Co-utilization of glucose and xylose by evolved Thermus thermophilus LC113 strain elucidated by (13)C metabolic flux analysis and whole genome sequencing

Abstract

We evolved Thermus thermophilus to efficiently co-utilize glucose and xylose, the two most abundant sugars in lignocellulosic biomass, at high temperatures without carbon catabolite repression. To generate the strain, T. thermophilus HB8 was first evolved on glucose to improve its growth characteristics, followed by evolution on xylose. The resulting strain, T. thermophilus LC113, was characterized in growth studies, by whole genome sequencing, and (13)C-metabolic flux analysis ((13)C-MFA) with [1,6-(13)C]glucose, [5-(13)C]xylose, and [1,6-(13)C]glucose+[5-(13)C]xylose as isotopic tracers. Compared to the starting strain, the evolved strain had an increased growth rate (~2-fold), increased biomass yield, increased tolerance to high temperatures up to 90°C, and gained the ability to grow on xylose in minimal medium. At the optimal growth temperature of 81°C, the maximum growth rate on glucose and xylose was 0.44 and 0.46h(-1), respectively. In medium containing glucose and xylose the strain efficiently co-utilized the two sugars. (13)C-MFA results provided insights into the metabolism of T. thermophilus LC113 that allows efficient co-utilization of glucose and xylose. Specifically, (13)C-MFA revealed that metabolic fluxes in the upper part of metabolism adjust flexibly to sugar availability, while fluxes in the lower part of metabolism remain relatively constant. Whole genome sequence analysis revealed two large structural changes that can help explain the physiology of the evolved strain: a duplication of a chromosome region that contains many sugar transporters, and a 5x multiplication of a region on the pVV8 plasmid that contains xylose isomerase and xylulokinase genes, the first two enzymes of xylose catabolism. Taken together, (13)C-MFA and genome sequence analysis provided complementary insights into the physiology of the evolved strain.

Keywords: Co-utilization; Glucose and xylose metabolism; Isotopic labeling; Metabolic fluxes; Thermophile.

Figure 1

Specific growth rates of wild-type T. thermophilus HB8 and the evolved strain T. thermophilus LC113 at different temperatures in medium containing 2 g/L of glucose or 2 g/L of xylose.

Figure 2

(A) Glucose, xylose and biomass profiles in a ¹³C-labeling experiment with 0.9 g/L of [1,6-¹³C]glucose + 0.9 g/L of [5-¹³C]xylose. (B) Biomass concentration plotted against glucose and xylose concentration demonstrates simultaneous utilization of glucose and xylose without carbon catabolite repression.

Figure 3

Measured biomass composition for T. thermophilus LC113 (mean ± stdev, n=2) compared to T. thermophilus HB27 (Lee et al., 2014).

Figure 4

Metabolic flux maps for T. thermophilus LC113 under three growth conditions: (A) glucose only, (B) glucose + xylose, (C) xylose only. Fluxes were determined by ¹³C-MFA (flux ± stdev; mmol/g_DW/h).

Figure 5

Coverage maps based on whole genome sequence analysis using T. thermophilus HB8 as a reference strain. Asterisks indicate locations where large structural changes were detected. Significant increases in coverage indicate replicated regions, and zero coverage indicates deletion of a region. Low coverage of pTT8 is in part due to plasmid size under the 10 kb size selection performed during SMRT library preparation.