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Song, Yoseb,Lee, Jin Soo,Shin, Jongoh,Lee, Gyu Min,Jin, Sangrak,Kang, Seulgi,Lee, Jung-Kul,Kim, Dong Rip,Lee, Eun Yeol,Kim, Sun Chang,Cho, Suhyung,Kim, Donghyuk,Cho, Byung-Kwan National Academy of Sciences 2020 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.117 No.13
<P><B>Significance</B></P><P>Despite sharing the first four reactions, coutilization of the Wood–Ljungdahl pathway (WLP) with the glycine synthase-reductase pathway (GSRP) and reductive glycine pathway (RGP) to fix C1 compounds has remained unknown. In this study, using <I>Clostridium drakei</I>, we elucidated the role of the GSRP and RGP in the presence of the WLP, via a genome-scale metabolic model, RNA-seq, <SUP>13</SUP>C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression. Overall, the data suggested the pathways are functional under autotrophic conditions. Along with the WLP, GSRP and RGP convert CO<SUB>2</SUB> to glycine and then to acetyl-phosphate and serine, which then obtain ATP by producing acetate and operate with limited reducing power. This is a unique coutilization of the pathways under autotrophic conditions in acetogens.</P><P>Among CO<SUB>2</SUB>-fixing metabolic pathways in nature, the linear Wood–Ljungdahl pathway (WLP) in phylogenetically diverse acetate-forming acetogens comprises the most energetically efficient pathway, requires the least number of reactions, and converts CO<SUB>2</SUB> to formate and then into acetyl-CoA. Despite two genes encoding glycine synthase being well-conserved in WLP gene clusters, the functional role of glycine synthase under autotrophic growth conditions has remained uncertain. Here, using the reconstructed genome-scale metabolic model <I>i</I>SL771 based on the completed genome sequence, transcriptomics, <SUP>13</SUP>C isotope-based metabolite-tracing experiments, biochemical assays, and heterologous expression of the pathway in another acetogen, we discovered that the WLP and the glycine synthase pathway are functionally interconnected to fix CO<SUB>2</SUB>, subsequently converting CO<SUB>2</SUB> into acetyl-CoA, acetyl-phosphate, and serine. Moreover, the functional cooperation of the pathways enhances CO<SUB>2</SUB> consumption and cellular growth rates via bypassing reducing power required reactions for cellular metabolism during autotrophic growth of acetogens.</P>
Shin, Jongoh,Song, Yoseb,Jin, Sangrak,Lee, Jung-Kul,Kim, Dong Rip,Kim, Sun Chang,Cho, Suhyung,Cho, Byung-Kwan Cold Spring Harbor Laboratory Press 2018 RNA Vol.24 No.12
<P>Acetogens synthesize acetyl-CoA via CO<SUB>2</SUB> or CO fixation, producing organic compounds. Despite their ecological and industrial importance, their transcriptional and post-transcriptional regulation has not been systematically studied. With completion of the genome sequence of <I>Acetobacterium bakii</I> (4.28-Mb), we measured changes in the transcriptome of this psychrotolerant acetogen in response to temperature variations under autotrophic and heterotrophic growth conditions. Unexpectedly, acetogenesis genes were highly up-regulated at low temperatures under heterotrophic, as well as autotrophic, growth conditions. To mechanistically understand the transcriptional regulation of acetogenesis genes via changes in RNA secondary structures of 5′-untranslated regions (5′-UTR), the primary transcriptome was experimentally determined, and 1379 transcription start sites (TSS) and 1100 5′-UTR were found. Interestingly, acetogenesis genes contained longer 5′-UTR with lower RNA-folding free energy than other genes, revealing that the 5′-UTRs control the RNA abundance of the acetogenesis genes under low temperature conditions. Our findings suggest that post-transcriptional regulation via RNA conformational changes of 5′-UTRs is necessary for cold-adaptive acetogenesis.</P>