Special Issue "Horizontal Gene Transfer in Bacteria"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 11416

Special Issue Editor

Dr. Christian Lesterlin
E-Mail Website
Guest Editor
Molecular Microbiology and Structural Biochemistry (MMSB), University of Lyon 1, CNRS, INSERM, UMR5086, F-69367 Lyon, France
Interests: horizontal gene transfer; bacterial DNA conjugation; live-cell fluorescence

Special Issue Information

Dear Colleagues,

Bacterial genomes are highly dynamic. Unlike eukaryotes, which evolve by gradual mutation, bacteria have the ability to acquire entire sets of genes through horizontal gene transfer mechanisms, which accelerates their diversification, adaptation and survival in changing environments. Analysis of an increasing number of the bacterial genome sequences helped realize the importance of gene transfer in the bacterial world. The newly acquired genetic information may encode new metabolic properties, including pathogenesis, environmental adaptation and symbiotic lifestyle, as well as resistance to antimicrobials, now recognized as one of the biggest threats to public health. In addition, gene transfer shapes the genetic dynamics of bacterial populations within microbiota and, consequently, affects the interactive equilibrium they establish with their plant or animal host.

This Special Issue in Genes on “Horizontal Gene Transfer in Bacteria” will address the mechanisms by which bacterial species acquire new genetic material and associated functions, providing an overview of recent developments in specialized research topics and critical perspectives on upcoming challenges.

Dr. Christian Lesterlin
Guest Editor

Manuscript Submission Information

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Keywords

  • Horizontal gene transfer in bacteria
  • Dissemination of bacterial properties
  • Cellular mechanisms of DNA transfer and maintenance
  • Bacterial genome evolution

Published Papers (5 papers)

