Reimann, J., Schreiber, K., Sierocinski, P., Teichmann, D., van Wolferen, M., von Jan, M., Wieloch, P., Albers, S. V., Driessen, A. J. M., Klenk, H-P., Schleper, C., Schomburg, D., van der Oost, J., Wright, P. C. & Siebers, B., Jan-2010, In : Extremophiles. 14, 1, p. 119-142 24 p.

Research output: Contribution to journalArticleAcademicpeer-review

  • Melanie Zaparty
  • Dominik Esser
  • Susanne Gertig
  • Patrick Haferkamp
  • Theresa Kouril
  • Andrea Manica
  • Trong K. Pham
  • Julia Reimann
  • Kerstin Schreiber
  • Pawel Sierocinski
  • Daniela Teichmann
  • Marleen van Wolferen
  • Mathias von Jan
  • Patricia Wieloch
  • Sonja V. Albers
  • Arnold J. M. Driessen
  • Hans-Peter Klenk
  • Christa Schleper
  • Dietmar Schomburg
  • John van der Oost
  • Phillip C. Wright
  • Bettina Siebers

Within the archaea, the thermoacidophilic crenarchaeote Sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. Within the Sulfolobus Systems Biology ("SulfoSYS")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic information for production of a silicon cell-model. The network under investigation is the central carbohydrate metabolism. The generation of high-quality quantitative data, which is critical for the investigation of biological systems and the successful integration of the different datasets, derived for example from high-throughput approaches (e.g., transcriptome or proteome analyses), requires the application and compliance of uniform standard protocols, e.g., for growth and handling of the organism as well as the "aEuro"omics" approaches. Here, we report on the establishment and implementation of standard operating procedures for the different wet-lab and in silico techniques that are applied within the SulfoSYS-project and that we believe can be useful for future projects on Sulfolobus or (hyper)thermophiles in general. Beside established techniques, it includes new methodologies like strain surveillance, the improved identification of membrane proteins and the application of crenarchaeal metabolomics.

Original languageEnglish
Pages (from-to)119-142
Number of pages24
JournalExtremophiles
Volume14
Issue number1
Publication statusPublished - Jan-2010

    Keywords

  • Crenarchaeon, Standard operating procedures, Genomics, Transcriptomics, Proteomics, Metabolomics, Biochemistry, Systems biology, ENTNER-DOUDOROFF PATHWAY, CENTRAL CARBOHYDRATE-METABOLISM, DNA MICROARRAY ANALYSIS, HYPERTHERMOPHILIC ARCHAEON, MEMBRANE PROTEOME, GENUS SULFOLOBUS, HIGH-TEMPERATURE, SYSTEMS BIOLOGY, SILICON CELL, KEY-ENZYME

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