"Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus.
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 "-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.
Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Lotharstrasse, 47057 Duisburg, Germany. melanie.zaparty@uni-due.de
Melanie
M
Zaparty
Dominik
D
Esser
Susanne
S
Gertig
Patrick
P
Haferkamp
Theresa
T
Kouril
Andrea
A
Manica
Trong K
TK
Pham
Julia
J
Reimann
Kerstin
K
Schreiber
Pawel
P
Sierocinski
Daniela
D
Teichmann
Marleen
M
van Wolferen
Mathias
M
von Jan
Patricia
P
Wieloch
Sonja V
SV
Albers
Arnold J M
AJ
Driessen
Hans-Peter
HP
Klenk
Christa
C
Schleper
Dietmar
D
Schomburg
John
J
van der Oost
Phillip C
PC
Wright
Bettina
B
Siebers
D023281:Genomics / Q000379:methods* / Q000592:standards*; D048229:Sulfolobus solfataricus / Q000235:genetics*