Mechanism Of Horizontal Gene Transfer Research Articles

The evolution of land plants: a perspective from horizontal gene transfer

Recent studies suggest that horizontal gene transfer (HGT) played a significant role in the evolution of eukaryotic lineages. We here review the mechanisms of HGT in plants and the importance of HGT in land plant evolution. In particular, we discuss the role of HGT in plant colonization of land, phototropic response, C<sub>4</sub> photosynthesis, and mitochondrial genome evolution.

The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer

The chloroplasts of heterokont algae such as diatoms are the result of a secondary endosymbiosis event, in which a red alga was engulfed by a non-photosynthetic eukaryote. The diatom chloroplast genomes sequenced to date show a high degree of similarity, but some examples of gene replacement or introduction of genes through horizontal gene transfer are known. The evolutionary origin of the gene transfers is unclear. We have sequenced and characterised the complete chloroplast genome and a putatively chloroplast-associated plasmid of the pennate diatom Seminavis robusta. The chloroplast genome contains two introns, a feature that has not previously been found in diatoms. The group II intron of atpB appears to be recently transferred from a Volvox-like green alga. The S. robusta chloroplast genome (150,905bp) is the largest diatom chloroplast genome characterised to date, mainly due to the presence of four large gene-poor regions. Open reading frames (ORFs) encoded by the gene-poor regions show similarity to putative proteins encoded by the chloroplast genomes of different heterokonts, as well as the plasmids pCf1 and pCf2 found in the diatom Cylindrotheca fusiformis. A tyrosine recombinase and a serine recombinase are encoded by the S. robusta chloroplast genome, indicating a possible mechanism for the introduction of novel genes. A plasmid with similarity to pCf2 was also identified. Phylogenetic analyses of three ORFs identified on pCf2 suggest that two of them are part of an operon-like gene cluster conserved in bacteria. Several genetic elements have moved through horizontal gene transfer between the chloroplast genomes of different heterokonts. Two recombinases are likely to promote such gene insertion events, and the plasmid identified may act as vectors in this process. The copy number of the plasmid was similar to that of the plastid genome indicating a plastid localization.

Staphylococcus aureus genomics and the impact of horizontal gene transfer

Whole genome sequencing and microarrays have revealed the population structure of Staphylococcus aureus, and identified epidemiological shifts, transmission routes, and adaptation of major clones. S. aureus genomes are highly diverse. This is partly due to a population structure of conserved lineages, each with unique combinations of genes encoding surface proteins, regulators, immune evasion and virulence pathways. Even more variable are the mobile genetic elements (MGE), which encode key proteins for antibiotic resistance, virulence and host-adaptation. MGEs can transfer at high frequency between isolates of the same lineage by horizontal gene transfer (HGT). There is increasing evidence that HGT is key to bacterial adaptation and success. Recent studies have shed light on new mechanisms of DNA transfer such as transformation, the identification of receptors for transduction, on integration of DNA pathways, mechanisms blocking transfer including CRISPR and new restriction systems, strategies for evasion of restriction barriers, as well as factors influencing MGE selection and stability. These studies have also lead to new tools enabling construction of genetically modified clinical S. aureus isolates. This review will focus on HGT mechanisms and their importance in shaping the evolution of new clones adapted to antibiotic resistance, healthcare, communities and livestock.

Horizontal Gene Transfer and Its Part in the Reorganisation of Genetics during the LUCA Epoch.

Currently there are five known mechanisms of horizontal gene transfer (HGT): transduction, conjugation, transformation, gene transfer agents and membrane vesicle transfer. The question here is: what part did HGT play in the reorganisation of genetics during the last universal common ancestor (LUCA) epoch? LUCA is a construct to explain the origin of the three domains of life; namely Archaea, Bacteria and Eukarya. This editorial offers a general introduction to the relevance and ultimate significance of HGT in relation to the LUCA.

