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肺炎衣原體核糖核酸酶H的功能研究

發(fā)布時(shí)間:2019-06-15 13:38
【摘要】:核糖核酸酶H (RNase H)能夠特異地水解RNA/DNA雜合雙鏈或DNA-RNA-DNA/DNA嵌合型底物中的RNA。根據(jù)氨基酸序列及空間結(jié)構(gòu)相似性,RNase H分為兩類(lèi),1型和2型。其中,1型RNaseH包括細(xì)菌的RNase HI及真核生物的RNase H1;2型RNase H包括細(xì)菌RNase HII、RNase HIII、古細(xì)菌RNase HII和真核生物RNase H2。 RNase HII/H2廣泛存在于各種生物體內(nèi),但RNase HI/H1和HIII只存留在部分生物體內(nèi)。目前人們普遍接受的看法是,RNase HI/H1和HIII只能切割含有四個(gè)(或更多)核糖核苷酸的DNA-(rN)n-DNA/DNA雙鏈(n≥4)或RNA/DNA雜合鏈底物,而RNase HII/H2不僅可以切這些底物,還能切割DNA-rN_1-DNA/DNA(rN_1,單個(gè)核糖核苷酸)雙鏈。 基因組全序列分析表明,肺炎衣原體沒(méi)有RNase HI,只有兩個(gè)2型的RNase H:CpRNase HII和CpRNase HIII,分別由CP0654和CP0782(NCBI序列號(hào))基因編碼。我們前期的體外生化研究證實(shí)純化后的CpRNase HII蛋白能切割DNA-rN_1-DNA/DNA底物;而CpRNase HIII可以切RNA/DNA底物。本研究發(fā)現(xiàn)CpRNase HIII在錳離子(Mn~(2+))存在時(shí)也能切割DNA-rN_1-DNA/DNA底物。這是RNase H領(lǐng)域中首次報(bào)道RNase HIII具有切割DNA-rN_1-DNA/DNA底物的能力。 體外生化實(shí)驗(yàn)證實(shí),兩種CpRNase H切割DNA-rN_1-DNA/DNA底物時(shí)對(duì)金屬離子的依賴(lài)性不同,CpRNase HIII依賴(lài)Mn~(2+),而CpRNase HII則偏愛(ài)鎂離子(Mg2+)且活性會(huì)受到Mn~(2+)抑制。進(jìn)一步研究表明,在切割DNA-rN_1-DNA/DNA底物時(shí),兩種酶對(duì)反應(yīng)體系中的鎂錳離子波動(dòng)敏感。另一方面,兩種CpRNase H切割其它底物(RNA/DNA雜合鏈及類(lèi)似岡崎片段的底物)時(shí)酶活性并不會(huì)因?yàn)殒V錳離子波動(dòng)受到明顯影響。這些結(jié)果表明鎂錳離子水平的變化會(huì)抑制一種CpRNase H切割DNA-rN_1-DNA/DNA底物的活性但同時(shí)激活另一種CpRNase H的活性。 在細(xì)菌體內(nèi),我們也證實(shí)了上述體外實(shí)驗(yàn)的結(jié)果。采用基因重組技術(shù)構(gòu)建了三株大腸桿菌rnh突變株,基因改造情況為:LZ1[DY329,ΔrnhA ΔrnhB:: CprnhB],LZ2[DY329, ΔrnhA:: CprnhC ΔrnhB::CprnhB],LZ3[DY329, ΔrnhA:: CprnhC ΔrnhB]。其中,CprnhB和CprnhC分別代表兩種CpRNase H (HII和HIII)的編碼基因;rnhA和rnhB分別表示大腸桿菌RNase HI和HII的編碼基因。CpRNase HII遺傳互補(bǔ)大腸桿菌RNase H缺失依賴(lài)于Mg2+,但培養(yǎng)基中添加0.2mM Mn~(2+)抑制了CpRNase HII的該功能,導(dǎo)致細(xì)菌生長(zhǎng)緩慢;相反,CpRNase HIII彌補(bǔ)大腸桿菌RNase H缺失則依賴(lài)于Mn~(2+)。對(duì)大腸桿菌突變株的基因組進(jìn)行堿敏感性分析發(fā)現(xiàn),,當(dāng)CpRNase H活性受到抑制而導(dǎo)致細(xì)菌生長(zhǎng)遲緩時(shí),其基因組對(duì)堿非常敏感,表明此時(shí)基因組中摻入了大量核糖核苷酸。考慮到體外實(shí)驗(yàn)證實(shí)CpRNase H酶切RNA/DNA雜合鏈、類(lèi)似岡崎片段的底物時(shí)不受緩沖液中鎂錳離子波動(dòng)的影響,突變株生長(zhǎng)遲緩的主因是體內(nèi)CpRNase H切割DNA-rN_1-DNA/DNA底物的活性受到抑制,導(dǎo)致基因組中摻入了過(guò)多的單個(gè)核糖核苷酸;而在生長(zhǎng)培養(yǎng)基內(nèi)添加對(duì)應(yīng)喜好的金屬離子則會(huì)恢復(fù)CpRNase H的活性從而使突變株恢復(fù)正常生長(zhǎng)。 培養(yǎng)基內(nèi)添加錳離子影響了細(xì)菌體內(nèi)CpRNase H的活性,這個(gè)結(jié)果暗示培養(yǎng)基內(nèi)添加錳時(shí)細(xì)菌胞內(nèi)的錳濃度發(fā)生了變化,我們提供了相關(guān)數(shù)據(jù)證實(shí)這一點(diǎn)。采用含有或不含錳的培養(yǎng)基培養(yǎng)這三株大腸桿菌突變株,用等離子發(fā)射光譜(ICP-AES)測(cè)定細(xì)菌胞內(nèi)錳離子濃度。結(jié)果表明含錳培養(yǎng)基培養(yǎng)的細(xì)菌相比不含錳培養(yǎng)基培養(yǎng)的,其胞內(nèi)錳離子濃度增加了5~14倍,對(duì)胞內(nèi)RNase H活性產(chǎn)生了明顯影響,即促進(jìn)CpRNase HIII活性、抑制CpRNase HII活性。另外,為了驗(yàn)證培養(yǎng)基中添加的錳是否會(huì)影響CpRNase H編碼基因的表達(dá),我們選擇在有錳和無(wú)錳時(shí)生長(zhǎng)有差異的突變株并提取其總RNA進(jìn)行實(shí)時(shí)定量PCR。采用管家基因gapA作為內(nèi)參基因做相對(duì)定量分析,結(jié)果證實(shí)基因表達(dá)并未因培養(yǎng)基中添加或缺少錳而有明顯差異,表明培養(yǎng)基中的錳影響突變株生長(zhǎng)是因?yàn)镃pRNase H的活性受到抑制,而不是CpRNase H編碼基因的表達(dá)受阻。 這些實(shí)驗(yàn)結(jié)果表明,兩種CpRNase H在體內(nèi)是合作互助的關(guān)系:在正常情況下由CpRNase HII執(zhí)行功能,去除基因組中摻入的單個(gè)核糖核苷酸;而在離子波動(dòng)的情況下,比如錳含量較高時(shí),CpRNase HII的活性受到抑制而由CpRNase HIII行使同樣的功能。肺炎衣原體采用了兩種2型RNase H很可能是因?yàn)樽陨砩姝h(huán)境復(fù)雜,在復(fù)雜多變的外界環(huán)境中兩種CpRNase H能夠合作、互補(bǔ),從而使細(xì)胞可以維持正常生理代謝。 在證實(shí)CpRNase HIII也具有酶切DNA-rN_1-DNA/DNA底物的活性之后,我們進(jìn)一步研究了CpRNase HIII識(shí)別、切割這類(lèi)底物的結(jié)構(gòu)基礎(chǔ)。