Data from: Alternative translation initiation codons for the plastid maturase MatK: unraveling the pseudogene misconception in the Orchidaceae

Background: The plastid maturase MatK has been implicated as a possible model for the evolutionary “missing link” between prokaryotic and eukaryotic splicing machinery. This evolutionary implication has sparked investigations concerning the function of this unusual maturase. Intron targets of MatK activity suggest that this is an essential enzyme for plastid function. The matK gene, however, is described as a pseudogene in many photosynthetic orchid species due to presence of premature stop codons in translations, and its high rate of nucleotide and amino acid substitution. Results: Sequence analysis of the matK gene from orchids identified an out-of-frame alternative AUG initiation codon upstream from the consensus initiation codon used for translation in other angiosperms. We demonstrate translation from the alternative initiation codon generates a conserved MatK reading frame. We confirm that MatK protein is expressed and functions in sample orchids currently described as having a matK pseudogene using immunodetection and reverse-transcription methods. We demonstrate using phylogenetic analysis that this alternative initiation codon emerged de novo within the Orchidaceae, with several reversal events at the basal lineage and deep in orchid history. Conclusion: These findings suggest a novel evolutionary shift for expression of matK in the Orchidaceae and support the function of MatK as a group II intron maturase in the plastid genome of land plants including the orchids.

背景：质体成熟酶MatK（plastid maturase MatK）被认为是原核与真核剪接机器之间进化"缺失环节"的潜在模型。这一进化关联引发了针对该特殊成熟酶功能的相关研究。针对MatK活性的内含子（intron）靶点的研究表明，该酶是质体功能行使所不可或缺的关键酶。然而，因其翻译过程中存在提前终止密码子（premature stop codon），且核苷酸（nucleotide）与氨基酸（amino acid）替换速率偏高，matK基因在众多光合兰科植物中被归类为假基因（pseudogene）。
结果：对兰科植物matK基因的序列分析显示，在其他被子植物（angiosperms）翻译所采用的共有起始密码子（initiation codon）上游，存在一个读码框偏移的替代性AUG起始密码子。本研究证实，从该替代性起始密码子启动翻译可生成保守的MatK读码框（reading frame）。我们通过免疫检测与反转录（reverse-transcription）实验方法，确认MatK蛋白在当前被归类为matK假基因的兰科样本植物中得以表达并发挥功能。通过系统发育分析（phylogenetic analysis），我们证实该替代性起始密码子是在兰科（Orchidaceae）中从头起源的，且在基部类群（basal lineage）与兰科演化的深层历史中发生过多次回复突变事件。
结论：本研究结果表明，兰科植物matK基因的表达存在一种全新的进化转变模式，同时证实MatK作为II型内含子成熟酶（group II intron maturase），在包括兰科植物在内的陆生植物质体基因组中发挥相应功能。