The Impact of Gene Silencing on Horizontal Gene Transfer and Bacterial Evolution

2016 ◽  
pp. 157-186 ◽  
Author(s):  
W.W. Navarre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Silencing ◽  
Bacterial Evolution ◽  
The Impact

Prediction of horizontal gene transfers in eukaryotes: approaches and challenges

2009 ◽  
Vol 37 (4) ◽  
pp. 792-795 ◽  
Author(s):  
John W. Whitaker ◽  
Glenn A. McConkey ◽  
David R. Westhead
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Present Review ◽  
Bacterial Evolution ◽  
Eukaryotic Evolution ◽  
Metabolic Evolution ◽  
Eukaryotic Genomes

HGT (horizontal gene transfer) is recognized as an important force in bacterial evolution. Now that many eukaryotic genomes have been sequenced, it has become possible to carry out studies of HGT in eukaryotes. The present review compares the different approaches that exist for identifying HGT genes and assess them in the context of studying eukaryotic evolution. The metabolic evolution resource metaTIGER is then described, with discussion of its application in identification of HGT in eukaryotes.

scholarly journals Beyond horizontal gene transfer: the role of plasmids in bacterial evolution

2021 ◽  
Author(s):  
Jerónimo Rodríguez-Beltrán ◽  
Javier DelaFuente ◽  
Ricardo León-Sampedro ◽  
R. Craig MacLean ◽  
Álvaro San Millán
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Bacterial Evolution

scholarly journals Adaptation by Ancient Horizontal Acquisition of Butyrate Metabolism Genes in Aggregatibacter actinomycetemcomitans

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Ahmed M. Moustafa ◽  
Senthil Kumar Velusamy ◽  
Lidiya Denu ◽  
Apurva Narechania ◽  
Daniel H. Fine ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Strong Association ◽  
Aggregatibacter Actinomycetemcomitans ◽  
Short Chain ◽  
Oral Microbiota ◽  
Content Type ◽  
History Of ◽  
The Impact

ABSTRACT Like the bacterial residents of the human gut, it is likely that many of the species in the human oral microbiota have evolved to better occupy and persist in their niche. Aggregatibacter actinomycetemcomitans (Aa) is both a common colonizer of the oral cavity and has been implicated in the pathogenesis of periodontal disease. Here, we present a whole-genome phylogenetic analysis of Aa isolates from humans and nonhuman primates that revealed an ancient origin for this species and a long history of association with the Catarrhini, the lineage that includes Old World monkeys (OWM) and humans. Further genomic analysis showed a strong association with the presence of a short-chain fatty acid (SCFA) catabolism locus (atoRDAEB) in many human isolates that was absent in almost all nonhuman OWM isolates. We show that this locus was likely acquired through horizontal gene transfer. When grown under conditions that are similar to those at the subgingival site of periodontitis (anaerobic, SCFA replete), Aa strains with atoRDAEB formed robust biofilms and showed upregulation of genes involved in virulence, colonization, and immune evasion. Both an isogenic deletion mutant and nonhuman primate isolates lacking the ato locus failed to grow in a robust biofilm under these conditions, but grew well under the carbohydrate-rich conditions similar to those found above the gumline. We propose that the acquisition of the ato locus was a key evolutionary step allowing Aa to utilize SCFAs, adapt, and modulate subgingival disease. IMPORTANCE There has been considerable interest in the impact of short-chain fatty acids (SCFAs) on inflammatory effects related to the microbiome. Here, we present evidence that SCFAs may also be important in disease by providing an energy source or disease-associated cue for colonizing pathogens. We propose that SCFAs allow Aggregatibacter actinomycetemcomitans (Aa) to adapt to the subgingival anaerobic environment, which is the site of human periodontitis. Under anaerobic, SCFA-rich conditions, human-derived Aa strains that possess butyrate metabolism genes form strong biofilms and upregulate virulence genes. Our phylogenetic analysis highlights a long history of evolution of Aa with its primate hosts and suggests that the acquisition of butyrate metabolism genes may have been a critical step in allowing Aa to colonize a new niche and cause disease in humans. Overall, this study highlights the important role that horizontal gene transfer may play in microbial adaptation and the evolution of infectious disease.

scholarly journals Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution

2004 ◽  
Vol 186 (19) ◽  
pp. 6575-6585 ◽  
Author(s):  
Pavel S. Novichkov ◽  
Marina V. Omelchenko ◽  
Mikhail S. Gelfand ◽  
Andrei A. Mironov ◽  
Yuri I. Wolf ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Orthologous Gene ◽  
Statistical Technique ◽  
Bacterial Evolution ◽  
Gene Sets ◽  
Genome Wide ◽  
Straight Line ◽  
Genome Scale ◽  
Bacterial Lineages

ABSTRACT We describe a simple theoretical framework for identifying orthologous sets of genes that deviate from a clock-like model of evolution. The approach used is based on comparing the evolutionary distances within a set of orthologs to a standard intergenomic distance, which was defined as the median of the distribution of the distances between all one-to-one orthologs. Under the clock-like model, the points on a plot of intergenic distances versus intergenomic distances are expected to fit a straight line. A statistical technique to identify significant deviations from the clock-like behavior is described. For several hundred analyzed orthologous sets representing three well-defined bacterial lineages, the α-Proteobacteria, the γ-Proteobacteria, and the Bacillus-Clostridium group, the clock-like null hypothesis could not be rejected for ∼70% of the sets, whereas the rest showed substantial anomalies. Subsequent detailed phylogenetic analysis of the genes with the strongest deviations indicated that over one-half of these genes probably underwent a distinct form of horizontal gene transfer, xenologous gene displacement, in which a gene is displaced by an ortholog from a different lineage. The remaining deviations from the clock-like model could be explained by lineage-specific acceleration of evolution. The results indicate that although xenologous gene displacement is a major force in bacterial evolution, a significant majority of orthologous gene sets in three major bacterial lineages evolved in accordance with the clock-like model. The approach described here allows rapid detection of deviations from this mode of evolution on the genome scale.

scholarly journals The proficiency of the original host species determines community-level plasmid dynamics

2020 ◽  
Author(s):  
Anastasia Kottara ◽  
James P.J. Hall ◽  
Michael A. Brockhurst
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Host Species ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Community Level ◽  
Mercury Resistance ◽  
Bacterial Evolution ◽  
Selection For ◽  
Selective Environment

ABSTRACTPlasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: Whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid. Plasmids reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid’s attributes and the selective environment, but also upon the proficiency of their host species.

scholarly journals Specificity and selective advantage of an exclusion system in the integrative and conjugative element ICEBs1 of Bacillus subtilis

2021 ◽  
Author(s):  
Kathleen P. Davis ◽  
Alan D. Grossman
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Cell Envelope ◽  
Donor Cell ◽  
High Specificity ◽  
Host Cells ◽  
Cell Contact ◽  
Bacterial Evolution ◽  
Potential Donor

AbstractIntegrative and conjugative elements (ICEs) are mobile genetic elements capable of transferring their own and other DNA. They contribute to the spread of antibiotic resistances and other important traits for bacterial evolution. Exclusion is a mechanism used by many conjugative plasmids and a few ICEs to prevent their host cell from acquiring a second copy of the cognate element. ICEBs1 of Bacillus subtilis has an exclusion mechanism whereby the exclusion protein YddJ in a potential recipient inhibits the activity of the ICEBs1-encoded conjugation machinery in a potential donor. The target of YddJ-mediated exclusion is the conjugation protein ConG (a VirB6 homolog). Here we defined the regions of YddJ and ConG that confer exclusion specificity and determined the importance of exclusion to host cells. Using chimeras that had parts of ConG from ICEBs1 and the closely related ICEBat1 we identified a putative extracellular loop of ConG that conferred specificity for exclusion by the cognate YddJ. Using chimeras of YddJ from ICEBs1 and ICEBat1 we identified two regions in YddJ needed for exclusion specificity. We also found that YddJ-mediated exclusion reduced death of donor cells following conjugation into recipients. Donor death was dependent on the ability of transconjugants to themselves become donors and was reduced under osmo-protective conditions, indicating that death was likely due to alterations in the donor cell envelope caused by excessive conjugation. We postulate that elements that can have high frequencies of transfer likely evolved exclusion mechanisms to protect the host cells from excessive death.ImportanceHorizontal gene transfer is a driving force in bacterial evolution, responsible for the spread of many traits, including antibiotic and heavy metal resistances. Conjugation, one type of horizontal gene transfer, involves DNA transfer from donor to recipient cells through conjugation machinery and direct cell-cell contact. Exclusion mechanisms allow conjugative elements to prevent their host from acquiring additional copies of the element, and are highly specific enabling hosts to acquire heterologous elements. We defined regions of the exclusion protein and its target in the conjugation machinery that convey high specificity of exclusion. We found that exclusion protects donors from cell death during periods of high transfer. This is likely important for the element to enter new populations of cells.

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