TABLE 1.

Significantly downregulated immune genes in BMDMs infected with the ΔbpdA mutant^a

Functional category	Gene symbol	Downregulation factor
		vs 16M	vs ΔcgsB mutant
Complement activation
Complement component 2 (within H-2S)	C2	0.40	0.44
Complement factor B	Cfb	0.31	0.29
MHC/antigen presentation
Histocompatibility 2, class II antigen A, beta 1	H2-Ab1	0.23	0.26
Histocompatibility 2, M region locus 2	H2-M2	0.24	0.18
Histocompatibility 2, O region alpha locus	H2-Oa	0.15	0.18
Histocompatibility 2, O region beta locus	H2-Ob	0.10	0.11
Proteasome (prosome, macropain) subunit, beta type 6	Psmb6	0.48	0.46
Proteasome (prosome, macropain) 26S subunit, non-ATPase, 8	Psmd8	0.50	0.50
Transporter 1, ATP-binding cassette, subfamily B (MDR/TAP)	Tap1	0.48	0.49
Interferon-induced genes
2′-5′ Oligoadenylate synthetase 3	Oas3	0.48	0.49
2′-5′ Oligoadenylate synthetase-like 1	Oasl1	0.14	0.17
2′-5′ Oligoadenylate synthetase-like 2	Oasl2	0.45	0.45
Chemokine (C-C motif) ligand 12	Ccl12	0.32	0.30
Chemokine (C-X-C motif) ligand 10	CXCL10	0.08	0.08
Chemokine (C-X-C motif) ligand 11	CXCL11	0.05	0.04
Guanylate binding protein 1	Gbp1	0.18	0.17
Guanylate binding protein 10	Gbp10	0.32	0.29
Guanylate binding protein 11	Gbp11	0.28	0.32
Guanylate binding protein 2	Gbp2	0.19	0.18
Guanylate binding protein 3	Gbp3	0.11	0.11
Guanylate binding protein 4	Gbp4	0.21	0.22
Guanylate binding protein 5	Gbp5	0.09	0.09
Guanylate binding protein 6	Gbp6	0.29	0.29
Guanylate binding protein 7	Gbp7	0.19	0.17
Guanylate binding protein 8	Gbp8	0.32	0.30
Guanylate binding protein 9	Gbp9	0.35	0.34
Interferon gamma-induced GTPase	Igtp	0.48	0.44
Interferon-induced protein with tetratricopeptide repeats 1B like 2	Ifit1bl2	0.35	0.31
Interferon-induced protein with tetratricpeptide repeats 1B like 1	Ifit1bl1	0.17	0.15
Interferon-inducible GTPase 1	Iigp1	0.40	0.33
Interferon-induced protein with tetratricopeptide repeats 1	Ifit1	0.27	0.25
Interferon-induced protein with tetratricopeptide repeats 2	Ifit2	0.21	0.21
Interferon-induced protein with tetratricopeptide repeats 3	Ifit3	0.39	0.36
MX dynamin-like GTPase 1	Mx1	0.27	0.29
MX dynamin-like GTPase 2	Mx2	0.19	0.20
TAP binding protein-like	Tapbpl	0.48	0.47
Inflammation
Chemokine (C-C motif) ligand 2	Ccl2	0.19	0.17
Chemokine (C-C motif) ligand 22	Ccl22	0.20	0.29
Chemokine (C-C motif) ligand 3	Ccl3	0.29	0.25
Chemokine (C-C motif) ligand 5	Ccl5	0.10	0.12
Chemokine (C-C motif) ligand 7	Ccl7	0.17	0.16
Chemokine (C-C motif) ligand 9	Ccl9	0.33	0.30
Chemokine (C-C motif) receptor 7	Ccr7	0.08	0.10
Chemokine (C-C motif) receptor-like 2	Ccrl2	0.12	0.11
Chemokine (C-X-C motif) ligand 1	CXCL1	0.23	0.21
Chemokine (C-X-C motif) ligand 2	CXCL2	0.27	0.25
Chemokine (C-X-C motif) ligand 3	CXCL3	0.27	0.32
Chemokine (C-X-C motif) receptor 4	Cxcr4	0.36	0.39
