Systemic understanding of $CO_2$ fixing eubacterium limosum for the production of biochemicals

Abstract

Bioconversion of $CO_2$ has received much attention to replace fossil fuels. Of the biocatalysts, phylogenetically diverse anaerobic acetogenic bacteria (acetogens) are considered to be the most efficient platform to produce biochemical with the capability to convert synthesis gas ($H_2$/CO/$CO_2$) into acetyl-CoA, an important central metabolite, via the reductive acetyl-CoA pathway, knowns as Wood-Ljungdahl pathway (WLP). Despite the advantages of acetogens in commercial application, a systemic understanding of acetogens at transcriptional and translational level is limited. Recently, genome sequencing of acetogens has profoundly examined, but only a few RNA sequencing (RNA-Seq) study has reported, which demonstrated need for more omics studies to identify engineering target to optimize acetogens. In this study, to systemically comprehend an acetogen at a molecular level during the autotrophic growth condition, first, a genome sequence of the syngas fermenting Eubacterium limosum ATCC8486 was completed and determined transcription start site (TSS), revealing 4.4 mega base pair (Mbp) long circular genome with 4,090 protein-encoding genes and 1,458 TSSs with 93 non-coding RNAs. Following, to find transcriptionally altered system, E. limosum under the autotrophic growth condition was explored, resulting transcriptional abundance in genes encoding WLP and the energy conservation system. Integrating the transcriptomic result to translatomic data, which obtained via ribosome profiling (Ribo-Seq), offered translation efficiency of genes during the autotrophic growth condition, revealing the transcriptionally abundant genes, such as the carbonyl branch of the WLP, the ion-translocating complex, and ATP synthase complexes, showed decreased translation efficiency caused by stable 5′ untranslated region (5′UTR) structures. Ultimately, using the obtained promoters and 5′UTR information from the omics analysis, a library set was constructed, then integrated to produce acetoin, resulting increased acetoin production from zero to 1.17 g/L. These findings provide systemic insights into comprehending $CO_2$ fixing acetogen and indicate a potential target for engineering the bacteria for biochemical production.