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H. pylori NikR: A New Nickel Regulatory Protein.

機(jī)譯：幽門(mén)螺桿菌NikR：一種新的鎳調(diào)節(jié)蛋白。

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My research has focused on understanding the mechanism of DNA recognition by the nickel regulatory protein NikR from Helicobacter pylori (HpNikR). H. pylori colonize the highly acidic gastric epithelium of the human stomach. One feature that enables H. pylori to survive under acidic conditions is the ability to release large quantities of ammonia, produced by the NikR regulated enzyme urease, to neutralize its immediate environment. HpNikR also regulates the expression of multiple other genes as either an activator or repressor including those involved in nickel ion homeostasis, acid adaptation and iron uptake. The genes for which direct regulation have been established contain variable recognition sequences; and the biophysical basis for DNA recognition and discrimination by HpNikR is currently unresolved. Crystallographic studies produced an unanticipated structure of Holo-HpNikR in which nickel ions are coordinated to two distinct binding sites: a 4-coordinate, square planar site (called the 4-site) and a 5/6-coordinate square-pyramidal/octahedral site (called the 5/6-site) in contrast to previous NikR structures where all four ions are coordinated to square planar sites. A mutant of HpNikR called H74A was designed to force all four nickels to the 4-sites, and the crystal structure confirmed singular coordination. DNA binding studies revealed that when Ni(II) is restricted from the 5/6 sites, DNA binding properties are abrogated compared to Holo-HpNikR. These data support a mechanism in which nickel coordination to the 5/6 site of HpNikR is critical for function. A reporter assay was also developed to monitor transcription of urease as a function of nickel concentration and promoter sequence directly within H. pylori. Unexpectedly, initial findings from this study directed us towards a novel cooperative effect in vivo where the presence of active HpArsR-P, from the ArsRS two component system, in conjunction with HpNikR leads to maximum Ni(II) dependent induction of urease. HpArsR is also able to bind the HpNikR PureA mutant operator sites in vitro as determined via fluorescence anisotropy at neutral pH with a high nanomolar to low micromolar affinity. Through the use of both in vitro and in vivo approaches, a novel model has been proposed for DNA recognition by HpNikR.
機(jī)譯：我的研究集中在了解幽門(mén)螺桿菌（HpNikR）的鎳調(diào)節(jié)蛋白NikR對(duì)DNA識(shí)別的機(jī)制。幽門(mén)螺桿菌定植在人胃的高酸性胃上皮中。使幽門(mén)螺桿菌能夠在酸性條件下生存的一項(xiàng)功能是能夠釋放由NikR調(diào)節(jié)的酶脲酶產(chǎn)生的大量氨，以中和其直接環(huán)境。 HpNikR還調(diào)節(jié)多種其他基因的表達(dá)，使其作為激活物或阻遏物，包括那些與鎳離子穩(wěn)態(tài)，酸適應(yīng)和鐵吸收有關(guān)的基因。已建立直接調(diào)控的基因包含可變識(shí)別序列； HpNikR識(shí)別和識(shí)別DNA的生物物理基礎(chǔ)目前尚未解決。晶體學(xué)研究產(chǎn)生了Holo-HpNikR的意外結(jié)構(gòu)，其中鎳離子與兩個(gè)不同的結(jié)合位點(diǎn)配位：一個(gè)4坐標(biāo)的方形平面位點(diǎn)（稱為4位）和一個(gè)5/6坐標(biāo)的方形金字塔形/八面體位點(diǎn)（稱為5/6位）與以前的NikR結(jié)構(gòu)相反，在該結(jié)構(gòu)中，所有四個(gè)離子都配位到方形平面位。設(shè)計(jì)了一個(gè)名為H74A的HpNikR突變體，將所有四個(gè)鎳都強(qiáng)迫到4位，并且晶體結(jié)構(gòu)證實(shí)了奇異的配位。 DNA結(jié)合研究表明，當(dāng)Ni（II）限制在5/6位時(shí)，與Holo-HpNikR相比，DNA結(jié)合特性被取消。這些數(shù)據(jù)支持了一種機(jī)制，其中鎳與HpNikR的5/6位點(diǎn)的配位對(duì)于功能至關(guān)重要。還開(kāi)發(fā)了一種報(bào)告基因測(cè)定法，以直接在幽門(mén)螺桿菌中監(jiān)測(cè)尿素酶的轉(zhuǎn)錄與鎳濃度和啟動(dòng)子序列的關(guān)系。出乎意料的是，這項(xiàng)研究的初步發(fā)現(xiàn)將我們引向了一種新的體內(nèi)協(xié)同效應(yīng)，其中來(lái)自ArsRS兩組分系統(tǒng)的活性HpArsR-P與HpNikR結(jié)合導(dǎo)致尿素酶的最大Ni（II）依賴性誘導(dǎo)。 HpArsR還能夠在體外結(jié)合HpNikR PureA突變體操作位點(diǎn)，該位點(diǎn)通過(guò)中性pH值下的熒光各向異性確定，具有高納摩爾至低微摩爾親和力。通過(guò)使用體外和體內(nèi)方法，已提出了一種新的模型用于HpNikR的DNA識(shí)別。

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  • 作者

    West, Abby L.;

  • 作者單位

    University of Maryland, Baltimore.;

  • 授予單位 University of Maryland, Baltimore.;
  • 學(xué)科 Chemistry Biochemistry.;Biology Microbiology.
  • 學(xué)位 Ph.D.
  • 年度 2012
  • 頁(yè)碼 265 p.
  • 總頁(yè)數(shù) 265
  • 原文格式 PDF
  • 正文語(yǔ)種 eng
  • 中圖分類(lèi) 地球物理學(xué);
  • 關(guān)鍵詞

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