在恶臭假单胞菌和比较基因组挖掘中发现新型 Tn4371-ICE 样元件。
Novel Tn4371-ICE like element in Ralstonia pickettii and genome mining for comparative elements.
机构信息
Microbiology Laboratory, Department of Chemical and Environmental Sciences, University of Limerick, Limerick, Ireland.
出版信息
BMC Microbiol. 2009 Nov 26;9:242. doi: 10.1186/1471-2180-9-242.
BACKGROUND
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.
RESULTS
Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several beta and gamma- 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.
CONCLUSION
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.
背景
整合共轭元件（ICEs）是微生物基因组可塑性的重要因素。在对 Ralstonia pickettii 12J 基因组的生物信息学搜索中发现了一个与 ICE Tn4371 相关的元件。对该元件进行了分析，并进一步进行了其他元件的搜索。设计了一种 PCR 方法，基于该支架和一个包含 58 株 Ralstonia pickettii 和 Ralstonia insidiosa 菌株的培养物集，来检测和表征这种新型元件。
结果
对细菌基因组的比较序列分析显示，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、可能的功能各不相同，并且具有质粒样和噬菌体样序列的镶嵌结构，这是 Tn4371 样 ICE 的典型特征。这些元件是在对 GenBank 数据库进行全面搜索后发现的。在 Ralstonia、Delftia、Acidovorax、Bordetella、Comamonas、Acidovorax、Congregibacter、Shewanella、Pseudomonas stenotrophomonas、Thioalkalivibrio sp. HL-EbGR7、Polaromonas、Burkholderia 和 Diaphorobacter sp. 中发现的元件共享一个共同的支架。设计了一种 PCR 方法（基于在 Ralstonia pickettii 12J 基因组中检测到的 Tn4371 样元件）来检测和表征这种新型元件。
结论
本研究中发现的所有元件都具有一个共同的核心基因支架，但包含不同的辅助基因。建议对 Tn4371 家族的 ICE 采用新的统一命名法。使用描述的新 PCR 方法，在来自实验室纯化水的两个不同的 Ralstonia pickettii 分离株中发现并表征了两个新的 Tn4371 样 ICE。
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