Acquired Genetic Mechanisms of a Multiresistant Bacterium Isolated from a Treatment Plant Receiving Wastewater from Antibiotic Production

The external environment, particularly wastewater treatment plants (WWTPs), where environmental bacteria meet human commensals and pathogens in large numbers, has been highlighted as a potential breeding ground for antibiotic resistance. We have isolated the extensively drug-resistant Ochrobactrum intermedium CCUG 57381 from an Indian WWTP receiving industrial wastewater from pharmaceutical production contaminated with high levels of quinolones. Antibiotic susceptibility testing against 47 antibiotics showed that the strain was 4 to >500 times more resistant to sulfonamides, quinolones, tetracyclines, macrolides, and the aminoglycoside streptomycin than the type strain O. intermedium LMG 3301T. Whole-genome sequencing identified mutations in the Indian strain causing amino acid substitutions in the target enzymes of quinolones. We also characterized three acquired regions containing resistance genes to sulfonamides (sul1), tetracyclines [tet(G) and tetR], and chloramphenicol/florfenicol (floR). Furthermore, the Indian strain harbored acquired mechanisms for horizontal gene transfer, including a type I mating pair-forming system (MPFI), a MOBP relaxase, and insertion sequence transposons. Our results highlight that WWTPs serving antibiotic manufacturing may provide nearly ideal conditions for the recruitment of resistance genes into human commensal and pathogenic bacteria.

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2–rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.

Subcellular location of the coupling protein TrwB and the role of its transmembrane domain

Conjugation is the most important mechanism for horizontal gene transfer and it is the main responsible for the successful adaptation of bacteria to the environment. Conjugative plasmids are the DNA molecules transferred and a multiprotein system encoded by the conjugative plasmid itself is necessary. The high number of proteins involved in the process suggests that they should have a defined location in the cell and therefore, they should be recruited to that specific point. One of these proteins is the coupling protein that plays an essential role in bacterial conjugation. TrwB is the coupling protein of R388 plasmid that is divided in two domains: i) The N-terminal domain referred as transmembrane domain and ii) a large cytosolic domain that contains a nucleotide-binding motif similar to other ATPases. To investigate the role of these domains in the subcellular location of TrwB, we constructed two mutant proteins that comprised the transmembrane (TrwBTM) or the cytoplasmic (TrwBΔN70) domain of TrwB. By immunofluorescence and GFP-fusion proteins we demonstrate that TrwB and TrwBTM mutant protein were localized to the cell pole independently of the remaining R388 proteins. On the contrary, a soluble mutant protein (TrwBΔN70) was localized to the cytoplasm in the absence of R388 proteins. However, in the presence of other R388-encoded proteins, TrwBΔN70 localizes uniformly to the cell membrane, suggesting that interactions between the cytosolic domain of TrwB and other membrane proteins of R388 plasmid may happen. Our results suggest that the transmembrane domain of TrwB leads the protein to the cell pole.

Prokaryotic diversity, electrified DNA, lightning waveforms, abiotic gene transfer, and the Drake equation: Assessing the hypothesis of lightning-driven evolution

In a review article in this journal [1], I discussed the feasibility of lightning-triggered electroporation and elec-trofusion acting as purely (bio)physical mechanisms of horizontal gene transfer and thus contributing to biologicalevolution, particularly among the prokaryotes. I would like to thank the authors of all commentaries on this article[2–6], and here I try to address the most important issues raised in them.Golberg [2] stresses that for different bacteria, the range of electric fields strengths causing reversible electropora-tion with ability for DNA uptake generally differs, and so does the range of electric field strengths causing irreversibleelectroporation with DNA release. This is true for prokaryotic organisms in general (both bacteria and archaea), andconsequently, in the area where some prokaryotic species are electroporated irreversibly, others may be electroporatedreversibly, avoiding the need for DNA to travel from the area where it is released from an irreversibly porated prokary-ote to the area where it can enter a reversibly porated prokaryote and transform it. As I tried to emphasize in the lastparagraph of Section 3.1 in my review article [1], the ranges of reversible and irreversible electroporation overlap evenfor prokaryotic organisms belonging to a single strain, because individual organisms vary in their size (due to beingin different stages of the division cycle) and in their orientation with respect to the field direction, and also becausepore formation is to some extent stochastic. But indeed, for two randomly sampled organisms belonging to differentstrains, there will – at least on average – be larger differences in their shape, size, as well as in composition of theirwall and membrane, than if the two organisms being compared are of the same strain. Furthermore, the more distantthe two strains are phylogenetically, the more pronounced – again, at least on average – most of these differenceswill be. With increasing differences between the donor and the acceptor, the availability of DNA released from the

Mechanisms of abiotic horizontal gene transfer: Comment on “Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer” by Tadej Kotnik

