Genome structural variation in Escherichia coli O157:H7.
Genome structural variation in Escherichia coli O157:H7.
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DOI：
10.1099/mgen.0.000682
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发表时间：
2021-11
影响因子：
3.9
通讯作者：
Gally DL
中科院分区：
文献类型：
--
作者：
Fitzgerald SF;Lupolova N;Shaaban S;Dallman TJ;Greig D;Allison L;Tongue SC;Evans J;Henry MK;McNeilly TN;Bono JL;Gally DL
人类人兽共患病原体 大肠杆菌 O157：H7是由其广泛的原噬菌体库定义的，包括编码滋贺毒素的那些，志贺毒素是负责诱导人类危及生命的病理学的因子。除了引入可以有助于菌株毒力的基因之外，原噬菌体还可以通过同源重组产生大染色体重排（LCR）。这项工作检查了O157：H7血清型的主要谱系中LCR的类型和频率。我们证明LCR是所有谱系中基因组变异的主要来源， E.杆菌 O157：H7，并通过使用光学作图和Oxford Nanopore长读测序，证明LCR是从单个菌落开始在实验室培养物中产生的，并且这些变体可以从定殖牛中回收。LCR偏向于基因组的末端区域，并且由共享与重组活性相关的大的序列同源性区域的特异性原噬菌体限制。RNA转录谱和特定结构变体的表型分析表明，重要的毒力表型，如志贺毒素的生产，3型分泌和运动性可以受到LCR的影响。总的来说， E.杆菌 随着时间的推移，O157：H7已经获得了多个原噬菌体区域，这些区域不断产生基因组的结构变体。这些发现提出了重要的问题，这种原噬菌体介导的基因组偶然性的意义，以提高环境之间的适应性。
The human zoonotic pathogen Escherichia coli O157:H7 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans. As well as introducing genes that can contribute to the virulence of a strain, prophage can enable the generation of large-chromosomal rearrangements (LCRs) by homologous recombination. This work examines the types and frequencies of LCRs across the major lineages of the O157:H7 serotype. We demonstrate that LCRs are a major source of genomic variation across all lineages of E. coli O157:H7 and by using both optical mapping and Oxford Nanopore long-read sequencing prove that LCRs are generated in laboratory cultures started from a single colony and that these variants can be recovered from colonized cattle. LCRs are biased towards the terminus region of the genome and are bounded by specific prophages that share large regions of sequence homology associated with the recombinational activity. RNA transcriptional profiling and phenotyping of specific structural variants indicated that important virulence phenotypes such as Shiga-toxin production, type-3 secretion and motility can be affected by LCRs. In summary, E. coli O157:H7 has acquired multiple prophage regions over time that act to continually produce structural variants of the genome. These findings raise important questions about the significance of this prophage-mediated genome contingency to enhance adaptability between environments.
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DOI：
10.1093/bioinformatics/btp097
发表时间：
2009-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Stewart AC;Osborne B;Read TD
通讯作者：
Read TD
影响因子：
5.8
作者：
Dallman, Timothy;Ashton, Philip;Grant, Kathie
通讯作者：
Grant, Kathie
影响因子：
9.4
作者：
Buvens, Glenn;De Gheldre, Yves;Pierard, Denis
通讯作者：
Pierard, Denis
影响因子：
4.4
作者：
Chen, Chun;Lewis, Carrie R.;Dudley, Edward G.
通讯作者：
Dudley, Edward G.
影响因子：
3.9
作者：
Cowley LA;Dallman TJ;Fitzgerald S;Irvine N;Rooney PJ;McAteer SP;Day M;Perry NT;Bono JL;Jenkins C;Gally DL
通讯作者：
Gally DL