Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655
Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli K-12 MG1655
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DOI：
10.1101/gr.10.7.959
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发表时间：
2000-07-01
期刊：
影响因子：
7
通讯作者：
Claverie, JM
中科院分区：
文献类型：
--
作者：
Alimi, JP;Poirot, O;Claverie, JM
尽管从广泛的门中取样的序列信息积累，新测序的基因组继续揭示高比例（50%-30%）的“未表征”基因，包括大量严格的“孤儿”基因，即，推定的开放阅读框（ORF），与先前确定的蛋白质编码序列没有任何相似之处。在数据库中发现的大多数基因只是通过计算机方法预测的，从未经过实验验证。虽然理论上的进化论支持基因的现实，当同源物被发现在各种遥远的物种，这不是孤儿基因的情况。在这里，我们报告的直接逆转录酶-聚合酶链反应检测25严格孤儿的开放阅读框的大肠杆菌。测试了两种生长条件，指数期和稳定期。共鉴定了19个孤儿基因的转录本，发现2个基因仅在两种生长条件之一中表达。我们的研究结果表明，绝大多数E。目前注释为“假设”的大肠杆菌ORF对应于真实的基因。推而广之，这意味着随机出现的“垃圾”ORF在密集E. coli基因组。
Despite the accumulation of sequence information sampling from a broad spectrum of phyla, newly sequenced genomes continue to reveal a high proportion (50%-30%) of "uncharacterized" genes, including a significant number of strictly "orphan" genes, i.e., putative open reading frames (ORFs] without any resemblance to previously determined protein-coding sequences. Most genes found in databases have only been predicted by computer methods and have never been experimentally validated. Although theoretical evolutionary arguments support the reality of genes when homologs are found in a variety of distant species, this is not the case for orphan genes. Here, we report the direct reverse transcriptase-polymerase chain reaction assay of 25 strictly orphan ORFs of Escherichia coli. Two growth conditions, exponential and stationary phases, were tested. Transcripts were identified for a total of 19 orphan genes, with 2 genes found to be expressed in only one of the two growth conditions. Our results suggest that a vast majority of E. coli ORFs presently annotated as "hypothetical" correspond to bona fide genes. By extension, this implies that randomly occurring "junk" ORFs have been actively counter selected during the evolution of the dense E. coli genome.