Comparative genomic assessment of the Cupriavidus necator species for one-carbon based biomanufacturing

Abstract

The transition from a petroleum-based manufacturing to biomanufacturing is an important step towards a sustainable bio-economy. In particular biotechnological processes which use one carbon (C1) compounds as feedstock represent an interesting avenue. Many bacterial species evolved naturally to thrive on such compounds, among them Cupriavidus necator, which has been studied in the past due to its range of metabolic capabilities in utilization and production of compounds of interest. Cupriavidus necator strain H16 is the reference laboratory strain for this species and by far the most extensively studied. In contrast, research efforts and genomic characterization of other strains within this species have been limited and sporadic. Therefore, the genomic diversity and full metabolic potential across the broader species remain poorly understood. In this work, we collected publicly available genomes along with newly sequenced ones. From a collection of 44 genomes we curated a final collection of 22 genomes deemed to be C. necator. We examined hallmark metabolic functions, including carbon dioxide fixation, formate assimilation, and hydrogen utilization. We identified methylation motifs and restriction modification systems. Finally, strains ATCC 25207, TA06, and 1978 are proposed as candidate strains of interest based on their genomic make-up and observations from literature. This work provides a comprehensive genomic resource for the C. necator species, facilitating its development as a biomanufacturing platform and advancing our understanding of its metabolic diversity and potential applications. ImportanceThe green transition from petroleum-based manufacturing to a biomanufacturing economy requires new solutions. One of these is the development of bacterial platforms for production of valuable chemicals, in particular from CO2 and derived molecules. In this context, Cupriavidus necator is one of the most studied platform strains, although the genomic potential of this species has been seldom explored. This work provides a curated set of C. necator genomes, collected from public repositories and additional newly sequenced genomes. Through multiple analyses, C. necator ATCC 25207, TA06, and 1978 are proposed as strains of interest for further use. These findings lay the groundwork for advancing C. necator as a key organism in sustainable biomanufacturing, highlighting its potential for efficient carbon fixation, formate assimilation, and hydrogen utilization. The identification of methylation motifs and restriction modification systems further supports genetic engineering efforts, making these strains highly valuable for future biotechnological applications.