以電腦模擬並剖析雙固碳循環作用於以氫氣為能量之自營大腸桿菌

固碳作用是無機碳以二氧化碳的形式進入生物圈最主要方式。加氧酶在大自然中是最豐富的蛋白質，加氧酶可以利用ATP的能量將二氧化碳中的碳接到醣類分子上。光自營生物透過卡爾文循環吸收大氣中的二氧化碳。然而加氧酶過慢的反應速率限制了整個卡爾文循環的進行。在本篇研究當中，我們嘗試整合並模擬還原性三羧酸循環和卡爾文循環進入到同一大腸桿菌中，希望以此改善固碳作用效率。我們加入了數個異源酶進入到大腸桿菌的代謝網路中，負責幫助細菌將二氧化碳轉換成生物能並將細菌轉換成使用氫氣做為能量來源。這樣的改變在大腸桿菌中形成了雙固碳循環也增加了它的生長速率。我們的實驗結果主要有以下幾點。(i)我們定義了兩種生長模式，碳源限制階段與氫氣限制階段。(ii)我們定義了當氫氣有限時固碳作用的不同階段。(iii)我們定義了還原性三羧酸循環當基因調控出現錯誤時會出現的次優生長模式。這些實驗結果。透過研究的成果，希望可以為未來相關的基因工程提供一個良好的研究方向。

關鍵字

固碳作用；大腸桿菌

並列摘要

Carbon fixation is the main route of inorganic carbon in the form of CO2 into the biosphere. In nature, RuBisCO is the most abundant protein that photosynthetic organisms use to fix CO2 from the atmosphere through the Calvin-Benson-Bassham (CBB) cycle. However, the CBB cycle is limited by its low catalytic rate and low energy eciency. In this work, we attempt to integrate the reductive tricarboxylic acid and CBB cycles in silico to further improve carbon fixation capacity. Key heterologous enzymes, mostly carboxylating enzymes, are inserted into the Esherichia coli core metabolic network to assimilate CO2 into biomass using hydrogen as energy source. Overall, such a strain shows enhanced growth yield with simultaneous running of dual carbon fixation cycles. Our key results include the following. (i) We identified two main growth states: carbon-limited and hydrogenlimited; (ii) we identified a hierarchy of carbon fixation usage when hydrogen supply is limited; and (iii) we identified the alternative sub-optimal growth mode while performing genetic perturbation. The results and modeling approach can guide bioengineering projects toward optimal production using such a strain as a microbial cell factory.