Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany.
Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland.
Nat Commun. 2020 Nov 16;11(1):5812. doi: 10.1038/s41467-020-19564-5.
Carbon fixation is one of the most important biochemical processes. Most natural carbon fixation pathways are thought to have emerged from enzymes that originally performed other metabolic tasks. Can we recreate the emergence of a carbon fixation pathway in a heterotrophic host by recruiting only endogenous enzymes? In this study, we address this question by systematically analyzing possible carbon fixation pathways composed only of Escherichia coli native enzymes. We identify the GED (Gnd-Entner-Doudoroff) cycle as the simplest pathway that can operate with high thermodynamic driving force. This autocatalytic route is based on reductive carboxylation of ribulose 5-phosphate (Ru5P) by 6-phosphogluconate dehydrogenase (Gnd), followed by reactions of the Entner-Doudoroff pathway, gluconeogenesis, and the pentose phosphate pathway. We demonstrate the in vivo feasibility of this new-to-nature pathway by constructing E. coli gene deletion strains whose growth on pentose sugars depends on the GED shunt, a linear variant of the GED cycle which does not require the regeneration of Ru5P. Several metabolic adaptations, most importantly the increased production of NADPH, assist in establishing sufficiently high flux to sustain this growth. Our study exemplifies a trajectory for the emergence of carbon fixation in a heterotrophic organism and demonstrates a synthetic pathway of biotechnological interest.
固碳是最重要的生化过程之一。大多数天然固碳途径被认为是由最初执行其他代谢任务的酶进化而来的。我们能否通过仅招募内源性酶在异养宿主中重新创造固碳途径的出现？在这项研究中，我们通过系统分析仅由大肠杆菌天然酶组成的可能的固碳途径来解决这个问题。我们确定 GED（Gnd-Entner-Doudoroff）循环是可以用高热力学驱动力运行的最简单途径。这种自动催化途径基于 6-磷酸葡萄糖酸脱氢酶（Gnd）对核酮糖 5-磷酸（Ru5P）的还原羧化作用，然后是 Entner-Doudoroff 途径、糖异生和戊糖磷酸途径的反应。我们通过构建大肠杆菌基因缺失菌株来证明这种新的天然途径的体内可行性，这些菌株的戊糖糖生长依赖于 GED 支路，这是 GED 循环的线性变体，不需要 Ru5P 的再生。几种代谢适应，最重要的是 NADPH 的产量增加，有助于建立足够高的通量来维持这种生长。我们的研究例证了异养生物中碳固定出现的轨迹，并展示了具有生物技术兴趣的合成途径。