Results suggestive of horizontal (lateral) gene transfer, attributed at the time to mutations, have been published since early 20th century [3]. Recent advances in gene sequencing technology have set on solid ground the idea that horizontal (lateral) gene transfer (HTG) is an important factor in evolution [10,11]. There is an increasing interest in this phenomenon [4,8,12], which is now thought to be largely responsible for the growing number of antibiotic resistant bacteria in the world [23]. In this issue, Kotnik, has developed a convincing hypothesis that lightning induced electroporation and electrofusion could be a mechanism for abiotic horizontal gene transfer [13]. Electroporation and electrofusion, described in detail in [13], are mechanisms that involve the application of certain electric fields across a cell and the consequent formation of defects in the cell membrane. These defects can be reversible or irreversible. Reversible electroporation is commonly used for gene transfection and cell fusion while irreversible electroporation is used for cell ablation [13]. Lightning produces a range of electric fields that include those for reversible electroporation, irreversible electroporation and fusion. It is reasonable to assume that microorganisms and viruses exposed to lightning could be exposed to a combination of electric fields that will produce abiotic horizontal gene transfer, as suggested by Kotnik [13]. In fact, the group of Rafael Lee has shown that lightning can cause irreversible electroporation injury to tissue [1,14]. The idea that lighting can cause abiotic lateral gene transfer is somewhat reminiscent of the idea of abiogenesis and the classical experiment of Miller and Urey [17,18]. Could other mechanisms proposed for abiogenesis be also involved in abiotic gene transfer? The clay hypothesis for abiogenesis proposed by Cairns-Smith [2] or the Wachtershauser [7] hypothesis for an iron sulfur world or Mulkidjanian’s [16] hypothesis of the Zn-world theory leads to thinking about micro and nano electroporation [5,6]. Clays and pyrite are structures with local electric charges. We have shown that when cells pass across surfaces with charges separated by nanometer distances the electric fields that are produced are sufficient to cause electroporation and electrolysis induced reversible and irreversible poration of the cell membrane [20,21]. We have also shown that it is sufficient for only part of the cell membrane to be exposed to electroporation fields for electroporation to occur [5,6]. Fig. 1 illustrates the electric field that would develop across a cell membrane when the cell flows across a substrate in which two small charges with a potential difference of 0.1 V are separated by a 100-nanometer gap. Even in the absence of native charges, an electrolytic process

The impact of pulsed electric fields on cells and biomolecules: Comment on “Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer” by Tadej Kotnik

The discovery of a horizontal gene transfer (HGT) revolutionized the evolutionary biology. Suddenly, a long developed concept of a phylogenetic tree, where all organisms share a common ancestor, could not describe the outcome of gene transfer between perceived unrelated organisms [1]. Consequently, a new concept – net of life – is emerging [1]. In the “net of life”, each organisms is a combination of shared ancestry and HGT [2]. T. Kotnik reviews the history of biological classification in the human history and positions the role of HGT in the transformation of “phylogenetic tree” to the “net of life” [3]. Although the most frequent mechanisms for HGT are biological: bacterial conjugation, bacterial competence for DNA uptake and viral transduction, T. Kotnik emphasized in this work the role of a physical phenomena – lightning – as a potential trigger of HGT. To answer the question, if HGT could happen before biological mechanisms had evolved, T. Kotnik analyzes the potential of lightening induced electroporation on HGT. Electroporation is the increase of biological cell membrane permeabilization by externally applied pulsed electric fields (PEF) [4], probably by the formation of aqueous pores in the cell membrane [5–7]. As described by T. Kotnik, the formation of pores leads to reversible electroporation (REP), electrofusion (EF), and irreversible electroporation (IEP). I would like to point out to two important properties of PEF: 1) heterogeneity of microbial population response to PEF and 2) the effects of PEF on biomolecules. In the natural marine and fresh water environments, more than two million bacteria species exist [8]. Research on food disinfection by PEF showed the tremendous variation in the different species resistance to PEF. Bacterial properties that affect the electroporation threshold are cell size and shape [9], membrane structure [10], membrane charge [11], cells concentration [12] and growth stage [13]. Given the large number of species of bacteria in marine environment it is likely that IEP, REP and EF happen simultaneously at the same depth. It appears that in nature, the number of species plays a significant role in the PEF induced effects in the population: increasing the number of species increases the probability of each of the IEP, REP and EF events. This is different from classical laboratory electroporation studies where PEF are applied on a single species to induce the desired single effect.

