scholarly journals Genome analysis and gene nblA identification of Microcystis aeruginosa myovirus (MaMV-DC) reveal the evidence for horizontal gene transfer events between cyanomyovirus and host

2015 ◽  
Vol 96 (12) ◽  
pp. 3681-3697 ◽  
Author(s):  
Tong Ou ◽  
Xiao-Chan Gao ◽  
San-Hua Li ◽  
Qi-Ya Zhang
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Microcystis Aeruginosa ◽  
Trna Gene ◽  
Genetic Characterization ◽  
Significant Decline ◽  
Lake Dianchi ◽  
Protein Coding ◽  
Efficient Expression ◽  
Insight Into

The genome sequence, genetic characterization and nblA gene function of Microcystis aeruginosa myovirus isolated from Lake Dianchi in China (MaMV-DC) have been analysed. The genome DNA is 169 223 bp long, with 170 predicted protein-coding genes (001L–170L) and a tRNA gene. About one-sixth of these genes have homologues in the host cyanobacteria M. aeruginosa. The genome carries a gene homologous to host nblA, which encodes a protein involved in the degradation of cyanobacterial phycobilisome. Its expression during MaMV-DC infection was confirmed by reverse transcriptase PCR and Western blot detection and abundant expression was companied by the significant decline of phycocyanin content and massive release of progeny MaMV-DC. In addition, expressing MaMV-DC nblA reduced the phycocyanin peak and the phycocyanin to chlorophyll ratio in model cyanobacteria. These results confirm that horizontal gene transfer events have occurred between cyanobacterial host and cyanomyovirus and suggest that MaMV-DC carrying host-derived genes (such as 005L, that codes for NblA) is responsible for more efficient expression of cyanophage genes and release of progeny cyanophage. This study provides novel insight into the horizontal gene transfer in cyanophage and the interactions between cyanophage and their host.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Extensive horizontal gene transfer in cheese-associated bacteria

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Kevin S Bonham ◽  
Benjamin E Wolfe ◽  
Rachel J Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Conjugative plasmids: vessels of the communal gene pool

2009 ◽  
Vol 364 (1527) ◽  
pp. 2275-2289 ◽  
Author(s):  
Anders Norman ◽  
Lars H. Hansen ◽  
Søren J. Sørensen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Significant Contribution ◽  
Prokaryotic Genome ◽  
Whole Genome ◽  
Adaptive Traits ◽  
Conjugative Plasmids ◽  
Environmental Setting ◽  
Genome Analyses ◽  
Insight Into

Comparative whole-genome analyses have demonstrated that horizontal gene transfer (HGT) provides a significant contribution to prokaryotic genome innovation. The evolution of specific prokaryotes is therefore tightly linked to the environment in which they live and the communal pool of genes available within that environment. Here we use the term supergenome to describe the set of all genes that a prokaryotic ‘individual’ can draw on within a particular environmental setting. Conjugative plasmids can be considered particularly successful entities within the communal pool, which have enabled HGT over large taxonomic distances. These plasmids are collections of discrete regions of genes that function as ‘backbone modules’ to undertake different aspects of overall plasmid maintenance and propagation. Conjugative plasmids often carry suites of ‘accessory elements’ that contribute adaptive traits to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes’.

scholarly journals CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Sara J. Weaver ◽  
Davi R. Ortega ◽  
Matthew H. Sazinsky ◽  
Triana N. Dalia ◽  
Ankur B. Dalia ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Natural Transformation ◽  
Domain Architecture ◽  
Genetic Material ◽  
Surface Binding ◽  
Exogenous Dna ◽  
Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

scholarly journals Traffic at the tmRNA Gene

2003 ◽  
Vol 185 (3) ◽  
pp. 1059-1070 ◽  
Author(s):  
Kelly P. Williams
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Trna Gene ◽  
Attachment Site ◽  
Trna Genes ◽  
Site Specificity ◽  
Bacterial Genomes ◽  
Transcriptional Terminator ◽  
Significant Bias ◽  
Attachment Sites

ABSTRACT A partial screen for genetic elements integrated into completely sequenced bacterial genomes shows more significant bias in specificity for the tmRNA gene (ssrA) than for any type of tRNA gene. Horizontal gene transfer, a major avenue of bacterial evolution, was assessed by focusing on elements using this single attachment locus. Diverse elements use ssrA; among enterobacteria alone, at least four different integrase subfamilies have independently evolved specificity for ssrA, and almost every strain analyzed presents a unique set of integrated elements. Even elements using essentially the same integrase can be very diverse, as is a group with an ssrA-specific integrase of the P4 subfamily. This same integrase appears to promote damage routinely at attachment sites, which may be adaptive. Elements in arrays can recombine; one such event mediated by invertible DNA segments within neighboring elements likely explains the monophasic nature of Salmonella enterica serovar Typhi. One of a limited set of conserved sequences occurs at the attachment site of each enterobacterial element, apparently serving as a transcriptional terminator for ssrA. Elements were usually found integrated into tRNA-like sequence at the 3′ end of ssrA, at subsites corresponding to those used in tRNA genes; an exception was found at the non-tRNA-like 3′ end produced by ssrA gene permutation in cyanobacteria, suggesting that, during the evolution of new site specificity by integrases, tropism toward a conserved 3′ end of an RNA gene may be as strong as toward a tRNA-like sequence. The proximity of ssrA and smpB, which act in concert, was also surveyed.

scholarly journals Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Rob J. L. Willems ◽  
Janetta Top ◽  
Willem van Schaik ◽  
Helen Leavis ◽  
Marc Bonten ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Enterococcus Faecium ◽  
Population Genetic ◽  
Effective Control ◽  
Phylogenomic Analysis ◽  
Content Type ◽  
Sequence Types ◽  
Insight Into

ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. IMPORTANCE Multiresistant Enterococcus faecium has become one of the most important nosocomial pathogens, causing increasing numbers of nosocomial infections worldwide. Here, we used Bayesian population genetic analysis to identify groups of related E. faecium strains and show a significant association of hospital and farm animal isolates to different genetic groups. We also found that hospital isolates could be divided into three lineages originating from sequence types (STs) 17, 18, and 78. We propose that, driven by the selective pressure in hospitals, the three hospital lineages have arisen through horizontal gene transfer, but once adapted to the distinct pathogenic niche, this population has become isolated and recombination with other populations declines. Elucidation of the population structure is a prerequisite for effective control of multiresistant E. faecium since it provides insight into the processes that have led to the progressive change of E. faecium from an innocent commensal to a multiresistant hospital-adapted pathogen.

scholarly journals Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus

2019 ◽  
Vol 11 (10) ◽  
pp. 2774-2788 ◽  
Author(s):  
Hsin-Han Lee ◽  
Huei-Mien Ke ◽  
Chan-Yi Ivy Lin ◽  
Tracy J Lee ◽  
Chia-Lin Chung ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Size Variation ◽  
Sequence Divergence ◽  
Intergenic Sequence ◽  
Protein Coding ◽  
Genetic Lineages ◽  
Basidiomycetous Fungus ◽  
Mitochondrial Dnas ◽  
Phellinus Noxius

Abstract Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes’ intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.

scholarly journals Exploring tRNA gene cluster in archaea

2018 ◽  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Trna Gene ◽  
Gene Clusters ◽  
Gene Organization ◽  
Trna Genes ◽  
Genomic Analyses ◽  
Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

scholarly journals Horizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 305 ◽  
Author(s):  
Pragya Tiwari ