Genereux Diane P, Logsdon John M
Department of Biology, Graduate Program in Population Biology, Ecology and Evolution, Emory University, 1510 Clifton Road, Atlanta, GA, USA.
Trends Genet. 2003 Apr;19(4):191-5. doi: 10.1016/S0168-9525(03)00055-6.
When the International Human Genome Sequencing Consortium (IHGSC) published its draft of the human genome in February 2001, several genes were identified as possible bacteria-to-vertebrate transfers (BVTs). These genes were identified by their highly significant sequence similarity to bacterial genes in BLAST searches, and by their lack of matches among non-vertebrate eukaryote genes. Many were later rejected as BVTs by several methods, including recovery of probable orthologs from the genomes of incompletely sequenced eukaryotes. Whereas the BVT issue has received considerable attention, there has been no compilation of all potential BVTs considered to date, nor any proposal of a single comprehensive method for rigorously establishing the veracity of a putative BVT. In reviewing the work to date, we list all of the proteins examined and propose systematic tests to investigate whether a vertebrate gene proposed as a BVT is indeed of bacterial origin. We use the proposed strategy to test--and reject--one of the BVTs from the original IHGSC list.
2001年2月,国际人类基因组测序联盟(IHGSC)公布了人类基因组草图,其中有几个基因被确定为可能是从细菌转移至脊椎动物的基因(BVTs)。这些基因是通过在BLAST搜索中与细菌基因具有高度显著的序列相似性,以及在非脊椎动物真核生物基因中缺乏匹配项而被识别出来的。后来,通过多种方法,包括从不完全测序的真核生物基因组中找回可能的直系同源基因,许多基因被排除在BVTs之外。尽管BVT问题受到了相当多的关注,但迄今为止,尚未对所有潜在的BVTs进行汇编,也没有提出一种单一的综合方法来严格确定一个假定的BVT的真实性。在回顾迄今为止的工作时,我们列出了所有检查过的蛋白质,并提出了系统测试,以调查一个被提议为BVT的脊椎动物基因是否确实起源于细菌。我们使用所提议的策略对原始IHGSC列表中的一个BVT进行了测试并予以否定。