Competence and natural transformation in vibrios

Natural transformation is a major mechanism of horizontal gene transfer in bacteria. By incorporating exogenous DNA elements into chromosomes, bacteria are able to acquire new traits that can enhance their fitness in different environments. Within the past decade, numerous studies have revealed that natural transformation is prevalent among members of the Vibrionaceae, including the pathogen Vibrio cholerae. Four environmental factors: (i) nutrient limitation, (ii) availability of extracellular nucleosides, (iii) high cell density and (iv) the presence of chitin, promote genetic competence and natural transformation in Vibrio cholerae by co-ordinating expression of the regulators CRP, CytR, HapR and TfoX respectively. Studies of other Vibrionaceae members highlight the general importance of natural transformation within this bacterial family.

Natural transformation as a mechanism of horizontal gene transfer among environmental Aeromonas species

Aeromonas species are common inhabitants of aquatic environments and relevant as human pathogens. Their potential as pathogens may be related in part to lateral transfer of genes associated with toxin production, biofilm formation, antibiotic resistance, and other virulence determinants. Natural transformation has not been characterized in aeromonads. DNA from wild-type, prototrophic strains that had been isolated from environmental sources was used as donor DNA in transformation assays with auxotrophs as the recipients. Competence was induced in 20% nutrient broth during the stationary phase of growth. Optimal transformation assay conditions for one chosen isolate were in Tris buffer with magnesium or calcium, pH 5–8, and a saturating concentration of 0.5μg of DNA per assay (3.3ng of DNA μl−1) at 30°C. Sodium was also required and could not be replaced with ammonium, potassium, or lithium. The maximal transformation frequency observed was 1.95×10−3 transformants (recipient cell)−1. A survey of environmental Aeromonas auxotrophic recipients (n=37), assayed with donor DNA from other wild-type environmental aeromonads under optimal assay conditions, demonstrated that 73% were able to act as recipients, and 100% were able to act as donors to at least some other aeromonads. Three different transformation groups were identified based on each isolates’ ability to transform other strains with its DNA. The transformation groups roughly corresponded to phylogenetic groups. These results demonstrate that natural transformation is a general property of Aeromonas environmental isolates with implications for the genetic structures of coincident Aeromonas populations.

Bacterial sex in dental plaque

Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

Characterization of Plasmid pML21 of Enterococcus faecalis ML21 from Koumiss

Plasmid mobilization has been recognized as the major mechanism for horizontal gene transfer in the evolution of antibiotic-resistant Enterococcus faecalis strains capable of causing human infection [1]. An investigation of plasmid distribution in E. faecalis and an analysis of their role in the dissemination of antimicrobial resistance can contribute to revealing the differences in the properties of clinically relevant versus probiotic strains of E. faecalis. Although a large number of E. faecalis plasmids have been sequenced and characterized, very few are from probiotic strains [2]. Many native plasmids from other lactic acid bacteria, such as lactobacilli and lactococci, have been used for the design of molecular tools, especially food-grade cloning and expression vectors [3, 4]. Although many E. faecalis strains isolated from food harbor abundant natural plasmids [5], only a few have been developed into valuable tools for biotechnological applications. Enterococcus faecalis strain ML21 (CGMCC No. 6166) was originally isolated from the koumiss produced by nomadic families of the Ili pastoral area of Xinjiang Uyghur Autonomous Region, China. Susceptibility testing by the agar disk diffusion method showed that the isolate is susceptible to vancomycin and some other antibiotics (e.g., erythromycin, chloramphenicol, and ampicillin). This susceptibility is remarkably different from the vast majority of enterococci from clinical cases [6]. E. faecalis ML21 harbors a native plasmid, designated pML21. DNA sequencing on an ABI 3730XL DNA Analyzer (Applied Biosystems Inc., Foster City, CA) showed that this plasmid is 5,598 bp in size with 32.9 % G?C, and is predicted to carry five putative open reading frames (ORFs) (Fig. 1a). Sequence analysis of the replicon region (ORF1, ORF2, and the sequence upstream of ORF1) of pML21 revealed that it is a member of the pCI305 family of plasmids, belonging to the group of lactococcal theta-type replicons [8], which differ from the rep9 family replicon plasmids that are prevalent in clinical strains of E. faecalis [2]. We therefore speculated that horizontal gene transfer might have occurred between E. faecalis ML21 and lactococcal strains in this niche, as the fermented dairy product koumiss contains a complex microbial ecological community. The plasmid also contains an e antitoxin component of the e/f-type toxin–antitoxin system (encoded by ORF5) but interestingly, no cognate toxin gene was detected on this plasmid. Based on homology blast, pML21 ORF3 was predicted to encode an abortive infection phage resistance (AIPR) protein which is often found in restriction–modification system operons. ORF3 and ORF4 were found likely to be under the control of a specific bidirectional promoter in pML21. ORF4 was predicted to encode a hypothetical MerR family transcriptional regulator protein, but its function remains unknown. The relative copy number of this plasmid was estimated to be about 137.81 ± 3.20 copies per cell, as determined by quantitative real-time PCR [9], higher than that of other closely related plasmids [10, 11]. To develop molecular tools using pML21, an Escherichia coli lactic acid bacteria shuttle vector designated pML23e was constructed (Fig. 1b). This vector was able to transform all tested lactic acid bacteria strains, including E. faecalis ML21, Lactococcus lactis subsp. cremoris MG1363, F. Zuo X. Feng X. Sun C. Du S. Chen (&) Key Laboratory of Functional Dairy Science of Chinese Ministry of Education and Municipal Government of Beijing, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, People’s Republic of China e-mail: swchen@cau.edu.cn

