Fis Protein Insulates the Gene from Uncontrolled Transcription

English version České info

The Escherichia coli curved DNA binding protein A (CbpA) is a poorly characterised nucleoid associated factor and co-chaperone. It is expressed at high levels as cells enter stationary phase. Using genetics, biochemistry, and genomics, we have examined regulation of, and DNA binding by, CbpA. We show that Fis, the dominant growth-phase nucleoid protein, prevents CbpA expression in growing cells. Regulation by Fis involves an unusual “insulation” mechanism. Thus, Fis protects cbpA from the effects of a distal promoter, located in an adjacent gene. In stationary phase, when Fis levels are low, CbpA binds the E. coli chromosome with a preference for the intrinsically curved Ter macrodomain. Disruption of the cbpA gene prompts dramatic changes in DNA topology. Thus, our work identifies a novel role for Fis and incorporates CbpA into the growing network of factors that mediate bacterial chromosome structure.

Vyšlo v časopise: Fis Protein Insulates the Gene from Uncontrolled Transcription. PLoS Genet 9(1): e32767. doi:10.1371/journal.pgen.1003152
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1003152

Souhrn

Zdroje

1. DillonSC, DormanCJ (2010) Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8: 185–195.

2. DormanCJ, BarrGC, Ni BhriainN, HigginsCF (1988) DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression. J Bacteriol 6: 2816–2826.

3. SobetzkoP, TraversA, MuskhelishviliG (2012) Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc Natl Acad Sci 109: E42–E50.

4. AzamTA, IwataA, NishimuraA, UedaS, IshihamaA (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361–6370.

5. AlmirónM, LinkAJ, FurlongD, KolterR (1992) A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev 6: 2646–2654.

6. WolfSG, FrenkielD, AradT, FinkelSE, KolterR, et al. (1999) DNA protection by stress-induced biocrystallization. Nature 400: 83–85.

7. CalhounLN, KwonYM (2011) Structure, function and regulation of the DNA-binding protein Dps and its role in acid and oxidative stress resistance in Escherichia coli: a review. J Appl Microbiol 110: 375–386.

8. GraingerDC, GoldbergMD, LeeDJ, BusbySJ (2008) Selective repression by Fis and H-NS at the Escherichia coli dps promoter. Mol Microbiol 68: 1366–1377.

9. UeguchiC, KakedaM, YamadaH, MizunoT (1994) An analogue of the DnaJ molecular chaperone in Escherichia coli. Proc Natl Acad Sci 91: 1054–1058.

10. AzamTA, IshihamaA (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 274: 33105–33113.

11. BirdJG, SharmaS, RoshwalbSC, HoskinsJR, WicknerS (2006) Functional analysis of CbpA, a DnaJ homolog and nucleoid-associated DNA-binding protein. J Biol Chem 281: 34349–34356.

12. ChintakayalaK, GraingerDC (2011) A conserved acidic amino acid mediates the interaction between modulators and co-chaperones in enterobacteria. J Mol Biol 411: 313–320.

13. ChaeC, SharmaS, HoskinsJR, WicknerS (2004) CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM. J Biol Chem 279: 33147–33153.

14. SarrafNS, BaardsnesJ, ChengJ, O'Connor-McCourtM, CyglerM, et al. (2010) Structural basis of the regulation of the CbpA co-chaperone by its specific modulator CbpM. J Mol Biol 398: 111–121.

15. CosgriffS, ChintakayalaK, ChimYT, ChenX, AllenS, et al. (2010) Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA. Mol Microbiol 77: 1289–1300.

16. SinghSS, TypasA, HenggeR, GraingerDC (2011) Escherichia coli σ70 senses sequence and conformation of the promoter spacer region. Nucleic Acids Res 39: 5109–5118.

17. AzamTA, HiragaS, IshihamaA (2000) Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 5: 613–626.

18. BrowningDF, ColeJA, BusbySJ (2004) Transcription activation by remodelling of a nucleoprotein assembly: the role of NarL at the FNR-dependent Escherichia coli nir promoter. Mol Microbiol 53: 203–215.

