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| Status |
Public on Apr 12, 2022 |
| Title |
Faster growth enhances low carbon fuels and commodity chemcial production through gas fermentation |
| Organism |
Clostridium autoethanogenum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Gas fermentation offers both fossil carbon-free sustainable production of fuels and chemicals and recycling of gaseous and solid waste using gas-fermenting microbes. Bioprocess development, systems-level analysis of biocatalyst metabolism, and engineering of cell factories are advancing the widespread deployment of the commercialised technology. Acetogens are particularly attractive biocatalysts but effects of the key physiological parameter – specific growth rate (μ) – on acetogen metabolism and the gas fermentation bioprocess have not been established yet. Here, we investigate the μ-dependent bioprocess performance of the model-acetogen Clostridium autoethanogenum in CO and syngas (CO+CO2+H2) grown chemostat cultures and assess systems-level metabolic responses using gas analysis, metabolomics, transcriptomics, and metabolic modelling. We were able to obtain steady-states up to μ ~2.8 day-1 (~0.12 h-1) and show that faster growth supports both higher yields and productivities for reduced by-products ethanol and 2,3-butanediol. Transcriptomics data revealed differential expression of 1,337 genes with increasing μ and suggest that C. autoethanogenum uses transcriptional regulation to a large extent for facilitating faster growth. Metabolic modelling showed significantly increased fluxes for faster growing cells that were, however, not accompanied by gene expression changes in key catabolic pathways for CO and H2 metabolism. Cells thus seem to maintain sufficient “baseline” gene expression to rapidly respond to CO and H2 availability without delays to kick-start metabolism. Our work advances understanding of transcriptional regulation in acetogens and shows that faster growth of the biocatalyst improves the gas fermentation bioprocess.
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| Overall design |
RNA sequencing of CO-grown or syngas-grown Clostridium autoethanogenum chemostat cultures at three specific growth rates; 20 samples in total with various number of biological replicate samples
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| Contributor(s) |
Lima LA, Ingelman H, Brahmbhatt K, Reinmets K, Barry C, Harris A, Marcellin E, Köpke M, Valgepea K |
| Citation(s) |
35497340 |
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| Submission date |
Feb 13, 2022 |
| Last update date |
May 05, 2022 |
| Contact name |
Kaspar Valgepea |
| E-mail(s) |
kaspar.valgepea@ut.ee
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| Organization name |
University of Tartu
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| Department |
Institute of Technology
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| Street address |
Nooruse 1, room 520
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| City |
Tartu |
| State/province |
Tartu |
| ZIP/Postal code |
50411 |
| Country |
Estonia |
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| Platforms (1) |
| GPL24458 |
Illumina NextSeq 500 (Clostridium autoethanogenum) |
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| Samples (20)
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| GSM5897148 |
D1, CO, rep4 |
| GSM5897149 |
D2, CO, rep1 |
| GSM5897150 |
D2, CO, rep2 |
| GSM5897151 |
D2, CO, rep3 |
| GSM5897152 |
D2.8, CO, rep1 |
| GSM5897153 |
D2.8, CO, rep2 |
| GSM5897154 |
D2.8, CO, rep3 |
| GSM5897155 |
D1, Syngas, rep1 |
| GSM5897156 |
D1, Syngas, rep2 |
| GSM5897157 |
D1, Syngas, rep3 |
| GSM5897158 |
D1, Syngas, rep4 |
| GSM5897159 |
D2, Syngas, rep1 |
| GSM5897160 |
D2, Syngas, rep2 |
| GSM5897161 |
D2, Syngas, rep3 |
| GSM5897162 |
D2.8, Syngas, rep1 |
| GSM5897163 |
D2.8, Syngas, rep2 |
| GSM5897164 |
D2.8, Syngas, rep3 |
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| Relations |
| BioProject |
PRJNA806656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196640_Compiled_RPKM_CO.txt.gz |
58.9 Kb |
(ftp)(http) |
TXT |
| GSE196640_Compiled_RPKM_Syngas.txt.gz |
58.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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