ArticlePloS one2016
DNA Sequence Determinants Controlling Affinity, Stability and Shape of DNA Complexes Bound by the Nucleoid Protein Fis.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
29 citing papers in PubMed, 46 citations in OpenAlex.
- Nucleoid-associated proteins: molecular mechanisms in microbial adaptation.World journal of microbiology & biotechnology · 2025Review
- Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression.Molecular microbiology · 2024Review
- Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding.Biophysical journal · 2024Article
- Dissection of integrated readout reveals the structural thermodynamics of DNA selection by transcription factors.Structure (London, England : 1993) · 2024Article
- Shedding Light on Bacterial Chromosome Structure: Exploring the Significance of 3C-Based Approaches.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Structures of theProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17.International journal of molecular sciences · 2023Article
- The DNA relaxation-dependent OFF-to-ON biasing of the type 1 fimbrial genetic switch requires the Fis nucleoid-associated protein.Microbiology (Reading, England) · 2023Article
- Facilitated dissociation of nucleoid-associated proteins from DNA in the bacterial confinement.Biophysical journal · 2022Article
- The importance of hydrophobic interactions in the structure of transcription systems.European biophysics journal : EBJ · 2021Article
- Fis Connects Two Sensory Pathways, Quorum Sensing and Surface Sensing, to Control Motility inFrontiers in microbiology · 2021Article
- The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.Nucleic acids research · 2020Article
- Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis.Journal of bacteriology · 2020Article
- Crystal structure of the nucleoid-associated protein Fis (PA4853) from Pseudomonas aeruginosa.Acta crystallographica. Section F, Structural biology communications · 2020Article
- A bacteriophage mimic of the bacterial nucleoid-associated protein Fis.The Biochemical journal · 2020Article
- Chromosome organization in bacteria: mechanistic insights into genome structure and function.Nature reviews. Genetics · 2020Review
- Fis protein forms DNA topological barriers to confine transcription-coupled DNA supercoiling in Escherichia coli.FEBS letters · 2020Article
- A report on DNA sequence determinants in gene expression.Bioinformation · 2020Article
- Architecture of the Escherichia coli nucleoid.PLoS genetics · 2019Article
- Cooperative DNA binding by proteins through DNA shape complementarity.Nucleic acids research · 2019Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequences in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. The affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.