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The shape of the DNA minor groove directs binding by the DNA-bending protein Fis.

Stella S, Cascio D, Johnson RC
Genes Dev 24 814-26 (2010)
Related entries: 3iv5, 3jr9, 3jra, 3jrb, 3jrc, 3jrd, 3jre, 3jrf, 3jrh, 3jri

Cited: 117 times
EuropePMC logo PMID: 20395367

Abstract

The bacterial nucleoid-associated protein Fis regulates diverse reactions by bending DNA and through DNA-dependent interactions with other control proteins and enzymes. In addition to dynamic nonspecific binding to DNA, Fis forms stable complexes with DNA segments that share little sequence conservation. Here we report the first crystal structures of Fis bound to high- and low-affinity 27-base-pair DNA sites. These 11 structures reveal that Fis selects targets primarily through indirect recognition mechanisms involving the shape of the minor groove and sequence-dependent induced fits over adjacent major groove interfaces. The DNA shows an overall curvature of approximately 65 degrees , and the unprecedented close spacing between helix-turn-helix motifs present in the apodimer is accommodated by severe compression of the central minor groove. In silico DNA structure models show that only the roll, twist, and slide parameters are sufficient to reproduce the changes in minor groove widths and recreate the curved Fis-bound DNA structure. Models based on naked DNA structures suggest that Fis initially selects DNA targets with intrinsically narrow minor grooves using the separation between helix-turn-helix motifs in the Fis dimer as a ruler. Then Fis further compresses the minor groove and bends the DNA to generate the bound structure.

Articles - 3jrg mentioned but not cited (2)

  1. Cooperative DNA binding by proteins through DNA shape complementarity. Hancock SP, Cascio D, Johnson RC. Nucleic Acids Res 47 8874-8887 (2019)
  2. Energy Transfer as A Driving Force in Nucleic Acid⁻Protein Interactions. Zavyalova E, Kopylov A. Molecules 24 1443 (2019)


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  1. Absence of a simple code: how transcription factors read the genome. Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Trends Biochem Sci 39 381-399 (2014)
  2. Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Browning DF, Grainger DC, Busby SJ. Curr Opin Microbiol 13 773-780 (2010)
  3. Bacterial chromosome organization and segregation. Badrinarayanan A, Le TB, Laub MT. Annu Rev Cell Dev Biol 31 171-199 (2015)
  4. Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability. Wang G, Vasquez KM. DNA Repair (Amst) 19 143-151 (2014)
  5. Chromosome organization in bacteria: mechanistic insights into genome structure and function. Dame RT, Rashid FM, Grainger DC. Nat Rev Genet 21 227-242 (2020)
  6. Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins. Rimsky S, Travers A. Curr Opin Microbiol 14 136-141 (2011)
  7. Bullied no more: when and how DNA shoves proteins around. Fogg JM, Randall GL, Pettitt BM, Sumners WL, Harris SA, Zechiedrich L. Q Rev Biophys 45 257-299 (2012)
  8. Role of DNA sequence based structural features of promoters in transcription initiation and gene expression. Bansal M, Kumar A, Yella VR. Curr Opin Struct Biol 25 77-85 (2014)
  9. Multilayer chromosome organization through DNA bending, bridging and extrusion. Gruber S. Curr Opin Microbiol 22 102-110 (2014)
  10. Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing. Stella S, Alcón P, Montoya G. Nat Struct Mol Biol 24 882-892 (2017)
  11. The λ Integrase Site-specific Recombination Pathway. Landy A. Microbiol Spectr 3 MDNA3-0051-2014 (2015)
  12. When is a transcription factor a NAP? Dorman CJ, Schumacher MA, Bush MJ, Brennan RG, Buttner MJ. Curr Opin Microbiol 55 26-33 (2020)
  13. Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium. Dorman CJ, Dorman MJ. Environ Microbiol 19 3834-3845 (2017)
  14. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Muskhelishvili G, Travers A. Biophys Rev 8 5-22 (2016)
  15. Towards quantitative analysis of gene regulation by enhancers. Nizovtseva EV, Todolli S, Olson WK, Studitsky VM. Epigenomics 9 1219-1231 (2017)
  16. Conservation of the three-dimensional structure in non-homologous or unrelated proteins. Sousounis K, Haney CE, Cao J, Sunchu B, Tsonis PA. Hum Genomics 6 10 (2012)
  17. Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology. Flores-Ríos R, Quatrini R, Loyola A. Comput Struct Biotechnol J 17 746-756 (2019)
  18. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Genes (Basel) 8 E192 (2017)
  19. The interplay between DNA topology and accessory factors in site-specific recombination in bacteria and their bacteriophages. Dorman CJ, Bogue MM. Sci Prog 99 420-437 (2016)
  20. Dps Is a Universally Conserved Dual-Action DNA-Binding and Ferritin Protein. Orban K, Finkel SE. J Bacteriol 204 e0003622 (2022)
  21. IHF and Fis as Escherichia coli Cell Cycle Regulators: Activation of the Replication Origin oriC and the Regulatory Cycle of the DnaA Initiator. Kasho K, Ozaki S, Katayama T. Int J Mol Sci 24 11572 (2023)
  22. Noncanonical binding of transcription factors: time to revisit specificity? Samee MAH. Mol Biol Cell 34 (2023)

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