TABLE 1.

Descriptions of S. pneumoniae promoters identified by DFI

Promoter designationaInduction ratiobNo. of ORFs in operonORF descriptioncMutant constructedd
BA001(NC_003028)1.480No ORF downstreamN
STS0061.98
BA002 (AE007482)1.51(AAK75982); hypothetical proteinN
BA003 (AE007410)2.323ORF1; PRPP synthetaseYe
OM0051.9 (CI)ORF2; aminotransferase (AAK75206)Yg
CO20034.8ORF3; hypothetical protein (AAK75205)
BA004 (AE007451)1.81Pyridine nucleotide-disulfide oxidoreductase family protein (AAK75650)N
IPC001 (AE007373)2.61Serine protease (AAK74791)Y
ISIP4561.5
IPC003 (AE007435)11ORF1; conserved hypothetical protein (AAK75476)Ye
ORF2; 3-dehydroquinate dehydratase (AAK75475)Yo
ORF3; shikimate dehydrogenase (AAK75474)
ORF4; 3-dehydroquinate synthase (AAK75473)
ORF5; chorismate synthase (AAK75472)
ORF6; prephenate dehydrogenase (AAK75471)
ORF7; hypothetical protein (AAK75470)
ORF8; 3-phosphoshikimate, 1-carboxyvinyl transferase (AAK75469)
ORF9; shikimate kinase (AAK75468)
ORF10; prephenate dehydratase (AAK75467)
ORF11; psr protein (AAK75466)
IPC002 (AE007451)2ORF1; hypothetical protein (AAK75645)Ye
ORF2; deg V (AAK75644)Yo
IPC004 (AE007391)1.31ORF1; DNA topoisomerase IV (AAK74981)N
RTI004
IPC005 (AE007448)16ORF1; Cof family protein/peptidyl-prolyl cis-trans isomerase (AAK75626)Ye
ORF2; general stress protein (AAK75625)Yo
ORF3; conserved hypothetical protein (AAK75624)
ORF4; conserved hypothetical protein (AAK75623)
ORF5; Mn-dependent pyrophosphatase (AAK75622)
ORF6; hypothetical ORF (AAK75621)
IPC006 (AE007466)0.34ORF1; conserved hypothetical protein (AAK75807)Ye
ORF2; hypothetical protein (AAK75806)Yo
ORF3; IS1381 transposase OrfB (AAK75996)
ORF4; hypothetical protein (AAK75805)
IPC022 (NC_003028)2.66Multiple very small ORFs (also known as transcriptional repressor)Ye
CO20023.21
SPIV016
SPIV005
IPC007 (AE007368)1.93ORF1; phenylalanyl tRNA synthetase, alpha chain (AAK74733)N
ORF2; acetyltransferase, GNAT family (AAK74734)
ORF3; phenylalanyl-tRNA synthetase, beta chain (AAK74735)
IPC008 (AE007321)321Phosphoribosylaminoimidazole-succinocarboxamide synthase (AAK74233)Y
SPIV014
IPC009 (AAK7423)1.61Integral membrane protein (AAK76084)Y
SPIV027
IPC010 (AE007507)0.52ORF1; chaperonin; heat shock protein (AAK76239)Ye
ORF2; NifR3/Smm1 in Bacillus subtilisYo
IPC011 (AE007349)0.252ORF1; recombination protein U (AAK74537)Ye
ORF2; penicillin binding pbpla gene in S. pneumoniae (AAK74536)Yo
IPC012 (AE007405)6.811ORF1; thymidine kinase (AAK75133)Yg
ORF2; spermidine acetyl transferase (AAK75134)
ORF3; peptide chain release factor (AAK75135)
ORF4; protoporphyrinogen oxidase/HEMK protein homolog (AAK75136)
ORF5; Sua5/YciO/YrdC family protein (AAK7513)
ORF6; acetyltransferase, GNAT family (AAK75138)
ORF7; serine hydroxymethyl transferase (AAK75139)
ORF8; hypothetical protein (AAK75140)
ORF9; conserved hypothetical protein (AAK75141)
ORF10; conserved hypothetical protein (AAK75142)
ORF11; RNA methyl transferase (AAK75144)
IPC013 (AE007487)1.41Putative membrane-spanning protein (AAK76039)Ye
OM0022.1 (CI)
IPC014 (AE007354)0.22ORF1; conserved hypothetical protein (AAK74596)N
OM0032.1 (CI)ORF2; translation elongation factor EF-P (AAK74597)
ORF3; transcription termination protein (AAK99194)
IPC015 (AE007318)1.13ORF1; GTP binding protein (AAK74197)Ye
OM006ORF2; peptidyl tRNA hydrolase (PTH gene) (AAK74198)Yo
ORF3; transcriptional-repair coupling factor (AAK99194)
IPC016 (AE007386)2.21Conserved hypothetical protein (AAK74938)Ye
IPC017 (AE007458)2.31Endopeptidase O (AAK75727)Y
SPIV001(Zn metalloprotease)
SPIV012
IPC018 (AE007356)8.32ORF1; amino acid ABC transporter; amino acid-binding protein/permease protein (AAK74614)Ye
ORF2; amino acid ABC transporter; ATP-binding protein (AAK74613)Yo
