scholarly journals Horizontal Gene Transfer and the Evolution of Microvirid Coliphage Genomes

2006 ◽  
Vol 188 (3) ◽  
pp. 1134-1142 ◽  
Author(s):  
D. R. Rokyta ◽  
C. L. Burch ◽  
S. B. Caudle ◽  
H. A. Wichman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Sparse Sampling ◽  
Apparent Difference ◽  
Genomic Evolution ◽  
Single Family ◽  
Bacterial Host ◽  
Double Stranded Dna ◽  
The Family

ABSTRACT Bacteriophage genomic evolution has been largely characterized by rampant, promiscuous horizontal gene transfer involving both homologous and nonhomologous source DNA. This pattern has emerged through study of the tailed double-stranded DNA (dsDNA) phages and is based upon a sparse sampling of the enormous diversity of these phages. The single-stranded DNA phages of the family Microviridae, including φX174, appear to evolve through qualitatively different mechanisms, possibly as result of their strictly lytic lifestyle and small genome size. However, this apparent difference could reflect merely a dearth of relevant data. We sought to characterize the forces that contributed to the molecular evolution of the Microviridae and to examine the genetic structure of this single family of bacteriophage by sequencing the genomes of microvirid phage isolated on a single bacterial host. Microvirids comprised 3.5% of the detectable phage in our environmental samples, and sequencing yielded 42 new microvirid genomes. Phylogenetic analysis of the genes contained in these and five previously described microvirid phages identified three distinct clades and revealed at least two horizontal transfer events between clades. All members of one clade have a block of five putative genes that are not present in any member of the other two clades. Our data indicate that horizontal transfer does contribute to the evolution of the microvirids but is both quantitatively and qualitatively different from what has been observed for the dsDNA phages.

scholarly journals A mobile genetic element increases bacterial host fitness by manipulating development

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Joshua M Jones ◽  
Ilana Grinberg ◽  
Avigdor Eldar ◽  
Alan D Grossman
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Mobile Genetic Elements ◽  
Selective Advantage ◽  
Host Cells ◽  
Bacterial Host ◽  
Host Fitness ◽  
Genetic Elements ◽  
Necessary And Sufficient ◽  
Integrative And Conjugative Element

Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element of Bacillus subtilis, provides to its host cells. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1 gene, devI (formerly ydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1 to increase host fitness, thereby increasing propagation of the element.

scholarly journals Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post–transfer refinement

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Joshua K Michener ◽  
Aline A Camargo Neves ◽  
Stéphane Vuilleumier ◽  
Françoise Bringel ◽  
Christopher J Marx
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Recombinant Strain ◽  
Mobile Genetic Element ◽  
Degradation Pathway ◽  
Environmental Isolates ◽  
Bacterial Host ◽  
Adaptive Process ◽  
Potential Applications ◽  
Effective Use

When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post–transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.

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 Gene Transfer of Functional Type VI Killing Genes by Natural Transformation

2017 ◽  
Author(s):  
Jacob Thomas ◽  
Samit S. Watve ◽  
William C. Ratcliff ◽  
Brian K. Hammer
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Direct Injection ◽  
Spatially Explicit ◽  
Type Vi Secretion System ◽  
Effector Genes ◽  
Type Vi Secretion ◽  
A Cell ◽  
Explicit Simulation

AbstractHorizontal gene transfer can have profound effects on bacterial evolution by allowing individuals to rapidly acquire adaptive traits that shape their strategies for competition. One strategy for intermicrobial antagonism often used by Proteobacteria is the genetically-encoded contact-dependent Type VI secretion system (T6SS); a weapon used to kill heteroclonal neighbors by direct injection of toxic effectors. Here, we experimentally demonstrate thatVibrio choleraecan acquire new T6SS effector genes via horizontal transfer and utilize them to kill neighboring cells. Replacement of one or more parental alleles with novel effectors allows the recombinant strain to dramatically outcompete its parent. Through spatially-explicit simulation modeling, we show that the HGT is risky: transformation brings a cell into conflict with its former clonemates, but can be adaptive when superior T6SS alleles are acquired. More generally, we find that these costs and benefits are not symmetric, and that high rates of HGT can act as hedge against competitors with unpredictable T6SS efficacy. We conclude that antagonism and horizontal transfer drive successive rounds of weapons-optimization and selective sweeps, dynamically shaping the composition of microbial communities.

scholarly journals Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists

2018 ◽  
Vol 84 (15) ◽  
Author(s):  
Reza Zolfaghari Emameh ◽  
Harlan R. Barker ◽  
Vesa P. Hytönen ◽  
Seppo Parkkila
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Carbonic Anhydrase ◽  
Horizontal Transfer ◽  
Bacterial Species ◽  
Critical Role ◽  
Genomic Islands ◽  
Ph Homeostasis ◽  
Gene Sequences ◽  
Biochemical Pathways

ABSTRACT Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. IMPORTANCE The evolutionary process is mediated by mobile genetic elements (MGEs), such as genomic islands (GIs). A gene or set of genes in the GIs is exchanged between and within various species through horizontal gene transfer (HGT). Based on the crucial role that GIs can play in bacterial survival and proliferation, they were introduced as environment- and pathogen-associated factors. Carbonic anhydrases (CAs) are involved in many critical biochemical pathways, such as the regulation of pH homeostasis and electrolyte transfer. Among the six evolutionary families of CAs, β-CA gene sequences are present in many bacterial species, which can be horizontally transferred to protists during evolution. This study shows the involvement of bacterial β-CA gene sequences in the GIs and suggests their horizontal transfer to protists during evolution.

