Fig. S1. Loop designed hybridization schemes of L. plantarum NC8 (A) and WCFS1 (B). Wild-type strains, cggR mutant strains and cggR-overexpressed strains are represented as Wt, ΔcggR and cggR-P25, respectively, and biological duplicates are indicated with A and B, and are represented in a circle. Strains grown on glucose are indicated by dark-grey boxes, whereas ribose-grown strains are indicated by grey boxes. The loop designs allow for the evaluation of putative dye effects.

Table S1. Bacterial strains and plasmids.

Table S2. Individual effects of the genes with significant CE, ME or IE in L. plantarum NC8.

Table S3. Genes with significant CE and OE in L. plantarum WCFS1.

Table S4. Cloning and sequencing primers used in the construction of cggR-engineered strains of L. plantarum.

Appendix S1. Experimental procedures.

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