DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence

Papapanagiotou, I.; Streeter, Simon; Cary, Peter D.; Kneale, Geoff

doi:10.1093/nar/gkm129

Cited by 21 publications

(37 citation statements)

References 30 publications

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“…Gels were post-stained with EtBr and DNA bands were visualized in gel documentation system. IHF bending angles were calculated as described previously (42). Mobilities of IHF bound DNA complex ( R b ) and the respective free DNA ( R f ) were calculated for all the restriction-digested fragments.…”

Section: Methodsmentioning

confidence: 99%

Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

Yoganand¹,

Sivathanu²,

Nimkar³

et al. 2016

Nucleic Acids Res

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CRISPR–Cas system epitomizes prokaryote-specific quintessential adaptive defense machinery that limits the genome invasion of mobile genetic elements. It confers adaptive immunity to bacteria by capturing a protospacer fragment from invading foreign DNA, which is later inserted into the leader proximal end of CRIPSR array and serves as immunological memory to recognize recurrent invasions. The universally conserved Cas1 and Cas2 form an integration complex that is known to mediate the protospacer invasion into the CRISPR array. However, the mechanism by which this protospacer fragment gets integrated in a directional fashion into the leader proximal end is elusive. Here, we employ CRISPR/dCas9 mediated immunoprecipitation and genetic analysis to identify Integration Host Factor (IHF) as an indispensable accessory factor for spacer acquisition in Escherichia coli. Further, we show that the leader region abutting the first CRISPR repeat localizes IHF and Cas1–2 complex. IHF binding to the leader region induces bending by about 120° that in turn engenders the regeneration of the cognate binding site for protospacer bound Cas1–2 complex and brings it in proximity with the first CRISPR repeat. This appears to guide Cas1–2 complex to orient the protospacer invasion towards the leader-repeat junction thus driving the integration in a polarized fashion.

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Section: Methodsmentioning

confidence: 99%

Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

Yoganand¹,

Sivathanu²,

Nimkar³

et al. 2016

Nucleic Acids Res

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show abstract

“…system (LI-COR) at 600 nm. The relative mobility of DNA fragments with or without protein was used to estimate the bend angle, , using the formulae, a= -b= 2c (1-cos ) as previously described [53].…”

Section: Accepted Manuscriptmentioning

confidence: 99%

AbiEi Binds Cooperatively to the Type IV abiE Toxin–Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation

Hampton

Jackson

Fagerlund

et al. 2018

Journal of Molecular Biology

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Bacteria resist phage infection using multiple strategies, including CRISPR-Cas and abortive infection (Abi) systems. Abi systems provide population-level protection from phage predation, via "altruistic" cell suicide. It has recently been shown that some Abi systems function via a toxin-antitoxin mechanism, such as the widespread AbiE family. The Streptococcus agalactiae AbiE system consists of a bicistronic operon encoding the AbiEi antitoxin and AbiEii toxin, which function as a Type IV toxin-antitoxin system. Here we examine the AbiEi antitoxin, which belongs to a large family of transcriptional regulators with a conserved N-terminal winged helix-turn-helix domain. This winged helix-turn-helix is essential for transcriptional repression of the abiE operon. The function of the AbiEi C-terminal domain is poorly characterized, but it contributes to transcriptional repression and is sufficient for toxin neutralization. We demonstrate that a conserved charged surface on one face of the C-terminal domain assists sequence-specific DNA binding and negative autoregulation, without influencing antitoxicity. Furthermore, AbiEi binds cooperatively to two inverted repeats within the abiE promoter and bends the DNA by 72°. These findings demonstrate that the mechanism of DNA binding by the widespread family of AbiEi antitoxins and transcriptional regulators can contribute to negative autoregulation.

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“…The homology between HipB and these proteins is confined to the four-helix bundle region as the β-lid is found only in HipB. Despite the similarities in DNA binding domains, these proteins bind their DNA sites differently as 434 Cro does not significantly distort its DNA site and biochemical data indicate that C.AhdI bends its DNA site by 47° (26–27). By contrast, HipB induces a large, 70° bend in its operator (Fig.…”

mentioning

confidence: 99%

Molecular Mechanisms of HipA-Mediated Multidrug Tolerance and Its Neutralization by HipB

Schumacher

Piro

et al. 2009

Science

298

359

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Summary Bacterial multidrug tolerance is largely responsible for the inability of antibiotics to eradicate infections and is caused by a small population of dormant bacteria called persisters. HipA is a critical Escherichia coli persistence factor that is normally neutralized by HipB, a transcription repressor, which also regulates hipBA expression. Here we report multiple structures of HipA and a HipA-HipB-DNA complex. HipA has a eukaryotic Ser/Thr kinase-like fold and can phosphorylate the translation factor, EF-Tu, suggesting a persistence mechanism via cell stasis. The HipA-HipB-DNA structure reveals the HipB-operator binding mechanism, ~70° DNA bending and unexpected HipA-DNA contacts. Dimeric HipB interacts with two HipA molecules to inhibit its kinase activity through sequestration and conformational inactivation. Combined, these studies suggest mechanisms for HipA-mediated persistence and its neutralization by HipB.

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DNA structural deformations in the interaction of the controller protein C.AhdI with its operator sequence

Cited by 21 publications

References 30 publications

Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system

AbiEi Binds Cooperatively to the Type IV abiE Toxin–Antitoxin Operator Via a Positively-Charged Surface and Causes DNA Bending and Negative Autoregulation

Molecular Mechanisms of HipA-Mediated Multidrug Tolerance and Its Neutralization by HipB

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