Key Points
-
This Analysis covers the ribbon–helix–helix (RHH) transcription-factor superfamily of proteins and focuses on the wealth of new structural information that has become available in the past year.
-
Instead of binding to DNA through the insertion of an α-helix into the DNA major groove — a motif which is used by the ubiquitous helix–turn–helix family of transcription factors — RHH proteins use an anti-parallel β-sheet to recognize specific nucleotide sequences and α-helices to anchor the β-sheet in the DNA major groove.
-
RHH proteins have a range of regulatory functions in prokaryotes and bacteriophages, several of which are of prime importance for human pathogen–host interactions.
-
A sequence and structural comparison of the characterized RHH-transcription factors is given for important motifs, which provides a better framework for bioinformatic studies of this protein family.
-
RHH proteins share a low sequence identity but have similar structures, despite multiple insertions and deletions between the α-helices of this small domain.
-
DNA binding does not alter the structure of RHH-transcription factors, and they are regulated in their affinity for DNA in various ways.
-
Prediction of a DNA-binding sequence is non-trivial based on knowledge of the RHH protein sequence. Different RHH proteins use the same amino-acid side chains to contact DNA bases, yet recognize unique DNA sequences.
Abstract
The ribbon–helix–helix (RHH) superfamily of transcription factors uses a conserved three-dimensional structural motif to bind to DNA in a sequence-specific manner. This functionally diverse protein superfamily regulates the transcription of genes that are involved in the uptake of metals, amino-acid biosynthesis, cell division, the control of plasmid copy number, the lytic cycle of bacteriophages and, perhaps, many other cellular processes. In this Analysis, the structures of different RHH transcription factors are compared in order to evaluate the sequence motifs that are required for RHH-domain folding and DNA binding, as well as to identify conserved protein–DNA interactions in this superfamily.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Perez-Rueda, E. & Collado-Vides, J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28, 1838–1847 (2000).
Wintjens, R. & Rooman, M. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J. Mol. Biol. 262, 294–313 (1996).
Harrison, S. C. & Aggarwal, A. K. DNA recognition by proteins with the helix–turn–helix motif. Annu. Rev. Biochem. 59, 933–969 (1990).
Brennan, R. G. & Matthews, B. W. The helix–turn–helix DNA binding motif. J. Biol. Chem. 264, 1903–1906 (1989).
Rafferty, J. B., Somers, W. S., Saint-Girons, I. & Phillips, S. E. Three-dimensional crystal structures of Escherichia coli met repressor with and without co-repressor. Nature 341, 705–710 (1989). The first determination of the structure of an RHH transcription factor, MetJ.
Jordan, S. R. & Pabo, C. O. Structure of the λ-complex at 2.5 Å resolution: details of the repressor–operator interactions. Science 242, 893–899 (1988).
Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 899–907 (1988).
Wolberger, C., Dong, Y. C., Ptashne, M. & Harrison, S. C. Structure of a phage 434 Cro/DNA complex. Nature 335, 789–795 (1988).
Breg, J. N., van Opheusden, J. H., Burgering, M. J., Boelens, R. & Kaptein, R. Structure of Arc repressor in solution: evidence for a family of β-sheet DNA-binding proteins. Nature 346, 586–589 (1990). The first proposal of a family of β-sheet DNA-binding proteins (the RHH superfamily), based on the NMR structure of Arc and biochemical results that showed that specificity-determinant residues reside in the β-sheet.
Knight, K. L., Bowie, J. U., Vershon, A. K., Kelley, R. D. & Sauer, R. T. The Arc and Mnt repressors. A new class of sequence-specific DNA-binding protein. J. Biol. Chem. 264, 3639–3642 (1989).
Knight, K. L. & Sauer, R. T. DNA binding specificity of the Arc and Mnt repressors is determined by a short region of N-terminal residues. Proc. Natl Acad. Sci. USA 86, 797–801 (1989).
Somers, W. S. & Phillips, S. E. Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature 359, 387–393 (1992). The first determination of the structure of a RHH transcription factor bound to operator DNA.
Raumann, B. E., Rould, M. A., Pabo, C. O. & Sauer, R. T. DNA recognition by β-sheets in the Arc repressor–operator crystal structure. Nature 367, 754–757 (1994).
Raumann, B. E., Brown, B. M. & Sauer, R. T. Major groove DNA recognition by β-sheets: the ribbon–helix–helix family of gene regulatory proteins. Curr. Opin. Struc. Biol. 4, 36–43 (1994). The first review of RHH transcription factors following the elucidation of the structures of Arc and MetJ in complex with DNA.