通過(guò)體外生化測(cè)活,鑒定突變的氨基酸對(duì)該蛋白切割、識(shí)別底物的重要性;結(jié)合同源模建、分子對(duì)接及分子動(dòng)力學(xué)模擬等計(jì)算機(jī)輔助的方法,闡明了CpRNase HIII識(shí)別DNA-rN_1-DNA/DNA底物的機(jī)制。CpRNase HIII的“GKG”基序負(fù)責(zé)識(shí)別單個(gè)核糖核苷酸,識(shí)別方式與RNase HII中“GR (K) G”基序相似,表明CpRNase HIII采納了與HII相似的底物識(shí)別機(jī)制。RNase HII/H2識(shí)別核糖核苷酸還需要一個(gè)高度保守的酪氨酸(Y),但通過(guò)分析氨基酸序列及同源模建得到的蛋白結(jié)構(gòu)模型,發(fā)現(xiàn)在CpRNase HIII對(duì)應(yīng)位置上沒(méi)有這樣一個(gè)Y殘基,通過(guò)分子動(dòng)力學(xué)模擬我們發(fā)現(xiàn)CpRNase HIII的第94位的絲氨酸(Ser94)與DNA-rN_1-DNA/DNA底物中嵌合的單個(gè)核糖核苷酸3′-端的脫氧核糖核苷酸形成穩(wěn)定氫鍵,將該脫氧核糖核苷酸拖拽地偏離了核糖核苷酸,同時(shí)使DNA雙螺旋的局部構(gòu)象發(fā)生了變動(dòng)。這個(gè)舉動(dòng)似乎執(zhí)行了RNase HII中酪氨酸的功能,援助“GKG”基序準(zhǔn)確地識(shí)別核糖核苷酸的2′-OH。在分子模擬結(jié)果的指導(dǎo)下,我們圍繞Ser94進(jìn)行了一系列生化實(shí)驗(yàn),證明了該Ser對(duì)酶活性的重要性。這部分研究結(jié)果闡釋了CpRNase HIII的底物識(shí)別機(jī)制。
[Abstract]:The RNase H (RNase H) is capable of specifically hydrolyzing the RNA/ DNA hybrid double-stranded or DNA-RNA-DNA/ DNA chimeric substrate. According to the amino acid sequence and spatial structure similarity, the RNase H is divided into two types: type 1 and type 2. Wherein, the type 1 RNaseH comprises the RNase HI of the bacterium and the RNase H1 of the eukaryote; the type 2 RNase H comprises the bacterial RNase HII, the RNase HIII, the archaea RNase HII and the eukaryote RNase H2. RNase HII/ H2 is widely present in various organisms, but RNase HI/ H1 and HIII remain only in some organisms It is generally accepted that RNase HI/ H1 and HIII can only cut DNA-(rN) n-DNA/ DNA double-stranded (n-4) or RNA/ DNA hybrid chain substrate containing four (or more) ribose nucleic acid, while RNase HII/ H2 can not only cut these substrates, but also cut DNA-rN _ 1-DNA/ DNA (rN _ 1, single ribose nucleic acid) bis The complete sequence analysis of the genome showed that the Chlamydia pneumoniae did not have RNase HI, only two of the two types of RNase H: CpRNase HII and CpRNase HIII, respectively, were based on CP0654 and CP0782 (NCBI serial number). For coding. In-vitro biochemical studies in the early stage confirmed that the purified CpRNase HII protein can cut the DNA-rN _ 1-DNA/ DNA substrate; and CpRNase HIII can cut the RNA/ DN A substrate. The present study found that CpRNase HIII can also cut DNA-rN _ 1-DNA/ DN in the presence of manganese ions (Mn ~ (2 +)) A substrate. This is the first time in the RNase H domain. The RNase HIII has the cleavage DNA-rN _ 1-DNA/ DNA substrate The ability of the two CpRNase H to cut the DNA-rN_1-DNA/ DNA substrate was different when the two CpRNase H cut the DNA-rN_1-DNA/ DNA substrate, and the CpRNase HIII was dependent on Mn ~ (2 +), while the CpRNase HII preferred the magnesium ion (Mg2 +) and the activity was affected by Mn ~ (2 +). 2 +) inhibition. Further studies have shown that, in the cleavage of DNA-rN _ 1-DNA/ DNA substrate, the two enzymes are separated from the magnesium and manganese in the reaction system. On the other hand, the enzyme activity is not affected by the fluctuation of magnesium-manganese ions when two CpRNase H cuts other substrates (the substrate of the RNA/ DNA hybrid chain and the similar Okazaki fragment). These results indicate that a change in the level of magnesium-manganese ions would inhibit the activity of a CpRNase H-cut DNA-rN _ 1-DNA/ DNA