Alimi J P, Poirot O, Lopez F, Claverie J M
Structural and Genetic Information Laboratory, Marseille, France.
Genome Res. 2000 Jul;10(7):959-66. doi: 10.1101/gr.10.7.959.
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.
尽管已经从广泛的门类中积累了序列信息样本，但新测序的基因组仍不断揭示出高比例（50%-30%）的“未表征”基因，其中包括大量严格意义上的“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。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。尽管理论上的进化观点支持当在多种远缘物种中发现同源物时基因的真实性，但孤儿基因并非如此。在此，我们报告了对大肠杆菌25个严格意义上的孤儿ORF进行的直接逆转录酶-聚合酶链反应分析。测试了两种生长条件，指数生长期和稳定期。总共鉴定出19个孤儿基因的转录本，其中2个基因仅在两种生长条件之一中表达。我们的结果表明，目前注释为“假设的”绝大多数大肠杆菌ORF对应于真正的基因。由此推断，这意味着在致密的大肠杆菌基因组进化过程中，随机出现的“垃圾”ORF已被积极地反向选择。