Bowie, J. U. & Sauer, R. T. TraY proteins of F and related episomes are members of the Arc and Mnt repressor family. J. Mol. Biol. 211, 5–6 (1990).
Lum, P. L. & Schildbach, J. F. Specific DNA recognition by F Factor TraY involves β-sheet residues. J. Biol. Chem. 274, 19644–19648 (1999).
Aravind, L., Anantharaman, V., Balaji, S., Babu, M. M. & Iyer, L. M. The many faces of the helix–turn–helix domain: transcription regulation and beyond. FEMS Microbiol. Rev. 29, 231–262 (2005).
Chivers, P. T. & Sauer, R. T. Regulation of high affinity nickel uptake in bacteria. Ni2+-dependent interaction of NikR with wild-type and mutant operator sites. J. Biol. Chem. 275, 19735–19741 (2000).
Saint-Girons, I., Duchange, N., Cohen, G. N. & Zakin, M. M. Structure and autoregulation of the metJ regulatory gene in Escherichia coli. J. Biol. Chem. 259, 14282–14285 (1984).
Youderian, P., Bouvier, S. & Susskind, M. M. Sequence determinants of promoter activity. Cell 30, 843–853 (1982).
Sauer, R. T., Krovatin, W., DeAnda, J., Youderian, P. & Susskind, M. M. Primary structure of the immI immunity region of bacteriophage P22. J. Mol. Biol. 168, 699–713 (1983).
Bowie, J. U. & Sauer, R. T. Equilibrium dissociation and unfolding of the Arc repressor dimer. Biochemistry 28, 7139–7143 (1989).
Phillips, K. & Phillips, S. E. Electrostatic activation of Escherichia coli methionine repressor. Structure 2, 309–316 (1994).
Buts, L., Lah, J., Dao-Thi, M. H., Wyns, L. & Loris, R. Toxin–antitoxin modules as bacterial metabolic stress managers. Trends Biochem. Sci. 30, 672–679 (2005).
Mattison, K., Wilbur, J. S., So, M. & Brennan, R. G. Structure of FitAB from Neisseria gonorrhoeae bound to DNA reveals a tetramer of toxin–antitoxin heterodimers containing Pin domains and ribbon–helix–helix motifs. J. Biol. Chem. 281, 37942–37951 (2006). The first determination of the structure of a toxin–RHH antitoxin complex bound to DNA.
Kamphuis, M. B. et al. Structure and function of bacterial kid–kis and related toxin–antitoxin systems. Protein Pept. Lett. 14, 113–124 (2007).
Schreiter, E. R., Wang, S. C., Zamble, D. B. & Drennan, C. L. NikR–operator complex structure and the mechanism of repressor activation by metal ions. Proc. Natl Acad. Sci. USA 103, 13676–13681 (2006). This study described the structure of the NikR–operator DNA complex and illustrated the mechanism of activation of NikR by nickel ions.
de la Hoz, A. B. et al. Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats. Nucleic Acids Res. 32, 3136–3147 (2004).
Weihofen, W. A., Cicek, A., Pratto, F., Alonso, J. C. & Saenger, W. Structures of omega repressors bound to direct and inverted DNA repeats explain modulation of transcription. Nucleic Acids Res. 34, 1450–1458 (2006).
Michael Gromiha, M., Siebers, J. G., Selvaraj, S., Kono, H. & Sarai, A. Intermolecular and intramolecular readout mechanisms in protein–DNA recognition. J. Mol. Biol. 337, 285–294 (2004).
Allemann, R. K. & Egli, M. DNA recognition and bending. Chem. Biol. 4, 643–650 (1997).
Marshall, B. J. & Warren, J. R. Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration. Lancet 1, 1311–1315 (1984).
Blaser, M. J. Helicobacter pylori and the pathogenesis of gastroduodenal inflammation. J. Infect. Dis. 161, 626–633 (1990).
Blaser, M. J. & Atherton, J. C. Helicobacter pylori persistence: biology and disease. J. Clin. Invest. 113, 321–333 (2004).
Forman, D. Helicobacter pylori infection: a novel risk factor in the etiology of gastric cancer. J. Natl Cancer. Inst. 83, 1702–1703 (1991).
Forman, D. et al. Association between infection with Helicobacter pylori and risk of gastric cancer: evidence from a prospective investigation. BMJ 302, 1302–1305 (1991).
van Vliet, A. H., Ernst, F. D. & Kusters, J. G. NikR-mediated regulation of Helicobacter pylori acid adaptation. Trends Microbiol. 12, 489–494 (2004).
van Vliet, A. H. et al. NikR mediates nickel-responsive transcriptional induction of urease expression in Helicobacter pylori. Infect. Immun. 70, 2846–2852 (2002).
