Eubacterium limosum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA382424 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5442630.fastq.gz | Fastqsanger.gz | |||
| SRR5442640.fastq.gz | Fastqsanger.gz | |||
| SRR5442631.fastq.gz | Fastqsanger.gz | |||
| SRR5442632.fastq.gz | Fastqsanger.gz | |||
| SRR5442633.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description: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.
2018-07-16 | GSE97613 | GEO
Project description:Some acetogenic bacteria, such as Eubacterium limosum, have the native ability to consume liquid C1 feedstocks, such as formate and methanol, as the sole substrate for growth. Due to high energy efficiency, and compatibility with existing infrastructure, this has sparked interest in the biotechnology industry. Previously, we reported limitations of this metabolism in batch fermentation. Here we undertook chemostat differential analysis to highlight key features and bottlenecks of metabolism. Our work serves as a reference dataset to advance understanding of liquid C1 metabolism in acetogens.
2023-04-13 | PXD040283 | Pride
Project description:Clostridium ljungdahlii not only utilizes CO, but also H2 as energy source during autotrophic growth. And C. ljungdahlii also grows in fructose fermentation. In theory, fructose is a more energetically favourable energy source than syngas in the fermentation of C. ljungdahlii. However, C. ljungdahlii grows insufficiently in fructose and produces less acetate and ethanol, compared to syngas fermentation. In this study, C. ljungdahlii wild type and mutants were fermented on fructose. C. ljungdahlii produced less ethanol than the ΔadhE1 mutant and consumed less fructose. The ΔadhE1+2 mutant cannot grow in the syngas fermentation and produced less ethanol among the three strains. The results showed that aldehyde dehydrogenase inactivation led to efficient metabolism in C. ljungdahlii and the bifunctional aldehyde/alcohol dehydrogenases inactivation led to decrease metabolism. Thus, comparative transcriptomes among cells grown on fructose of three strains were performed to investigate gene expression profiles based on three biological replicates.
2023-06-27 | E-MTAB-13020 | biostudies-arrayexpress
Project description:Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood-Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.
| S-EPMC7079680 | biostudies-literature
Project description:Unlike gaseous C1 feedstocks for acetogenic bacteria, there has been less attention on liquid C1 feedstocks, despite benefits in terms of energy efficiency, mass transfer and integration within existing fermentation infrastructure. Here, we present growth of Eubacterium limosum ATCC8486 using methanol and formate as substrates, finding evidence for the first time of native butanol production. We varied ratios of methanol-to-formate in batch serum bottle fermentations, showing butyrate is the major product (maximum specific rate 220 ± 23 mmol-C gDCW-1 day-1 ). Increasing this ratio showed methanol is the key feedstock driving the product spectrum towards more reduced products, such as butanol (maximum titre 2.0 ± 1.1 mM-C). However, both substrates are required for a high growth rate (maximum 0.19 ± 0.011 h-1 ) and cell density (maximum 1.2 ± 0.043 gDCW l-1 ), with formate being the preferred substrate. In fact, formate and methanol are consumed in two distinct growth phases - growth phase 1, on predominately formate and growth phase 2 on methanol, which must balance. Because the second growth varied according to the first growth on formate, this suggests butanol production is due to overflow metabolism, similar to 2,3-butanediol production in other acetogens. However, further research is required to confirm the butanol production pathway in E. limosum, particularly given, unlike other substrates, methanol likely results in mostly NADH generation, not reduced ferredoxin.
| S-EPMC9049608 | biostudies-literature
Project description:Eubacterium limosum KIST612 is an anaerobic acetogenic bacterium that uses CO as the sole carbon/energy source and produces acetate, butyrate, and ethanol. To evaluate its potential as a syngas microbial catalyst, we have sequenced the complete 4.3-Mb genome of E. limosum KIST612.
| S-EPMC3019962 | biostudies-literature
Project description:Acetogenic bacteria are an increasingly popular choice for producing fuels and chemicals from single carbon (C1) substrates. Eubacterium limosum is a promising acetogen with several native advantages, including the ability to catabolize a wide repertoire of C1 feedstocks and the ability to grow well on agar plates. However, despite its promise as a strain for synthetic biology and metabolic engineering, there are insufficient engineering tools and molecular biology knowledge to leverage its native strengths for these applications. To capitalize on the natural advantages of this organism, here we extended its limited engineering toolbox. We evaluated the copy number of three common plasmid origins of replication and devised a method of controlling copy number and heterologous gene expression level by modulating antibiotic concentration. We further quantitatively assessed the strength and regulatory tightness of a panel of promoters, developing a series of well-characterized vectors for gene expression at varying levels. In addition, we developed a black/white colorimetric genetic reporter assay and leveraged the high oxygen tolerance of E. limosum to develop a simple and rapid transformation protocol that enables benchtop transformation. Finally, we developed two new antibiotic selection markers-doubling the number available for this organism. These developments will enable enhanced metabolic engineering and synthetic biology work with E. limosum.
| S-EPMC9559302 | biostudies-literature
Project description:To understand transcriptional regulation of Eubacterium limosum KIST612 across different carbon/energy/electron sources, RNAseq analysis was carried out over different substrate conditions (glucose, CO, H2/CO2).
2020-04-25 | GSE149269 | GEO