Collins L J, Moulton V, Penny D
Institute of Molecular BioSciences, Massey University, Private Bag 11222 Palmerston North, New Zealand.
J Mol Evol. 2000 Sep;51(3):194-204. doi: 10.1007/s002390010081.
Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison of secondary structures support the identity of an RNase P-like sequence in the maize chloroplast genome. Overall, it is concluded that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned with confidence.
通过评估二级结构来确定催化RNA分子之间的进化关系，这些分子亲缘关系极远，几乎无法比对。核糖核蛋白核糖核酸酶P（P）和核糖核酸酶MRP（MRP）由于功能和二级结构上的相似性，被认为在进化上有关联。然而，它们的RNA序列无法可靠地比对，这导致从序列推断的任何进化树都存在不确定性。我们报告了几种利用二级结构推断进化树的方法，并强调了定量测试，以证明进化信息可以被恢复。对于P和MRP，考虑了三种关联性假设。第一种是MRP在早期真核生物中源自P。第二种是MRP源自早期内共生体中的P。第三种是P和MRP都在RNA世界中进化（此后原核生物中不再需要MRP）。对pRNA和mrpRNA二级结构的定量比较发现，MRP起源于细胞器的可能性不大。此外，二级结构的比较支持了玉米叶绿体基因组中类似核糖核酸酶P序列的一致性。总体而言，得出的结论是，即使对于无法可靠比对的序列，RNA二级结构对于评估进化关联性也是有用的。
