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破伤风梭菌的一种选择性剪接的组 II 内含子的新型 RNA 结构特征。

Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani.

机构信息

Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.

出版信息

RNA. 2014 Jun;20(6):855-66. doi: 10.1261/rna.042440.113. Epub 2014 Apr 21.

DOI:10.1261/rna.042440.113
PMID:24751650
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4024640/
Abstract

Group II introns are ribozymes in bacterial and organellar genomes that function as self-splicing introns and as retroelements. Previously, we reported that the group II intron C.te.I1 of Clostridium tetani alternatively splices in vivo to produce five distinct coding mRNAs. Accurate fusion of upstream and downstream reading frames requires a shifted 5' splice site located 8 nt upstream of the usual 5' GUGYG motif. This site is specified by the ribozyme through an altered intron/exon-binding site 1 (IBS1-EBS1) pairing. Here we use mutagenesis and self-splicing assays to investigate in more detail the significance of the structural features of the C.te.I1 ribozyme. The shifted 5' splice site is shown to be affected by structures in addition to IBS1-EBS1, and unlike other group II introns, C.te.I1 appears to require a spacer between IBS1 and the GUGYG motif. In addition, the mechanism of 3' exon recognition is modified from the ancestral IIB mechanism to a IIA-like mechanism that appears to be longer than the typical single base-pair interaction and may extend up to 4 bp. The novel ribozyme properties that have evolved for C.te.I1 illustrate the plasticity of group II introns in adapting new structural and catalytic properties that can be utilized to affect gene expression.

摘要

Group II introns 是细菌和细胞器基因组中的核酶，它们既能自我剪接，也能作为逆转录元件发挥作用。此前，我们曾报道过破伤风梭菌的 Group II intron C.te.I1 在体内选择性剪接，从而产生五种不同的编码 mRNA。上游和下游阅读框的准确融合需要一个位于通常的 5' GUGYG 基序上游 8 个核苷酸的移位 5' 剪接位点。该位点通过改变的核酶内含子/外显子结合位点 1（IBS1-EBS1）配对来指定。在这里，我们使用诱变和自我剪接实验更详细地研究了 C.te.I1 核酶的结构特征的重要性。移位的 5' 剪接位点除了 IBS1-EBS1 之外还受到其他结构的影响，而且与其他 Group II introns 不同，C.te.I1 似乎需要在 IBS1 和 GUGYG 基序之间有一个间隔物。此外，3' 外显子识别的机制已经从原始的 IIB 机制修改为类似于 IIA 的机制，这种机制似乎比典型的单碱基对相互作用更长，可能延伸至 4 个碱基。为 C.te.I1 进化而来的新型核酶特性说明了 Group II introns 在适应新的结构和催化特性方面的可塑性，这些特性可用于影响基因表达。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/18ca978b7c92/855f06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/c4fbf0a0158b/855f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/3c919c1fecbc/855f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/15c585411e7d/855f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/d12fe2d08ae9/855f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/76979a7e8a71/855f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/18ca978b7c92/855f06.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/c4fbf0a0158b/855f01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/3c919c1fecbc/855f02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/15c585411e7d/855f03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/d12fe2d08ae9/855f04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/76979a7e8a71/855f05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/cb96/4024640/18ca978b7c92/855f06.jpg

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本文引用的文献

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2
Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties.全面的细菌 group II 内含子编码的 ORF 缺乏 DNA 内切酶结构域的系统发育分析揭示了新的变种。
PLoS One. 2013;8(1):e55102. doi: 10.1371/journal.pone.0055102. Epub 2013 Jan 23.
3
Database for bacterial group II introns.
细菌组 II 内含子数据库。
Nucleic Acids Res. 2012 Jan;40(Database issue):D187-90. doi: 10.1093/nar/gkr1043. Epub 2011 Nov 10.
4
Recurrent insertion of 5'-terminal nucleotides and loss of the branchpoint motif in lineages of group II introns inserted in mitochondrial preribosomal RNAs.线粒体前核糖体 RNA 插入的 II 组内含子谱系中 5' 端核苷酸的反复插入和分支点模体的缺失。
RNA. 2011 Jul;17(7):1321-35. doi: 10.1261/rna.2655911. Epub 2011 May 25.
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A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases.对 II 组内含子 RNA 和内含子编码的逆转录酶进行广泛的系统发育分析。
Mol Biol Evol. 2009 Dec;26(12):2795-808. doi: 10.1093/molbev/msp193. Epub 2009 Aug 27.
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A conserved 3' extension in unusual group II introns is important for efficient second-step splicing.异常II组内含子中保守的3'延伸对于高效的第二步剪接很重要。
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