Form III RubisCO in autotrophic CO2 assimilation in Bacteria and Archaea

尽管对于不同的生物体来说，同一生物体中存在两种不同的自养CO2固定途径已被多次提出，但一直没有得到充分的证实。通常，人们提出了还原三元酸循环和Calvin-Benson循环共存的观点。在这里，我们研究了两个自养途径共存的另一个例子：德根山龙虾基因组同时拥有Wood-Ljugdahl途径和Calvin-Benson循环的基因。在第一个资助期，我们发现德氏艾美耳球虫依靠氢分压(氧化还原电位)来平衡其代谢，控制其还原铁氧还蛋白的能力。在有利于铁氧还蛋白还原的高H2条件下，它使用铁氧还蛋白依赖的Wood-LJungdahl途径，但在低H2条件下的生长过程中切换到效率较低但不依赖铁氧还蛋白的Calvin-Benson循环。我们的初步数据表明，德根霉的Calvin-Benson循环功能被修改，使用转醛缩酶反应生成七硫代磷酸-7-磷酸，而不是七硫-1，7-二磷酸缩醛酶和七硫-1，7-二磷酸磷酸酶反应。此外，Rubisco被认为在未培养的异养藻中参与了一种新的二氧化碳代谢途径，并在候选辐射门的细菌中发挥了核苷降解途径的作用。这些建议是基于生物信息学分析，生化研究是必要的，以评估其有效性。在这一更新项目中，我们将进一步评估影响德根藻和硫酸盐还原古生菌利用不同CO2固定途径的因素，为德根藻中是否存在海藻糖-1，7-二磷酸磷酸酶反应提供生化证据，并研究Rubisco在异养藻和候选辐射门细菌代谢中的作用。我们的目的是加深我们对不同自养途径共存现象的理解，并扩大我们对形式III Rubisco酶在微生物代谢中的功能的认识。

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.