Biology subjects

Wakashima, T.

Publications and source records attributed to Wakashima, T..

3 recordsLinked to original sources

bioRxiv2025

Direct carbon monoxide fixation via the bacterial and archaeal Wood-Ljungdahl pathways

The Wood-Ljungdahl (WL) pathway, which is widely distributed in both archaea and bacteria, is an ancient carbon fixation pathway from CO2. CO2 fixation proceeds via two branches of pathway: progressive reduction to the methyl group in the methyl branch and one-step reduction to CO in the carbonyl branch. In the final step of the pathway, the methyl group, CO, and CoA are combined into a carbon monoxide dehydrogenase (CODH)/acetyl-CoA synthase (ACS) complex to form acetyl-CoA. Here, we show direct CO fixation to the carbonyl group of acetyl-CoA in both archaeal and bacterial WL pathways under hydrogenogenic growth conditions using 13C tracer-based metabolomics. A combination of metabolomics and proteomics suggested that the hydrogenotrophically grown Thermodesulfatator indicus and Archaeoglobus sp. strain MCR cells, directly fixed CO using free-form ACS in the carbonyl branch with relatively low CO availability. In contrast, carboxydotrophically grown Archaeoglobus cells utilize the CODH/ACS complex for CO2 fixation rather than CO fixation. Direct CO fixation by free-form ACS is more advantageous for conserving reduced ferredoxin compared with the thermodynamically challenged CO2 reduction by CODH. These findings provide further insight into the origin and evolution of the most ancient inorganic carbon fixation pathway and geochemical cycles on early Earth.

microbiology↗

bioRxiv2025

Molecular evolution of the Wood-Ljungdahl pathway and the reductive glycine pathway in Thermodesulfobacteriota

Carbon fixation is a fundamental metabolic process that sustains ecosystems, yet its origins and evolutionary history remain largely unresolved. In this study, we focused on the Wood-Ljungdahl (WL) pathway, which is considered one of the most ancient carbon fixation pathways and the reductive glycine (rGly) pathway, which shares several reactions with the WL pathway. The evolutionary scenario of the two carbon fixation pathways was inferred in the phylum Thermodesulfobacteriota, which includes microorganisms that operate either the WL pathway or the rGly pathway for autotrophic growth. The timing of gene gain and loss events was inferred by gene presence/absence analyses for both pathways, together with phylogenetic analyses of their key enzymes. Our results suggested that the common ancestor of Thermodesulfobacteriota possessed all genes encoding key enzymes of both pathways; formate dehydrogenase, the carbon monoxide dehydrogenase/acetyl-CoA synthase complex and the glycine cleavage system. Furthermore, analyses of complete gene sets for the WL and rGly pathway, together with downstream genes required for amino acid biosynthesis, supported the possibility that the common ancestor of this phylum had been capable of autotrophic growth through these carbon fixation pathways. Then, multiple lineages have lost the WL and rGly pathway genes independently during subsequent evolution. Gene replacements also occurred in the glycine cleavage system by regaining genes by horizontal gene transfer. These results suggest that carbon fixation pathways in extant organisms in the phylum Thermodesulfobacteriota arose through a combination of vertical inheritance, gene loss, and horizontal gene transfer.

bioinformatics↗

bioRxiv2025

Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria

The Wood-Ljungdahl (WL) pathway and reductive tricarboxylic acid (rTCA) cycle are the dominant chemolithotrophic CO2 fixation pathways in bacteria inhabiting aphotic geothermal and deep-sea hydrothermal ecosystems. However, the activity of these bacterial metabolic systems in ecosystems with available organic carbons remains unclear. Here, we examined the impact of extracellular acetate on the CO2-fixation pathways of three thermophilic hydrogen-oxidizing and non-acetogenic bacteria using 13C tracer-based metabolomics. Under chemolithoautotrophic conditions, Thermodesulfatator indicus and Hydrogenobacter thermophilus fixed CO2 through the WL pathway and rTCA cycle, respectively, whereas Thermovibrio ammonificans, which has been suggested to operate both of these pathways, exhibited significant CO2 fixation through only the rTCA cycle. Under chemolithomixotrophic conditions with acetate, H. thermophilus and T. ammonificans assimilated both CO2 and acetate via the rTCA cycle. In contrast, acetate suppressed CO2 fixation through the WL pathway in T. indicus and was used as the primary carbon source under chemolithomixotrophic conditions. These results suggest that the contribution of the WL pathway for CO2 fixation might be overestimated in ecosystems where acetate is available. Moreover, the present findings indicate that simultaneous CO2 fixation through both the WL pathway and rTCA cycle in a cell, which has been proposed as a possible metabolic strategy for CO2-fixation in ancestral life, is not advantageous in extant microorganisms.

microbiology↗