携带污染物降解基因的可移动基因元件及其介导的生物修复

可移动基因元件(mobile genetic elements,MGEs)在环境微生物群落中的水平转移是细菌基因组进化和适应特定环境压力的重要机制.在污染土壤和水体中接种携带具有降解基因MGEs的菌株后,随着MGEs的水平基因转移,可使降解基因转移至具有竞争性的土著微生物中并在其中表达,从而不必考虑供体菌在环境中是否能够长期存活.这种由可移动降解基因元件水平转移介导的生物修复为探索新的生物修复途径提供了可行性.本文重点综述了环境样品中携带降解基因MGEs的多样性及其在促进污染物降解过程中的重要作用,介绍了从环境样品中分离代谢MGEs的方法,并列举了在污染土壤、活性污泥、其他生物反应器等生态系统中MGEs水平转移的几个实例.     

Gene transfer, speciation, and the evolution of bacterial genomes.

Studies in microbial evolution have focused on the origin and vertical transmission of genetic variation within populations experiencing limited recombination. Genomic analyses have highlighted the importance of horizontal genetic transfer in shaping the composition of microbial genomes, providing novel metabolic capabilities, and catalyzing the diversification of bacterial lineages.     

Host-bacterial coevolution and the search for new drug targets

Understanding the coevolution between humans and our microbial symbionts and pathogens requires complementary approaches, ranging from community analysis to in-depth analysis of individual genomes. Here we review the evidence for coevolution between symbionts and their hosts, the role of horizontal gene transfer in coevolution, and genomic and metagenomic approaches to identify drug targets. Recent studies have shown that our symbiotic microbes confer many metabolic capabilities that our mammalian genomes lack, and that targeting mechanisms of horizontal gene transfer is a promising new direction for drug discovery. Gnotobiotic ('germ-free') mice are an especially exciting new tool for unraveling the function of microbes, whether individually or in the context of complex communities.     

Transposable Elements Cross Kingdom Boundaries and Contribute to Inflammation and Ageing

The de-repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell-autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well-evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under-reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed.     

Insights into the evolutionary process of genome degradation

Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.     

SIGI: score-based identification of genomic islands

Background  

Genomic islands can be observed in many microbial genomes. These stretches of DNA have a conspicuous composition with regard to sequence or encoded functions. Genomic islands are assumed to be frequently acquired via horizontal gene transfer. For the analysis of genome structure and the study of horizontal gene transfer, it is necessary to reliably identify and characterize these islands.     

Transformation and DNA repair: linkage by DNA recombination

The stability of microbial genomes is constantly challenged by horizontal gene transfer, recombination and DNA damage. Mechanisms for rapid genome variation, adaptation and maintenance are a necessity to ensure microbial fitness and survival in changing environments. Indeed, genome sequences reveal that most, if not all, bacterial species have numerous gene functions for DNA repair and recombination. These important topics were addressed at the Second Genome Maintenance Meeting (GMM2).     

Very early evolution from the perspective of microbial ecology

The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.     

Non-clonal evolution of microbes

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to interorganismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes have shown, however, that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the horizontal movement of genes across vast phylogenetic distances. © 2003 The Linnean Society of London. Biological Journal of the Linnean Society , 2003, 79 , 27–32.     

Assessing evolutionary relationships among microbes from whole-genome analysis

The determination and analysis of complete genome sequences have recently enabled many major advances to be made in the area of microbial evolutionary biology. These include the determination of the first genome of a Crenarchaeota, the suggestion that horizontal gene transfer may be the rule rather than the exception, and revelations about how genomes evolve on short timescales.     

A new computational method for the detection of horizontal gene transfer events

In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.     

The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so widespread that it might be the “essence of phylogeny” and might leave the treelike form of genealogy in doubt. On the other hand, possible biased estimation of HGT extent and the findings of coherent phylogenetic patterns indicate that phylogeny of life is well represented by tree graphs. Here, we reexamine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to 40 microbial genomes in the Clusters of Orthologous Groups database over a curated set of 297 orthologous gene clusters, and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative of HGT. We propose that HGT events, even when relatively common, still leave the treelike history of phylogenies intact, much like cobwebs hanging from tree branches.     

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

Background  

Horizontal gene transfer (HGT) played an important role in shaping microbial genomes. In addition to genes under sporadic selection, HGT also affects housekeeping genes and those involved in information processing, even ribosomal RNA encoding genes. Here we describe tools that provide an assessment and graphic illustration of the mosaic nature of microbial genomes.     

A database of phylogenetically atypical genes in archaeal and bacterial genomes,identified using the <Emphasis Type="Italic">DarkHorse</Emphasis> algorithm

Background  

The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. DarkHorse, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not.     

Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus

The recently sequenced genome of the predatory delta-proteobacterium Bdellovibrio bacteriovorus provides many insights into its metabolism and evolution. Because its genes are reasonably uniform in G+C content, it was suggested that B. bacteriovorus actively resists recombination with foreign DNA and horizontal transfer of DNA from other bacteria. To investigate this further, we carried out a variety of phylogenetic and comparative genomics analyses using data from >200 microbial genomes, including several published delta-proteobacteria. Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent.     

Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom

Unlike crown eukaryotic species, microbial species are created by continual processes of gene loss and acquisition promoted by horizontal genetic transfer. The amounts of foreign DNA in bacterial genomes, and the rate at which this is acquired, are consistent with gene transfer as the primary catalyst for microbial differentiation. However, the rate of successful gene transfer varies among bacterial lineages. The heterogeneity in foreign DNA content is directly correlated with amount of genetic headroom intrinsic to a bacterial species. Genetic headroom reflects the amount of potentially dispensable information--reflected in codon usage bias and codon context bias--that can be transiently sacrificed to allow experimentation with functions introduced by gene transfer. In this way, genetic headroom offers a potential metric for assessing the propensity of a lineage to speciate.     

Stable tRNA-based phylogenies using only 76 nucleotides

tRNAs are among the most ancient, highly conserved sequences on earth, but are often thought to be poor phylogenetic markers because they are short, often subject to horizontal gene transfer, and easily change specificity. Here we use an algorithm now commonly used in microbial ecology, UniFrac, to cluster 175 genomes spanning all three domains of life based on the phylogenetic relationships among their complete tRNA pools. We find that the overall pattern of similarities and differences in the tRNA pools recaptures universal phylogeny to a remarkable extent, and that the resulting tree is similar to the distribution of bootstrapped rRNA trees from the same genomes. In contrast, the trees derived from tRNAs of identical specificity or of individual isoacceptors generally produced trees of lower quality. However, some tRNA isoacceptors were very good predictors of the overall pattern of organismal evolution. These results show that UniFrac can extract meaningful biological patterns from even phylogenies with high level of statistical inaccuracy and horizontal gene transfer, and that, overall, the pattern of tRNA evolution tracks universal phylogeny and provides a background against which we can test hypotheses about the evolution of individual isoacceptors.     

Horizontal gene transfer

This review explores examples of horizontal genetic transfer in eukaryotes and prokaryotes. The best understood of these involves various conserved families of transposable elements, but examples of non-transposable-element-based movement of genes or gene clusters have also been identified in prokaryotic genomes. A unifying theme is the structural and DNA-sequence homology of transposable elements from widely unrelated genomes, suggesting evolutionarily conserved mechanisms for horizontal transfer. This is reinforced by the fundamental similarity in the enzymatic mechanisms of retro viral integration (by integrases) and of transposition (by transposases). The review deals with various types of horizontal transfer, the mechanisms available for such transfer, potential barriers, and the evolutionary significance of horizontal genetic transfer.     

Systematic Detection of Large-Scale Multigene Horizontal Transfer in Prokaryotes

Horizontal gene transfer (HGT) is central to prokaryotic evolution. However, little is known about the “scale” of individual HGT events. In this work, we introduce the first computational framework to help answer the following fundamental question: How often does more than one gene get horizontally transferred in a single HGT event? Our method, called HoMer, uses phylogenetic reconciliation to infer single-gene HGT events across a given set of species/strains, employs several techniques to account for inference error and uncertainty, combines that information with gene order information from extant genomes, and uses statistical analysis to identify candidate horizontal multigene transfers (HMGTs) in both extant and ancestral species/strains. HoMer is highly scalable and can be easily used to infer HMGTs across hundreds of genomes. We apply HoMer to a genome-scale data set of over 22,000 gene families from 103 Aeromonas genomes and identify a large number of plausible HMGTs of various scales at both small and large phylogenetic distances. Analysis of these HMGTs reveals interesting relationships between gene function, phylogenetic distance, and frequency of multigene transfer. Among other insights, we find that 1) the observed relative frequency of HMGT increases as divergence between genomes increases, 2) HMGTs often have conserved gene functions, and 3) rare genes are frequently acquired through HMGT. We also analyze in detail HMGTs involving the zonula occludens toxin and type III secretion systems. By enabling the systematic inference of HMGTs on a large scale, HoMer will facilitate a more accurate and more complete understanding of HGT and microbial evolution.     

The cytoplasmic structure hypothesis for ribosome assembly,vertical inheritance,and phylogeny

Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to “boot,” i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell “body” into which genomes are placed.