Mapping the Transition State for DNA Bending by IHF

Vivas, Paula; Velmurugu, Yogambigai; Kuznetsov, Serguei V.; Rice, Phoebe A.; Ansari, Anjum

doi:10.1016/j.jmb.2012.02.028

Cited by 30 publications

(70 citation statements)

References 81 publications

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“…The biochemical data, combined with the crystal structures, have shown that E. coli IHF␣␤ binds to the minor groove of DNA and bends the double helix by Ͼ160° (14,67,68). Other studies have shown that E. coli IHF ␣␤ binding to DNA, and subsequently DNA bending, occurs in a concerted fashion (67)(68)(69).…”

Section: Discussionmentioning

confidence: 98%

“…Since its discovery (4), E. coli IHF␣␤ has attracted considerable attention because of its role in various DNA transactions, wherein IHF-induced sharp bends or DNA loops coordinate the cooperative assembly of multicomponent nucleoprotein complexes (2,3,8). The biochemical data, combined with the crystal structures, have shown that E. coli IHF␣␤ binds to the minor groove of DNA and bends the double helix by Ͼ160° (14,67,68). Other studies have shown that E. coli IHF ␣␤ binding to DNA, and subsequently DNA bending, occurs in a concerted fashion (67)(68)(69).…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Sharadamma

Harshavardhana

Ravishankar

et al. 2014

Journal of Biological Chemistry

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Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF␣␤. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts.

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Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Sharadamma

Harshavardhana

Ravishankar

et al. 2014

Journal of Biological Chemistry

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“…Deletion of ihfA in S. Typhimurium severely decreases csrB expression, similar to the case for a uvrY deletion, although it does not affect csrC expression. IHF typically modifies DNA architecture, affecting DNA supercoiling, duplex stabilization, and global gene expression (88). It commonly regulates transcription from promoters that are directly regulated by multiple transcription factors.…”

Section: Regulation Of the Csr/rsm Systemmentioning

confidence: 99%

Regulation of Bacterial Virulence by Csr (Rsm) Systems

Vakulskas

Potts

Babitzke

et al. 2015

Microbiol Mol Biol Rev

295

400

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SUMMARY Most bacterial pathogens have the remarkable ability to flourish in the external environment and in specialized host niches. This ability requires their metabolism, physiology, and virulence factors to be responsive to changes in their surroundings. It is no surprise that the underlying genetic circuitry that supports this adaptability is multilayered and exceedingly complex. Studies over the past 2 decades have established that the CsrA/RsmA proteins, global regulators of posttranscriptional gene expression, play important roles in the expression of virulence factors of numerous proteobacterial pathogens. To accomplish these tasks, CsrA binds to the 5′ untranslated and/or early coding regions of mRNAs and alters translation, mRNA turnover, and/or transcript elongation. CsrA activity is regulated by noncoding small RNAs (sRNAs) that contain multiple CsrA binding sites, which permit them to sequester multiple CsrA homodimers away from mRNA targets. Environmental cues sensed by two-component signal transduction systems and other regulatory factors govern the expression of the CsrA-binding sRNAs and, ultimately, the effects of CsrA on secretion systems, surface molecules and biofilm formation, quorum sensing, motility, pigmentation, siderophore production, and phagocytic avoidance. This review presents the workings of the Csr system, the paradigm shift that it generated for understanding posttranscriptional regulation, and its roles in virulence networks of animal and plant pathogens.

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“…Error bars represent the standard error of the mean and were calculated from at least three independent experiments. *p<0.05, **p<0.01 the integration host factor (IHF) (Gamas et al 1987), which in turn, has been shown to have a higher affinity for intrinsically bent/kinked DNA (Vivas et al 2012). These findings are in line with our observations of abrupt shifts in GC skew, and both support a scenario similar to the one of IS2, in which intrinsically bent/kinked conformations are necessary both at the level of minicircle junction and cognate target DNA for binding site recognition (Lewis et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

Gonçalves

Oliveira

Gomes

et al. 2014

Appl Microbiol Biotechnol

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Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a metaanalysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly, extend this requirement to other families of IS elements. Using this information, we were able to pinpoint regions with high propensity for transposition and to predict and detect, de novo, a novel IS2 insertion event in the 3′ region of the gfp gene of a reporter plasmid. We also found that during amplification of this plasmid, process parameters such as scale, culture growth phase, and medium composition exacerbate IS2 transposition, leading to contamination levels with potentially detrimental clinical effects. Overall, our findings provide new insights into the role of target DNA structure in the mechanism of transposition of IS elements and extend our understanding of how culture conditions are a relevant factor in the induction of genetic instability.

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Mapping the Transition State for DNA Bending by IHF

Cited by 30 publications

References 81 publications

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Regulation of Bacterial Virulence by Csr (Rsm) Systems

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

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