Wolfram, L., Haas, E. & Bauerfeind, P. Nickel represses the synthesis of the nickel permease NixA of Helicobacter pylori. J. Bacteriol. 188, 1245–1250 (2006).
Contreras, M., Thiberge, J. M., Mandrand-Berthelot, M. A. & Labigne, A. Characterization of the roles of NikR, a nickel-responsive pleiotropic autoregulator of Helicobacter pylori. Mol. Microbiol. 49, 947–963 (2003).
van Vliet, A. H., Kuipers, E. J., Stoof, J., Poppelaars, S. W. & Kusters, J. G. Acid-responsive gene induction of ammonia-producing enzymes in Helicobacter pylori is mediated via a metal-responsive repressor cascade. Infect. Immun. 72, 766–773 (2004).
Dosanjh, N. S., Hammerbacher, N. A. & Michel, S. L. Characterization of the Helicobacter pylori NikR-PureA DNA interaction: metal ion requirements and sequence specificity. Biochemistry 46, 2520–2529 (2007).
Abraham, L. O., Li, Y. & Zamble, D. B. The metal- and DNA-binding activities of Helicobacter pylori NikR. J. Inorg. Biochem. 100, 1005–1014 (2006).
Dian, C. et al. Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states. J. Mol. Biol. 361, 715–730 (2006).
Jayaraman, S., Joo, N. S., Reitz, B., Wine, J. J. & Verkman, A. S. Submucosal gland secretions in airways from cystic fibrosis patients have normal [Na+] and pH but elevated viscosity. Proc. Natl Acad. Sci. USA 98, 8119–8123 (2001).
Matsui, H. et al. Evidence for periciliary liquid layer depletion, not abnormal ion composition, in the pathogenesis of cystic fibrosis airways disease. Cell 95, 1005–1015 (1998).
Evans, L. R. & Linker, A. Production and characterization of the slime polysaccharide of Pseudomonas aeruginosa. J. Bacteriol. 116, 915–924 (1973).
Govan, J. R. & Harris, G. S. Pseudomonas aeruginosa and cystic fibrosis: unusual bacterial adaptation and pathogenesis. Microbiol. Sci. 3, 302–308 (1986).
Baynham, P. J., Brown, A. L., Hall, L. L. & Wozniak, D. J. Pseudomonas aeruginosa AlgZ, a ribbon–helix–helix DNA-binding protein, is essential for alginate synthesis and algD transcriptional activation. Mol. Microbiol. 33, 1069–1080 (1999).
Yu, H., Mudd, M., Boucher, J. C., Schurr, M. J. & Deretic, V. Identification of the algZ gene upstream of the response regulator algR and its participation in control of alginate production in Pseudomonas aeruginosa. J. Bacteriol. 179, 187–193 (1997).
Tart, A. H., Blanks, M. J. & Wozniak, D. J. The AlgT-dependent transcriptional regulator AmrZ (AlgZ) inhibits flagellum biosynthesis in mucoid, nonmotile Pseudomonas aeruginosa cystic fibrosis isolates. J. Bacteriol. 188, 6483–6489 (2006).
Baynham, P. J., Ramsey, D. M., Gvozdyev, B. V., Cordonnier, E. M. & Wozniak, D. J. The Pseudomonas aeruginosa ribbon–helix–helix DNA-binding protein AlgZ (AmrZ) controls twitching motility and biogenesis of type IV pili. J. Bacteriol. 188, 132–140 (2006).
DeLano, W. L. The PyMol Molecular Graphics System, [online] (2002).
Gomis-Ruth, F. X. et al. The structure of plasmid-encoded transcriptional repressor CopG unliganded and bound to its operator. EMBO J. 17, 7404–7415 (1998).
Costa, M. et al. Plasmid transcriptional repressor CopG oligomerises to render helical superstructures unbound and in complexes with oligonucleotides. J. Mol. Biol. 310, 403–417 (2001).
Murayama, K., Orth, P., de la Hoz, A. B., Alonso, J. C. & Saenger, W. Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 Å resolution. J. Mol. Biol. 314, 789–796 (2001).
Schreiter, E. R. et al. Crystal structure of the nickel-responsive transcription factor NikR. Nature Struct. Biol. 10, 794–799 (2003).
Madl, T. et al. Structural basis for nucleic acid and toxin recognition of the bacterial antitoxin CcdA. J. Mol. Biol. 364, 170–185 (2006).
