Genome-wide detection of conservative site-specific recombination in bacteria.
Genome-wide detection of conservative site-specific recombination in bacteria.
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DOI：
10.1371/journal.pgen.1007332
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发表时间：
2018-04
期刊：
影响因子：
4.5
通讯作者：
Camilli A
中科院分区：
文献类型：
--
作者：
Sekulovic O;Mathias Garrett E;Bourgeois J;Tamayo R;Shen A;Camilli A
克隆细菌群体产生基因组和表型异质性的能力被认为对许多细菌和病原菌非常重要。一种有助于多样性形成的常见机制依赖于通常称为保守位点特异性重组的过程中小基因组DNA片段的倒位。已知这种现象发生在几种细菌谱系中，然而由于缺乏保守特征，它仍然非常难以识别。在这里，我们报告了一个易于实现的方法，基于高通量配对末端测序的全基因组检测保守位点特异性重组的单核苷酸水平上。我们证明了该方法的有效性，通过成功地检测几个新的倒置网站在流行性分离的肠道病原体艰难梭菌。使用实验方法，我们验证了所有检测到的网站在C的反转潜力。difficile并量化其在体外指数和静止生长期间的患病率。此外，我们证明了主重组酶RecV负责一些但不是所有可逆位点的反转。使用荧光基因报告系统，我们表明，至少有一个基因从一个双组分系统位于旁边的可逆网站的开关模式，让人想起相位变化的表达。我们通过挖掘209个公开的测序数据集进一步证明了我们方法的适用性，并表明保守的位点特异性重组在细菌领域很常见，但在某些谱系中似乎不存在。最后，我们表明，与反转位点相关的基因内容是多样的，超越了传统上描述的表面组件。总的来说，我们的方法为检测细菌中的保守位点特异性重组提供了一个强大的平台，并为全球探索这一重要现象开辟了新的途径。许多生态环境中的细菌都面临着不可预测的环境波动的共同挑战。快速适应挑战性条件对于细菌存活和成功增殖至关重要。通过DNA倒位改变基因表达是许多细菌物种采用的一种常见机制，其允许快速产生具有改变的适应性的不同亚群。这些系统的特性超出了一些经典的情况下是滞后的，由于难以准确地检测到这样的反转的人口水平。在这项研究中，我们实现了一个易于使用的方法来检测细菌基因组中的小基因组倒位。我们成功地应用我们的方法来检测已知的和新的倒位位点在C。很难我们进一步表明，所有检测到的网站进行反转，并存在于不同的频率在体外。几个位点的倒位似乎依赖于主重组酶RecV。我们将我们的分析扩展到大量的细菌和古细菌菌株，并表明我们的方法可以在全球范围内应用于检测小的基因组倒位。总之，这项研究提高了描述这一重要现象的能力。
The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria. One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to as conservative site-specific recombination. This phenomenon is known to occur in several bacterial lineages, however it remains notoriously difficult to identify due to the lack of conserved features. Here, we report an easy-to-implement method based on high-throughput paired-end sequencing for genome-wide detection of conservative site-specific recombination on a single-nucleotide level. We demonstrate the effectiveness of the method by successfully detecting several novel inversion sites in an epidemic isolate of the enteric pathogen Clostridium difficile. Using an experimental approach, we validate the inversion potential of all detected sites in C. difficile and quantify their prevalence during exponential and stationary growth in vitro. In addition, we demonstrate that the master recombinase RecV is responsible for the inversion of some but not all invertible sites. Using a fluorescent gene-reporter system, we show that at least one gene from a two-component system located next to an invertible site is expressed in an on-off mode reminiscent of phase variation. We further demonstrate the applicability of our method by mining 209 publicly available sequencing datasets and show that conservative site-specific recombination is common in the bacterial realm but appears to be absent in some lineages. Finally, we show that the gene content associated with the inversion sites is diverse and goes beyond traditionally described surface components. Overall, our method provides a robust platform for detection of conservative site-specific recombination in bacteria and opens a new avenue for global exploration of this important phenomenon. Bacteria in many ecological niches experience a common challenge in the form of unpredictable environmental fluctuations. Rapid adaptation to challenging conditions is important for bacterial survival and successful proliferation. Altering gene expression through DNA inversion is a common mechanism adopted by many bacterial species that allows quick generation of distinct subpopulations with altered fitness. The characterization of these systems beyond a few classical cases is lagging due to the difficulties to accurately detect such inversion on a population level. In this study, we implement an easy-to-use method for detecting small genomic inversions in bacterial genomes. We successfully applied our approach to detect known and novel inversion sites in C. difficile. We further show that all detected sites undergo inversion and exist at different frequencies in vitro. The inversion of several sites seems dependent on the master recombinase RecV. We expand our analysis to a large collection of bacterial and archaeal strains and show that our method can be globally applied for detection of small genomic inversions. Taken together, this study advances the ability to characterize this important phenomenon.
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影响因子：
6.7
作者：
Chopra-Dewasthaly R;Spergser J;Zimmermann M;Citti C;Jechlinger W;Rosengarten R
通讯作者：
Rosengarten R
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.7
作者：
Dziewanowska K;Settles M;Hunter S;Linquist I;Schilkey F;Hartzell PL
通讯作者：
Hartzell PL
DOI：
10.1038/nrmicro2145
发表时间：
2009-07
期刊：
Nature reviews. Microbiology
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.7
作者：
Blomfield, Ian C.
通讯作者：
Blomfield, Ian C.