Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene)
Insights into the Origin of Clostridium botulinum Strains: Evolution of Distinct Restriction Endonuclease Sites in rrs (16S rRNA gene)
复制标题
DOI：
10.1007/s12088-015-0514-z
复制
发表时间：
2015-06-01
影响因子：
3
通讯作者：
Kalia, Vipin Chandra
中科院分区：
文献类型：
--
作者：
Bhushan, Ashish;Mukherjee, Tanmoy;Kalia, Vipin Chandra
由于存在 9-22 个 rrs（16S rRNA 基因）拷贝，导致肉毒梭菌菌株的多样性分析变得复杂。需要挖掘遗传标记来识别非常密切相关的菌株。 13 个肉毒梭菌菌株 212 rrs 的核苷酸序列的多重比对揭示了基因组内和基因组间的异质性。 rrs 中的低基因组异质性在菌株 230613、Alaska E43、Okra、Eklund 17B、Langeland、657、Kyoto、BKT015925 和 Loch Maree 中很明显。最异质的 rrs 序列是肉毒梭菌菌株 ATCC 19397、Hall、H04402065 和 ATCC 3502 的序列。使用 137 种 II 型限制性内切核酸酶 (RE) 可以观察到这些 rrs 序列的计算机限制性图谱。这些 RE 位点的核苷酸变化 (NC) 导致出现不同的额外位点，以及某些其他位点的丢失。在 rrs 基因的不同位置记录了由于 NC 导致的 RE 位点的从头出现。 Loch Maree 肉毒杆菌和 657 的 rrs 中的核苷酸转变 A > G 分别导致产生 4 个和 10 个不同的 RE 位点。转变 A > G、G > A 和 T > C 导致 RE 位点丢失。仔细阅读整个 NC 和肉毒杆菌菌株 rrs 的计算机 RE 图谱，可以深入了解其进化。基于 rrs RE 消化模式的菌株分离通过涉及 6 个管家基因的分支分析得到验证：dnaN、gyrB、metG、prfA、pyrG 和 Rho。
Diversity analysis of Clostridium botulinum strains is complicated by high microheterogeneity caused by the presence of 9-22 copies of rrs (16S rRNA gene). The need is to mine genetic markers to identify very closely related strains. Multiple alignments of the nucleotide sequences of the 212 rrs of 13 C. botulinum strains revealed intra- and inter-genomic heterogeneity. Low intragenomic heterogeneity in rrs was evident in strains 230613, Alaska E43, Okra, Eklund 17B, Langeland, 657, Kyoto, BKT015925, and Loch Maree. The most heterogenous rrs sequences were those of C. botulinum strains ATCC 19397, Hall, H04402065, and ATCC 3502. In silico restriction mapping of these rrs sequences was observable with 137 type II Restriction endonucleases (REs). Nucleotide changes (NC) at these RE sites resulted in appearance of distinct and additional sites, and loss in certain others. De novo appearances of RE sites due to NC were recorded at different positions in rrs gene. A nucleotide transition A > G in rrs of C. botulinum Loch Maree and 657 resulted in the generation of 4 and 10 distinct RE sites, respectively. Transitions A > G, G > A, and T > C led to the loss of RE sites. A perusal of the entire NC and in silico RE mapping of rrs of C. botulinum strains provided insights into their evolution. Segregation of strains on the basis of RE digestion patterns of rrs was validated by the cladistic analysis involving six house keeping genes: dnaN, gyrB, metG, prfA, pyrG, and Rho.