substrate, but also activate another CpRNas e H. In the bacterial body, we also confirmed the above The results of in vitro experiments were as follows: The gene recombination technique was used to construct the rnh mutant of Sanzhu. The transformation of the gene was as follows: LZ1[DY329,[rnhA, rnhB:: CprnhB], LZ2[DY329, and rnhA:: CprnhC, rnhB:: CprnhB], LZ3[DY329]: Cprnh: Cprnh C. rnhB], where CprnhB and Cprnhc represent the coding genes of two CpRNase H (HII and HIII), respectively; and rnhA and rnhB represent E. coli RNase HI and H, respectively. The addition of 0.2 mM Mn to (2 +) in the culture medium inhibited the function of the CpRNase HII, resulting in a slow growth of the bacteria; on the contrary, the deletion of the RNase H in the E.coli was dependent on the CpRNase HIII. The analysis of the alkali sensitivity of the genome of the mutant strain of E. coli found that when the activity of the CpRNase H was inhibited and the growth of the bacteria was retarded, its genome was very sensitive to the base, indicating that the genome was incorporated. Large amount of ribose nucleic acid. Considering in vitro experiments that the CpRNase H enzyme digestion RNA/ DNA hybrid chain is confirmed, the substrate with similar Okazaki fragment is not affected by the fluctuation of the magnesium-manganese ions in the buffer solution, the main reason for the growth retardation of the mutant strain is the in vivo CpRNase H cleavage DNA-rN_1-DNA/ DNA substrate, The activity is inhibited, leading to the incorporation of too much of a single ribose nucleic acid in the genome; while adding corresponding preferred metal ions in the growth medium will restore the activity of CpRNase H to make the mutation The addition of manganese ions in the culture medium affected the activity of CpRNase H in the bacteria. The results suggested that the manganese concentration in the bacteria was changed when the manganese was added to the culture medium, and we provided it. This was confirmed by the relevant data. The three strains of E. coli were cultured using a medium containing or without manganese, and measured by plasma emission spectroscopy (ICP-AES). The results showed that the concentration of manganese ion in the cell was increased by 5-14 times compared with that of the culture of the manganese-containing medium, and the activity of the intracellular RNase H was significantly affected, that is to promote the activity of CpRNase HIII and to inhibit the CpR. Nase HII activity. In addition, in order to verify that the added manganese in the medium will affect the expression of the CpRNase H-encoding gene, we choose to grow a mutant strain that is different in the presence of manganese and manganese and to extract its total RNA Real-time quantitative PCR was carried out. The relative quantitative analysis was carried out using the housekeeping gene gapA as the internal reference gene, and the results showed that the expression of the gene was not significantly different from the addition or absence of manganese in the culture medium, indicating that the manganese in the culture medium affected the growth of the mutant strain because of CpRNas. The activity of e H is inhibited, not CpRNase H The expression of the coding gene is