Bae Jiyun, Lee Donghwi, Park Chanho, Jung Hyunwoo, Huh Minkyu, Kang Seulgi, Gwak Ye Jin, Lee Hyo Jung, Jung You-Jung, Yoon Hyeokjun, Hur Moonsuk, Jin Sangrak, Cho Suhyung, Cho Byung-Kwan
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
mSystems. 2025 Aug 6:e0045125. doi: 10.1128/msystems.00451-25.
KIAC is a novel acetogen isolated from cattle feces that exhibits rapid CO utilization. To investigate the molecular basis of this phenotype, we performed a comprehensive multi-omics analysis, including Genome-seq, RNA-seq, dRNA-seq, and Term-seq, to map its transcriptome architecture. We identified 2,158 transcription start sites and 2,275 transcript 3' ends, enabling high-resolution reconstruction of the transcriptional landscape and associated regulatory features. This analysis uncovered key -regulatory elements and an expanded regulatory role for the alternative sigma factor SigH in controlling acetogenesis-related genes. Notably, KIAC harbors nine functionally diverse hydrogenases-a greater diversity than observed in other acetogens-likely contributing to its rapid CO utilization. Heterologous expression of KIAC-derived hydrogenases in led to doubled H and CO consumption rates, increased growth rates, and notably, the first reported butyrate production under energy-limited H/CO conditions. These improvements stem from enhanced H oxidation, which supplies additional reducing equivalents for growth and biochemical production. Our findings provide critical insights into the genetic basis for rapid autotrophic growth in acetogens. The discovery of the expanded regulatory role of SigH and the energetic advantages of diverse hydrogenases offers new strategies for enhanced CO bioconversion of acetogens.IMPORTANCEAcetogens offer a promising solution for sustainable CO bioconversion into multicarbon biochemicals through the Wood-Ljungdahl pathway, the most energy-efficient carbon fixation route known in nature. However, an incomplete understanding of their metabolism and regulatory systems has limited metabolic engineering efforts to achieve superior CO fixation efficiency. In this study, we investigated KIAC, a newly isolated acetogen with rapid CO utilization, to uncover the molecular mechanisms underlying its superior performance. By revealing an expanded regulatory role for an alternative sigma factor and a highly diverse set of hydrogenases, our findings provide a foundation for engineering acetogens with enhanced CO conversion efficiency under energy-limited conditions.
KIAC是一种从牛粪中分离出的新型产乙酸菌，具有快速利用CO的能力。为了研究这种表型的分子基础，我们进行了全面的多组学分析，包括基因组测序、RNA测序、dRNA测序和Term测序，以绘制其转录组图谱。我们鉴定出2158个转录起始位点和2275个转录本3'末端，从而能够对转录图谱和相关调控特征进行高分辨率重建。该分析揭示了关键调控元件以及替代sigma因子SigH在控制产乙酸相关基因方面扩大的调控作用。值得注意的是，KIAC含有九种功能多样的氢化酶——比其他产乙酸菌中观察到的多样性更高——这可能有助于其快速利用CO。将KIAC来源的氢化酶在[此处原文缺失受体信息]中进行异源表达，导致H₂和CO₂消耗速率加倍，生长速率提高，并且值得注意的是，在能量受限的H₂/CO₂条件下首次报道了丁酸盐的产生。这些改善源于增强的H₂氧化，它为生长和生化产物提供了额外的还原当量。我们的数据为产乙酸菌快速自养生长的遗传基础提供了关键见解。SigH扩大的调控作用以及多样氢化酶的能量优势的发现，为提高产乙酸菌的CO₂生物转化提供了新策略。重要性产乙酸菌通过伍德-Ljungdahl途径将CO₂可持续生物转化为多碳生物化学物质提供了一个有前景的解决方案，这是自然界中已知的最节能的碳固定途径。然而，对其代谢和调控系统的不完全理解限制了实现卓越CO₂固定效率的代谢工程努力。在本研究中，我们研究了KIAC，一种新分离的具有快速CO₂利用能力的产乙酸菌，以揭示其卓越性能背后的分子机制。通过揭示替代sigma因子和一组高度多样的氢化酶的扩大调控作用，我们的发现为在能量受限条件下工程化改造具有更高CO₂转化效率的产乙酸菌奠定了基础。
