TABLE 3.

Sequences upstream of or within pneumococcal target genes related to the YycF consensus binding site proposed for B. subtilis and S. aureusa

SiteSequence
Proposed consensus (B. subtilis and S. aureus)5′-TGT(A/T)A(A/T/C)>-N5-TGT(A/T)A(A/T/C)>-3′
    59 bp upstream of pcsBb5′-TGTAAC>-AAAGG-CGTAAT>-ATTT-3′
    125 bp within pcsBc3′-ATTG-<AATTGT-CGTGT-<TGTTGT-5′
    85 bp upstream of pspAb5′-TGTAAC>-AAAAA-TGTAAT>-ATAA-3′
    44 bp upstream of spr0096b5′-TGTCAA>-GAAAC-GGTAAT>-ATTT-3′
    50 bp upstream of spr0709b,d5′-TGTAAC>-CTTTC-TGTAAT>-AATT-3′
    148 bp upstream of spr1875b3′-AAAA-<CACTGT-CTCTG-<GATTGT-5′
    108 bp upstream of spr1875c3′-CAAA-<CAATGT-TCCTT-<ATCTGT-5′
    15 bp upstream of fabRc5′-TGTAAA>-AGTTT-TTTGAA>-GAAG-3′
Pneumococcal consensus5′-TGT(A/C/T)A′(A/G/C)>-(A/C/G)(A/T)(A/C/T)(A/T/G)(A/C/G)- (G/T/C)GT(A/C)A(T/C)>-A(A/T)(A/T)(A/T)-3′
5′-TGTNAN>-N(A/T)NNN-NGT(A/C)A(C/T)>-A(A/T)(A/T)(A/T)-3′
  • a Locations are from the 3′ ends of the sequence shown and A in the start codons of each gene. Mismatches with the proposed consensus in B. subtilis and S. aureus (11, 22) are underlined. Orientations of the direct repeats relative to downstream genes are indicated by >> and << for same and opposite directions, respectively. Invariant nucleotides in consensus sequences are in boldface.

  • b Used for pneumococcal consensus at the bottom of the table. The consensus-related sequences for these genes are identical in strain R6 (21) and serotype 4 strain TIGR4 (60), except for pspA (spr0121 in R6 and sp0117 in TIGR4). The sequence upstream of pspA in TIGR4 is 5′-TGTAAT>-AAAAA-TGTAAT>-ATAA-3′.

  • c Specific binding of VicR or VicR-P was not detected in footprinting experiments (see text).

  • d Not tested in footprinting experiments, but the pattern of binding of VicR and VicR-P to the single site upstream of spr0709 was similar to those shown for other binding sites in Fig. 7.