到目前為止，科學(xué)家已經(jīng)積累了大量的基因組數(shù)據(jù)“礦藏”,。而那些被忽略的數(shù)據(jù)則可能揭示出非比尋常的重要信息,。
現(xiàn)在，美國(guó)能源部聯(lián)合基因組研究所(DOE JGI)進(jìn)行的一項(xiàng)對(duì)大量微生物基因組序列數(shù)據(jù)的系統(tǒng)性的再次分析正是這樣的一個(gè)絕佳例子,。
這項(xiàng)研究鑒定出了殺死了測(cè)序過(guò)程中使用的細(xì)菌的基因,。該研究還給出了發(fā)現(xiàn)新抗生素的可能策略。這項(xiàng)研究發(fā)現(xiàn)刊登在10月19日的《科學(xué)》雜志上,。
在自然界中,，各種混雜的微生物很容易分享遺傳信息，因此使得利用基因來(lái)推斷它們?cè)?ldquo;生命樹”上的位置變得非常困難?，F(xiàn)在,，DOE JGI的研究人員通過(guò)鑒定出殺死傳遞的受體細(xì)菌的基因而無(wú)需考量細(xì)菌捐體（bacterial donor）類型的方法解決了這些障礙。這些致死性基因還為構(gòu)建系統(tǒng)演化樹（證實(shí)生物體間進(jìn)化關(guān)系的方法）提供了更好的參考點(diǎn),。
研究人員表示,，在測(cè)序一個(gè)基因組時(shí)，永遠(yuǎn)都不能一下子就構(gòu)建出完整的基因組,。通常在組裝過(guò)程中會(huì)有一些“缺口”。測(cè)序過(guò)程復(fù)雜而又花費(fèi)昂貴,，人們不得不進(jìn)一步了解這些缺口并解開這些疑惑,。這項(xiàng)新研究則是了解缺口發(fā)生的一個(gè)重大突破——一些基因不能被轉(zhuǎn)移到大腸桿菌中，因?yàn)樗鼈儠?huì)殺死大腸桿菌,。
研究人員對(duì)80個(gè)不同的基因中的超過(guò)90億個(gè)核苷酸進(jìn)行篩選并估計(jì)缺口,。他們發(fā)現(xiàn)相同的基因一次又一次造成這種“缺口”，即它們不能被轉(zhuǎn)移到大腸桿菌中,。
隨著技術(shù)的進(jìn)步,，越來(lái)越多的物種完成了基因組的測(cè)序，與此同時(shí)累積大量的數(shù)據(jù),。而如果利用這些數(shù)據(jù)探索生命奧秘,、造福人類健康則是我們面臨的更為艱巨的任務(wù)。
原始出處:
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: [email protected]
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.
