Structural Classification of HTH DNA-binding Domains and Protein – DNA Interaction Modes

Simeonov

Proc. Natl. Acad. Sci. U.S.A.

et al. 2002

Anti-sigma factors regulate prokaryotic gene expression through interactions with specific sigma factors. The bacteriophage T4 anti-sigma factor AsiA is a molecular switch that both inhibits transcription from bacterial promoters and phage early promoters and promotes transcription at phage middle promoters through its interaction with the primary sigma factor of Escherichia coli, 70 . AsiA is an all-helical, symmetric dimer in solution. The solution structure of the AsiA dimer reveals a novel helical fold for the protomer. Furthermore, the AsiA protomer, surprisingly, contains a helix-turn-helix DNA binding motif, predicting a potential new role for AsiA. The AsiA dimer interface includes a substantial hydrophobic component, and results of hydrogen͞deuterium exchange studies suggest that the dimer interface is the most stable region of the AsiA dimer. In addition, the residues that form the dimer interface are those that are involved in binding to 70 . The results promote a model whereby the AsiA dimer maintains the active hydrophobic surfaces and delivers them to 70 , where an AsiA protomer is displaced from the dimer via the interaction of 70 with the same residues in AsiA that constitute the dimer interface. R egulation of prokaryotic transcription involves the interaction of sigma ( ) factors, which bind to the core RNA polymerase to impart promoter recognition specificity, with cognate anti-sigma (anti-) factors that inhibit function. Most of the numerous examples of ͞anti-pairs involve alternative factors, those activated in response to specific stimuli, as opposed to primary factors, which are essential for survival and responsible for the bulk of transcription, including the housekeeping genes (reviewed in refs. 1-4). An important exception is the interaction of 70 of Escherichia coli, namesake for a family of sequence conserved primary factors, with the anti-factor AsiA.The bacteriophage T4-encoded AsiA protein, product of the asiA gene (5), and the first anti-factor to be discovered, binds tightly to the 70 subunit of the E. coli RNA polymerase holoenzyme (6-10), altering the specificity of the complex toward both phage and host promoters. Following infection by bacteriophage T4, the E. coli RNA polymerase is recruited to sequentially transcribe genes from the T4 early, middle, and late promoters. T4 early promoters contain bacterial-like consensus DNA sequences that allow for their immediate recognition by the unmodified RNA polymerase, and the T4 early genes include the asiA gene. Shortly thereafter, transcription at early promoters is inhibited, along with transcription at bacterial promoters, by phage-induced modifications of the RNA polymerase, one of which is the tight association of AsiA with 70 . This interaction inhibits 70 -dependent transcription at early promoters by blocking recognition by 70 of the conserved sequence element centered at position Ϫ35 (11). Furthermore, AsiA not only has the ability to function as an anti-factor, it also has the ability to promote transcription. In conce...

“…2a). The turn between H R-1 and H R in AsiA is a loop (HTH loop ) (53). We were unable to find examples of proteins with helices superimposable with helices 5, 4, and 3 of AsiA.…”

Section: Resultsmentioning

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Solution structure and stability of the anti-sigma factor AsiA: Implications for novel functions

Simeonov

Proc. Natl. Acad. Sci. U.S.A.

et al. 2002

Journal of Molecular Evolution

“…Although the protein sequence has changed significantly within the families clustered in the supergroup, the variation in the protein backbone has been smaller within the HTH structure (Wintjens and Rooman 1997). This smaller variation would reflect the functional conservation among several members of the supergroup.…”

Section: Discussionmentioning

confidence: 99%

“…The pattern is 40 amino acid residues long, located in all cases at the N terminus of the proteins, except in Crp and Fnr, where it is at the C terminus. It contains the core of the HTH motif and a bordering region that in some proteins corresponds to a third ␣-helix (Suzuki et al 1995;Wintjens and Rooman 1997). The convergence of the PROBE iterations motivates the proposal of a supergroup of DNA binding Tf's where proteins from different families were clustered, probably sharing a common evolutionary history.…”

Section: The Supergroup Of Repressor Proteinsmentioning

confidence: 93%

Common History at the Origin of the Position-Function Correlation in Transcriptional Regulators in Archaea and Bacteria

