Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution.
Identification of novel MITEs (miniature inverted-repeat transposable elements) in Coxiella burnetii: implications for protein and small RNA evolution.
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DOI：
10.1186/s12864-018-4608-y
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发表时间：
2018-04-11
期刊：
影响因子：
4.4
通讯作者：
Minnick MF
中科院分区：
文献类型：
--
作者：
Wachter S;Raghavan R;Wachter J;Minnick MF
伯内特柯克斯体是一种革兰氏阴性γ变形菌，也是Q热的人畜共患病原体。 C. burnetii的基因组包含大量的假基因和大量自私的遗传元件。 MITE（微型反向重复转座元件）是存在于生命各个领域的非自主转座子，被认为是失去转座酶功能的插入序列（IS）。与大多数转座元件 (TE) 一样，MITE 被认为通过插入和删除活动改变基因功能和表达，从而在进化中发挥积极作用。然而，有关细菌 MITE 的信息有限。我们描述了在 C.burnetii 的小非编码 RNA (sRNA) 研究过程中发现的两个 MITE 家族。两种 sRNA（Cbsr3 和 Cbsr13）被发现源自一个新的 MITE 家族，称为 QMITE1。另一种 sRNA CbsR16 被发现源自一个独立的新型 MITE 家族，称为 QMITE2。每个家族的成员在评估的菌株中出现约 50 次。 QMITE1 是一种典型的 300-400 bp 的 MITE，具有可变序列的短 (2-3 nt) 直接重复序列 (DR)，并且经常发现重叠注释的开放阅读框 (ORF)。此外，QMITE1 元件拥有 sigma-70 启动子，并且在多个位点具有转录活性，可能影响附近基因的表达。 QMITE2 较小 (150-190 bps)，但具有较长 (7-11 nt) 的可变序列 DR，主要存在于带注释的 ORF 和基因间区域的 3' 非翻译区中。 QMITE2 包含一个 GTAG 重复外源回文 (REP)，用作 IS1111 TE 插入的目标。 QMITE1 和 QMITE2 均表现出株间连锁和序列保守性，表明它们具有适应性并且在 C. burnetii 菌株分化之前就存在。我们发现了两个新的 C. burnetii MITE 家族。我们发现 MITE 作为 sRNA 的来源是新颖的。 QMITE2 具有独特的结构，有大版本或小版本，具有独特的 DR，显示菌株之间的连锁和序列保守性，从而可以跟踪基因组重排。假设 QMITE1 和 QMITE2 拷贝通过转录干扰和核糖核酸酶加工影响参与 DNA 修复和毒力的邻近基因的表达。本文的在线版本 (10.1186/s12864-018-4608-y) 包含补充材料，可供授权用户使用。
Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii’s genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities. However, information regarding bacterial MITEs is limited. We describe two MITE families discovered during research on small non-coding RNAs (sRNAs) of C. burnetii. Two sRNAs, Cbsr3 and Cbsr13, were found to originate from a novel MITE family, termed QMITE1. Another sRNA, CbsR16, was found to originate from a separate and novel MITE family, termed QMITE2. Members of each family occur ~ 50 times within the strains evaluated. QMITE1 is a typical MITE of 300-400 bp with short (2-3 nt) direct repeats (DRs) of variable sequence and is often found overlapping annotated open reading frames (ORFs). Additionally, QMITE1 elements possess sigma-70 promoters and are transcriptionally active at several loci, potentially influencing expression of nearby genes. QMITE2 is smaller (150-190 bps), but has longer (7-11 nt) DRs of variable sequences and is mainly found in the 3′ untranslated region of annotated ORFs and intergenic regions. QMITE2 contains a GTAG repetitive extragenic palindrome (REP) that serves as a target for IS1111 TE insertion. Both QMITE1 and QMITE2 display inter-strain linkage and sequence conservation, suggesting that they are adaptive and existed before divergence of C. burnetii strains. We have discovered two novel MITE families of C. burnetii. Our finding that MITEs serve as a source for sRNAs is novel. QMITE2 has a unique structure and occurs in large or small versions with unique DRs that display linkage and sequence conservation between strains, allowing for tracking of genomic rearrangements. QMITE1 and QMITE2 copies are hypothesized to influence expression of neighboring genes involved in DNA repair and virulence through transcriptional interference and ribonuclease processing. The online version of this article (10.1186/s12864-018-4608-y) contains supplementary material, which is available to authorized users.
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影响因子：
3.1
作者：
MOOS, A;HACKSTADT, T
通讯作者：
HACKSTADT, T
影响因子：
3.2
作者：
HOOVER, TA;VODKIN, MH;WILLIAMS, JC
通讯作者：
WILLIAMS, JC
影响因子：
3.2
作者：
Hicks, Linda D.;Warrier, Indu;Minnick, Michael F.
通讯作者：
Minnick, Michael F.
影响因子：
3.3
作者：
Delihas N
通讯作者：
Delihas N
影响因子：
64.5
作者：
FRIEDMAN, DI
通讯作者：
FRIEDMAN, DI