Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae.
Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae.
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DOI：
10.1534/g3.113.009597
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发表时间：
2014-04-16
期刊：
影响因子：
--
通讯作者：
Redfield RJ
中科院分区：
文献类型：
--
作者：
Mell JC;Lee JY;Firme M;Sinha S;Redfield RJ
天然感受态细菌物种主动摄取环境DNA，并可通过同源重组将其整合到其染色体中。这可以将遗传变异从环境DNA带到受体染色体，通常在多个长的“供体”片段中。在这里，我们报告了96个实验室流感嗜血杆菌菌株的菌落的基因组测序结果，该菌株已通过实验由来自分歧的临床分离株的DNA转化。供体片段平均为6.9 kb（跨越几个基因），并聚集成约19.5 kb的重组区。单个菌落已替换了0.1 - 3.2%的染色体，并且约1/3的所有供体特异性单核苷酸变体存在于至少一个重组体中。我们发现，核苷酸的分歧并没有明显限制的重组域的位置，虽然有小，但显着减少重组断点的分歧。虽然插入缺失偶尔转化为较长的重组区的一部分，但它们在断点处很常见，这表明插入缺失通常会阻止链交换的进展。一些菌落具有重组区，其中变体位置包含供体和受体等位基因的混合物。这些束聚集在复制起点周围，并被解释为原始转化细胞中异源双链体分离的结果。最后，中试实验证明了自然转化在遗传解剖自然表型变异中的实用性。我们讨论了我们的研究结果的背景下，合并实验和人口遗传学的方法，使细菌基因转移的一个更全面的了解。
Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long “donor” segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer.
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影响因子：
12.3
作者：
Hogg JS;Hu FZ;Janto B;Boissy R;Hayes J;Keefe R;Post JC;Ehrlich GD
通讯作者：
Ehrlich GD
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC
影响因子：
3.2
作者：
LACKS, S;NEUBERGER, M
通讯作者：
NEUBERGER, M
影响因子：
3.6
作者：
Krueger, Nora-Johanna;Stingl, Kerstin
通讯作者：
Stingl, Kerstin
DOI：
10.1093/bioinformatics/btq413
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Guy L;Kultima JR;Andersson SG
通讯作者：
Andersson SG