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首页> 外文期刊>BMC Genomics >GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes
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GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes

机译：GTAG和CGTC标记的回文DNA在原核生物中重复

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Background REPs (Repetitive Extragenic Palindromes) are small (20–40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. Results We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in multiple species. Conclusions CGTC REPs apparently lack a dedicated transposase. Future work will clarify whether these elements may be mobilized by RAYTs or other transposases, and assess if de-novo formation of either GTAG or CGTC repeats type still occurs.
机译：背景REP（重复性外源回文）是在某些原核基因组中以高拷贝形式发现的小回文重复（20–40 bp），据推测在DNA超螺旋，转录终止，mRNA稳定化中起作用。结果我们监测了原核基因组中的大量REP元件，发现大多数可以分为两个大的DNA超家族，因为它们的一端具有适合GTAG或CGTC共有的未配对基序。已在8个不同门的80多个物种中识别出带标记的REP。 GTAG和CGTC重复分别主要存在于变形杆菌的γ和α分裂的微生物中。然而，在更深的分支门如蓝细菌和扁平菌中鉴定两个超家族的成员支持了REPs是细菌染色体的老组成部分的观点。根据序列内容和整体结构，已分别将GTAG和CGTC重复序列分配给24和4个家族。其中，有些是特定物种的，有些则居住在多个物种中，并且几种生物包含不同的REP类型。在许多家庭中，大多数单元在相反的方向上彼此靠近，并且可能会折叠成更大的二级结构。在不同的富含REP的基因组中，重复序列主要位于单向和会聚转录的ORF之间。 REP主要位于编码区的下游，并且许多REP可能被转录并充当RNA元件。位于基因内部的REP已在几种物种中鉴定。许多位于复制和整体基因组修复基因之内。假设GTAG REPs是被称为RAYTs（REP相关酪氨酸转座酶）的特定转座酶动员的微型转座子。 RAYT基因的侧翼是GTAG重复序列或与GTAG重复序列无关的长末端反向重复序列（TIR）。已在多种物种中确定了中等数量的TIR家族。结论CGTC REPs显然缺乏专用的转座酶。未来的工作将阐明RAYT或其他转座酶是否可以调动这些元件，并评估是否仍会发生GTAG或CGTC重复类型的新型形成。

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