Helicobacter Pylori's plasticity zones are novel transposable elements.
Helicobacter Pylori's plasticity zones are novel transposable elements.
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DOI：
10.1371/journal.pone.0006859
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发表时间：
2009-09-03
期刊：
影响因子：
3.7
通讯作者：
Berg DE
中科院分区：
文献类型：
--
作者：
Kersulyte D;Lee W;Subramaniam D;Anant S;Herrera P;Cabrera L;Balqui J;Barabas O;Kalia A;Gilman RH;Berg DE
只有在细菌物种的某些菌株中存在的基因才能强烈影响细胞表型和进化潜力。通过比较前两个幽门螺杆菌基因组序列(菌株26695和J99)，发现了一个似乎特别富含菌株特有基因的片段，并将其命名为“可塑性带”。我们通过在另外五个螺杆菌菌株中对可塑性区域进行测序，确定它们在其他菌株中的位置，并在最近公布的基因组序列中识别它们，来研究可塑性区域的性质和进化。它们以离散的单位出现，插入在许多染色体上，通常由5‘AAGAATG的直接重复序列组成，在其他菌株中，该序列通常也以一个拷贝的形式存在于未被占据的位置。这表明塑性区是可转位的元素，被称为TnPZ。每个全长TnPZ包含一个IV型蛋白分泌基因簇(TFS3)、一个酪氨酸重组酶家族基因(“xerT”)、一个编码带有解旋酶和≥甲基酶结构域的蛋白质的大的(DNA2800密码子)orf，以及额外的与已知功能基因没有同源性的ORF。发现几种不同的TnPZ类型在基因排列或DNA序列上存在差异。我们的分析还表明，首次发现的塑性区(在菌株26695和J99中)是TnPZ残基的复杂马赛克，由TnPZ多次插入形成，以及自发和转座元件介导的缺失。使用实验室产生的缺失进行的测试表明，TnPZ对活性并不是必不可少的，但发现了一种TnPZ，它在小鼠感染期间对细菌生长起到了定量作用，另一种TnPZ影响了细胞培养中促炎症细胞因子的合成。我们认为可塑性区域基因存在于共轭转座子(TnPZ)或其残留物中，TnPZ插入由XerT重组酶介导，某些TnPZ基因影响细菌的表型和适合性。
Genes present in only certain strains of a bacterial species can strongly affect cellular phenotypes and evolutionary potentials. One segment that seemed particularly rich in strain-specific genes was found by comparing the first two sequenced Helicobacter pylori genomes (strains 26695 and J99) and was named a “plasticity zone”. We studied the nature and evolution of plasticity zones by sequencing them in five more Helicobacter strains, determining their locations in additional strains, and identifying them in recently released genome sequences. They occurred as discrete units, inserted at numerous chromosomal sites, and were usually flanked by direct repeats of 5′AAGAATG, a sequence generally also present in one copy at unoccupied sites in other strains. This showed that plasticity zones are transposable elements, to be called TnPZs. Each full length TnPZ contained a cluster of type IV protein secretion genes (tfs3), a tyrosine recombinase family gene (“xerT”), and a large (≥2800 codon) orf encoding a protein with helicase and DNA methylase domains, plus additional orfs with no homology to genes of known function. Several TnPZ types were found that differed in gene arrangement or DNA sequence. Our analysis also indicated that the first-identified plasticity zones (in strains 26695 and J99) are complex mosaics of TnPZ remnants, formed by multiple TnPZ insertions, and spontaneous and transposable element mediated deletions. Tests using laboratory-generated deletions showed that TnPZs are not essential for viability, but identified one TnPZ that contributed quantitatively to bacterial growth during mouse infection and another that affected synthesis of proinflammatory cytokines in cell culture. We propose that plasticity zone genes are contained in conjugative transposons (TnPZs) or remnants of them, that TnPZ insertion is mediated by XerT recombinase, and that some TnPZ genes affect bacterial phenotypes and fitness.
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DOI：
10.1073/pnas.0808424106
发表时间：
2009-01-27
影响因子：
11.1
作者：
Dillehay, Tom D.
通讯作者：
Dillehay, Tom D.
影响因子：
4.5
作者：
Eppinger, Mark;Baar, Claudia;Schuster, Stephan C.
通讯作者：
Schuster, Stephan C.
影响因子：
64.5
作者：
Barabas, Orsolya;Ronning, Donald R.;Dyda, Fred
通讯作者：
Dyda, Fred
影响因子：
64.8
作者：
Alm, RA;Ling, LSL;Trost, TJ
通讯作者：
Trost, TJ
影响因子：
11.4
作者：
Atmakuri, Krishnamohan;Cascales, Eric;Christie, Peter J.
通讯作者：
Christie, Peter J.