Antibiotic Resistance: From Darwin to Lederberg to Keynes

The emergence and spread of antibiotic-resistant bacteria reflects both, a gradual, completely Darwinian evolution, which mostly yields slight decreases in antibiotic susceptibility, along with phenotypes that are not precisely characterized as "resistance"; and sudden changes, from full susceptibility to full resistance, which are driven by a vast array of horizontal gene transfer mechanisms. Antibiotics select for more than just antibiotic resistance (i.e., increased virulence and enhanced gene exchange abilities); and many non-antibiotic agents or conditions select for or maintain antibiotic resistance traits as a result of a complex network of underlying and often overlapping mechanisms. Thus, the development of new antibiotics and thoughtful, integrated anti-infective strategies is needed to address the immediate and long-term threat of antibiotic resistance. Since the biology of resistance is complex, these new drugs and strategies will not come from free-market forces, or from "incentives" for pharmaceutical companies.

Diversity of integrating conjugative elements in actinobacteria

Conjugation is certainly the most widespread and promiscuous mechanism of horizontal gene transfer in bacteria. During conjugation, DNA translocation across membranes of two cells forming a mating pair is mediated by two types of mobile genetic elements: conjugative plasmids and integrating conjugative elements (ICEs). The vast majority of conjugative plasmids and ICEs employ a sophisticated protein secretion apparatus called type IV secretion system to transfer to a recipient cell. Yet another type of conjugative DNA translocation machinery exists and to date appears to be unique to conjugative plasmids and ICEs of the Actinomycetales order, a sub-group of high G + C Gram-positive bacteria. This conjugative system is reminiscent of the machinery that allows segregation of chromosomal DNA during bacterial cell division and sporulation, and relies on a single FtsK-homolog protein to translocate double-stranded DNA molecules to the recipient cell. Recent thorough sequence analyses reveal that while this latter strategy appears to be used by the majority of ICEs in Actinomycetales, the former is also predicted to be important in exchange of genetic material in actinobacteria.

Connecting Environment and Genome Plasticity in the Characterization of Transformation-Induced SOS Regulation and Carbon Catabolite Control of the Vibrio cholerae Integron Integrase

The human pathogen Vibrio cholerae carries a chromosomal superintegron (SI). The SI contains an array of hundreds of gene cassettes organized in tandem which are stable under conditions when no particular stress is applied to bacteria (such as during laboratory growth). Rearrangements of these cassettes are catalyzed by the activity of the associated integron integrase. Understanding the regulation of integrase expression is pivotal to fully comprehending the role played by this genetic reservoir for bacterial adaptation and its connection with the development of antibiotic resistance. Our previous work established that the integrase is regulated by the bacterial SOS response and that it is induced during bacterial conjugation. Here, we show that transformation, another horizontal gene transfer (HGT) mechanism, also triggers integrase expression through SOS induction, underlining the importance of HGT in genome plasticity. Moreover, we report a new cyclic AMP (cAMP)-cAMP receptor protein (CRP)-dependent regulation mechanism of the integrase, highlighting the influence of the extracellular environment on chromosomal gene content. Altogether, our data suggest an interplay between different stress responses and regulatory pathways for the modulation of the recombinase expression, thus showing how the SI remodeling mechanism is merged into bacterial physiology.

