Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

Donati, Claudio; Hiller, N Luisa; Tettelin, Hervé; Muzzi, Alessandro; Croucher, Nicholas J; Angiuoli, Samuel V; Oggioni, Marco; Dunning Hotopp, Julie C; Hu, Fen Z; Riley, David R; Covacci, Antonello; Mitchell, Tim J; Bentley, Stephen D; Kilian, Morgens; Ehrlich, Garth D; Rappuoli, Rino; Moxon, E Richard; Masignani, Vega

doi:10.1186/gb-2010-11-10-r107

Table 2 Presence, cellular localization and level of conservation of a selection of genes that are either surface exposed, or known to be involved in interaction with the host and virulence

From: Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

TIGR ID	R6 Id	INV104B	Length	Annotation	Predicted cell localization	Presence in Spn strains	Conservation (average % ID)	Present in S. mitis^a	Present in S. oralis	Present in S. infantis
Frameshifted^b	spr1536		1,035	Neuraminidase A (NanA)	LPXTG cell-wall anchored	44	92.59	Yes	Yes	Yes
SP_0057	spr0057		1,312	Beta-N-acetylhexosaminidase (StrH)	LPXTG cell-wall anchored	44	97.59	No	Yes	Yes
SP_0069	Absent		211	Choline binding protein I (CbpI)	Choline binding, surface	6	85.73	Yes	No	No
SP_0071	Absent		1,856	Zinc metalloprotease ZmpC	LPXTG cell-wall anchored	6	89.79	Yes	No	No
SP_0082	spr0075		857	Cell wall surface anchor family protein	LPXTG cell-wall anchored	44	91.92	Yes	Yes	Yes
SP_0117	spr0097		744	Pneumococcal surface protein A (PspA)	Choline binding, surface	44	81.35	No	No	No
SP_0268	spr0247		1,280	Alkaline amylopullulanase, putative	LPXTG cell-wall anchored	44	97.53	Yes	Yes	No
SP_0314	spr0286		1,066	Hyaluronidase (HysA)	LPXTG cell-wall anchored	44	99.38	No	No	No
SP_0368	spr0328		1,767	Cell wall surface anchor family protein	LPXTG cell-wall anchored	44	96.96	No	Yes	Yes
SP_0377	spr0337		340	Choline binding protein C (CbpC)	Choline binding, surface	31	93.86	Yes	Yes	No
SP_0378	Absent		332	Choline binding protein J (CbpJ)	Choline binding, surface	36	88.97	Yes	Yes	Yes
SP_0390	spr0349		285	Choline binding protein G (CbpG)	Choline binding, surface	44	95.21	No	No	No
SP_0391	spr0350		340	Choline binding protein F (CbpF)	Choline binding, surface	16	90.33	Yes	Yes	Yes
SP_0462	Absent		893	RrgA pilus subunit, adhesin	LPXTG cell-wall anchored	8	91.66	No	No	No
SP_0463	Absent		665	RrgB pilus subunit, backbone	LPXTG cell-wall anchored	8	66.5	No	No	No
SP_0464	Absent		393	RrgC pilus subunit	LPXTG cell-wall anchored	8	99.09	No	No	No
SP_0498	spr0440		1,659	Endo-beta-N-acetylglucosaminidase, putative	LPXTG cell-wall anchored	44	97.02	Yes	Yes	Yes
SP_0641	spr0561		2,140	Serine protease, subtilase family	LPXTG cell-wall anchored	44	96.54	Yes	Yes	No
SP_0648	spr0565		2,233	Beta-galactosidase (BgaA)	LPXTG cell-wall anchored	44	96.54	Yes	Yes	No
SP_0664	spr0581		1,881	Zinc metalloprotease, putative (ZmpB)	LPXTG cell-wall anchored	43	71.13	Yes	No	Yes
SP_0667	spr0583		332	Pneumococcal surface protein, putative	Choline binding, surface	44	90	Yes	No	Yes
