Natural History Museum, Department for Research and Collections, University of Oslo, 0318 Oslo, Norway.
BMC Evol Biol. 2010 Jan 4;10:3. doi: 10.1186/1471-2148-10-3.
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.
卫星 DNA 的序列、长度、复杂性和丰度差异巨大，使得难以将其功能归因于这种基因组成分。最近的研究表明，卫星 DNA 可以被转录，并参与调控染色质结构和基因表达。一些卫星 DNA，如多刺洞穴蟋蟀中的 pDo500 序列家族，在每个重复序列中都具有催化锤头（HH）核酶结构和活性。
我们评估了来自代表 12 种多刺洞穴蟋蟀的 38 个不同种群的 pDo500 序列中 HH 核酶的系统发育足迹。HH 区域比 pDo500 重复的非锤头（NHH）区域更保守。此外，茎比环更保守。在茎中，检测到了一些维持碱基配对的补偿性突变。HH 核酶的核心区域受到的核苷酸取代很少，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，大多数多刺洞穴蟋蟀种群和物种中都存在潜在活性的 HH 核酶。
系统发育足迹表明，pDo500 序列家族的 HH 区域在多刺洞穴蟋蟀中是为功能而选择的。然而，真核生物中 HH 核酶的功能作用尚不清楚。其可能的功能与 RNA 靶物的转切割有关，通过核糖核蛋白进行，以及对基因表达的调控。多刺洞穴蟋蟀中的 HH 核酶是否参与类似的功能仍有待研究。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锤头的催化效率。
