Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth

Abstract

BackgroundAcetogenic bacteria constitute promising biocatalysts for the conversion of CO2/H2 or synthesis gas (H2/CO/CO2) into biofuels and value-added biochemicals. These microorganisms are naturally capable of autotrophic growth via unique acetogenesis metabolism. Despite their biosynthetic potential for commercial applications, a systemic understanding of the transcriptional and translational regulation of the acetogenesis metabolism remains unclear.ResultsBy integrating genome-scale transcriptomic and translatomic data, we explored the regulatory logic of the acetogenesis to convert CO2 into biomass and metabolites in Eubacterium limosum. The results indicate that majority of genes associated with autotrophic growth including the Wood-Ljungdahl pathway, the reduction of electron carriers, the energy conservation system, and gluconeogenesis were transcriptionally upregulated. The translation efficiency of genes in cellular respiration and electron bifurcation was also highly enhanced. In contrast, the transcriptionally abundant genes involved in the carbonyl branch of the Wood-Ljungdahl pathway, as well as the ion-translocating complex and ATP synthase complex in the energy conservation system, showed decreased translation efficiency. The translation efficiencies of genes were regulated by 5′UTR secondary structure under the autotrophic growth condition.ConclusionsThe results illustrated that the acetogenic bacteria reallocate protein synthesis, focusing more on the translation of genes for the generation of reduced electron carriers via electron bifurcation, rather than on those for carbon metabolism under autotrophic growth.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5238-0) contains supplementary material, which is available to authorized users.

Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei

“…To confirm the functional role of a pathway, a reconstruction of C. drakei to modify the pathways is required to confirm the prior result, but, unfortunately, developing a genetic modification tool for the strain was infeasible. As an alternative, a genetically modifiable acetogen, the Eubacterium limosum ATCC 8486 strain with the absence of GSRP-coding genes in its genome, was examined for the heterogeneous introduction of the pathway (8,31). To confirm the functional role, the GSRP-encoding gene cluster from the C. drakei genome was cloned into a plasmid, which was then introduced into E. limosum (the GSRP strain), and the same plasmid backbone without the gene cluster was introduced into E. limosum as a control strain (SI Appendix, Fig.…”

Transcriptome Analysis of Ice Plant Growth-Promoting Endophytic Bacterium Halomonas sp. Strain MC1 to Identify the Genes Involved in Salt Tolerance

“…GO functional enrichment and KEGG pathway analyses were performed with Goatools (Available online: https:// github.com/tanghaibao/Goatools) and KOBAS (Available online: http://kobas.cbi.pku.edu.cn/home.do), respectively, to understand the functions of the DEGs. The DEGs were considered significantly enriched in GO terms and metabolic pathways in accordance with the reported method under multiple test corrections [32] when their corrected p-value was less than 0.05 using Fisher's test. In order to improve statistical significance, the q-value was used to estimate the false discovery rate (FDR).…”

Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide

“…Subsequently, the assembled plasmid (pJIR750_alsD) was linearized by SacI and BamHI, and was then assembled with the amplified alsS by In-Fusion cloning Kit, generating the pJIR750_alsS_alsD plasmid. To control the gene expressions, promoters of ELIM_c2885 (pyruvate:ferredoxin oxidoreductase) and ELIM_c1121 ([Fe] hydrogenase) were selected as the two genes were constitutively expressed with high expression levels in E. limosum (Song et al, 2018). The native promoters were amplified from genomic DNA of E. limosum and inserted in the pJIR750_alsS_alsD plasmid, resulting in the construction of pJIR750_alsS_U_1121_P1121_P2885_U1121_alsD plasmid.…”

“…To investigate the strain capacity to produce biochemicals, acetoin was selected as a target chemical, which is widely utilized in various industries from cosmetics, food flavoring, and pharmaceuticals (Werpy and Petersen, 2004;Bao et al, 2015). Interestingly, in E. limosum, the acetoin biosynthetic pathway coding genes are located, but the production was not detected under CO and other conditions, such as glucose and H 2 /CO 2 conditions (Song et al, 2017(Song et al, , 2018. In the presence of the genes, E. limosum is capable of synthesizing acetoin; however, the insignificant transcriptional and translational expressions under the heterotrophic and autotrophic conditions prevent the production, according to a previous study (Song et al, 2018).…”

“…Interestingly, in E. limosum, the acetoin biosynthetic pathway coding genes are located, but the production was not detected under CO and other conditions, such as glucose and H 2 /CO 2 conditions (Song et al, 2017(Song et al, , 2018. In the presence of the genes, E. limosum is capable of synthesizing acetoin; however, the insignificant transcriptional and translational expressions under the heterotrophic and autotrophic conditions prevent the production, according to a previous study (Song et al, 2018). Thus, activation of the biosynthetic pathway coding genes using novel bio-parts potentially produce acetoin in E. limosum, and then determine whether ECO_acsA is a superior platform to produce the biochemical compounds.…”