Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria

Thomas, Christopher M.; Nielsen, Kaare M.

doi:10.1038/nrmicro1234

Cited by 1,707 publications

(1,482 citation statements)

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“…In silico analyses of gene transfer patterns indicate that HGT is much more frequent between closely related organisms than between distantly related ones 9,11,71 . This is consistent with the idea that GTAs have played an important part in creating such HGT patterns, as GTA-mediated HGT requires specific interactions between the host and the GTA particle for successful attachment and injection of the DNA 72 , as well as DNA sequence similarity to facilitate incorporation of a transferred allele by homologous recombination 14 .…”

Section: Transfer Of Packaged Dna Into Recipient Cellssupporting

confidence: 87%

“…For illegitimate recombination, in which the incoming DNA is not homologous to the recipient DNA, the frequency is expected to be orders of magnitude lower than the frequency for homologous sequences, especially for linear fragments as opposed to circular molecules, as reviewed elsewhere 14 . In silico analyses of gene transfer patterns indicate that HGT is much more frequent between closely related organisms than between distantly related ones 9,11,71 .…”

Section: Transfer Of Packaged Dna Into Recipient Cellsmentioning

confidence: 99%

“…6,9,11,12 . Such patterns are probably a consequence of existing barriers to HGT, which have been reviewed in detail elsewhere 13,14 . …”

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Gene transfer agents: phage-like elements of genetic exchange

2012

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Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.The prevalence of horizontal gene transfer (HGT), in which DNA is exchanged between closely or distantly related lineages, has altered the way we think about evolution 1,2 , having profound effects on our views of the evolutionary relationships among living organisms. It has caused a shift from a bifurcating 'tree of life' view to a 'net of life' or 'web of life' view [3][4][5] , in which "highways of gene sharing" (REF. 6) represent major connections, with genes (or DNA segments) viewed as "public goods, available for all organisms to integrate into their genomes" (REF. 7). HGT occurs within and between all three domains of life, and it has been estimated that 0.05-80% of genes in bacterial and archaeal genomes have been affected by HGT, depending on the analytical method used and the genome analysed [8][9][10] . Although HGT is widespread, it is not random: patterns of preferential gene exchange among specific groups of organisms that share ancestry or habitat have been * Present address. aslang@mun.ca; olgazh@dartmouth.edu; j.beatty@mail.ubc.ca Competing interests statementThe authors declare no competing financial interests. 6,9,11,12 . Such patterns are probably a consequence of existing barriers to HGT, which have been reviewed in detail elsewhere 13,14 . FURTHER INFORMATIONAlthough we have known about some HGT mechanisms for decades, novel processes that expand the existing repertoire of gene exchange methods are continually being identified. Transformation was the first mechanism of gene exchange to be discovered 15 , wherein DNA is taken up directly from the environment (reviewed elsewhere 16,17 ). In transduction, DNA transfer is mediated by viral particles (BOX 1). In conjugation, which was discovered in the 1940s 18 , DNA is transferred from a donor to a recipient cell during cell-to-cell contact; conjugation is used in the transfer of plasmids, transposons, integrons, and integrative and conjugative elements (ICEs) [19][20][21] . There are other modes of gene exchange that do not fit well into any of these three canonical mechanisms, including temporary cell fusion followed by chromosomal recombination and plasmid exchange 22 , intercellular connection through nanotubes 23 , and the release of membrane vesicles containing chromosomal, plasmid and phage DNA that can then merge with nearby cells 24 . In addition, a novel mechanism of gene transfer that has feature...

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Section: Transfer Of Packaged Dna Into Recipient Cellssupporting

confidence: 87%

Section: Transfer Of Packaged Dna Into Recipient Cellsmentioning

confidence: 99%

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Gene transfer agents: phage-like elements of genetic exchange

2012

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“…The first group of T4S systems are called conjugative T4S systems and members of this group transfer DNA from a donor to a recipient cell (de la Cruz et al , 2010). This process contributes to the spread of antibiotic resistance genes among different bacterial species and is also instrumental in bacterial adaptation to environmental changes (Thomas & Nielsen, 2005). The second group of T4S systems are responsible for DNA release or uptake to or from the extracellular milieu, respectively: these T4S systems operate in bacterial species such as Neisseria gonorrhoeae and Helicobacter pylori (Karnholz et al , 2006; Ramsey et al , 2011).…”

Section: Introductionmentioning

confidence: 99%

Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery

et al. 2017

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Type IV secretion (T4S) systems are versatile bacterial secretion systems mediating transport of protein and/or DNA. T4S systems are generally composed of 11 VirB proteins and 1 VirD protein (VirD4). The VirB1‐11 proteins assemble to form a secretion machinery and a pilus while the VirD4 protein is responsible for substrate recruitment. The structure of VirD4 in isolation is known; however, its structure bound to the VirB1‐11 apparatus has not been determined. Here, we purify a T4S system with VirD4 bound, define the biochemical requirements for complex formation and describe the protein–protein interaction network in which VirD4 is involved. We also solve the structure of this complex by negative stain electron microscopy, demonstrating that two copies of VirD4 dimers locate on both sides of the apparatus, in between the VirB4 ATPases. Given the central role of VirD4 in type IV secretion, our study provides mechanistic insights on a process that mediates the dangerous spread of antibiotic resistance genes among bacterial populations.

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“…the shiga-like toxin encoding genes in the O157 plasmid of E. coli) might increase the sensitivity of the test with respect to genomic sequences, being plasmids present in multiple copies in each cell. However, the use of these sequences as target could lead to the incorrect classification of the detected bacteria, due to the high ratio of horizontal plasmid transfer, even between different species [56].…”

Section: Choice Of the Target Genementioning

confidence: 99%

Potentials and limitations of molecular diagnostic methods in food safety

Lauri

Mariani

2008

Genes Nutr

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Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed.

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Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria

Cited by 1,707 publications

References 161 publications

Gene transfer agents: phage-like elements of genetic exchange

Gene transfer agents: phage-like elements of genetic exchange

Structure of a VirD4 coupling protein bound to a VirB type IV secretion machinery

Potentials and limitations of molecular diagnostic methods in food safety

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