Genomic insights to facilitate the construction of a high-xylose-utilization Enterococcus faecalis OPS2 for 2,3-BDO production

Sustainable bioconversion of plant biomass sugars for 2,3-butanediol (2,3-BDO) production is a carbon-neutral practice, however, its economic feasibility has been hindered by inefficient utilization of xylose. In this study, a novel Enterococcus faecalis strain OPS1 was isolated from palm oil-polluted soil, which assimilates xylose for 2,3-BDO production. While this wild-type strain OPS1 was suppressed with an increase in xylose concentration (60 g/L), strain OPS2, constructed using an adaptive laboratory evolution, achieved a desirable 2,3-BDO production with high-xylose (>100 g/L) tolerance. Whole-genome sequencing analysis reconstructed the metabolic pathways facilitating xylose utilization and 2,3-BDO production in these two novel strains that evolved within from a lactic acid-producing genus Enterococcus. A rpiB gene encoded for ribose-5-phosphate isomerase B enzyme of xylose metabolism in these two strains was identified to be horizontally acquired from a different family Enterobacteriaceae. The detection of a bacteriocin gene UviB and an antitoxin gene hicB in strain OPS1 and OPS2 which are absent in the E. faecalis type strain indicates their beneficial probiotic and antitoxin features. A mutation in uge (UDP-xylose 4-epimerase) was identified between strain OPS1 and OPS2 which may cater to the high-xylose stress. The evolved E. faecalis OPS2 showed a 3-fold increase in xylose consumption rate (2.19 g/L/h) with 0.67 g/L/h 2,3-BDO productivity than OPS1. For the first time, a maximum of 65.3 g/L 2,3-BDO was successfully produced via fed batch xylose fermentation. These results provide the genomic insights to the xylose regulatory metabolism in Enterococci and pave the way for industrial implication as a microbial biocatalyst in a 2,3-BDO biorefinery.

Automated summary

In this study, a novel Enterococcus faecalis strain OPS2 was isolated from palm oil-polluted soil, which showed high-xylose tolerance and desirable 2,3-BDO production. Whole-genome sequencing analysis revealed the metabolic pathways and identified genes related to xylose utilization and 2,3-BDO production. OPS2 showed better performance than OPS1, providing genomic insights for industrial implication as a microbial biocatalyst in a 2,3-BDO biorefinery.