Table 4.

ΔrisA in non-modulating (Bvg+) conditions.

Cluster	risAD60N vs. WT Non-Mod	ΔrisA vs. WT Non-Mod	ΔrisAS vs. WT Non-Mod	WT Non-Mod vs. Mod	risAD60N Non-Mod vs. Mod	ΔrisA Non-Mod vs. Mod	ΔrisAS Non-Mod vs. Mod	Description	Gene
a	NS	NS	NS	Down	NS	NS	NS	Vrgs not regulated by RisAS and/or phosphorylation of RisA during non-modulating (Bvg+) conditions and require RisAS and phosphorylation of RisA for modulation	wcbA (capsular polysaccharide)
b	Up	Up	Up	Down	NS	NS	NS	Vrgs repressed by RisAS and phosphorylation of RisA during non-modulating (Bvg+) conditions and require RisAS and phosphorylation of RisA for modulation	flaA (flagellar protein)
c	Up	Up	Up	Down	Down	Down	Down	Vrgs repressed by RisA and phosphorylation of RisAS during non-modulating (Bvg+) conditions but do not require RisAS and phosphorylation of RisA for modulation	livK (leucine transport)
d	NS	NS	NS	Up	Up	Up	Up	Vags not regulated by RisAS and/or phosphorylation of RisA during non-modulating (Bvg+) conditions and require RisAS and phosphorylation of RisA for maintaining an expected vag transcriptional response	FHA and PRN
e	Down	Down	Down	Up	NS	NS	NS	Vags that require RisAS and phosphorylation of RisA for full expression in non-modulating (Bvg+) conditions and for maintaining an expected vag transcriptional response	osmC
f	Down	Down	Down	Up	Up	Up	Up	Vags that require RisAS and phosphorylation of RisA for full expression in non-modulating (Bvg+) conditions but do not require RisA and phosphorylation of RisA Maxbites01!	bopN (T3SS)

Transcriptional response of genes within clusters identified from comparisons used to evaluate the differential expression of the ΔrisA mutant in non-modulating (Bvg+) conditions. Yellow, indicates genes upregulated (Up) (log2fc > 1); blue, indicates genes downregulated (Down) (log2fc < −1); white, no significant change or NS in gene expression (log2fc < 1, but > −1).