Figure 2

Left panel: Sequence motifs of predicted LacI-family TF specific operators in L. plantarum. Right panel: The protein sequence motif of the DNA-binding region of the LacI-family TFs per GOOFE. The numbering of the protein residues deviates slightly from that in the various crystal structures. This relates to the fact that the alignment includes some gaps that are necessary to accommodate all the LacI protein sequences that have been compared by us. The visualization of the sequences was created using Weblogo [99]. remark: NMR studies have shown that the hinge helix plays an important role in kinking the DNA whilst forming an alpha-helix (helix 4) and thereby stabilizing the induced fit of the recognition helix within the major groove of the operator [33,81]. In fact, the 3D-structures of operator-bound CcpA and LacI implicate many residues of helix 3 and 4 in the contact of the TF with the operator [56,57]. Moreover, the 3D-structures indicate that in both CcpA and LacI the same residues are involved. The DNA-protein contacts are indicated with triangles. The blue triangles mark the residues interacting with the phosphate backbone and the red triangles mark the residues interacting directly with a nucleotide (the position of the nucleotide is indicated in a box). In the case of Lp_0188 (SacR), a well-conserved guanine and corresponding cytidine are found at positions -7 and 7 of the operator, respectively. This suggests that the operator recognized by Lp_0188 (SacR) and its orthologs, is two nucleotides wider than that recognized by other 'CcpA-like' LacI-TFs. The 'EbgR-like' LacI-family TFs carry a conserved insertion before helix 3 and seem to lack the characteristic conserved alanine and leucine (or methionine in the case of RbsR) at position 60 of the hinge helix in the 'CcpA-like' LacI-family TFs. The absence of these residues coincides perfectly with the absence of the central CG nucleotide pair in the predicted Lp_3470 (LacR), Lp_3479 (GalR) and Lp_3488 (RafR) operators.