IPC020 (AE007442)5.83ORF1; spoU rRNA methylase family protein (AAK75551)Ye
ORF2; tRNA guanosine methyl transferase (AAL00115)Yo
ORF3; no match in database
IPC021 (AE007341)2.11Cof family protein (AAK74464)N
SPIV002
SPIV026
CO2001 (AE007386)4.83ORF1; aminopeptidase N (AAK74934)Yo
ORF2; regulator ciaR (AAK74935)
ORF3; histidine kinase ciaH (AAK74936)
CO2004 (NC_003028)4.3No ORF downstreamN
CO2006 (NC_003028)4.5No ORF downstreamN
HOI021 (AE007337)0.23ORF1; lactose-specific IIA component of PTS system (AAK74427)Yg
ISIP0692ORF2; cellobiose phosphotransferase system enzyme (AAK74428)
ORF3; PTS system; cellobiose-specific IIC component (AAK74429)
HOI042 (AE007509)0.7510ORF1; conserved hypothetical protein (AAK76273)Ye
ORF2; peptidase, M16 family (AAK76272)Yg
ORF3; conserved hypothetical protein (AAK76271)
ORF4; phosphotidylglycerophosphate synthase (AAK76270)
ORF5; ATP-binding protein (AAK76269)
ORF6; ATP-binding protein (AAK76268)
ORF7; conserved hypothetical protein (AAK76267)
ORF8; cell shape-determining protein (AAK76266)
ORF9; rod shape-determining protein MreD; putative (AAK76265)
ORF10; putative secreted protein (AAK76264)
HOI101 (AE008513)0.21Adenine phosphoribosyl transferase (AAL00239)Y
ISIP454 (AE007321)3.72ORF1; competence factor transporting ATP-binding/permease protein ComA (AAK74231)Yg
ORF2; competence factor transport protein ComB (AAK74232)
ISIP741 (AE007364)1.74ORF1; ABC transporter (CAC18585)Yg
ORF2; ABC transporter (CAC18584)
ORF3; ABC transporter (CAC18583)
ORF4; ABC transporter (AAK74687)
ISIP409 (AE007325)1.51Uridine phosphorylase (AAK74264)Y
ISIP485 (NC_003028)1.53ORF1; no match in databaseYg
ORF2; no match in database
ORF3; no match in database
ISIP497 (AE007320)1.64ORF1; hypothetical protein (AAK74215)Yg
SPIV010ORF2; no match in database
SPIV011ORF3; hypothetical protein (AAK74217)
ORF4; PRPP synthetase (AAK74218)
ISIP747 (AE007449)1.74ORF1; polypeptide deformylase (AAK75636)N
SPIV003ORF2; hypothetical protein (AAK75635)
SPIV028ORF3; hypothetical protein (AAL00210)
ISIP870 (AE007337)2.12ORF1; transcriptional regulator, DeoR family (AAK74425)Yg
ORF2; transcriptional regulator (AAK74426)
OM001 (AE007492)2.1 (CI)3ORF1; preprotein translocase, YajC subunit (AAK76094)Yo
SPIV017ORF2; protein tyrosine phosphatase (AAK76093)
ORF3; conserved hypothetical protein (AAK76092)
OM004 (AE007443)2.3 (CI)2ORF1; peptidoglycan GLcNAc deacetylase (AAK75573)Ye
ORF2; oxidoreductase; aldo/keto reductase family (AAK75572)
RTI001 (AE007401)2ORF1; oligopeptidase F (AAK75100)N
ORF2; methyltransferase (AAK75101)
RTI002 (NC_003028)1No match in databaseN
RTI005 (AE007434)5ORF1; homoserine kinase homolog (AAK75458)N
ORF2; hypothetical protein
ORF3; peptide methionine sulfoxide reductase (AAK75457)
ORF4; ATP-binding protein (AAK75456)
ORF5; putative ABC transporter (AAK75455)
RTI006 (AE007477)2ORF1; choline transporter (AAK75933)Yg
ORF2; choline transporter (AAK75932)
RTI007 (NC_003028)1No match in databaseN
RTI008 (AE007440)3ORF1; conserved hypothetical protein (AAK75533)N
ORF2; cation ABC transporter (AAK75534)
ORF3; Spn1 putative transposase (NP_345810)
RTI009 (AE007511)1SPSpoJ (AAK76287)Y
RTI010 (NC_003028)1No match in databaseN
RTI011 (NC_003028)1No match in databaseN
RTI012 (NC_003028)0No match in databaseN
RTI013 (NC_003028)0No match in databaseN
SPIV004 (AE007376)2ORF1; hypothetical protein (AAK74808)Yg
SPIV009ORF2; putative zinc metalloproteinase (AAK74809)
SPIV015
SPIV007 (AE007330)4ORF1; unknown protein (AAK74324)N
SPIV023ORF2; conserved domain protein (AAK74325)
ORF3; hypothetical protein (AAK74326)
ORF4; conserved hypothetical protein (AAK74327)
SPIV008 (AE007367)3ORF1; licT (AAK74730)N