Colony-stimulating factor 3 (granulocyte)	Csf3	0.05	0.03
Colony-stimulating factor 3 receptor (granulocyte)	Csf3r	0.48	0.47
Interleukin 1 alpha	Il1a	0.06	0.06
Interleukin 1 receptor antagonist	Il1rn	0.04	0.03
Interleukin 10	IL-10	0.19	0.13
Interleukin 11 receptor, alpha chain 1	IL-11ra1	0.36	0.36
Interleukin 12a	IL-12a	0.09	0.09
Interleukin 12b	IL-12b	0.02	0.02
Interleukin 13 receptor, alpha 1	IL-13ra1	0.28	0.27
Interleukin 15 receptor, alpha chain	IL-15ra	0.12	0.11
Interleukin 17 receptor A	IL-17ra	0.30	0.24
Interleukin 18	IL-18	0.38	0.42
Interleukin 27	IL-27	0.12	0.11
Interleukin 6	IL-6	0.04	0.04
Interleukin 7 receptor	IL-7r	0.12	0.10
Killer cell lectin-like receptor subfamily K, member 1	Klrk1	0.40	0.36
Nitric oxide synthase 2, inducible	Nos2	0.01	0.01
Tumor necrosis factor	TNF	0.28	0.28
Tumor necrosis factor (ligand) superfamily, member 10	Tnfsf10	0.43	0.41
Tumor necrosis factor (ligand) superfamily, member 15	Tnfsf15	0.17	0.17
Tumor necrosis factor (ligand) superfamily, member 9	Tnfsf9	0.22	0.28
Tumor necrosis factor receptor superfamily, member 12a	Tnfrsf12a	0.22	0.27
Tumor necrosis factor receptor superfamily, member 1b	Tnfrsf1b	0.40	0.43
Tumor necrosis factor receptor superfamily, member 8	Tnfrsf8	0.24	0.25
Tumor necrosis factor receptor superfamily, member 9	Tnfrsf9	0.03	0.03
Immune signaling
CCAAT/enhancer binding protein beta	Cebpb	0.40	0.49
CD164 antigen	Cd164	0.45	0.43
CD200 antigen	Cd200	0.08	0.06
CD24a antigen	Cd24a	0.01	0.00
CD274 antigen	Cd274	0.17	0.16
CD300 antigen-like family member F	Cd300lf	0.08	0.09
CD33 antigen	Cd33	0.47	0.39
CD40 antigen	Cd40	0.10	0.11
CD69 antigen	Cd69	0.41	0.39
CD83 antigen	Cd83	0.23	0.25
CD86 antigen	Cd86	0.19	0.19
Fas death domain-associated protein	Daxx	0.44	0.46
Fc receptor, IgG, low affinity IIb	Fcgr2b	0.38	0.37
Interferon regulatory factor 7	Irf7	0.46	0.47
Janus kinase 2	Jak2	0.47	0.43
Nucleotide-binding oligomerization domain containing 1	Nod1	0.43	0.43
Secretory leukocyte peptidase inhibitor	Slpi	0.35	0.23
Signal transducer and activator of transcription 3	Stat3	0.49	0.50
Signaling lymphocytic activation molecule family member 1	Slamf1	0.01	0.01
SLAM family member 7	Slamf7	0.20	0.19
SLAM family member 8	Slamf8	0.21	0.18
Suppressor of cytokine signaling 1	Socs1	0.28	0.31
Suppressor of cytokine signaling 3	Socs3	0.32	0.32
TNF receptor-associated factor 1	Traf1	0.29	0.29
TNF receptor-associated factor 5	Traf5	0.32	0.32
TNF receptor-associated factor 6	Traf6	0.34	0.35
Toll-like receptor 3	TLR3	0.43	0.37
Tumor necrosis factor, alpha-induced protein 3	Tnfaip3	0.22	0.21

^aAll genes presented are at least 2-fold different in the ΔbpdA mutant versus 16M and the ΔbpdA mutant versus the ΔcgsB mutant and are statistically significant (P < 0.001).