Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler

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Ler, a member of the H-NS protein family, is the master regulator of the LEE pathogenicity island in virulent Escherichia coli strains. Here, we determined the structure of a complex between the DNA-binding domain of Ler (CT-Ler) and a 15-mer DNA duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor groove formed by two consecutive regions which are narrower and wider, respectively, compared with standard B-DNA. The compressed region, associated with an AT-tract, is sensed by the side chain of Arg90, whose mutation abolishes the capacity of Ler to bind DNA. The expanded groove allows the approach of the loop in which Arg90 is located. This is the first report of an experimental structure of a DNA complex that includes a protein belonging to the H-NS family. The indirect readout mechanism not only explains the capacity of H-NS and other H-NS family members to modulate the expression of a large number of genes but also the origin of the specificity displayed by Ler. Our results point to a general mechanism by which horizontally acquired genes may be specifically recognized by members of the H-NS family.

Vyšlo v časopise: Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler. PLoS Pathog 7(11): e32767. doi:10.1371/journal.ppat.1002380
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1002380

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Zdroje

1. CroxenMAFinlayBB 2010 Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 8 26 38

2. MelliesJLBarronAMCarmonaAM 2007 Enteropathogenic and enterohemorrhagic Escherichia coli virulence gene regulation. Infect Immun 75 4199 4210

3. ElliottSJSperandioVGirónJAShinSMelliesJL 2000 The locus of enterocyte effacement (LEE)-encoded regulator controls expression of both LEE- and non-LEE-encoded virulence factors in enteropathogenic and enterohemorrhagic Escherichia coli. Infect Immun 68 6115 6126

4. FriedbergDUmanskiTFangYRosenshineI 1999 Hierarchy in the expression of the locus of enterocyte effacement genes of enteropathogenic Escherichia coli. Mol Microbiol 34 941 952

5. ZhuCFengSThateTEKaperJBBoedekerEC 2006 Towards a vaccine for attaching/effacing Escherichia coli: a LEE encoded regulator (ler) mutant of rabbit enteropathogenic Escherichia coli is attenuated, immunogenic, and protects rabbits from lethal challenge with the wild-type virulent strain. Vaccine 24 3845 3855

6. TorresAGLópez-SánchezGNMilflores-FloresLPatelSDRojas-LópezM 2007 Ler and H-NS, regulators controlling expression of the long polar fimbriae of Escherichia coli O157:H7. J Bacteriol 189 5916 5928

7. AbeHMiyaharaAOshimaTTashiroKOguraY 2008 Global regulation by horizontally transferred regulators establishes the pathogenicity of Escherichia coli. DNA Res 15 25 38

8. HaackKRRobinsonCLMillerKJFowlkesJWMelliesJL 2003 Interaction of Ler at the LEE5 (tir) operon of enteropathogenic Escherichia coli. Infect Immun 71 384 392

9. BañosRCViveroAAznarSGarcíaJPonsM 2009 Differential regulation of horizontally acquired and core genome genes by the bacterial modulator H-NS. PLoS Genet 5 e1000513 doi:10.1371/journal.pgen.1000513

10. SperandioVMelliesJLDelahayRMFrankelGCrawfordJA 2000 Activation of enteropathogenic Escherichia coli (EPEC) LEE2 and LEE3 operons by Ler. Mol Microbiol 38 781 793

11. BarbaJBustamanteVHFlores-ValdezMADengWFinlayBB 2005 A positive loop controls expression of the locus of enterocyte effacement-encoded regulatos Ler and GrlA. J Bacteriol 187 7918 7930

12. TauschekMYangJHockingDAzzopardiKTanA 2010 Transcriptional analysis of the grlRA virulence operon from Citrobacter rodentium. J Bacteriol 192 3722 3734

13. SchwidderMHenselMSchmidtH 2011 Regulation of nleA in shiga toxin-producing Escherichia coli O84:H4 strain 4795/97. J Bacteriol 193 832 841

14. Rojas-LópezMArenas-HernándezMMPMedrano-LópezAMartínez de la PeñaCFPuenteJL 2011 Regulatory control of the Escherichia coli O157:H7 lpf1 operon by H-NS and Ler. J Bacteriol 193 1622 1632

15. LangBBlotNBouffartiguesEBuckleMGeertzM 2007 High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res 35 6330 6337

16. YerushalmiGNadlerCBerdichevskiTRosenshineI 2008 Mutational analysis of the locus of enterocyte effacement-encoded regulator (Ler) of enteropathogenic Escherichia coli. J Bacteriol 190 7808 7818

17. BertinPHommaisFKrinESoutourinaOTendengC 2001 H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism. Biochimie 83 235 241

18. MelliesJLLarabeeFJZarrMAHorbackKJLorenzenE 2008 Ler interdomain linker is essential for anti-silencing activity in enteropathogenic Escherichia coli. Microbiology 154 3624 3638

19. ShindoHIwakiTIedaRKurumizakaHUeguchiC 1995 Solution structure of the DNA binding domain of a nucleoid-associated protein, H-NS, from Escherichia coli. FEBS Lett 360 125 131

20. HaranTEMohantyU 2009 The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 42 41 81

21. ShindoHOhnukiAGinbaHKatohEUeguchiC 1999 Identification of the DNA binding surface of H-NS protein from Escherichia coli by heteronuclear NMR spectroscopy. FEBS Lett 455 63 69