Pérez‐Rueda

Collado‐Vides

2001

Abstract. Regulatory proteins in Escherichia coliwith a helix-turn-helix (HTH) DNA binding motif show a position-function correlation such that repressors have this motif predominantly at the N terminus, whereas activators have the motif at the C-terminus extreme. Using this initial collection we identified by sequence comparison the exhaustive set of transcriptional regulators in 17 bacterial and 6 archaeal genomes. This enlarged set shows the same position-function correlation. The main question we address is whether this correlation is the result of common origin in evolution or the result of convergence. Evidence is presented supporting a common history at the origin of this correlation. We show the existence of a supergroup of eight repressor protein families sharing a conserved extended sequence comprising the classic HTH. Two of these repressor families (MarR and AsnC) originated before the divergence of Archaea and Bacteria. They are proposed at the origin of HTHbearing transcriptional regulators currently present in Bacteria. The group of LysR proteins, with the HTH also at the N terminus, offers a control to the argument, since it shows clearly distinctive structural, functional, and evolutionary properties. This group of activator proteins, suggested to have originated within the Bacteria, has an advantageous gene organization to facilitate its horizontal transfer-used to conquer some Archaea-as well as negative autoregulation convenient for homeostasis, all of which agrees with this being the largest family in Bacteria. These results suggest that if shuffling of motifs occurred in Bacteria, it occurred only early in the history of these proteins, as opposed to what is observed in eukaryotic regulators.

Proc. Natl. Acad. Sci. U.S.A.

“…In Gram-positive bacteria, such as Bacilli and Cocci, new quorum-sensing regulators have been found that, unlike in most described quorum-sensing systems, are controlled by their direct interaction with a reimported signaling peptide: Rap proteins involved in the development of competence and sporulation in Bacilli (2); the necrotrophic response regulator NprR, which enables necrotrophism in Bacillus thuringiensis (3); the sex pheromone receptor PrgX involved in the control of conjugation in Enterococcus faecalis (4); and the transcription regulator PlcR responsible for the production of virulence factors in B. thuringiensis and Bacillus cereus (5). These proteins share structural similarities: tetratricopeptide repeats (TPRs) forming a peptide binding domain (6) and a helix-turn-helix (HTH) DNA-binding domain (7) in the case of transcriptional regulators. They have been grouped in a new family of quorum sensors called RNPP, for Rap, NprR, PrgX, and PlcR (8).…”

mentioning

confidence: 99%

Structural basis for the activation mechanism of the PlcR virulence regulator by the quorum-sensing signal peptide PapR

Grenha

Slamti

Nicaise

et al. 2012

The quorum-sensing regulator PlcR is the master regulator of most known virulence factors in Bacillus cereus. It is a helix-turn-helix (HTH)-type transcription factor activated upon binding of its cognate signaling peptide PapR on a tetratricopeptide repeat-type regulatory domain. The structural and functional properties of PlcR have defined a new family of sensor regulators, called the RNPP family (for Rap, NprR, PrgX, and PlcR), in Gram-positive bacteria. To fully understand the activation mechanism of PlcR, we took a closer look at the conformation changes induced upon binding of PapR and of its target DNA, known as PlcR-box. For that purpose we have determined the structures of the apoform of PlcR (Apo PlcR) and of the ternary complex of PlcR with PapR and the PlcR-box from the plcA promoter. Comparison of the apoform of PlcR with the previously published structure of the PlcR-PapR binary complex shows how a small conformational change induced in the C-terminal region of the tetratricopeptide repeat (TPR) domain upon peptide binding propagates via the linker helix to the N-terminal HTH DNA-binding domain. Further comparison with the PlcR-PapR-DNA ternary complex shows how the activation of the PlcR dimer allows the linker helix to undergo a drastic conformational change and subsequent proper positioning of the HTH domains in the major groove of the two half sites of the pseudopalindromic PlcR-box. Together with random mutagenesis experiments and interaction measurements using peptides from distinct pherogroups, this structural analysis allows us to propose a molecular mechanism for this functional switch