根據(jù)二項(xiàng)由加州大學(xué)柏克來分校所發(fā)表的新研究，科學(xué)家發(fā)現(xiàn)基因分布于不同種類的狀態(tài)是超乎尋常地混亂,，原始的有機(jī)生物之間分享基因的情況更明顯,，而且它們共享的往往不只幾個(gè)基因,，而是整個(gè)基因群。
這種基因在不同物種間流動的現(xiàn)象,，稱為基因水平轉(zhuǎn)移,，在細(xì)菌中經(jīng)常可以觀察到,，這種現(xiàn)象使得致病性細(xì)菌可以將抗藥性基因與其它細(xì)菌交換共享,。
最近，研究人員發(fā)現(xiàn)二種不同種類的植物也會分享基因,。問題是,，這種現(xiàn)象有多普遍，這是怎么發(fā)生的,。根據(jù)這篇發(fā)表于PNAS的文章,，加州大學(xué)伯克來分校和勞倫斯柏克來國家實(shí)驗(yàn)室(LBNL)的研究人員，分析了超過基因8,000種不同的基因家族,，這些基因編碼的蛋白質(zhì)可代表所有生物中,，數(shù)以百萬計(jì)的蛋白質(zhì)，藉以評估基因水平轉(zhuǎn)移的發(fā)生率,。
他們發(fā)現(xiàn)一半以上最原始的有機(jī)生物,，古菌(Archaea)，有一個(gè)以上的蛋白質(zhì)基因是經(jīng)由基因水平轉(zhuǎn)移而獲得的,，相較于百分之30 到50的細(xì)菌經(jīng)由這種方式獲得基因,。真核生物則只有百分之10。
第二篇發(fā)表于3月7 日Nature網(wǎng)絡(luò)版的報(bào)告,，則提出了生活在加州酸性紅泥土中的二種細(xì)菌發(fā)現(xiàn)分享一大群基因,。這些基因編碼的蛋白質(zhì)具有合作的功能，所以這二種細(xì)菌分享的基因也是一大群的。因此研究人員認(rèn)為,，這可以幫助細(xì)菌適應(yīng)同樣類型的新環(huán)境,。而這項(xiàng)研究也是第一次觀察到一大群基因發(fā)生基因水平轉(zhuǎn)移的現(xiàn)象。
(資料來源 : Bio.com)
部分英文原文：
Published online before print March 7, 2007, 10.1073/pnas.0611557104
PNAS | March 13, 2007 | vol. 104 | no. 11 | 4489-4494
Global extent of horizontal gene transfer
In-Geol Choi*, and Sung-Hou Kim
Physical Biosciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, CA 94720
Contributed by Sung-Hou Kim, December 28, 2006 (received for review July 1, 2006)
Abstract
Horizontal gene transfer (HGT) is thought to play an important role in the evolution of species and innovation of genomes. There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT. Here, we present a method of identifying HGT events within a given protein family and estimate the global extent of HGT in all curated protein domain families (8,000) listed in the Pfam database. The results suggest four conclusions: (i) for all protein domain families in Pfam, the fixation of genes horizontally transferred is not a rampant phenomenon between organisms with substantial phylogenetic separations (1.1–9.7% of Pfam families surveyed at three taxonomic ranges studied show indication of HGT); (ii) however, at the level of domains, >50% of Archaea have one or more protein domains acquired by HGT, and nearly 30–50% of Bacteria did the same when examined at three taxonomic ranges. But, the equivalent value for Eukarya is <10%; (iii) HGT will have very little impact in the construction of organism phylogeny, when the construction methods use whole genomes, large numbers of common genes, or SSU rRNAs; and (iv) there appears to be no strong preference of HGT for protein families of particular cellular or molecular functions.
protein domain family | protein sequence family | lateral gene transfer
One of the new important concepts that emerged from a large number of genomic sequences in the last decade is that of horizontal gene transfer (HGT): gene transfer among organisms of different species. HGT has been found to have occurred in all three domains: Archaea, Bacteria, and Eukarya. The concept of HGT has been evoked to interpret various evolutionary processes ranging from speciation and the adaptation of organisms to uncertainties in phylogenetic inference of the tree of life (1–9). Although HGT has been regarded as a driving force in the innovation and evolution of genomes, especially in prokaryotes, its extent and impact on the evolutionary process and phylogeny of organisms or species remains controversial (8–10).
There have been several methods developed to detect HGT, including (i) difference between gene trees derived from a limited number of gene families and the reference trees such as the small-subunit ribosomal RNA (SSU rRNA) tree (11–13) or whole genome tree (14); (ii) unexpectedly high sequence similarity of a gene from two distant genomes compared with those among homologous genes in closely related genomes (15); and (iii) unusual nucleotide composition or codon usages of a gene compared with the rest of the genes within a genome (16, 17). Many factors affect the detection of HGT, such as lineage-specific gene loss (18, 19), unequal rates of base substitution (1), loss of signal due to amelioration processes (16), and others (1, 15).
It has been suggested that HGT may have been "rampant" in primitive genomes (6, 20), but, for modern organisms, it may not be a dominant factor in speciation, because HGT has less effect on overall genome phylogeny (10, 21).
There have been many convincing evidences for HGT for specific genes or gene families, but there has been no estimate of the global extent of HGT in terms of protein domains. Here, we present a statistical method to identify the member(s) in a protein family that may have joined the family by HGT events and examine the global extent of HGT events for all protein domain families of known curated sequences at various ranges of taxonomic levels.
A protein (sequence) domain is a functionally independent unit in protein sequence. The gene coding for it often behaves like a modular genetic element that transfers within or between genomes, sometimes forming a new gene coding for a multiple domain protein (22–24). Because the fixation of a new gene during evolution depends mostly on its advantage for survival, we focus on HGT of the genetic module coding for the sequence domains, rather than the entire genes. At present, there are 1.2 million curated protein domain sequences from three domains of life (Archaea, Bacteria, and Eukarya) in the Pfam (release 16.0) (25).
英文全文鏈接：www.pnas.org/cgi/content/full/104/11/4489
Letter
Nature advance online publication 7 March 2007 | doi:10.1038/nature05624; Received 16 November 2006; Accepted 26 January 2007; Published online 7 March 2007
Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
Ian Lo1, Vincent J. Denef1, Nathan C. VerBerkmoes2, Manesh B. Shah2, Daniela Goltsman1, Genevieve DiBartolo1, Gene W. Tyson1, Eric E. Allen1, Rachna J. Ram1, J. Chris Detter3, Paul Richardson3, Michael P. Thelen4, Robert L. Hettich2 and Jillian F. Banfield1
University of California, Berkeley, California 94720, USA
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
Joint Genome Institute, Walnut Creek, California 94598, USA
Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Correspondence to: Jillian F. Banfield1 Correspondence and requests for materials should be addressed to J.F.B. (Email: [email protected]).
Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems1, 2, 3 and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis4, 5, 6 of microorganisms in the natural environment.