scholarly journals Horizontal Transfer of Bacterial Cytolethal Distending Toxin B Genes to Insects

2019 ◽  
Vol 36 (10) ◽  
pp. 2105-2110 ◽  
Author(s):  
Kirsten I Verster ◽  
Jennifer H Wisecaver ◽  
Marianthi Karageorgi ◽  
Rebecca P Duncan ◽  
Andrew D Gloss ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Natural Enemies ◽  
Larval Stage ◽  
Horizontal Transfer ◽  
Parasitoid Wasps ◽  
Cytolethal Distending Toxin ◽  
Toxin B ◽  
Genes Encoding ◽  
Hamiltonella Defensa

Abstract Horizontal gene transfer events have played a major role in the evolution of microbial species, but their importance in animals is less clear. Here, we report horizontal gene transfer of cytolethal distending toxin B (cdtB), prokaryotic genes encoding eukaryote-targeting DNase I toxins, into the genomes of vinegar flies (Diptera: Drosophilidae) and aphids (Hemiptera: Aphididae). We found insect-encoded cdtB genes are most closely related to orthologs from bacteriophage that infect Candidatus Hamiltonella defensa, a bacterial mutualistic symbiont of aphids that confers resistance to parasitoid wasps. In drosophilids, cdtB orthologs are highly expressed during the parasitoid-prone larval stage and encode a protein with ancestral DNase activity. We show that cdtB has been domesticated by diverse insects and hypothesize that it functions in defense against their natural enemies.

scholarly journals Horizontal Transfer and the Evolution of Host-Pathogen Interactions

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Elena de la Casa-Esperón
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dna Sequences ◽  
Horizontal Transfer ◽  
Close Contact ◽  
Dna Transfer ◽  
Host Pathogen Interactions ◽  
Important Impact ◽  
Host Pathogen

Horizontal gene transfer has been long known in viruses and prokaryotes, but its importance in eukaryotes has been only acknowledged recently. Close contact between organisms, as it occurs between pathogens and their hosts, facilitates the occurrence of DNA transfer events. Once inserted in a foreign genome, DNA sequences have sometimes been coopted by pathogens to improve their survival or infectivity, or by hosts to protect themselves against the harm of pathogens. Hence, horizontal transfer constitutes a source of novel sequences that can be adopted to change the host-pathogen interactions. Therefore, horizontal transfer can have an important impact on the coevolution of pathogens and their hosts.

scholarly journals Exploring Antibiotic Susceptibility, Resistome and Mobilome Structure of Planctomycetes from Gemmataceae Family

2021 ◽  
Vol 13 (9) ◽  
pp. 5031
Author(s):  
Anastasia A. Ivanova ◽  
Kirill K. Miroshnikov ◽  
Igor Y. Oshkin
Keyword(s):  
Gene Transfer ◽  
Antimicrobial Resistance ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Antibiotic Susceptibility ◽  
Large Genome ◽  
Antimicrobial Resistance Genes ◽  
The Family ◽  
Terrestrial Environments ◽  
Environmental Bacteria

The family Gemmataceae accomodates aerobic, chemoorganotrophic planctomycetes with large genome sizes, is mostly distributed in freshwater and terrestrial environments. However, these bacteria have recently also been found in locations relevant to human health. Since the antimicrobial resistance genes (AMR) from environmental resistome have the potential to be transferred to pathogens, it is essential to explore the resistant capabilities of environmental bacteria. In this study, the reconstruction of in silico resistome was performed for all nine available gemmata genomes. Furthermore, the genome of the newly isolated yet-undescribed strain G18 was sequenced and added to all analyses steps. Selected genomes were screened for the presence of mobile genetic elements. The flanking location of mobilizable genomic milieu around the AMR genes was of particular interest since such colocalization may appear to promote the horizontal gene transfer (HGT) events. Moreover the antibiotic susceptibility profile of six phylogenetically distinct strains of Gemmataceae planctomycetes was determined.

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 Horizontal Transfer of Domains in ssrA gene Among Enterobacteriaceae

2021 ◽  
Author(s):  
Tamilmaran Nagarajan ¹ ◽  
Ramamoorthy Sankaranarayanan ¹ ◽  
Punitha Selvakumar ◽  
M. Hussain Munavar Munavar
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Horizontal Transfer ◽  
Messenger Rna ◽  
Recombination Detection Program ◽  
Recognition Sites ◽  
Detection Program ◽  
Functional Relevance ◽  
High Level

Abstract BackgroundThe tmRNA (transfer messenger RNA), encoded by ssrA gene, is involved in rescuing of stalled ribosomes by a process called trans-translation. Additionally, regions of the ssrA gene act as recognition sites for various integrases. Variations in ssrA genes were widely reported among the members of Enterobacteriaceae, but the functional relevance in the course of evolution are not well understood. In this study, we investigated the horizontal gene transfer of tmRNA among the members of Enterobacteriaceae. Methods and ResultsHorizontal gene transfer in tmRNA was found by predicting recombination signals in the tmRNA belong to Enterobacteriaceae using recombination detection program (RDP5). Our results revealed 7 recombination signals in tmRNA among different species. We further showed that the recombination signals was more in the domains present in the 3’ end than the domains in the 5’ end of tmRNA. Of note, the mRNA region, which codes for the peptide tag was reported in many recombination signals. Further, members belonging to genera Yersinia, Erwinia, Dickeya, and Enterobacter were highly represented in the recombination signatures.Conclusions Taken together, our results revealed a high level of recombination among specific regions of tmRNA of Enterobacteriaceae and suggest the possible role of recombination in the diversification of SsrA function in proteolysis and other pathways.

Sign in / Sign up

Export Citation Format

Share Document