scholarly journals Genomic Background Governs Opposing Responses to Nalidixic Acid Upon Megaplasmid Acquisition in Pseudomonas

2019 ◽  
Author(s):  
David A. Baltrus ◽  
Caitlin Smith ◽  
MacKenzie Derrick ◽  
Courtney Leligdon ◽  
Zoe Rosenthal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nalidixic Acid ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Horizontal Gene Transfer Event ◽  
Genetic Material ◽  
Fitness Costs ◽  
Transfer Event ◽  
Phenotypic Changes

AbstractHorizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of a ∼1Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid, but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance.ImportanceNumerous studies have demonstrated that gene transfer events (e.g. plasmid acquisition) can entail a variety of costs that arise as byproducts of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide new a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

scholarly journals Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in Pseudomonas

mSphere ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
David A. Baltrus ◽  
Caitlin Smith ◽  
MacKenzie Derrick ◽  
Courtney Leligdon ◽  
Zoe Rosenthal ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nalidixic Acid ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Genetic Material ◽  
Fitness Costs ◽  
Transfer Event ◽  
Content Type ◽  
Phenotypic Changes

ABSTRACT Horizontal gene transfer is a significant driver of evolutionary dynamics across microbial populations. Although the benefits of the acquisition of new genetic material are often quite clear, experiments across systems have demonstrated that gene transfer events can cause significant phenotypic changes and entail fitness costs in a way that is dependent on the genomic and environmental context. Here, we test for the generality of one previously identified cost, sensitization of cells to the antibiotic nalidixic acid after acquisition of an ∼1-Mb megaplasmid, across Pseudomonas strains and species. Overall, we find that the presence of this megaplasmid sensitizes many different Pseudomonas strains to nalidixic acid but that this same horizontal gene transfer event increases resistance of Pseudomonas putida KT2440 to nalidixic acid across assays as well as to ciprofloxacin under competitive conditions. These phenotypic results are not easily explained away as secondary consequences of overall fitness effects and appear to occur independently of another cost associated with this megaplasmid, sensitization to higher temperatures. Lastly, we draw parallels between these reported results and the phenomenon of sign epistasis for de novo mutations and explore how context dependence of effects of plasmid acquisition could impact overall evolutionary dynamics and the evolution of antimicrobial resistance. IMPORTANCE Numerous studies have demonstrated that gene transfer events (e.g., plasmid acquisition) can entail a variety of costs that arise as by-products of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize the presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here, we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer (HGT) event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

scholarly journals Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 543-558
Author(s):  
Shai Slomka ◽  
Itamar Françoise ◽  
Gil Hornung ◽  
Omer Asraf ◽  
Tammy Biniashvili ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Growth Yield ◽  
Genomic Variation ◽  
Bacterial Populations ◽  
Flagellar Proteins ◽  
Foreign Dna

Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.

scholarly journals Extensive Phenotypic Changes Associated with Large-scale Horizontal Gene Transfer

2013 ◽  
Author(s):  
Kevin Dougherty ◽  
Brian A Smith ◽  
Autum F Moore ◽  
Shannon Maitland ◽  
Chris Fanger ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Pseudomonas Stutzeri ◽  
Transfer Event ◽  
Small Plasmid ◽  
Phenotypic Changes ◽  
Evolutionary Trajectories ◽  
Evolutionary Consequences

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e. changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmid and phage, little is known about how size of the acquired region affects the magnitude or number of such costs. Here we describe an amazing breadth of phenotypic changes which occur after a large-scale horizontal transfer event (~1Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.

scholarly journals Horizontal transfer of the n-TASE gene cluster in Burkholderia seminalis TC3.4.2R3 inferred from phylogenetic and molecular methods

2021 ◽  
Author(s):  
Sarina Tsui ◽  
Welington Luiz Araújo
Keyword(s):  
Comparative Genomics ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Horizontal Gene Transfer Event ◽  
Donor Strain ◽  
Biotechnological Applications ◽  
Transfer Event ◽  
Species Phylogeny ◽  
Homologous Genes

Abstract This study describes the n-TASE cluster in Burkholderia seminalis TC3.4.2R3, which was present in B. contaminans (CP046609.1), but absent in other related Burkholderia species. Phylogeny, comparative genomics and molecular analysis indicated it is not common to B. seminalis species, presenting similarity with homologous genes presents Aquamicrobium sp. SK-2 and B. contaminans LMG23361, probably acquired by an HGT (Horizontal Gene Transfer) event. It was not possible to determine which was the most likely donor strain of the n-TASE cluster. The HGT event did not occur in all strains of the Bcc group, nor in the B. seminalis, but it did occur punctually in the strain B. seminalis TC34.2R3. It has a correlation in biotechnological applications related processes. Aiming at understanding the involvement of the n-TASE cluster in the interaction of this bacterium in the environment, genes in this cluster will be inactivated, next.

scholarly journals Features of a novel protein, rusticalin, from the ascidian Styela rustica reveal ancestral horizontal gene transfer event

