Turlin Justine, Alván-Vargas Maria V G, Puiggené Òscar, Donati Stefano, Wenk Sebastian, Nikel Pablo I
The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
mBio. 2025 Aug 18:e0197625. doi: 10.1128/mbio.01976-25.
Formate and methanol are promising alternatives to sugar-based feedstocks for biotechnological applications. These one-carbon (C) substrates can be sustainably produced from CO and renewable electricity and assimilated by both native and engineered microbial systems. However, their broader adoption is limited by the narrow range of bacterial hosts capable of efficient methanol and formate utilization. In this study, the industrially relevant soil bacterium was metabolically engineered to assimilate formate and methanol as sole carbon and energy sources via the linear reductive glycine pathway. Initial strains were optimized for formate assimilation using acetate for energy conservation through adaptive laboratory evolution (ALE), leading to a substantial reduction in doubling time under mixotrophic conditions. Key mutations emerged in the promoter regions of synthetic pathway genes and within the native genome. Strictly formatotrophic growth, with a doubling time of ca. 28 h, was achieved by integrating a formate dehydrogenase gene either on a plasmid or chromosomally as a mini-Tn module, combined with growth-coupled selection. The resulting strain, rG·F, was then re-engineered by replacing the formate dehydrogenase with an engineered methanol dehydrogenase from . Following ALE, an isolate displaying full methylotrophy, rG·M, grew on methanol with a doubling time of ca. 24 h. These efforts demonstrate the feasibility of constructing robust C-assimilating strains and highlight the substrate versatility of this bacterium for bioproduction. Integrating evolutionary engineering with synthetic biology tools has expanded the range of viable microbial hosts for efficient C feedstock utilization.IMPORTANCESoluble C feedstocks, such as formate and methanol, have gained attention as sustainable substrates for biotechnology, with the potential to reduce greenhouse gas emissions and reliance on sugar-based resources. Despite their promise, the metabolic assimilation of these compounds remains uncharacterized in robust bacterial hosts beyond a few model species. , known for its metabolic versatility and industrial relevance, has lacked the ability to grow solely on C compounds. This study is a first-case example of strict synthetic formatotrophy and methylotrophy in any species, enabling growth on formate and methanol as sole carbon and energy sources. Through pathway rewiring and adaptive laboratory evolution, key metabolic and regulatory adaptations were identified that enabled efficient C assimilation. These findings not only expand the known capabilities of but also open directions for its deployment in carbon-efficient biomanufacturing. This study sets a precedent for leveraging non-model microorganisms in the development of scalable, carbon-efficient bioprocesses.
在生物技术应用中,甲酸盐和甲醇是有前景的糖基原料替代品。这些一碳(C)底物可由一氧化碳和可再生电力可持续生产,并可被天然和工程化微生物系统同化。然而,它们的更广泛应用受到能够有效利用甲醇和甲酸盐的细菌宿主范围狭窄的限制。在本研究中,对具有工业相关性的土壤细菌进行代谢工程改造,使其通过线性还原甘氨酸途径将甲酸盐和甲醇作为唯一碳源和能源进行同化。最初的菌株通过适应性实验室进化(ALE),以乙酸盐为能量源优化甲酸盐同化,从而在混合营养条件下大幅缩短了倍增时间。关键突变出现在合成途径基因的启动子区域和天然基因组内。通过将甲酸盐脱氢酶基因整合到质粒上或作为mini-Tn模块整合到染色体上,并结合生长偶联选择,实现了严格的甲酸盐营养生长,倍增时间约为28小时。然后,通过用来自[具体来源]的工程化甲醇脱氢酶替换甲酸盐脱氢酶,对所得菌株rG·F进行重新工程改造。经过ALE后,一个表现出完全甲基营养的分离株rG·M以约24小时的倍增时间在甲醇上生长。这些努力证明了构建强大的C同化[细菌名称]菌株的可行性,并突出了该细菌在生物生产中的底物多功能性。将进化工程与合成生物学工具相结合,扩大了有效利用C原料的可行微生物宿主范围。
重要性
可溶性C原料,如甲酸盐和甲醇,作为生物技术的可持续底物受到关注,具有减少温室气体排放和减少对糖基资源依赖的潜力。尽管它们有前景,但除了少数模式物种外,这些化合物在强大的细菌宿主中的代谢同化仍未得到充分研究。[细菌名称]以其代谢多功能性和工业相关性而闻名,但缺乏仅在C化合物上生长的能力。本研究是[细菌名称]中严格的合成甲酸盐营养和甲基营养的首个实例,使其能够以甲酸盐和甲醇作为唯一碳源和能源生长。通过途径重新布线和适应性实验室进化,确定了实现高效C同化的关键代谢和调控适应。这些发现不仅扩展了[细菌名称]的已知能力,还为其在碳高效生物制造中的应用开辟了方向。本研究为在可扩展的碳高效生物过程开发中利用非模式微生物树立了先例。