Retroids in Archaea: Phylogeny and lateral origins
Retroids in Archaea: Phylogeny and lateral origins
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DOI：
10.1093/molbev/msg135
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发表时间：
2003-07-01
影响因子：
10.7
通讯作者：
Mindell, DP
中科院分区：
文献类型：
--
作者：
Rest, JS;Mindell, DP
直到最近，还没有人知道带有逆转录酶（retroids）的不同元素来自于黑曲霉。然而，在最近发表的利用乙酸盐的古生产甲烷菌基因组中，食乙酸甲烷八叠球菌（Methanosarcina acetivorans）和M。Mazei中，几个开放阅读框（ORF）被注释为逆转录酶（RT）。这些注释使我们确定了一个retron和13个retrointrons，包括3个twintrons，聚集在7个位点的M。acetivorans基因组中的两个位点上有4个反转录内含子。Mazei基因组基于RT ORF的同源性，我们推断这些retroids从细菌到细菌的四个横向基因转移（LGT）和细菌基因组内的retrointron迁移。我们的系统发育分析还在细菌群Firmicutes、Fusobacteria、Cyanobacteria和beta-Proteobacteria以及M.食醋动物。由于细菌的LGT，在大肠杆菌中发现了逆转录内含子，这表明它们并不起源于原基因组，并与剪接体起源的“线粒体种子”理论相一致。将已知的retroids的系统发育分布扩展到古生物，与它们在整个生命树的基因组进化中发挥重要作用的观点一致。
Until recently, none of the diverse elements bearing reverse transcriptase (retroids) have been known from Archaea. However, in the recently published genomes of the acetate-utilizing archaeal methanogens, Methanosarcina acetivorans and M. mazei, several open reading frames (ORFs) are annotated as reverse transcriptase (RT). These annotations led us to the characterization of a retron and 13 retrointrons, including three twintrons, clustered at seven loci of the M. acetivorans genome, and four retrointrons at two loci of the M. mazei genome. Based on a phylogeny of the RT ORFs, we infer four lateral gene transfers (LGT) of these retroids from Bacteria to Archaea and of retrointron mobility within the Archaea genomes. Our phylogenetic analysis also identifies several novel retrons from GenBank in the bacterial groups Firmicutes, Fusobacteria, Cyanobacteria and beta-Proteobacteria, as well as in M. acetivorans. The discovery of retrointrons in Archaea as a consequence of LGT from Bacteria suggests that they did not originate in the progenote and parallels the "mitochondrial seed" theory of the origin of spliceosomes. Extending the known phylogenetic distribution of retroids to Archaea is consistent with the view that they have played a significant role in evolution of genomes throughout the tree of life.