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| Status |
Public on Jul 16, 2018 |
| Title |
Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth |
| Organism |
Eubacterium limosum |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Autotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and translational regulation of the corresponding genes is highly demanded. Here, we complete a genome sequence of Eubacterium limosum ATCC8466 in a circular form of 4.4 Mb, followed by integrating genome-scale measurements of its transcriptome and translatome. Interestingly, the transcriptionally abundant genes encoding the Wood-Ljungdahl pathway were regulated at translational level with decreased translation efficiency (TE). To understand the regulation, the primary transcriptome was augmented, which determined 1,458 transcription start sites (TSS) and 1,253 5’-untranslated regions (5′UTR). The data supports that under the autotrophic condition the TE of genes for the Wood-Ljungdahl pathway and the energy conservation system were regulated by 5′UTR secondary structure. In addition, it was illustrated that the strain reallocates protein synthesis and energy economically, focusing more on translation of energy conservation system rather than on carbon metabolism under autotrophic growth. Thus, our results provide potential route for strain engineering to enhance syngas fermenting capacity.
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| Overall design |
Transcription abundance and ribosomal profiling analysis of Eubacterium limosum in heterotrophic and autotrophic condition
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| Contributor(s) |
Song Y, Shin J, Jeong Y, Jin S, Sung BH, Kim DR, Kim SC, Cho S, Cho B |
| Citation(s) |
30470174, 33563990 |
| Submission date |
Apr 10, 2017 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Yoseb Song |
| E-mail(s) |
yosebiback@gmail.com
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| Organization name |
KAIST
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| Street address |
291 Daehak-ro
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| City |
Yuseong-gu |
| State/province |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
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| Platforms (2) |
| GPL23275 |
Illumina MiSeq (Eubacterium limosum) |
| GPL23276 |
Illumina HiSeq 2500 (Eubacterium limosum) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA382424 |
| SRA |
SRP103784 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97613_Eubacterium_limosum_cDNA.fa.gz |
1.1 Mb |
(ftp)(http) |
FA |
| GSE97613_RAW.tar |
12.7 Mb |
(http)(custom) |
TAR (of GFF, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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