TABLE 2

Genes present in commensal Streptococcus species but absent from S. pneumoniae

Locus no. in S. mitisAnnotation and commentsPresence (%) in:Size of protein (aa)
S. mitisS. pseudopneum.S. oralisS. infantis
SM12261_0091-2Gram-positive cell wall surface anchor family protein (YSIRK family); one reading frame in all other strains; N-terminal 199 nt show 87% identity, whereas remaining part shows no significant homology to S. pneumoniae950100100657
SM12261_0140MarR family transcriptional regulator (phosphoenolpyruvate-protein phosphotransferase); absent from S. oralis subsp. dentisani; pseudogene in S. pneumoniae; regulators with the MarR-type HTH domain control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents, and regulation of the virulence factor synthesis in pathogens100065081
SM12261_0266Oligopeptide-binding protein SarA; present in four of five S. oralis subsp. dentisani isolates, ATCC 6249, and SK6431000240654
SM12261_0268Amino acid permease 2 superfamily; APC (amino acid/polyamine/organocation) family permease (solute:cation symporter) involved in the uptake of a specific amino acid and/or polyamine substrate with the concomitant import of a proton900100100614
SM12261_0489-91Queuosine biosynthesis proteins QueC, QueD, and QueE; queuosine is a hypermodified guanosine analog; pseudogene of QueC consisting of first 213 bp is present in S. pneumoniae strains1001008267217, 147, 226
SM12261_0495-6LrgA + LrgB; homologs of LrgA and LrgB/CidA and CidB in Streptococcus mutans and Staphylococcus aureus; substantial influence on properties involved in colonization and persistence in dental biofilms and under oxidative stress conditions (99, 100)100100100100124–134, 231
SM12261_0576-9Iron chelate uptake ABC transporter (FeCT family) (permease, ATP-binding protein, oligopeptide-binding protein) and putative esterase (predicted hydrolase of the alpha/beta superfamily)10001000348, 251, 336, 230
SM12261_0615Beta-glucosidase 2, glycosyl-hydrolase family 116 N-terminal domain10010010083102–127
SM12261_0623Virulence factor BrkB; a homolog in Bordetella pertussis is essential for resistance to complement-dependent killing by serum900100100286–294
SM12261_10763-Isopropylmalate dehydratase, large subunit (LeuC); this enzyme performs the second step in the biosynthesis of leucine; the prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit; LeuD (591 nt) occurs downstream from LeuC; LeuD is present in strains of S. pneumoniae in a truncated version (N-terminal 360 bp) in an otherwise syntenic area100100100100460
SM12261_1129Glycerophosphoryl diester phosphodiesterase100000587
SM12261_1229PF08002 family protein of unknown function9505950153–181
SM12261_1300Amino acid permease (LysP superfamily: l-asparagine transporter and related permeases)1000100100445–470
SM12261_1517Oligopeptide-binding protein AliD (SarA); located immediately upstream of the cps locus, in some strains flanked by the paralog aliC; pseudogene in association with cps loci of S. pneumoniae serotypes 25A, 25F, and 38 (104); SarA mutant in S. gordonii is defective in serum-induced aggregation, competence, growth on complex nitrogen sources, and ability to colonize the oral cavity (103)9501000652
SM12261_1764Hypothetical protein; contains DNA polymerase III subunits gamma and tau domain; predicted coiled-coil domain-containing protein (DUF2360)95100100100227–232
B6:smi_1070-3ABC transporter, ATP-binding protein + ABC-2 transporter family protein + histidine kinase + response regulator receiver domain protein951007133302, 250, 292, 225