SP_0930	spr0831		627	Choline binding protein E (CbpE)	Choline binding, surface	44	96.64	Yes	No	No
SP_0965	spr0867		658	Endo-beta-N-acetylglucosaminidase (LytB)	Choline binding, surface	44	98.42	Yes	No	No
SP_0981	spr0884		313	Putative protease maturation protein (PpmA)	Lipoprotein	44	96.77	Yes	Yes	Yes
SP_1003	spr0907		839	Histidine triad protein	Lipoprotein	39	91.34	Yes	Yes	Yes
SP_1004	spr0908		1,039	Histidine triad protein	Lipoprotein	44	99.67	Yes	Yes	Yes
SP_1154	spr1042		2,004	Immunoglobulin A1 protease	LPXTG cell-wall anchored	44	79.85	Yes	Yes	No
SP_1174	Absent		819	Histidine triad protein	Lipoprotein	16	95.39	Yes	Yes	Yes
SP_1175	spr1061		802	Histidine triad protein	Lipoprotein	33	92.95	Yes	Yes	Yes
SP_1326	Absent		740	Putative neuraminidase (NanC)	Outer membrane/secreted	16	94.21	No	No	No
SP_1492	spr1345		202	Cell wall surface anchor family protein	LPXTG cell-wall anchored	44	91	Yes	Yes	Yes
SP_1572	spr1430		178	Non-heme iron-containing ferritin (PppA)	Surface	44	94.5	Yes	Yes	Yes
SP_1573	spr1431		490	Lysozyme (LytC)	Choline binding, surface	44	96.46	Yes	No	No
SP_1650	spr1494		309	Manganese ABC transporter, manganese-binding adhesion liprotein (PsaA)	Lipoprotein	44	97.92	Yes	Yes	Yes
SP_1687	spr1531		697	Neuraminidase B (NanB)	Surface	43	93.85	Yes	No	No
SP_1732	spr1577			Serine threonine kinase protein (StkP)	Membrane	44	95.33	Yes	Yes	Yes
SP_1772	Absent		4,776	Cell wall surface anchor family protein (PsrP)	LPXTG cell-wall anchored	14	99.7	No	No	No
SP_1833	spr1652		708	Cell wall surface anchor family protein	LPXTG cell-wall anchored	44	97.63	Yes	No	Yes
SP_1923	spr1739		471	Pneumolysin (Ply)	Secreted	44	99.5	Yes	No	No
SP_1937	spr1754		318	Autolysin (LytA)	Choline binding, surface	44	98.74	Yes	No	No
SP_1992	spr1806		221	Cell wall surface anchor family protein	LPXTG cell-wall anchored	44	99.01	No	No	No
SP_2136	spr1945		621	Choline binding protein PcpA (PcpA)	Choline binding, surface	32	99.05	Yes	No	No
SP_2190^c	spr1995		693	Choline binding protein A (CbpA) (PspC)	Choline binding, surface	44		Yes	No	No
SP_2201	Absent		448	Choline binding protein D (CbpD)	Choline binding, surface	43	98.94	Yes	No	No
SP_2216	spr2021		392	Secreted 45 kDa protein (PcsB)	Secreted	44	96.75	Yes	Yes	Yes
Absent	Absent	SPNINV104_08710	410	PitB pilus 2 subunit, backbone	LPXTG cell-wall anchored	8	100	No	Yes	No
Absent	Absent	SPNINV104_08690	589	PitA pilus 2 subunit, ancillary	LPXTG cell-wall anchored	8	100	No	Yes	No

Due to the presence of unfinished genomes, we considered genes present in 43 S. pneumoniae genomes to be core. ^a'Yes' indicates genes that are present in at least one of the strains of S. mitis, while 'no' indicates genes that are absent in the four analyzed strains. ^bNanA is annotated as frameshifted in the TIGR4 strain, but it is known to be expressed by all pneumococcal strains. ^cPspC has been classified in 11 major variants that cannot be aligned due to different gene organization.

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