Systems Biology of Caldicellulosiruptor saccharolyticus: Analysis of the metabolic network leading to hydrogen formation.

Hydrogen produced from renewable resources is considered to be a potent future biofuel. Caldicellulosiruptor saccharolyticus, an anaerobic thermophilic bacterium, is capable of efficiently converting a wide range of biomass components (cellulose, xylan, pectin, starch etc.) into hydrogen. Moreover, unlike mesophilic hydrogen producers, less reduced end products are produced leading to a relatively high hydrogen yield.

Recently, we have been able to sequence and annotate the complete genome of C. saccharolyticus, which revealed its central metabolic pathways 1 (Figure 1).As a part of the fermentative metabolism, it is necessary to dispose of produced reducing equivalents (NADH and reduced ferredoxin). This is accomplished through the production of reduced end products like hydrogen, lactate or ethanol. However the regulation of the reductant disposal and the identity of responsible hydrogenases and dehydrogenases are not known.

Figure 2 en 3.png

Project aim

Our research focuses on the main sugar degradation pathways. Cultures aregrown under chemostatic conditions allowing control over growth parameters (growth rate, pH, limiting substrate) safeguarding identical metabolic states of the produced cells. The analysis of the metabolome, transcriptome (Figure 2) and proteome under different growth conditions will reveal key regulatory enzymes of the central metabolic pathways and their interactions.

Additionally a mathematical model describing the relevant interactionswithin the central metabolism will be made, based on the -omics results. The model can direct further research and will by fine-tuned by the additional results (Figure 3).

Our main aim is to elucidate C. saccharolyticus’ regulatory mechanismscontrolling the metabolic network involved in hydrogen formation and to derive a mathematical model describing this network.

Techniques involved

Working under anaerobic conditions, continuous and batch cultivation, sample processing for -omics analysis: Quenching, GC-MS, LC-ESI-FTMS, DNAmicroarray, protein purification and enzyme assays. Matlab programming (Cobra)

Student projects/internships

Students are welcome to participate in this project. Experience in field of microbiology is an advantage. So if you’re interested feel free to contact me at: Bram Bielen