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Research

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Article
Vertical and Horizontal Transmission of ESBL Plasmid from Escherichia coli O104:H4
Genes 2020, 11(10), 1207; https://doi.org/10.3390/genes11101207 - 16 Oct 2020
Cited by 1 | Viewed by 1764
Abstract
Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. [...] Read more.
Multidrug resistance (MDR) often results from the acquisition of mobile genetic elements (MGEs) that encode MDR gene(s), such as conjugative plasmids. The spread of MDR plasmids is founded on their ability of horizontal transference, as well as their faithful inheritance in progeny cells. Here, we investigated the genetic factors involved in the prevalence of the IncI conjugative plasmid pESBL, which was isolated from the Escherichia coli O104:H4 outbreak strain in Germany in 2011. Using transposon-insertion sequencing, we identified the pESBL partitioning locus (par). Genetic, biochemical and microscopic approaches allowed pESBL to be characterized as a new member of the Type Ib partitioning system. Inactivation of par caused mis-segregation of pESBL followed by post-segregational killing (PSK), resulting in a great fitness disadvantage but apparent plasmid stability in the population of viable cells. We constructed a variety of pESBL derivatives with different combinations of mutations in par, conjugational transfer (oriT) and pnd toxin-antitoxin (TA) genes. Only the triple mutant exhibited plasmid-free cells in viable cell populations. Time-lapse tracking of plasmid dynamics in microfluidics indicated that inactivation of pnd improved the survival of plasmid-free cells and allowed oriT-dependent re-acquisition of the plasmid. Altogether, the three factors—active partitioning, toxin-antitoxin and conjugational transfer—are all involved in the prevalence of pESBL in the E. coli population. Full article
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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Article
ShadowCaster: Compositional Methods under the Shadow of Phylogenetic Models to Detect Horizontal Gene Transfers in Prokaryotes
Genes 2020, 11(7), 756; https://doi.org/10.3390/genes11070756 - 07 Jul 2020
Cited by 4 | Viewed by 1795
Abstract
Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex [...] Read more.
Horizontal gene transfer (HGT) plays an important role for evolutionary innovations within prokaryotic communities and is a crucial event for their survival. Several computational approaches have arisen to identify HGT events in recipient genomes. However, this has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Phylogenetic reconstruction methods turned out to be the most reliable ones, but they are not extensible to all genes/species and are computationally demanding when dealing with large datasets. In contrast, the so-called surrogate methods that use heuristic solutions either based on nucleotide composition patterns or phyletic distribution of BLAST hits can be applied easily to the genomic scale, but they fail in identifying common HGT events. Here, we present ShadowCaster, a hybrid approach that sequentially combines nucleotide composition-based predictions by support vector machines (SVMs) under the shadow of phylogenetic models independent of tree reconstruction, to improve the detection of HGT events in prokaryotes. ShadowCaster successfully predicted close and distant HGT events in both artificial and bacterial genomes. ShadowCaster detected HGT related to heavy metal resistance in the genome of Rhodanobacter denitrificans with higher accuracy than the most popular state-of-the-art computational approaches, encompassing most of the predicted cases made by other methods. ShadowCaster is released at the GitHub platform as an open-source software under the GPLv3 license. Full article
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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Article
Direct Visualization of Horizontal Gene Transfer by Transformation in Live Pneumococcal Cells Using Microfluidics
Genes 2020, 11(6), 675; https://doi.org/10.3390/genes11060675 - 20 Jun 2020
Cited by 3 | Viewed by 1372
Abstract
Natural genetic transformation is a programmed mechanism of horizontal gene transfer in bacteria. It requires the development of competence, a specialized physiological state during which proteins involved in DNA uptake and chromosomal integration are produced. In Streptococcus pneumoniae, competence is transient. It [...] Read more.
Natural genetic transformation is a programmed mechanism of horizontal gene transfer in bacteria. It requires the development of competence, a specialized physiological state during which proteins involved in DNA uptake and chromosomal integration are produced. In Streptococcus pneumoniae, competence is transient. It is controlled by a secreted peptide pheromone, the competence-stimulating peptide (CSP) that triggers the sequential transcription of two sets of genes termed early and late competence genes, respectively. Here, we used a microfluidic system with fluorescence microscopy to monitor pneumococcal competence development and transformation, in live cells at the single cell level. We present the conditions to grow this microaerophilic bacterium under continuous flow, with a similar doubling time as in batch liquid culture. We show that perfusion of CSP in the microfluidic chamber results in the same reduction of the growth rate of individual cells as observed in competent pneumococcal cultures. We also describe newly designed fluorescent reporters to distinguish the expression of competence genes with temporally distinct expression profiles. Finally, we exploit the microfluidic technology to inject both CSP and transforming DNA in the microfluidic channels and perform near real time-tracking of transformation in live cells. We show that this approach is well suited to investigating the onset of pneumococcal competence together with the appearance and the fate of transformants in individual cells. Full article
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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Article
Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids
Genes 2019, 10(11), 850; https://doi.org/10.3390/genes10110850 - 28 Oct 2019
Cited by 3 | Viewed by 1515
Abstract
Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, [...] Read more.
Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp. Full article
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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Review

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Review
Plasmid Transfer by Conjugation in Gram-Negative Bacteria: From the Cellular to the Community Level
Genes 2020, 11(11), 1239; https://doi.org/10.3390/genes11111239 - 22 Oct 2020
Cited by 39 | Viewed by 4549
Abstract
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of [...] Read more.
Bacterial conjugation, also referred to as bacterial sex, is a major horizontal gene transfer mechanism through which DNA is transferred from a donor to a recipient bacterium by direct contact. Conjugation is universally conserved among bacteria and occurs in a wide range of environments (soil, plant surfaces, water, sewage, biofilms, and host-associated bacterial communities). Within these habitats, conjugation drives the rapid evolution and adaptation of bacterial strains by mediating the propagation of various metabolic properties, including symbiotic lifestyle, virulence, biofilm formation, resistance to heavy metals, and, most importantly, resistance to antibiotics. These properties make conjugation a fundamentally important process, and it is thus the focus of extensive study. Here, we review the key steps of plasmid transfer by conjugation in Gram-negative bacteria, by following the life cycle of the F factor during its transfer from the donor to the recipient cell. We also discuss our current knowledge of the extent and impact of conjugation within an environmentally and clinically relevant bacterial habitat, bacterial biofilms. Full article
(This article belongs to the Special Issue Horizontal Gene Transfer in Bacteria)
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