“Hot standards” for the thermoacidophilic archaeon Sulfolobus solfataricus

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

doi:10.1007/s00792-009-0280-0

Cited by 54 publications

(94 citation statements)

References 70 publications

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“…S. solfataricus strain P2 cells were grown on modified Brock medium supplemented with 0.1% (wt/vol) tryptone and 0.4% (wt/vol) sucrose (41). Cell lysates were prepared as described previously (1).…”

Section: Methodsmentioning

confidence: 99%

An HflX-Type GTPase from Sulfolobus solfataricus Binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States

et al. 2011

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HflX GTPases are found in all three domains of life, the Bacteria, Archaea, and Eukarya. HflX from Escherichia coli has been shown to bind to the 50S ribosomal subunit in a nucleotide-dependent manner, and this interaction strongly stimulates its GTPase activity. We recently determined the structure of an HflX ortholog from the archaeon Sulfolobus solfataricus (SsoHflX). It revealed the presence of a novel HflX domain that might function in RNA binding and is linked to a canonical G domain. This domain arrangement is common to all archaeal, bacterial, and eukaryotic HflX GTPases. This paper shows that the archaeal SsoHflX, like its bacterial orthologs, binds to the 50S ribosomal subunit. This interaction does not depend on the presence of guanine nucleotides. The HflX domain is sufficient for ribosome interaction. Binding appears to be restricted to free 50S ribosomal subunits and does not occur with 70S ribosomes engaged in translation. The fingerprint 1 H-15 N heteronuclear correlation nuclear magnetic resonance (NMR) spectrum of SsoHflX reveals a large number of well-resolved resonances that are broadened upon binding to the 50S ribosomal subunit. The GTPase activity of SsoHflX is stimulated by crude fractions of 50S ribosomal subunits, but this effect is lost with further high-salt purification of the 50S ribosomal subunits, suggesting that the stimulation depends on an extrinsic factor bound to the 50S ribosomal subunit. Our results reveal common properties but also marked differences between archaeal and bacterial HflX proteins.

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Section: Methodsmentioning

confidence: 99%

An HflX-Type GTPase from Sulfolobus solfataricus Binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States

et al. 2011

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“…Gluconate dehydratase catalyzes the dehydration of D-gluconate or D-galactonate, forming KDG/KDGal, the characteristic intermediate of the archaeal modified ED pathway (289,290,502).…”

Section: Sulfolobus Solfataricusmentioning

confidence: 99%

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Bräsen

Esser

Rauch

et al. 2014

Microbiol Mol Biol Rev

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SUMMARY The metabolism of Archaea , the third domain of life, resembles in its complexity those of Bacteria and lower Eukarya . However, this metabolic complexity in Archaea is accompanied by the absence of many “classical” pathways, particularly in central carbohydrate metabolism. Instead, Archaea are characterized by the presence of unique, modified variants of classical pathways such as the Embden-Meyerhof-Parnas (EMP) pathway and the Entner-Doudoroff (ED) pathway. The pentose phosphate pathway is only partly present (if at all), and pentose degradation also significantly differs from that known for bacterial model organisms. These modifications are accompanied by the invention of “new,” unusual enzymes which cause fundamental consequences for the underlying regulatory principles, and classical allosteric regulation sites well established in Bacteria and Eukarya are lost. The aim of this review is to present the current understanding of central carbohydrate metabolic pathways and their regulation in Archaea . In order to give an overview of their complexity, pathway modifications are discussed with respect to unusual archaeal biocatalysts, their structural and mechanistic characteristics, and their regulatory properties in comparison to their classic counterparts from Bacteria and Eukarya . Furthermore, an overview focusing on hexose metabolic, i.e., glycolytic as well as gluconeogenic, pathways identified in archaeal model organisms is given. Their energy gain is discussed, and new insights into different levels of regulation that have been observed so far, including the transcript and protein levels (e.g., gene regulation, known transcription regulators, and posttranslational modification via reversible protein phosphorylation), are presented.

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“…solfataricus cells grown on glucose under standardized growth conditions at 70 or 80°C, respectively, as described previously [49, 51]. S .…”

Section: Methodsmentioning

confidence: 99%

Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus

et al. 2017

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Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80°C and pH 2–4. It catabolizes specific carbon sources, such as D-glucose, to pyruvate via the modified Entner-Doudoroff (ED) pathway. This pathway has two parallel branches, the semi-phosphorylative and the non-phosphorylative. However, the strategy of S.solfataricus to endure in such an extreme environment in terms of robustness and adaptation is not yet completely understood. Here, we present the first dynamic mathematical model of the ED pathway parameterized with quantitative experimental data. These data consist of enzyme activities of the branched pathway at 70°C and 80°C and of metabolomics data at the same temperatures for the wild type and for a metabolic engineered knockout of the semi-phosphorylative branch. We use the validated model to address two questions: 1. Is this system more robust to perturbations at its optimal growth temperature? 2. Is the ED robust to deletion and perturbations? We employed a systems biology approach to answer these questions and to gain further knowledge on the emergent properties of this biological system. Specifically, we applied deterministic and stochastic approaches to study the sensitivity and robustness of the system, respectively. The mathematical model we present here, shows that: 1. Steady state metabolite concentrations of the ED pathway are consistently more robust to stochastic internal perturbations at 80°C than at 70°C; 2. These metabolite concentrations are highly robust when faced with the knockout of either branch. Connected with this observation, these two branches show different properties at the level of metabolite production and flux control. These new results reveal how enzyme kinetics and metabolomics synergizes with mathematical modelling to unveil new systemic properties of the ED pathway in S.solfataricus in terms of its adaptation and robustness.

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“Hot standards” for the thermoacidophilic archaeon Sulfolobus solfataricus

Cited by 54 publications

References 70 publications

An HflX-Type GTPase from Sulfolobus solfataricus Binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States

An HflX-Type GTPase from Sulfolobus solfataricus Binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States

Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus

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