Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.
Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.
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DOI：
10.1371/journal.pgen.1007410
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发表时间：
2018-06
期刊：
影响因子：
4.5
通讯作者：
Hanage WP
中科院分区：
文献类型：
--
作者：
Cowley LA;Petersen FC;Junges R;Jimson D Jimenez M;Morrison DA;Hanage WP
遗传转化模式生物肺炎链球菌中的同源重组被认为在该病原体的适应和进化中是重要的。虽然有能力的肺炎球菌能够复制添加到实验室培养物中的DNA，但在这些条件下，多个kb的大规模转移是罕见的。我们使用全基因组测序（WGS）来绘制重组体中的转移，这些转移是由感受态细胞与非感受态“靶”细胞接触引起的，使用具有已知基因组的菌株，通过总共约16，000个SNP来区分。设计用于探索环境对大规模重组事件的影响的实验使用饱和的纯化供体DNA、Millipore过滤器上的短期细胞聚集体和成熟的生物膜混合培养物。每个环境的22个重组体的WGS映射了重组体和供体之间相同但不是受体之间相同的所有SNP。平均重组事件的大小被发现是显着更大的细胞间接触培养物（4051 bp的过滤器组装和3938 bp的生物膜共培养与1815 bp的饱和DNA）。通过20个重组事件，高达5.8%的基因组被转移到单个受体，其中最大的单个事件整合了29，971bp。我们还发现，一些重组事件是成簇的，这些簇更可能发生在细胞与细胞接触的环境中，并且它们导致基因连锁的显著增加，远至60，000bp。我们的结论是，肺炎球菌通过同源重组的演变是更有可能发生在一个更大的规模在环境中，允许细胞与细胞接触。细菌基因重组的频率远低于人类，基因或性状更直接地与单个细菌亲本细胞相关联，而不是与参与有性繁殖的两个亲本相关联。然而，细菌偶尔也会以同源重组的形式发生性行为，即通过吸收外部DNA并将其整合到它们的基因组中。这种情况发生的频率远远低于人类世代的有性生殖，但这是细菌进行“水平基因转移”的一种已知方式。这意味着基因可以在不被遗传的情况下获得。在这项研究中，我们表明，这种形式的水平基因转移更可能发生在某些环境中的肺炎链球菌比其他人。特别是，我们表明，这是更有可能发生在环境中，密切反映鼻咽，这是自然栖息地的S。肺炎。
Homologous recombination in the genetic transformation model organism Streptococcus pneumoniae is thought to be important in the adaptation and evolution of this pathogen. While competent pneumococci are able to scavenge DNA added to laboratory cultures, large-scale transfers of multiple kb are rare under these conditions. We used whole genome sequencing (WGS) to map transfers in recombinants arising from contact of competent cells with non-competent ‘target’ cells, using strains with known genomes, distinguished by a total of ~16,000 SNPs. Experiments designed to explore the effect of environment on large scale recombination events used saturating purified donor DNA, short-term cell assemblages on Millipore filters, and mature biofilm mixed cultures. WGS of 22 recombinants for each environment mapped all SNPs that were identical between the recombinant and the donor but not the recipient. The mean recombination event size was found to be significantly larger in cell-to-cell contact cultures (4051 bp in filter assemblage and 3938 bp in biofilm co-culture versus 1815 bp with saturating DNA). Up to 5.8% of the genome was transferred, through 20 recombination events, to a single recipient, with the largest single event incorporating 29,971 bp. We also found that some recombination events are clustered, that these clusters are more likely to occur in cell-to-cell contact environments, and that they cause significantly increased linkage of genes as far apart as 60,000 bp. We conclude that pneumococcal evolution through homologous recombination is more likely to occur on a larger scale in environments that permit cell-to-cell contact. Bacteria shuffle their genes far less often than humans do and genes or traits are more directly linked with the singular bacterial parent cell rather than the two parents that are involved in sexual reproduction. However, bacteria do occasionally have sex in the form of homologous recombination by taking up external DNA and incorporating it into their genomes. This happens far less regularly than sexual reproduction happens in human generations but is a known way that bacteria undergo ‘Horizontal gene transfer’. This means that genes can be acquired without being inherited. In this study we show that this form of horizontal gene transfer is more likely to happen in certain environments over others in Streptococcus pneumoniae. In particular, we show that this is more likely to happen in environments that closely mirror the nasopharynx which is the natural habitat of S. pneumoniae.
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影响因子：
5.4
作者：
Croucher NJ;Hanage WP;Harris SR;McGee L;van der Linden M;de Lencastre H;Sá-Leão R;Song JH;Ko KS;Beall B;Klugman KP;Parkhill J;Tomasz A;Kristinsson KG;Bentley SD
通讯作者：
Bentley SD
影响因子：
4.5
作者：
Croucher NJ;Kagedan L;Thompson CM;Parkhill J;Bentley SD;Finkelstein JA;Lipsitch M;Hanage WP
通讯作者：
Hanage WP
影响因子：
9.4
作者：
Andam, Cheryl P.;Mitchell, Patrick K.;Hanage, William P.
通讯作者：
Hanage, William P.
影响因子：
6.7
作者：
Croucher, Nicholas J.;Harris, Simon R.;Bentley, Stephen D.
通讯作者：
Bentley, Stephen D.
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.