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Maria A. Daugavet ◽  
Sergey Shabelnikov ◽  
Alexander Shumeev ◽  
Tatiana Shaposhnikova ◽  
Leonid S. Adonin ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Gene Transfer Event ◽  
Transfer Event ◽  
Styela Rustica ◽  
Novel Protein

scholarly journals The Phylogenomics of CRISPR-Cas System in Salmonella: an evolutionary race with housekeeping genes

2020 ◽  
Author(s):  
Simran Krishnakant Kushwaha ◽  
Chandrajit Lahiri ◽  
Bahaa Abdella ◽  
Sandhya Amol Marathe
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Virulence Factors ◽  
Horizontal Gene Transfer Event ◽  
Housekeeping Genes ◽  
Broad Host Range ◽  
Evolutionary Patterns ◽  
Transfer Event ◽  
Serovar Typhimurium ◽  
Cas Genes

AbstractSalmonellae display intricate evolutionary patterns comprising over 2500 serovars having diverse pathogenic profiles. The acquisition/exchange of various virulence factors influence the evolutionary framework. To gain insights into evolution of Salmonella as a pathogen in association with the CRISPR-Cas genes we performed phylogenetic surveillance across strains of 22 Salmonella serovars. The strains assorted into two main clades, pertaining to the differences in their CRISPR1-leader and cas operon. Considering Salmonella enterica subsp. enterica serovar Typhimurium and serovar Typhi as signature serovars, we classified the clades as CRISPR1-STM/cas-STM and CRISPR1-STY/cas-STY, respectively. Serovars of the two clades displayed better relatedness, concerning CRISPR-1 leader and cas operon, across genera than between themselves. This signifies the acquisition of CRISPR1/Cas region a horizontal gene transfer event owing to the presence of mobile genetic elements flanking CRISPR1 array. The CRISPR2 tree does not show such relation. Spacer mapping of the two CRISPR arrays suggests the construct to be canonical, with only 8.8% spacer conservation among the serovars. As opposed to broad-host-range serovars, the host-specific serovars harbor fewer spacers. All typhoidal serovars have CRISPR1-STY/cas-STY system. Comparison of CRISPR and cas phenograms with that of multilocus sequence typing (MLST) suggests differential evolution of CRISPR/Cas system implying supplementary roles beyond immunity.

scholarly journals Identification of a Tyrosine Decarboxylase Gene (tdcA) inStreptococcus thermophilus1TT45 and Analysis of Its Expression and Tyramine Production in Milk

2010 ◽  
Vol 77 (3) ◽  
pp. 1140-1144 ◽  
Author(s):  
Federica La Gioia ◽  
Lucia Rizzotti ◽  
Franca Rossi ◽  
Fausto Gardini ◽  
Giulia Tabanelli ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Gene Transfer Event ◽  
Streptococcus Thermophilus ◽  
Its Sequence ◽  
Tyrosine Decarboxylase ◽  
Critical Levels ◽  
Lactobacillus Curvatus ◽  
Transfer Event

ABSTRACTIn this study, a tyrosine decarboxylase gene (tdcA) was identified in 1 among 83Streptococcus thermophilusstrains tested. Its sequence, nearly identical to that of atdcAofLactobacillus curvatus, indicated a horizontal gene transfer event. Transcription in milk and the formation of critical levels of tyramine were observed in the presence of tyrosine.

scholarly journals Experimental determination of evolutionary barriers to horizontal gene transfer

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Hande Acar Kirit ◽  
Mato Lagator ◽  
Jonathan P. Bollback
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Protein Interactions ◽  
Evolutionary Dynamics ◽  
Horizontal Transmission ◽  
Protein Protein Interactions ◽  
New Host ◽  
Transfer Event ◽  
Fitness Effects ◽  
Serovar Typhimurium

Abstract Background Horizontal gene transfer, the acquisition of genes across species boundaries, is a major source of novel phenotypes that enables microbes to rapidly adapt to new environments. How the transferred gene alters the growth – fitness – of the new host affects the success of the horizontal gene transfer event and how rapidly the gene spreads in the population. Several selective barriers – factors that impact the fitness effect of the transferred gene – have been suggested to impede the likelihood of horizontal transmission, however experimental evidence is scarce. The objective of this study was to determine the fitness effects of orthologous genes transferred from Salmonella enterica serovar Typhimurium to Escherichia coli to identify the selective barriers using highly precise experimental measurements. Results We found that most gene transfers result in strong fitness costs. Previously identified evolutionary barriers — gene function and the number of protein-protein interactions — did not predict the fitness effects of transferred genes. In contrast, dosage sensitivity, gene length, and the intrinsic protein disorder significantly impact the likelihood of a successful horizontal transfer. Conclusion While computational approaches have been successful in describing long-term barriers to horizontal gene transfer, our experimental results identified previously underappreciated barriers that determine the fitness effects of newly transferred genes, and hence their short-term eco-evolutionary dynamics.

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