Table 1.

Functional categorization of OM and periplasmic proteins statistically significantly over- and underrepresented in SOMVs

Functional category and protein name or NMB designation	Function	Fold SOMV/OM changea	Relative amt in SOMVsb
OM proteins overrepresented
Autotransporter proteins
App	Adhesion and penetration protein	4.72	213.33
AusI	Autotransporter, serine-type peptidase	4.10	116.33
NalP	Autotransporter protease	3.10	19
Iga	IgA-specific serine endopeptidase	2.71	278
NadA	Putative adhesin/invasin	2.04	19
Complement regulatory proteins
fHbp	Factor H-binding protein	3.78	84
Opc	Class 5 OM protein	3.16	2,132
NspA	OM protein	3.10	36.67
NhbA	Heparin-binding protein A	2.32	5.67
Two-partner secretion proteins
HprA	TPSS,c secreted component	2.71	6
HprB	TPSS, transporter protein	1.94	16.67
Tr metal (iron, zinc, others) binding and uptake proteins
Tbp2	Transferrin-binding protein 2	3.80	10.67
Tbp1	Transferrin-binding protein 1	1.99	130.33
LbpA	Lactoferrin-binding protein A	1.78	5
HpuB	Hemoglobin receptor	1.38	36
ZnuD	Zinc uptake component D	1.66	220.33
FetA	Iron-regulated OM protein FrpB	1.56	17.67
FetB	Iron(III) ABC transporter, periplasmic binding protein	1.06	4
NMB1829	TonB-dependent receptor	1.32	7.33
Autolysin OMPLA	OM phospholipase A	1.49	30.67
Unknown function
NMB1578	Conserved hypothetical protein	1.96
NMB2139	Conserved hypothetical protein	1.79	7.67
NMB0035	Conserved hypothetical protein	1.13	25.67
NMB2134	Conserved hypothetical protein	1.06	13.67
NMB1212	Hypothetical protein	1.85	2.33
NMB0841	Hypothetical protein	1.68	5
NMB1084	Hypothetical protein	1.63	43.67
NMB1035	Hypothetical protein	1.46	22.67
NMB1213	Putative lipoprotein	1.74	14.33
NMB0204	Putative lipoprotein	1.73	17
NMB0873	Putative OM protein	1.63	10.67
NMB2091	Putative hemolysin	1.58	40.67
NMB0707	Putative rare lipoprotein B	1.53	20.67
NMB1898	Lipoprotein	1.40	21.67
Other transporters
PotD-3	Spermidine/putrescine ABC transporter	2.06	5.67
PotD-1	Spermidine/putrescine ABC transporter	1.61	34
NMB0787	Amino acid ABC transporter	1.23	46
NMB0623	Spermidine/putrescine ABC transporter	1.18	22.67
OM proteins underrepresented
Porins
PorA	Major OM protein PorA	0.70	621.33
PorB	Major OM protein PorB	0.69	1,604
Membrane integrity protein RmpM	OM protein class 4	0.58	46.67
Drug efflux protein MtrE	Multidrug efflux pump channel protein	0.31	22
Pilus-related protein PilQ	Pilus pore protein PilQ	0.44	69
Other
Mip	Macrophage infectivity potentiator	0.77	24.33
Unknown function
NMB0086	Hypothetical protein	0.92	2.67
NMB1369	Hypothetical protein	0.82	2.33
NMB1592	Putative lipoprotein	0.81	7.67
Periplasmic proteins overrepresented
Transporter proteins
NMB0041	ABC transporter, periplasmic solute binding protein	3.43	17
FbpA	Iron(III) ABC transporter, periplasmic binding protein	3.27	74.33
ZnuA	Zinc uptake component A	2.05	14
NMB1017	Sulfate ABC transporter, periplasmic sulfate-binding protein	1.20	22.67
Functional maturation of proteins
DsbC	Thiol-disulfite interchange protein	3.41	10.67
NMB0006	Thioredoxin-related protein	3.05	5.67
DsbA3	Thiol-disulfite interchange protein	2.85	2
Unknown function
NMB1030	Conserved hypothetical protein	3.44	17
NMB1963	Conserved hypothetical protein	3.39	11.67
NMB0355	Conserved hypothetical protein	3.35	8.33
NMB0783	Conserved hypothetical protein	3.33	5.33
NMB0345	Putative cell-binding factor	3.27	52.67
NMB1475	Conserved hypothetical protein	3.13	55.33
NMB2074	Hypothetical protein	1.85	11.67
NMB1557	Conserved hypothetical protein	1.83	2
NMB0088	Putative OM protein P1	1.5	157.33
NMB0872	Conserved hypothetical protein	1.28	5.67
NMB0313	Conserved hypothetical protein	1.26	25.33
Cell wall biogenesis protein NMB1620	Putative muramoyltetrapeptide carboxypeptidase	1.35	3
Periplasmic proteins underrepresented
Cell wall remodeling
MltA	Membrane-bound lytic murein transglycosylase A	0.89	6
MltB	Membrane-bound lytic murein transglycosylase B	0.75	0
Slt	Putative soluble lytic murein transglycosylase	0.75	22.33
Functional maturation of proteins
DsbA1	Thiol-disulfite interchange protein	0.81	3.33
DsbA2	Thiol-disulfite interchange protein	0.78	14
Membrane integrity protein NMB0109	Putative PG-binding periplasmic protein	0.79	27

^aRatio of relative SOMV and OM protein abundances obtained by MS quantification against the metabolically labeled internal standard.

^bRelative amount of protein within the SOMV fraction based on NSAFs. Statistical significance was calculated with Student's t test. P < 0.05 was defined as statistically significant.

^cTPSS, two-partner secretion system.