Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
Genome Biol. 2011;12(4):R38. doi: 10.1186/gb-2011-12-4-r38. Epub 2011 Apr 13.
As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional.
Using an improved version of the gene-finding program tRNAscan-SE, comparative analyses and experimental verifications, we have now identified four novel trans-spliced tRNA genes, each in a different species of the Desulfurococcales branch of the Archaea: tRNA(Asp(GUC)) in Aeropyrum pernix and Thermosphaera aggregans, and tRNA(Lys(CUU)) in Staphylothermus hellenicus and Staphylothermus marinus. Each of these includes features surprisingly similar to previously studied split tRNAs, yet comparative genomic context analysis and phylogenetic distribution suggest several independent, relatively recent splitting events. Additionally, we identified the first examples of permuted tRNA genes in Archaea: tRNA(iMet(CAU)) and tRNA(Tyr(GUA)) in Thermofilum pendens, which appear to be permuted in the same arrangement seen previously in red alga.
Our findings illustrate that split tRNAs are sporadically spread across a major branch of the Archaea, and that permuted tRNAs are a new shared characteristic between archaeal and eukaryotic species. The split tRNA discoveries also provide new clues to their evolutionary history, supporting hypotheses for recent acquisition via viral or other mobile elements.
与真核生物一样，古菌的前体 tRNA 通常含有内含子，这些内含子在 tRNA 成熟过程中被切除。两种不相关的古菌物种以分裂 tRNA 基因的形式表现出独特的前 tRNA 加工复杂性，其中两个到三个 tRNA 片段从不同的基因座转录，然后经过转剪接形成成熟的 tRNA。另一种罕见的前 tRNA 类型仅存在于真核藻类中，是被置换的，其中 3' 半部分位于 5' 半部分的上游，并且必须经过加工才能具有功能。
使用改进版的基因发现程序 tRNAscan-SE，比较分析和实验验证，我们现在已经在古菌的脱硫球菌目中的不同物种中鉴定出了四个新的转剪接 tRNA 基因，每个基因都包含一个：Aeropyrum pernix 和 Thermosphaera aggregans 中的 tRNA(Asp(GUC))，以及 Staphylothermus hellenicus 和 Staphylothermus marinus 中的 tRNA(Lys(CUU))。这些基因都具有与之前研究的分裂 tRNA 非常相似的特征，但比较基因组上下文分析和系统发育分布表明这是几个独立的、相对较新的分裂事件。此外，我们还在古菌中鉴定出了第一个被置换的 tRNA 基因的例子：Thermofilum pendens 中的 tRNA(iMet(CAU))和 tRNA(Tyr(GUA))，它们似乎是以与先前在红藻中观察到的相同排列方式被置换的。
我们的发现表明，分裂 tRNA 零星分布在古菌的一个主要分支中，而置换 tRNA 是古菌和真核生物之间的一个新的共有特征。分裂 tRNA 的发现也为它们的进化历史提供了新的线索，支持了最近通过病毒或其他移动元件获得的假说。