19. HengenPN, BartramSL, StewartLE, SchneiderTD (1997) Information analysis of Fis binding sites. Nucleic Acids Res 25: 4994–5002.

20. HirvonenCA, RossW, WozniakCE, MarascoE, AnthonyJR, et al. (2001) Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J Bacteriol 183: 6305–6314.

21. ShaoY, Feldman-CohenLS, OsunaR (2008) Functional characterisation of the Escherichia coli Fis-DNA binding sequence. J Mol Biol 376: 771–785.

22. GraingerDC, HurdD, GoldbergMD, BusbySJ (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 34: 4642–4652.

23. ChoBK, KnightEM, BarrettCL, PalssonBØ (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18: 900–910.

24. KahramanoglouC, SeshasayeeAS, PrietoAI, IbbersonD, SchmidtS, et al. (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39: 2073–2091.

25. AtteyA, BelyaevaT, SaveryN, HoggettJ, FujitaN, et al. (1994) Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the Escherichia coli galactose operon P1 promoter. Nucleic Acids Res 22: 4375–4380.

26. XuM, BusbySJ, BrowningDF (2009) Activation and repression at the Escherichia coli ynfEFGHI operon promoter. J Bacteriol 191: 3172–3176.

27. SquireDJ, XuM, ColeJA, BusbySJ, BrowningDF (2009) Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters. Biochem J 420: 249–257.

28. HollandsK, LeeDJ, LloydGS, BusbySJ (2010) Activation of sigma 28-dependent transcription in Escherichia coli by the cyclic AMP receptor protein requires an unusual promoter organization. Mol Microbiol 75: 1098–1111.

29. PedersenAG, JensenLJ, BrunakS, StaerfeldtHH, UsseryDW (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299: 907–930.

30. ConterA (2003) Plasmid DNA supercoiling and survival in long-term cultures of Escherichia coli: role of NaCl. J Bacteriol 185: 5324–5327.

31. ConterA, MenchonC, GutierrezC (1997) Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. J Mol Biol 273: 75–83.

32. YamashinoT, KakedaM, UeguchiC, MizunoT (1994) An analogue of the DnaJ molecular chaperone whose expression is controlled by σS during the stationary phase and phosphate starvation in Escherichia coli. Mol Microbiol 13: 475–483.

33. DornenburgJE, DevitaAM, PalumboMJ, WadeJT (2010) Widespread antisense transcription in Escherichia coli. mBio 1(1): e00024–10 doi:10.1128/mBio.00024-10.

34. SharmaCM, HoffmannS, DarfeuilleF, ReignierJ, FindeissS, et al. (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250–255.

35. KawanoM, StorzG, RaoBS, RosnerJL, MartinRG (2005) Detection of low-level promoter activity within open reading frame sequences of Escherichia coli. Nucleic Acids Res 33: 6268–6276.

36. OhniwaRL, MorikawaK, KimJ, OhtaT, IshihamaA, et al. (2006) Dynamic state of DNA topology is essential for genome condensation in bacteria. EMBO J 25: 5591–5602.

37. Miller J (1972) Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

38. LloydGS, HollandsK, GodfreyRE, BusbySJ (2008) Transcription initiation in the Escherichia coli K-12 malI-malX intergenic region and the role of the cyclic AMP receptor protein. FEMS Microbiol Lett 288: 250–7.

39. KolbA, KotlarzD, KusanoS, IshihamaA (1995) Selectivity of the Escherichia coli RNA polymerase E sigma 38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res 23: 819–826.

40. GraingerDC, OvertonTW, ReppasN, WadeJT, TamaiE, et al. (2004) Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J Bacteriol 186: 6938–6943.

41. CarverT, ThomsonN, BleasbyA, BerrimanM, ParkhillJ (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119–120.

42. ShpigelmanES, TrifonovEN, BolshoyA (1993) CURVATURE: software for the analysis of curved DNA. Comput Appl Biosci 9: 435–440.

43. BallCA, OsunaR, FergusonKC, JohnsonRC (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli.. J Bacteriol 174: 8043–8056.