Required Gene Set for Autotrophic Growth of Clostridium autoethanogenum

Abstract

Although microbial genome sequences are relatively easily determined, assigning gene function remains a bottleneck. Consequently, relatively few genes are well characterized, leaving the function of many as either hypothetical or entirely unknown.

Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum

“…1 D and Dataset S4 ). This number is close to the 404 and 439 essential genes reported in Clostridium difficile ( 26 ) and C. autoethanogenum ( 19 ), respectively. For example, ribosomal, chaperone, aminoacyl-tRNA biosynthesis, and DNA replication proteins were included in the core essential genes and consistent with gene essentiality in E. coli ( 27 ) ( Fig.…”

“…Although the required gene set for autotrophic growth has been identified in C. autoethanogenum ( 19 ), significant gaps remain in our understanding of the functions of other genes in heterotrophic and autotrophic acetogenesis. Under autotrophic growth conditions, the electrochemical sodium gradient across the cytoplasmic membrane is essential for cellular bioenergetics because the F 1 F 0 ATP synthase and Rnf complex strictly rely only on the sodium ion potential ( 31 , 44 ).…”

“…3 A ). However, TIS results in C. autoethanogenum showed that the W–L pathway was not essential in heterotrophic conditions ( 19 ), suggesting that the role of the W–L pathway among acetogenic strains may be different during heterotrophic growth.…”

“…Recently, gene essentiality of Clostridium autoethanogenum was determined using high-throughput random transposon insertion sequencing (TIS). The study showed that the W–L pathway, the Rnf complex, and Nfn are essential for autotrophic growth ( 19 ). However, there are limitations to comparing heterotrophic and autotrophic specific gene sets.…”

Metabolic changes of the acetogen Clostridium sp. AWRP through adaptation to acetate challenge

“…Most genes involved in glycolysis/gluconeogenesis, the pentose phosphate pathway, and the incomplete TCA cycle ( Figure 5A ) were found to be down-regulated. Other auxiliary enzymes for energy conservation including the Hyt hydrogenase, the NADH-dependent ferredoxin:NADP + oxidoreductase (Nfn), and the Rnf complex, all of which are essential for autotrophic growth in CO 2 + H 2 ( Tremblay et al, 2013 ; Woods et al, 2022 ), were also significantly down-regulated in 46 T-a ( Figure 5B ). Regarding ethanol production, two of three genes encoding aldehyde:ferredoxin oxidoreductase (AOR; DMR38_10295 and DMR38_10330), which were actively transcribed in AWRP, were significantly down-regulated in 46 T-a at the stationary phase ( Figure 5C ).…”