Table 2.

Selected RpoS-regulated genes also regulated by BosR in mammalian host-adapted (DMC-cultivated) B. burgdorferi.

Genes activated by RpoS and BosR†
Locus tag‡	Gene‡	Product‡	Fold change in WT vs ΔbosR§	Fold change in WT vs bosR-R39AΔrpoS/irpoS¶
BBF0041	vlsE1	Outer surface protein VlsE1	1006.21	1.28
BBA25	dbpB	Decorin binding protein B	27.58	2.97
BBA34	oppA5	Extracellular solute-binding protein OppA5	9.28	6.41
BBK32	-	Fibronectin-binding protein	8.74	3.03
BBB19	ospC	Outer surface protein C	7.50	1.75
BBA24	dbpA	Decorin binding protein A	6.45	2.95
BB0681	mcp5	Methyl-accepting chemotaxis protein Mcp5	5.35	2.55
BB0680	mcp4	Methyl-accepting chemotaxis protein Mcp4	4.44	2.12
BB0669	cheA2	Chemotaxis protein CheA2	2.94	2.51
Genes repressed by RpoS and BosR†
Locus tag‡	Gene‡	Product‡	Fold change in WT vs ΔbosR§	Fold change in WT vs bosR-R39AΔrpoS/irpoS¶
BBJ09	ospD	Outer surface protein D	−650.90	−581.81
BBA74	bba74	Osm28	−296.74	−170.51
BBA15	ospA	Outer surface protein A	−281.17	−152.92
BBA68	BBCRASP-1	Complement regulator-acquiring surface protein 1	−203.17	−46.49
BBA16	ospB	Outer surface protein B	−187.10	−100.20
BBA62	bba62	6.6 kDa lipoprotein	−156.60	−80.01
BBI39	-	PFam_54/60	−144.65	−62.16
BBI38	-	PFam_54/60	−20.16	−44.43
BBD18	-	BBD18	−8.05	−13.10
BB0240	glpF	Glycerol uptake facilitator	−7.01	−13.41
BBB29	malX2	PTS system transporter subunit IIBC	−4.96	−1.93
BB0241	glpK	Glycerol kinase	−4.58	−10.00
BB0330	oppA3	Oligopeptide ABC transporter periplasmic oligopeptide-binding protein (OppA3)	−3.72	−5.93
BB0243	glpD	Glycerol-3-phosphate dehydrogenase	−2.93	−5.42

^†Genes were selected based on their predicted or experimentally validated functions and prior identification as RpoS-regulated in multiple studies. A complete list of RpoS-regulated genes within the mammalian-phase BosR regulon is provided in Table S3.

^‡Locus tags, gene names, and product descriptions are derived from the B. burgdorferi strain B31 RefSeq genome annotation and/or UniProt/InterPro analyses.

^§Fold changes in gene expression were determined by comparing WT to ΔbosR strains in DMCs (Table S3). Only genes showing ≥2-fold differences with q < 0.05 were considered significantly regulated. All genes shown meet the q<0.05 threshold.

^¶Fold changes in gene expression were determined by comparing WT to bosR-R39AΔrpoS/irpoS +IPTG strains in DMCs (Table S3). Only genes showing ≥2-fold differences with q < 0.05 were considered significantly regulated. All genes shown meet the threshold, except those shaded in pale peach color.