期刊
EXTREMOPHILES
卷 14, 期 1, 页码 119-142出版社
SPRINGER JAPAN KK
DOI: 10.1007/s00792-009-0280-0
关键词
Crenarchaeon; Standard operating procedures; Genomics; Transcriptomics; Proteomics; Metabolomics; Biochemistry; Systems biology
资金
- Federal Ministry of Education and Resarch (BMBF), Germany
- Netherlands Organization for Scientific Research (NWO)
- Research Council of Norway (RCN)
- Biotechnology, Biological Research Council (BBSRC), United Kingdom
- University of Bergen (Norway)
- University of Duisburg-Essen (Germany)
- Wageningen University and University of Groningen (The Netherlands)
- University of Sheffield and the University of Manchester (The United Kingdom)
- Free University Amsterdam (The Netherlands)
- SulfoSYS-project [SysMo P N-01-09-23]
- BBSRC [BB/F003420/1] Funding Source: UKRI
- EPSRC [EP/E036252/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/F003420/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/E036252/1] Funding Source: researchfish
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 aEuroomics 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.
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