Stem Loop Sequences Specific to Transposable Element IS605 Are Found Linked to Lipoprotein Genes in Borrelia Plasmids
Stem Loop Sequences Specific to Transposable Element IS605 Are Found Linked to Lipoprotein Genes in Borrelia Plasmids
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DOI：
10.1371/journal.pone.0007941
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发表时间：
2009-11-20
期刊：
影响因子：
3.7
通讯作者：
Delihas, Nicholas
中科院分区：
文献类型：
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作者：
Delihas, Nicholas
背景：疏螺旋体属的质粒是动态结构，含有大量重复基因、基因片段和基因融合体。此外，转座元件 IS605/200 家族以及该 IS 元件的简并形式也很普遍。在幽门螺杆菌中，IS605 转座酶基因的侧翼区域包含折叠成相同小茎环的序列。这些在单链 DNA 水平上发挥转座作用。方法/主要发现：在此报告的工作中，生物信息学技术用于扫描疏螺旋体质粒基因组中的 IS605 转座元件特异性茎环序列。在转座酶基因的左右侧翼区域发现了两个变异的茎环基序。这两个基序似乎分散在质粒基因组中，并且被发现是“独立的”并且在系统发育上是保守的，没有相关的 IS605 转座酶基因或相邻的侧翼序列。重要的是，在脂蛋白基因（PFam12 和 PFam60）的 3' 端也发现了 IS605 特异性茎环序列，但是左侧和右侧序列似乎发展了自己的进化模式。脂蛋白基因连接的左侧茎环序列保持了IS605 茎环基序存在于直向同源物中，但仅在 RNA 水平上。这些突变表明变异体折叠成包含摆动非沃森-克里克 G-U 碱基配对的 RNA 型茎环。同源物的比较表明，IS605 茎环基序迅速消失，但其内部似乎出现了更复杂的二级结构。结论/意义：转座元件 IS605 特异的茎环序列存在于缺乏转座酶基因的质粒区域，并且显着地被发现与疏螺旋体质粒中的脂蛋白基因相关。研究结果表明，IS605 茎环序列是多方面的，并且在转座元件消失时在进化过程中选择性保守。
Background: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level.Methodology/Principal Findings: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing'' and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60), however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place.Conclusions/Significance: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in an RNA format. The findings show that IS605 stem loop sequences are multifaceted and are selectively conserved during evolution when the transposable element dissipates.