Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).
Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).
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DOI：
10.1186/1471-2148-10-3
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发表时间：
2010-01-04
影响因子：
3.4
通讯作者：
Bachmann L
中科院分区：
文献类型：
--
作者：
Martinsen L;Johnsen A;Venanzetti F;Bachmann L
卫星DNA在序列、长度、复杂性和丰度上的巨大差异使得很难将任何功能归因于这一基因组组成部分。近年来的研究表明，卫星DNA可以转录并参与染色质结构和基因表达的调控。一些卫星dna，如洞蟋蟀的pDo500序列家族，在每个重复序列中都嵌入了催化锤头（HH）核酶结构和活性。我们评估了来自12个种类的38个不同种群的pDo500序列中HH核酶的系统发育足迹。HH区明显比pDo500重复序列的非锤头区（NHH）保守。此外，茎比环更保守。在茎中，检测到一些维持碱基配对的补偿性突变。HH核酶的核心区域受到很少的核苷酸取代的影响，在198个序列中仅改变了一次切割位置。HH序列的RNA折叠表明，在大多数Dolichopoda种群和物种中都可以发现潜在的活性HH核酶。系统发育足迹表明，pDo500序列家族的HH区在洞蟋蟀中被选中发挥功能。然而，HH核酶在真核生物中的功能作用尚不清楚。可能的功能与核糖核蛋白对RNA靶标的反式切割和基因表达的调节有关。Dolichopoda的HH核酶是否参与类似的功能还有待研究。未来的研究需要证明观察到的核苷酸变化和进化约束如何影响双髻鲨的催化效率。
The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat. We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.
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影响因子：
4.1
作者：
Allegrucci, G;Todisco, V;Sbordoni, V
通讯作者：
Sbordoni, V
影响因子：
7.8
作者：
EPSTEIN, LM;MAHON, KA;GALL, JG
通讯作者：
GALL, JG
影响因子：
11.4
作者：
Martens, JHA;O'Sullivan, RJ;Jenuwein, T
通讯作者：
Jenuwein, T
影响因子：
5.3
作者：
Ferbeyre, G;Smith, JM;Cedergren, R
通讯作者：
Cedergren, R
DOI：
10.1016/s0169-328x(98)00343-x
发表时间：
1999-03-20
期刊：
MOLECULAR BRAIN RESEARCH
影响因子：
--
作者：
Komine, Y;Tanaka, NK;Yamamori, T
通讯作者：
Yamamori, T