Comparative Genomics of Firmicutes reveals probable adaptations for xylose fermentation in Thermoanaerobacterium saccharolyticum

Abstract Second-generation (2G) ethanol is one potential biofuel that could be used to achieve the goal of reducing greenhouse gas emissions. Many challenges still need to be overcome for the feasibility of this technology, most of them related to consumption of xylose, a pentose sugar not easily metabolized by industrial microorganisms. Thus, exploring genes, pathways and other organisms that can ferment xylose is a strategy implemented to solve industrial bottlenecks. Thermoanaerobacterium saccharolyticum ( T. sac ) is an organism from the firmicutes phylum, capable of naturally fermenting compounds of industrial interest, such as xylan and xylose. Understanding evolutionary adaptations may help not only to solidify this bacterium as a potential substitute to the yeast Saccharomyces cerevisiae in industry, but also bring novel genes and information that can be used for yeast, enhance its fermenting capabilities, and increase production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improve T. sac as a new microbial cell factory, which may help to solve current problems found in the biofuels industry.