Department of Ecogenetics and Systems Biology - Division of Archaea Biology and Ecogenomics


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SYSMO

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SYSMO: A Silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Temperature changes are not only most difficult to deal with for organisms, it is also unclear how biological networks can withstand and respond to such changes. Even slight differences between the rates of individual reactions in metabolic pathways should cause rapid accumulation or depletion of intermediates with various deleterious effects. With a change in temperature, the rates of individual reactions in metabolic pathways must therefore change by precisely the same extent. Organisms could adapt by (i) having identical temperature coefficients of the enzymes, (ii) metabolic regulation, (iii) adjusting Vmax-s (e.g. through enzyme phosphorylation), (iv) adjusting translation or protein stability, (v) adjusting transcription or mRNA stability, (vi) rerouting the metabolic flow, (vii) formation of compatible solutes, (viii) export of overflow metabolites or (ix) going into dormancy. We hypothesize that several of theses mechanisms contribute to different extents and will try to quantify each of these adaptations in a systems biology approach. As the issue should be most acute for thermophiles, we will perform these studies with a thermophilic archaeon.

The archaeal model organism of choice for this systems biology approach is Sulfolobus solfataricus, a thermoacidophilic Crenarchaeon that grows at around 80°C and pH 3 [2]. S. solfataricus uses an unusual branched Entner-Doudoroff (ED) pathway for glucose catabolism [3]. Life at high temperature requires a very efficient adaptation to temperature changes, which is most difficult to deal with for organisms and it is unclear how biological networks can withstand and respond to such changes. In this sysmo project,10 partner laboratories will study the central carbohydrate metabolism (CCM), i.e. the branched ED pathway of S. solfataricus and its regulation under temperature variation by the integration of genomic, transcriptomic, proteomic, metabolomic, kinetic and biochemical information. The long term goal of the project is to build a sufficiently precise replica for this part of the living cell (“a Silicon Cell”) to enable computation of life, particular its robustness to changes in temperature, at the system level.

Selected publications
[1] Siebers & Schönheit (2005) Curr. Opin. Microbiol. 8, 695-705
2] Zillig et al. (1980) Arch. Microbiol. 125, 259-269
[3] Ahmed et al. (2005) Biochem. J. 390.

Duration: 01.11.2007 - 30.09.2010


Funding: European Commission Research: The Reasearch Council of Norway 182901/S10

Participants: Christa Schleper, Andrea Manica

Publications:
Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJM, Grogan DW, Albers SV, Schleper C (2011) UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili. Molecular Microbiology 82(4): 807-817.

Reeve JN, Schleper C (2011) Archaea: very diverse, often different but never bad?Current Opinion in Microbiology 14(3): 271-273.

Manica A, Zebec Z, Teichmann D, Schleper C (2011) In vivo activity of CRISPR-mediated virus defence in a hyperthermophilic archaeon. Molecular Microbiology 80(2): 481-491.

Zaparty M, Esser D, Gertig S, Haferkamp P, Kouril T, Manica A, Pham TK, Reimann J, Schreiber K, Sierocinski P, Teichmann D, van Wolferen M, von Jan M, Wieloch P, Albers SV, Driessen AJ, Klenk HP, Schleper C, Schomburg D, van der Oost J, Wright PC, Siebers B (2009) "Hot standards" for the thermoacidophilic archaeon Sulfolobus solfataricus. Extremophiles 14(1): 119-142.

Redder P, Peng X, Brügger K, Shah SA, Roesch F, Greve B, She Q, Schleper C, Forterre P, Garrett RA, Prangishvili D (2009) Four newly isolated fuselloviruses from extreme geothermal environments reveal unusual morphologies and a possible interviral recombination mechanism. Environmental Microbiology 11(11): 2849-2862.

Albers SV, Birkeland NK, Driessen AJ, Gertig S, Haferkamp P, Klenk HP, Kouril T, Manica A, Pham TK, Ruoff P, Schleper C, Schomburg D, Sharkey KJ, Siebers B, Sierocinski P, Steuer R, van der Oost J, Westerhoff HV, Wieloch P, Wright PC, Zaparty M SulfoSYS (Sulfolobus Systems Biology) (2009) Towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation. Biochemical Society Transactions 37(Pt 1): 58-64.

Perevalova AA, Kolganova TV, Birkeland NK, Schleper C, Bonch-Osmolovskaya EA, Lebedinsky AV (2008) Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland. Applied and Environmental Microbiology 74(24): 7620-7628.

Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, Boekema, Driessen AJM, Schleper C, Albers SV (2008) UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation. Molecular Microbiololy 70(4): 938-52.

Fröls S, Gordon PM, Panlilio MA, Duggin ID, Bell SD, Sensen CW, Schleper C (2007) Response of the hyperthermophilic Archaeon Sulfolobus solfataricus to UV damage. Journal of Bacteriology 189: 8708-8718.

Fröls S, Gordon PM, Panlilio MA, Schleper C, Sensen CW (2007) Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365: 48-59.

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