22. SetteMSpurioRTrottaEBrandiziCBrandiA 2009 Sequence-specific recognition of DNA by the C-terminal domain of nucleoid-associated protein H-NS. J Biol Chem 284 30453 30462

23. RohsRWestSMSosinskyALiuPMannRS 2009 The role of DNA shape in protein-DNA recognition. Nature 461 1248 1253

24. WestSMRohsRManRSHonigB 2010 Electrostatic interactions between arginines and the minor groove in the nucleosome. J Biomol Struct Dyn 27 861 866

25. GordonBRGLiYWangLSintsovaAvan BakelH 2010 Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 107 5154 5159

26. TraversAA 2004 The structural basis of DNA flexibility. Phil Transat A Math Phys Eng Sci 362 1423 1438

27. RimskySZuberFBuckleMBucH 2001 A molecular mechanism for the repression of transcription by the H-NS protein. Mol Microbiol 42 1311 1323

28. BouffartiguesEBuckleMBadautCTraversARimskyS 2007 H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat Struct Mol Biol 14 441 448

29. KahramanoglouCSeshasayeeASPrietoAIIbbersonDSchmidtS 2011 Direct and indirect effects of H-NS and FIS on global gene expression control in Escherichia coli. Nucleic Acids Res 39 2073 2091

30. NietoJMMadridCMiquelayEParraJLRodríguezS 2002 Evidence for direct protein-protein interaction between members of the enterobacterial Hha/YmoA and H-NS family of proteins. J Bacteriol 184 629 635

31. NeriDSzyperskiTOttingOSennHWuthrichK 1989 Stereo-specific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 Repressor by biosynthetically directed fractional 13C labeling. Biochemistry 28 7510 7516

32. SzyperskiTNeriDLeitingBOttingGWüthrichK 1992 Support of 1H NMR assignments in proteins by biosynthetically directed fractional 13C-labeling. J Biomol NMR 2 323 334

33. CordeiroTNGarcíaJPonsJIAznarSJuárezA 2008 A single residue loop mutation enhancing Hha binding to nucleoid associated protein H-NS results in loss of Hha regulatory properties. FEBS Lett 20 3139 3144

34. RoehrlMWangJWagnerG 2004 A general Framework and data analysis of competitive high-throughput screens for small-molecule inhibitors of protein-protein interactions by fluorescence Polarization. Biochemistry 43 16056 16066

35. DelaglioFGrzesiekSVuisterGWZhuGPfeiferJ 1995 NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6 277 293

36. JohnsonBA 2004 Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278 313 352

37. KellerRLJ 2004 The Computer Aided Resonance Assignment Tutorial. Goldau (Switzerland) CANTINA

38. IwaharaJWojciakJMClubbRT 2001 Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized istope-filtered NOESY experiment. J Biomol NMR 19 231 241

39. IkuraMBaxA 1992 Isotope-filtered 2D NMR of a protein-peptide complex: study of a skeletal muscle myosin light chain kinase fragment bound to calmodulin. J Am Chem Soc 114 2433 2440

40. HerrmannTGüntertPWüthrichK 2002 Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS. J Biomol NMR 24 171 189

41. HerrmannTGüntertPWüthrichK 2002 Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319 209 227

42. ZwahlenCLegaultPVincentSJFGreenblattJKonratR 1997 Methods for measurement of intermolecular NOEs by Multinuclear NMR spectroscopy: application to a bacteriophage λ N-peptide/boxB RNA complex. J Am Chem Soc 119 6711 6721

43. CornilescuGDelaglioFBaxA 1999 Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13 289 302

44. VuisterGWBaxA 1993 Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HN-Hα) coupling constants in 15N-enriched proteins. J Am Chem Soc 115 7772 7777

45. GüntertP 2004 Automated NMR structured calculation using CYANA. Methods Mol Biol 278 353 378

46. BrungerATAdamsPDCloreGMDeLanoWLGrosP 1998 Crystallography & NMR System (CNS). A new software suite for macromolecular structure determination. Acta Crystallogr D 54 905 921

47. NederveenAJDoreleijersJFVrankenWMillerZSpronkCA 2005 RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins 59 662 672

48. UlyanovNBSchmitzUJamesTL 1993 Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure. J Biomol NMR 3 547 568

49. WangJCieplakPKollmanPA 2000 How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21 1049 1074

50. DominguezCBoelensRBonvinAM 2003 HADDOCK: a protein-protein docking aproach based on biochemical or biophysical information. J Am Chem Soc 125 1731 1737

51. ZhengGLuXJOlsonWK 2009 Web 3DNA-a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res 37 W240 W246

52. RocchiaWSridharanSNichollsAAlexovEChiabreraA 2002 Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23 128 137

53. RoessleMWKlaeringRRistauURobrahnBJahnD 2007 Upgrade of the small-angle X-ray scattering beamline X33 at the European Molecular Biology Laboratory, Hamburg. J Appl Crystallogr 40 S190 S194

54. KonarevPVVolkovVVSokolovaAVKochMHJSvergunDI 2003 PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36 1277 1282

55. SvergunDIBarberatoCKochMHJ 1995 CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28 768 773

56. BlackburnGMGaitMJLoakesDWilliansDM 2006 Nucleic Acids in Chemistry and Biology. Cambridge, UK RSC Publishing 3rd ed

57. LaskowskiRAMacArthurMWMossDSThorntonJM 1993 PROCHECK – a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26 283 291