Ho Wing Sze, Ou Hong-Yu, Yeo Chew Chieng, Thong Kwai Lin
Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, 200030, Shanghai, China.
BMC Genomics. 2015 Mar 17;16(1):199. doi: 10.1186/s12864-015-1421-8.
Strains of Escherichia coli that are non-typeable by pulsed-field gel electrophoresis (PFGE) due to in-gel degradation can influence their molecular epidemiological data. The DNA degradation phenotype (Dnd(+)) is mediated by the dnd operon that encode enzymes catalyzing the phosphorothioation of DNA, rendering the modified DNA susceptible to oxidative cleavage during a PFGE run. In this study, a PCR assay was developed to detect the presence of the dnd operon in Dnd(+) E. coli strains and to improve their typeability. Investigations into the genetic environments of the dnd operon in various E. coli strains led to the discovery that the dnd operon is harboured in various diverse genomic islands.
The dndBCDE genes (dnd operon) were detected in all Dnd(+) E. coli strains by PCR. The addition of thiourea improved the typeability of Dnd(+) E. coli strains to 100% using PFGE and the Dnd(+) phenotype can be observed in both clonal and genetically diverse E. coli strains. Genomic analysis of 101 dnd operons from genome sequences of Enterobacteriaceae revealed that the dnd operons of the same bacterial species were generally clustered together in the phylogenetic tree. Further analysis of dnd operons of 52 E. coli genomes together with their respective immediate genetic environments revealed a total of 7 types of genetic organizations, all of which were found to be associated with genomic islands designated dnd-encoding GIs. The dnd-encoding GIs displayed mosaic structure and the genomic context of the 7 islands (with 1 representative genome from each type of genetic organization) were also highly variable, suggesting multiple recombination events. This is also the first report where two dnd operons were found within a strain although the biological implication is unknown. Surprisingly, dnd operons were frequently found in pathogenic E. coli although their link with virulence has not been explored.
Genomic islands likely play an important role in facilitating the horizontal gene transfer of the dnd operons in E. coli with 7 different types of islands discovered so far.
由于凝胶内降解而无法通过脉冲场凝胶电泳（PFGE）分型的大肠杆菌菌株会影响其分子流行病学数据。DNA降解表型（Dnd(+)）由dnd操纵子介导，该操纵子编码催化DNA硫代磷酸化的酶，使修饰后的DNA在PFGE电泳过程中易受氧化切割。在本研究中，开发了一种PCR检测方法来检测Dnd(+)大肠杆菌菌株中dnd操纵子的存在并提高其分型能力。对各种大肠杆菌菌株中dnd操纵子的遗传环境进行研究后发现，dnd操纵子存在于各种不同的基因组岛中。
通过PCR在所有Dnd(+)大肠杆菌菌株中检测到dndBCDE基因（dnd操纵子）。添加硫脲可使Dnd(+)大肠杆菌菌株使用PFGE的分型能力提高到100%，并且在克隆和基因多样的大肠杆菌菌株中均能观察到Dnd(+)表型。对来自肠杆菌科基因组序列的101个dnd操纵子进行基因组分析发现，同一细菌物种的dnd操纵子在系统发育树中通常聚集在一起。对52个大肠杆菌基因组的dnd操纵子及其各自的直接遗传环境进行进一步分析，共发现7种遗传组织类型，所有这些类型均与指定为dnd编码基因岛（dnd-encoding GIs）的基因组岛相关。dnd编码基因岛呈现镶嵌结构，7个岛（每种遗传组织类型有1个代表性基因组）的基因组背景也高度可变，表明发生了多次重组事件。这也是首次报道在一个菌株中发现两个dnd操纵子，尽管其生物学意义尚不清楚。令人惊讶的是，dnd操纵子在致病性大肠杆菌中经常被发现，尽管尚未探索它们与毒力的联系。
基因组岛可能在促进大肠杆菌中dnd操纵子的水平基因转移方面发挥重要作用，目前已发现7种不同类型的岛。
