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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>
Determination of single nucleotide variants in Escherichia coli DH5α by using short-read sequencing
Song, Yoseb,Lee, Bo-Rahm,Cho, Suhyung,Cho, Yoo-Bok,Kim, Seon-Won,Kang, Taek Jin,Kim, Sun Chang,Cho, Byung-Kwan Published by Elsevier/North Holland on behalf of t 2015 FEMS microbiology letters Vol.362 No.11
Fabrication and characterization of thermochemical hydrogen sensor with laminated structure
Kim, Seil,Song, Yoseb,Lim, Hyo-Ryoung,Kwon, Young-Tae,Hwang, Tae-Yeon,Song, Eunpil,Lee, Songjun,Lee, Young-In,Cho, Hong-Baek,Choa, Yong-Ho Elsevier 2017 International journal of hydrogen energy Vol.42 No.1
<P><B>Abstract</B></P> <P>In this study, we reported the simple and cost-effective fabrication of thermochemical hydrogen (TCH) sensors composed of chalcogenide thin films and Pt/Al<SUB>2</SUB>O<SUB>3</SUB> powders. Chalcogenide thin films of two types, composed of Bi<SUB>2</SUB>Te<SUB>3</SUB> (monomorphic-type) and Bi<SUB>2</SUB>Te<SUB>3</SUB> Sb<SUB>2</SUB>Te<SUB>3</SUB> (four-leg PN junction-type), were prepared by electrochemical deposition. The Pt/Al<SUB>2</SUB>O<SUB>3</SUB> powder, which acts as a heating catalyst, was synthesized by impregnation of an Al<SUB>2</SUB>O<SUB>3</SUB> powder with an aqueous solution of platinum (IV) chloride pentahydrate. Its heating process was optimized via a hydrogen-sensing evaluation to control the size of the Pt particles. The monomorphic-type TCH sensor showed an output signal of 14.2 μV in response to 10 vol% hydrogen gas, whereas an output signal of 39.6 μV was obtained from a four-leg PN junction–type TCH sensor. Even though the n–p junction-type had the same deposition area as that of the monomorphic-type, the output signal of the n–p junction TCH sensor was greater by a factor of 2.8. In addition, the monomorphic-type TCH sensor had an inferior response time (T<SUB>90</SUB>) of 31 s and a longer recovery time (D<SUB>10</SUB>) of 38 s; the four-leg PN junction-type TCH sensor had a lowest response time of 27 s and a fastest recovery time of 9 s (in 3% H<SUB>2</SUB>/air at room temperature).</P> <P><B>Highlights</B></P> <P> <UL> <LI> Thermochemical hydrogen sensor composed of chalcogenide thin film and Pt/Al<SUB>2</SUB>O<SUB>3</SUB> catalyst was fabricated. </LI> <LI> Voltage signal of the n–p junction type sensor was higher than monomorphic type sensor. </LI> <LI> Heat dissipation of n–p junction type sensor was superior to that of monomorphic type one. </LI> <LI> Response and recovery time of n–p junction type sensor were 27.4 and 9.6 s in 3% H<SUB>2</SUB>/air. </LI> </UL> </P>
Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome.
Lee, Sooin,Song, Yoseb,Choe, Donghui,Cho, Suhyung,Yu, Seok Jong,Cho, Yongseong,Kim, Sun Chang,Cho, Byung-Kwan American Scientific Publishers 2015 Journal of Nanoscience and Nanotechnology Vol.15 No.5
<P>Clostridium aceticum is an anaerobic homoacetogen, able to reduce CO2 to multi-carbon products using the reductive acetyl-CoA pathway. This unique ability to use CO2 or CO makes the microbe a potential platform for the biotech industry. However, the development of genetically engineered homoacetogen for the large-scale production of commodity chemicals is hampered by the limited amount of their genetic and metabolic information. Here we exploited next-generation sequencing to reveal C. aceticum genome. The short-read sequencing produced 44,871,196 high quality reads with an average length of 248 bases. Following sequence trimming step, 30,256,976 reads were assembled into 12,563 contigs with 168-fold coverage and 1,971 bases in length using de Bruijn graph algorithm. Since the k-mer hash length in the algorithm is an important factor for the quality of output contigs, a window of k-mers (k-51 to k-201) was tested to obtain high quality contigs. In addition to the assembly metrics, the functional annotation of the contigs was investigated to select the k-mer optimum. Metabolic pathway mapping using the functional annotation identified the majority of central metabolic pathways, such as the glycolysis and TCA cycle. Further, these analyses elucidated the enzymes consisting of Wood-Ljungdahl pathway, in which CO2 is fixed into acetyl-CoA. Thus, the metabolic reconstruction based on the draft genome assembly provides a foundation for the functional genomics required to engineer C. aceticum.</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>
Kim, Seil,Song, Yoseb,Hwang, Tae-Yeon,Lim, Jae-Hong,Choa, Yong-Ho Pergamon Press 2019 International journal of hydrogen energy Vol.44 No.21
<P><B>Abstract</B></P> <P>A novel method for fabrication of a thermochemical hydrogen (TCH) gas sensor composed of platinum (Pt)-decorated graphene sheets and a thermoelectric (TE) polymer nanocomposite was investigated. The hydrogen sensing characterization for the device included gas response, response time (T<SUB>90</SUB>), recovery time (D<SUB>10</SUB>), and reliability testing, which were systematically conducted at room temperature with a relative humidity of 55%. Here, the Pt-decorated graphene sheets act as both an effective hydrogen oxidation surface and a heat-transfer TE polymer nanocomposite having low thermal conductivity. This property plays an important role in generating output voltage signal with a temperature difference between the top and bottom surfaces of the nanocomposite. As a result, our TCH gas sensor can detect the range of hydrogen from 100 ppm to percentage level with good linearity. The best response and recovery time revealed for the optimized TCH gas sensor were 23 s and 17 s under 1000 ppm H<SUB>2</SUB>/air, respectively. This type of sensor can provide an important component for fabricating thermoelectric-based gas sensors with favorable gas sensing performance.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A novel-type of TE composite-based hydrogen gas sensor was fabricated. </LI> <LI> Gas response of the sensor was considerably linear at low- and high concentrations. </LI> <LI> The sensor has a detection limit of 100 ppm with high signal to noise ratio. </LI> <LI> The response/recovery times were 23 s and 17 s under 1000 ppm H<SUB>2</SUB>/air, respectively. </LI> </UL> </P>