Laboratory evolution and reverse engineering of Clostridium thermocellum for growth on glucose and fructose

ABSTRACT

The native ability of Clostridium thermocellum to efficiently solubilize cellulose makes it an interesting platform for sustainable biofuel production through consolidated bioprocessing. Together with other improvements, industrial implementation of C. thermocellum, as well as fundamental studies into its metabolism, would benefit from improved and reproducible consumption of hexose sugars. To investigate growth of C. thermocellum on glucose or fructose, as well as the underlying molecular mechanisms, laboratory evolution was performed in carbon-limited chemostats with increasing concentrations of glucose or fructose and decreasing cellobiose concentrations. Growth on both glucose and fructose was achieved with biomass yields of 0.09 ± 0.00 and 0.18 ± 0.00 g_biomass g_substrate⁻¹, respectively, compared to 0.15 ± 0.01 g_biomass g_substrate⁻¹ for wild type on cellobiose. Single-colony isolates had no or short lag times on the monosaccharides, whilst wild type showed 42 ± 4 hours on glucose and >80 hours on fructose. With good growth on glucose, fructose, and cellobiose, the fructose isolates were chosen for genome sequence-based reverse metabolic engineering. Deletion of a putative transcriptional regulator (Clo1313_1831), which upregulated fructokinase activity, reduced lag time on fructose to 12 hours with a growth rate of 0.11 ± 0.01 h⁻¹ and resulted in immediate growth on glucose at 0.24 ± 0.01 h⁻¹. Additional introduction of a cbpA^G148V mutation resulted in immediate growth on fructose at 0.32 ± 0.03 h⁻¹. These insights can guide engineering of strains for fundamental studies into transport and the upper glycolysis, as well as maximizing product yields in industrial settings.

Importance. C. thermocellum is an important candidate for sustainable and cost-effective production of bioethanol through consolidated bioprocessing. In addition to unsurpassed cellulose deconstruction, industrial application and fundamental studies would benefit from improvement of glucose and fructose consumption. This study demonstrated that C. thermocellum can be evolved for reproducible constitutive growth on glucose or fructose. Subsequent genome sequencing, gene editing and physiological characterization identified two underlying mutations with a role in (regulation of) transport or metabolism of the hexose sugars. In light of these findings, such mutations have likely (and unknowingly) also occurred in previous studies with C. thermocellum using hexose-based media with possible broad regulatory consequences. By targeted modification of these genes, industrial and research strains of C. thermocellum can be engineered to i) reduce glucose accumulation, ii) study cellodextrin transport systems in vivo, iii) allow experiments at >120 g L⁻¹ soluble substrate concentration, or iv) reduce costs for labelling studies.