SPIV025ORF2; beta-glucoside-specific IIABC PTS system component (AAK74731)
ORF3; beta-glucosidase (AAK74732)
SPIV013 (AE007496)1ABC transporter; ATP-binding protein (AAK76137)Y
SPIV018 (AE007497)3ORF1; response regulator pnpR (AAK76142)Ye
ORF2; histidine kinase pnpS (AAK76143)Yg
ORF3; phosphate-binding protein pstS (AAL00697)
SPIV019 (AE007352)2ORF1; RNase HII (AAK74566)Yo
SPIV029ORF2, signal peptidase 1; lep (AAK74565)
SPIV020 (NC_003028)0No ORF downstreamN
SPIV021 (AE007429)1Flavodoxin (AAK75401)N
SPIV022 (AE007405)14-Oxalocrotonate tautomerase (AAK75132)N
SPIV024 (NC_003028)0No match in databaseN
SPIV030 (AE007402)1Hypothetical protein (AAK75106)N
STS001 (AE008461)7.963ORF1; dihydroorotate dehydrogenase electron transfer subunit (AAK99669)Yg
ORF2; dihydroorotate dehydrogenase B, catalytic subunit (AAK99670)
ORF3; endo-beta-N-acetylglucosaminidase (AAK19156)
STS002 (AE007325)44.771PII-type cell wall-associated proteinase precursor (AAK74270)Ye
STS003 (AE007481)2.731RNA methyl transferase homolog (AAK75972)N
STS004 (AE007356)2.071Hypothetical protein (AAK74615)Y
STS005 (AE007359)24.11Lactose permease IIBC component, lactose-specific PTS system (AAK74637)Ye
STS007 (AE008443)2.031Unknown conserved protein (AAK99455)N
STS008 (AE007485)2.511Nucleoside diphosphate kinase (AAK76026)Y
STS009 (AE007433)1.922ORF1; no match in databaseN
ORF2; no match in database
STS010 (NC_003028)2.90No ORF downstreamN
STS011 (NC_003028)10.81No match in databaseN
STS012 (AE007379)2.492ORF1; orotidine 5′- phosphate decarboxylase (pyrF) (AAK74844)Yo
ORF2; orotate phosphoribosyl transferase (pyrE) (AAK74845)
STS013 (AE007355)2.813ORF1; glutamyl tRNA amidotransferase subunit A (AAK74599)Ye
ORF2; glutamyl tRNA amidotransferase subunit B (AAK74598)Yo
ORF3; translation elongation factor P (AAK74597)
STS014 (AE007350)2.474ORF1; FMN-dependent dehydrogenase family protein (AAK74551)Ye
ORF2; hypothetical protein (AAK74552)Yo
ORF3; sensor histidine kinase; putative (AAK74553)
ORF4; response regulator (AAK74554)
STS016 (AE007482)2.882ORF1; hypothetical protein (AAK75983)N
ORF2; hypothetical protein (AAK75982)
STS017 (AE007438)1.664ORF1; Hpr (Ser) kinase/phosphatase (AAK75511)N
ORF2; prolipoprotein diacylglyceryl transferase (AAK75510)
ORF3; conserved hypothetical protein (AAK75509)
ORF4; conserved hypothetical protein (AAK75508)
STS018 (AE007333)2.764ORF1; riboflavin biosynthetic protein ribD (AAK74359)Yo
ORF2; riboflavin synthase alpha chain (AAK74358)
ORF3; 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (AAK74357)
ORF4; riboflavin synthase beta chain (AAK74356)
  • a Prefix indicates identifying DFI screen (CO2, carbon dioxide shift; HOI, high osmolarity; IPC, intraperitoneal chamber; ISIP, iron starvation; OM, otitis media infection; RTI and SPIV, respiratory tract infection; STS, static temperature shift); accession number (in parentheses) refers to chromosomal location.

  • b Ratio of induced MCF to uninduced MCF under conditions under which clone was originally identified, except for clones labeled “CI,” which were assayed in vivo in the intraperitoneal chamber implant.

  • c Accession number (in parentheses) refers to protein.

  • d Result of replacement mutagenesis. Y, replacement mutant constructed; Yg, mutant constructed by replacing first gene in operon; Yo, mutant constructed by replacing entire operon; Ye, replacement mutant construction was attempted but was unsuccessful, indicating that downstream gene is essential; N, no replacement mutant was constructed because downstream gene(s) was essential by literature search, there was no ORF downstream of clone homology, or there was no sequence homology to anything in the S. pneumoniae database downstream of clone homology.