Form III RubisCO in autotrophic CO2 assimilation in Bacteria and Archaea

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Although the co-occurrence of two different autotrophic CO2 fixation pathways in one organism has been proposed for different organisms many times, it has never been fully confirmed. Usually, the co-existence of the reductive tricarboxylic acid cycle and the Calvin-Benson cycle has been proposed. Here, we study another example of the co-occurrence of two autotrophic pathways: Ammonifex degensii genome possesses genes for both the Wood-Ljungdahl pathway and the Calvin-Benson cycle. In the first funding period, we showed that A. degensii balances its metabolism depending on H2 partial pressure (redox potential), governing its capability to reduce ferredoxin. At high-H2 conditions favoring ferredoxin reduction, it uses the ferredoxin-dependent Wood-Ljungdahl pathway but switches to the less efficient but ferredoxin-independent Calvin-Benson cycle during growth at low-H2 conditions. Our preliminary data indicate that the Calvin-Benson cycle functioning in A. degensii is modified, using transaldolase reaction for the formation of sedoheptulose-7-phosphate instead of sedoheptulose-1,7-bisphosphate aldolase and sedoheptulose-1,7-bisphosphate phosphatase reactions. Furthermore, RubisCO was proposed to function in a novel CO2 metabolism pathway in uncultured heterotrophic Thaumarchaeota and in the nucleoside degradation pathway in bacteria of the candidate phyla radiation. These proposals are based on bioinformatic analysis, and biochemical studies are necessary to evaluate their validity. In this renewal project, we are going to further evaluate factors governing the usage of different CO2 fixation pathways in A. degensii and sulfate-reducing Archaea, to provide biochemical evidence whether the sedoheptulose-1,7-bisphosphate phosphatase reaction present in A. degensii or not, and to study functions of RubisCO in metabolism of heterotrophic Thaumarchaeota and bacteria of the candidate phyla radiation. We aim to deepen our understanding of the phenomenon of the co-occurrence of different autotrophic pathways and to expand our knowledge of the functions of form III RubisCO enzymes in microbial metabolism.