Fig. 2: Reprogramming xylose catabolism by BETTER.
a Xylose catabolism pathway. Three target genes and the corresponding reactions are highlighted in blue. E4P erythrose 4-phosphate, F6P fructose 6-phosphate, G3P glyceraldehyde 3-phosphate, R5P ribose 5-phosphate, Ru5P ribulose 5-phosphate, S7P sedoheptulose 7-phosphate. b Components of RBS libraries before (0) and after six passages (sixth) of serial cultivation in xylose. Three colonies were used for base editing and the cells were mixed with an equal proportion before extraction of genomic DNAs, PCR amplification, and NGS. c Serial cultivation for screening genetic combinations that favor growth on xylose. The numbers above columns represent the passages of serial cultivation. d Discreteness change of genetic combinations during serial cultivation. KL divergence was used to evaluate the discreteness of genetic combinations. e The matrixes show the coverage and discreteness of 256 G/A-containing RBS variants in the RBS libraries generated by BETTER before (0) and after six passages (sixth) of serial cultivation in xylose. Scale bar represents log2(relative proportion). Blue squares represent the enriched GAAAGGAA RBSxylA. f RBS variants with the largest ten proportions for each passage of serial cultivation. g Xylose utilization by a screened strain from the sixth passage and a rationally built strain with the same xylA, xylB, and tkt RBSs as the screened strain. Values and error bars reflect the mean ± s.d. of three biological replicates (n = 3). Statistical evaluation (P value) was performed by a two-sided t test. NS nonsignificant (P ≥ 0.05), n = 3. h Strength of RBSs enriched during serial cultivation in xylose using a chromosomal GFP reporter. The tailored RBS (GGGGGGGG) and a strong RBS (GAAAGGAG) were used as controls. Values and error bars reflect the mean ± s.d. of three biological replicates (n = 3). Source data underlying Fig. 2c–h are provided as a Source Data file.