Burgering, M. J. et al. Solution structure of dimeric Mnt repressor (1–76). Biochemistry 33, 15036–15045 (1994).
Golovanov, A. P., Barilla, D., Golovanova, M., Hayes, F. & Lian, L. Y. ParG, a protein required for active partition of bacterial plasmids, has a dimeric ribbon–helix–helix structure. Mol. Microbiol. 50,
Larson, J. D. et al. Crystal structures of the DNA-binding domain of Escherichia coli proline utilization A flavoprotein and analysis of the role of Lys9 in DNA recognition. Protein Sci. 15, 2630–2641 (2006).
Popescu, A., Karpay, A., Israel, D. A., Peek, R. M. Jr & Krezel, A. M. Helicobacter pylori protein HP0222 belongs to Arc/MetJ family of transcriptional regulators. Proteins 59, 303–311 (2005).
Oberer, M., Lindner, H., Glatter, O., Kratky, C. & Keller, W. Thermodynamic properties and DNA binding of the ParD protein from the broad host-range plasmid RK2/RP4 killing system. Biol. Chem. 380, 1413–1420 (1999).
Oberer, M., Zangger, K., Prytulla, S. & Keller, W. The anti-toxin ParD of plasmid RK2 consists of two structurally distinct moieties and belongs to the ribbon–helix–helix family of DNA-binding proteins. Biochem. J. 361, 41–47 (2002).
Pavlov, N. A., Cherny, D. I., Nazimov, I. V., Slesarev, A. I. & Subramaniam, V. Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri. Nucleic Acids Res. 30, 685–694 (2002).
Moncalian, G. & de la Cruz, F. DNA binding properties of protein TrwA, a possible structural variant of the Arc repressor superfamily. Biochim. Biophys. Acta 1701, 15–23 (2004).
Schildbach, J. F., Robinson, C. R. & Sauer, R. T. Biophysical characterization of the TraY protein of Escherichia coli F factor. J. Biol. Chem. 273, 1329–1333 (1998).
Acknowledgements
The authors acknowledge support from the National Institutes of Health grants RR016439 and GM69857.
Author information
Authors and Affiliations
Corresponding author
Glossary
- Promoter
-
A region of DNA that is upstream of a gene or operon and that is required for its transcription. In bacteria, RNA polymerase and an associated σ factor protein bind the promoter and initiate transcription. Promoters can also contain regulatory regions of DNA, such as operators, that are recognized by transcription factors.
- Motif
-
A pattern of residues with biological significance. A sequence motif refers to a linear sequence of nucleotides or amino acids, whereas a structural motif can refer to residues that are not consecutive but are in close proximity in the natively folded molecule.
- Operator
-
The DNA sequence that is specifically recognized by a transcription factor. Often, operator DNA sequences contain either direct or inverted repeats of smaller DNA sub-sites, which multiple molecules of the transcription factor bind to cooperatively.
- Root mean square deviation
-
(RMSD). A metric unit that represents the similarity between two structures and that is calculated by comparing the positions of atoms in one structure with the positions of the equivalent atoms in another. Here, RMSD is measured in units of Ångströms (Å) or 10−10 m. For two perfectly identical structures, the RMSD value would be 0 Å; for two randomly chosen dissimilar proteins, the RMSD is likely to be 10 Å or higher.
- Hydrophobic core
-
The interior portion of a folded globular protein that is composed of primarily hydrophobic amino-acid side chains. The burial of hydrophobic side chains is a primary driving force for protein folding.
- Toxin–antitoxin
-
A post-segregational cell-killing system that is usually composed of a pair of plasmid-encoded proteins that form a complex. If a plasmid-free cell arises, the antitoxin cannot be replenished and the liberated toxin causes cell death or severe growth impairment.
Rights and permissions
About this article
Cite this article
Schreiter, E., Drennan, C. Ribbon–helix–helix transcription factors: variations on a theme. Nat Rev Microbiol 5, 710–720 (2007). https://doi.org/10.1038/nrmicro1717
Issue Date:
DOI: https://doi.org/10.1038/nrmicro1717
This article is cited by
-
CvkR is a MerR-type transcriptional repressor of class 2 type V-K CRISPR-associated transposase systems
Nature Communications (2023)
-
Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120
Communications Biology (2023)
-
Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems
Communications Biology (2022)
-
Auxiliary interfaces support the evolution of specific toxin–antitoxin pairing
Nature Chemical Biology (2021)
-
Comprehensive analysis of IncC plasmid conjugation identifies a crucial role for the transcriptional regulator AcaB
Nature Microbiology (2020)