The distribution of plasmids that carry virulence and resistance genes in Staphylococcus aureus is lineage associated

BackgroundStaphylococcus aureus is major human and animal pathogen. Plasmids often carry resistance genes and virulence genes that can disseminate through S. aureus populations by horizontal gene transfer (HGT) mechanisms. Sequences of S. aureus plasmids in the public domain and data from multi-strain microarrays were analysed to investigate (i) the distribution of resistance genes and virulence genes on S. aureus plasmids, and (ii) the distribution of plasmids between S. aureus lineages.ResultsA total of 21 plasmid rep gene families, of which 13 were novel to this study, were characterised using a previously proposed classification system. 243 sequenced plasmids were assigned to 39 plasmid groups that each possessed a unique combination of rep genes. We show some resistance genes (including ermC and cat) and virulence genes (including entA, entG, entJ, entP) were associated with specific plasmid groups suggesting there are genetic pressures preventing recombination of these genes into novel plasmid groups. Whole genome microarray analysis revealed that plasmid rep, resistance and virulence genes were associated with S. aureus lineages, suggesting restriction-modification (RM) barriers to HGT of plasmids between strains exist. Conjugation transfer (tra) complex genes were rare.ConclusionThis study argues that genetic pressures are restraining the spread of resistance and virulence genes amongst S. aureus plasmids, and amongst S. aureus populations, delaying the emergence of fully virulent and resistant strains.

The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons

Bacteria are key in the biodegradation of polycyclic aromatic hydrocarbons (PAH), which are widespread environmental pollutants. At least six genotypes of PAH degraders are distinguishable via phylogenies of the ring-hydroxylating dioxygenase (RHD) that initiates bacterial PAH metabolism. A given RHD genotype can be possessed by a variety of bacterial genera, suggesting horizontal gene transfer (HGT) is an important process for dissemination of PAH-degrading genes. But, mechanisms of HGT for most RHD genotypes are unknown. Here, we report in silico and functional analyses of the phenanthrene-degrading bacterium Delftia sp. Cs1-4, a representative of the phnAFK2 RHD group. The phnAFK2 genotype predominates PAH degrader communities in some soils and sediments, but, until now, their genomic biology has not been explored. In the present study, genes for the entire phenanthrene catabolic pathway were discovered on a novel ca. 232 kb genomic island (GEI), now termed the phn island. This GEI had characteristics of an integrative and conjugative element with a mobilization/stabilization system similar to that of SXT/R391-type GEI. But, it could not be grouped with any known GEI, and was the first member of a new GEI class. The island also carried genes predicted to encode: synthesis of quorum sensing signal molecules, fatty acid/polyhydroxyalkanoate biosynthesis, a type IV secretory system, a PRTRC system, DNA mobilization functions and >50 hypothetical proteins. The 50% G + C content of the phn gene cluster differed significantly from the 66.7% G + C level of the island as a whole and the strain Cs1-4 chromosome, indicating a divergent phylogenetic origin for the phn genes. Collectively, these studies added new insights into the genetic elements affecting the PAH biodegradation capacity of microbial communities specifically, and the potential vehicles of HGT in general.

Widespread impact of horizontal gene transfer on plant colonization of land.

In complex multicellular eukaryotes such as animals and plants, horizontal gene transfer is commonly considered rare with very limited evolutionary significance. Here we show that horizontal gene transfer is a dynamic process occurring frequently in the early evolution of land plants. Our genome analyses of the moss Physcomitrella patens identified 57 families of nuclear genes that were acquired from prokaryotes, fungi or viruses. Many of these gene families were transferred to the ancestors of green or land plants. Available experimental evidence shows that these anciently acquired genes are involved in some essential or plant-specific activities such as xylem formation, plant defence, nitrogen recycling as well as the biosynthesis of starch, polyamines, hormones and glutathione. These findings suggest that horizontal gene transfer had a critical role in the transition of plants from aquatic to terrestrial environments. On the basis of these findings, we propose a model of horizontal gene transfer mechanism in nonvascular and seedless vascular plants.