到目前为止，科学家已经积累了大量的基因组数据“矿藏”。而那些被忽略的数据则可能揭示出非比寻常的重要信息。
现在，美国能源部联合基因组研究所(DOE JGI)进行的一项对大量微生物基因组序列数据的系统性的再次分析正是这样的一个绝佳例子。
这项研究鉴定出了杀死了测序过程中使用的细菌的基因。该研究还给出了发现新抗生素的可能策略。这项研究发现刊登在10月19日的《科学》杂志上。
在自然界中，各种混杂的微生物很容易分享遗传信息，因此使得利用基因来推断它们在“生命树”上的位置变得非常困难。现在，DOE JGI的研究人员通过鉴定出杀死传递的受体细菌的基因而无需考量细菌捐体（bacterial donor）类型的方法解决了这些障碍。这些致死性基因还为构建系统演化树（证实生物体间进化关系的方法）提供了更好的参考点。
研究人员表示，在测序一个基因组时，永远都不能一下子就构建出完整的基因组。通常在组装过程中会有一些“缺口”。测序过程复杂而又花费昂贵，人们不得不进一步了解这些缺口并解开这些疑惑。这项新研究则是了解缺口发生的一个重大突破——一些基因不能被转移到大肠杆菌中，因为它们会杀死大肠杆菌。
研究人员对80个不同的基因中的超过90亿个核苷酸进行筛选并估计缺口。他们发现相同的基因一次又一次造成这种“缺口”，即它们不能被转移到大肠杆菌中。
随着技术的进步，越来越多的物种完成了基因组的测序，与此同时累积大量的数据。而如果利用这些数据探索生命奥秘、造福人类健康则是我们面临的更为艰巨的任务。
原始出处:
Published Online October 18, 2007
Science DOI: 10.1126/science.1147112
Submitted on June 27, 2007
Accepted on October 9, 2007
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
Rotem Sorek 1, Yiwen Zhu 2, Christopher J. Creevey 3, M. Pilar Francino 4, Peer Bork 3, Edward M. Rubin 1*
1 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA.; Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
2 Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
3 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
4 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, USA.
* To whom correspondence should be addressed.
Edward M. Rubin , E-mail: EMRubin@lbl.gov
Bacteria that grow normally on a plate (left) cannot grow when a toxic gene is transferred into them (right). Photo by Rotem Sorek, JGI
Horizontal gene transfer, in which genetic material is transferred from the genome of one organism to another, has been investigated in microbial species mainly through computational sequence analyses. To address the lack of experimental data, we studied the attempted movement of 246,045 genes from 79 prokaryotic genomes into Escherichia coli and identified genes that consistently fail to transfer. We studied the mechanisms underlying transfer inhibition by placing coding regions from different species under the control of inducible promoters. Our data suggest that toxicity to the host inhibited transfer regardless of the species of origin and that increased gene dosage and associated increased expression may be a predominant cause for transfer failure. While these experimental studies examined transfer solely into E. coli, a computational analysis of gene transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life.