blocked. The results of these experiments show that the two kinds of CpRNase H are the relationship of mutual assistance in the body: in the normal case, the function of CpRNase HII is performed to remove the single ribose nucleic acid which is incorporated in the genome, while in the condition of the ion fluctuation If, for example, the manganese content is high, the activity of CpRNase HII is inhibited and the activity of CpRNase HII is inhibited by CpRNase. The same function is exercised by HIII. Two types of RNase H are used by Chlamydia pneumoniae because of their complex living environment, and the two species of CpRNase H can be co-operative and complementary in a complex and changeable environment. The cell can maintain normal physiological metabolism. After confirming that CpRNase HIII also has the activity of the enzyme-cut DNA-rN _ 1-DNA/ DNA substrate, we further studied CpRNase HIII. The structure of this kind of substrate is not cut, and the importance of the substrate is identified by the in vitro biochemical measurement, the amino acid of the mutation is identified and the protein is cut, the importance of the substrate is identified, and the identification of the DNA-rN _ 1 by the CpRNase HIII is clarified by means of computer-aided methods such as the homologous mode construction, the molecular docking and the molecular dynamics simulation. -The mechanism of the DNA/ DNA substrate. The "GKG" motif of the CpRNase HIII was responsible for the identification of a single ribose nucleic acid, similar to the "GR (K) G" motif in the RNase HII, indicating that CpRNase HIII was adopted The substrate recognition mechanism similar to HII. The RNase HII/ H2 recognizes that the ribose nucleic acid also requires a highly conserved tyrosine (Y), but by analyzing the protein structure model obtained by the amino acid sequence and the homologous model, it is found that in the case of CpRNase HIII, There was no such Y residue in position, and by molecular dynamics simulation we found that the 94-bit serine (Ser94) of the CpRNase HIII and the deoxyribose nucleic acid 3--terminal of the DNA-rN _ 1-DNA/ DNA substrate form a stable hydrogen bond, and the deoxyribose core The acid is dragged by the acid of the ribose nucleic acid, while the DNA is allowed to The local conformation of the double helix has changed. This action appears to have performed the function of tyrosine in the RNase HII, and the aid of the "GKG" motif is accurate. In the guidance of the molecular simulation results, we carried out a series of biochemical experiments around Ser94 to prove that The importance of the Ser to the activity of the enzyme is given. The results of this study illustrate the CpRNa
【學(xué)位授予單位】:上海交通大學(xué)
【學(xué)位級(jí)別】:博士
【學(xué)位授予年份】:2012
【分類(lèi)號(hào)】:R374

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5 倪安平;崔京濤;汪曉巍;;4種國(guó)產(chǎn)大環(huán)內(nèi)酯類(lèi)抗菌藥物體外抗沙眼衣原體和肺炎衣原體作用的研究[A];中華醫(yī)學(xué)會(huì)第七次全國(guó)檢驗(yàn)醫(yī)學(xué)學(xué)術(shù)會(huì)議資料匯編[C];2008年

6 糜祖煌;秦玲;;肺炎衣原體套式PCR檢測(cè)及其臨床意義[A];第五屆全國(guó)優(yōu)生科學(xué)大會(huì)論文匯編[C];2000年

7 蘇世斌;林勤益;郭浩然;;臺(tái)灣成年人肺炎衣原體和新陳代謝癥候群之相關(guān)研究[A];第七屆海峽兩岸心血管科學(xué)研討會(huì)論文集[C];2009年

8 楊玲;吳移謀;周洲;鄧仲良;劉R

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