Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements.
Dinoflagellate spliced leader RNA genes display a variety of sequences and genomic arrangements.
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DOI：
10.1093/molbev/msp083
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发表时间：
2009-08
影响因子：
10.7
通讯作者：
Huan Zhang;D. Campbell;N. R. Sturm;Senjie Lin
中科院分区：
文献类型：
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作者：
Huan Zhang;D. Campbell;N. R. Sturm;Senjie Lin
剪接前导（SL）反式剪接是甲藻中一种常见的mRNA加工机制，它将一段22个核苷酸的序列从小的非编码RNA（SL RNA）的5 '端转移到mRNA分子的5'端。虽然SL RNA基因最初被证明是组织为串联重复，转录本为50-60 nt，比其他生物中的大多数对应物短，但随后报道了其他基因组织和转录本长度。为了解决基因组织复杂性的进化梯度，我们彻底研究了SL RNA的转录本和基因组织在一个遗传和生态多样的甲藻代表四个订单。所有这些甲藻具有SL RNA转录的50-60 nt，虽然在一个物种的额外的转录高达92 nt也被检测到。在基因组水平上，采用聚合酶链反应扩增了6种甲藻的SL RNA和5S rRNA串联基因阵列的不同组合，包括SL RNA-only、5S rRNA-only和混合SL RNA-5S rRNA（SL-5S）簇。在这些物种中，没有检测到SL-5S簇的最小原甲藻，只有Karenia brevis显示U6小核RNA基因与这些混合阵列。在三种甲藻中也发现了仅含5S rRNA的阵列，沿着在另外两种物种中发现了两个SL-5S相邻排列，这可能代表了连接。两个物种含有多聚体SL外显子重复，没有相关的内含子。这些结果表明：1）SL RNA串联重复序列和SL-5S簇基因组结构是甲藻门中“古老”和广泛的特征; 2）在每个甲藻谱系中，猖獗的基因组复制和重组独立地进行，导致SL RNA基因的高度复杂和多样化的基因组排列，同时保留功能性SL RNA的长度和结构。
Spliced leader (SL) trans-splicing is a common mRNA processing mechanism in dinoflagellates, in which a 22-nt sequence is transferred from the 5'-end of a small noncoding RNA, the SL RNA, to the 5'-end of mRNA molecules. Although the SL RNA gene was shown initially to be organized as tandem repeats with transcripts of 50-60 nt, shorter than most of their counterparts in other organisms, other gene organizations and transcript lengths were reported subsequently. To address the evolutionary gradient of gene organization complexity, we thoroughly examined transcript and gene organization of the SL RNA in a phylogenetically and ecologically diverse group of dinoflagellates representing four Orders. All these dinoflagellates possessed SL RNA transcripts of 50-60 nt, although in one species additional transcripts of up to 92 nt were also detected. At the genomic level, various combinations of SL RNA and 5S rRNA tandem gene arrays, including SL RNA-only, 5S rRNA-only, and mixed SL RNA-5S rRNA (SL-5S) clusters, were amplified by polymerase chain reaction for six dinoflagellates, containing intergenic spacers ranging from 88 bp to over 1.2 kb. Of these species, no SL-5S cluster was detected in Prorocentrum minimum, and only Karenia brevis showed the U6 small nuclear RNA gene associated with these mixed arrays. The 5S rRNA-only array was also found in three dinoflagellates, along with two SL-5S-adjacent arrangements found in two other species that could represent junctions. Two species contained multimeric SL exon repeats with no associated intron. These results suggest that 1) both the SL RNA tandem repeat and the SL-5S cluster genomic organizations are an "ancient" and widespread feature within the phylum of dinoflagellates and 2) rampant genomic duplication and recombination are ongoing independently in each dinoflagellate lineage, giving rise to the highly complex and diversified genomic arrangements of the SL RNA gene, while conserving the length and structure of the functional SL RNA.