Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements.
Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements.
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DOI：
10.1186/1471-2180-9-242
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发表时间：
2009-11-26
期刊：
影响因子：
4.2
通讯作者：
Adley CC
中科院分区：
文献类型：
--
作者：
Ryan MP;Pembroke JT;Adley CC
整合接合元件（ICE）是微生物基因组可塑性的重要因素。在对 Ralstonia pickettii 12J 基因组进行生物信息学搜索时发现了与 ICE Tn4371 相关的元件。对该元素进行了分析，并进一步搜索其他元素。设计了一种基于该支架的 PCR 方法来检测和表征该类型的新元件，并对 58 个 Ralstonia pickettii 和 Ralstonia insidiosa 菌株的培养物保藏进行了分析，以确定该元件的存在。细菌基因组的比较序列分析揭示了几种β和γ-变形菌的基因组中存在许多未表征的Tn4371样ICE。这些元件的大小、GC 含量、推定功能各不相同，并且具有质粒和噬菌体样序列的马赛克样结构，这是 Tn4371 样 ICE 的典型特征。这些元素是在对 GenBank 数据库进行彻底搜索后发现的。这些元素存在于 Ralstonia、Delftia、Acidovorax、Bordetella、Comamonas、Acidovorax、Congregibacter、Shewanella、Pseudomonas Stenotropicomonas、Thioalkalivibrio sp. 中。 HL-EbGR7、偏单胞菌、伯克霍尔德杆菌和迪亚弗罗杆菌属。共享一个共同的脚手架。设计了一种 PCR 方法（基于 Ralstonia pickettii 12J 基因组中检测到的 Tn4371 样元件）来检测和表征该类型的新元件。本研究中发现的所有元素都拥有共同的核心基因支架，但包含不同的辅助基因。建议为 Tn4371 系列 ICE 采用新的统一命名法。使用实验室纯化水中两种不同的皮氏拉尔斯顿氏菌分离物中描述的新型 PCR 方法，发现并表征了两种新型 Tn4371 ICE。
Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several β and γ- Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371- like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.
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影响因子：
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