Chapter 3 : AraC Family Regulators and Transcriptional Control of Bacterial Virulence Determinants

Structures of Rob and MarA in complex with target DNA sequences. The structurally similar N-terminal DNA binding domains are colored orange in the ribbon diagrams. The C-terminal domain unique to Rob is blue. MicF and MarA sequences used for cocrystallization are shown with Abox sequences in orange and B-box sequences in light blue type. Only the Nterminal HTH motif of Rob directly contacts bases of the binding sequence. MarA bends the DNA target so that both HTH motifs are located in adjacent major groove surfaces on one side of the DNA. From reference 8 with permission. (See Color Plates following p. 256.)

Regulatory region of the araBAD operon, the binding sites for AraC (I1, I2, O1, and O2), and promoters p C and p BAD . The domains of AraC consisting of the N-terminal arm, the dimerization domain, the linker domain, and the DNAbinding domain are marked. The light switch mechanism is illustrated. In the absence of arabinose the N-terminal arms interact with the DNAbinding domain and cause the protein to assume an extended conformation and preferential binding to distal I1 and O2 sites, forming a DNA loop and repressing transcription from p BAD and p C . Arabinose-binding changes the orientation of the arms and allows binding to adjacent I1 and I2 sites. AraC bound to the O1 site in the presence of arabinose is shown in gray to illustrate partial occupancy. From reference 6 with permission.

The operons of Pseudomonas aeruginosa type III secretion system and effector toxins ExoU, ExoS, ExoT, and ExoY are shown. Individual gene products are indicated as colored arrows (the sizes of protein products are approximate and not to scale). Different colors are used to identify operons based on promoter mapping, transcriptional fusion, or DNA-binding analyses. The toxins and known chaperone proteins are located in different chromosomal locations than the set of operons that encode the secretory, translocation, and regulatory proteins. ExsA consensus and imperfect binding sites are illustrated. (See Color Plates following p. 256.)

Location and orientation of the consensus binding sites for members of the AraC protein family: (A) ExsA, (B) UreR, and (C) Rns. Open reading frames are represented by open arrows. Bent arrows illustrate experimentally defined transcriptional start sites, and filled boxes indicate the sigma-70 promoter hexamers. A striped bar indicates a putative promoter region identified by sequence homology. An asterisk located within the ureDABCEFG operon is used to identify a UreR + urea-dependent start site present only in the plasmid-encoded locus. Positions of the Rns-binding sites 1, 2, and 3 and sites I and II are numbered relative to the transcriptional start sites. The two binding sites within rns are numbered relative to the translational start codon. Putative Rns-binding sites that overlap with the -35 hexamer or are within the cotB coding region are marked with a # sign. Information used to assemble this summary figure was derived from references 7 , 10 , 11 , and 16 . Figure is not to scale.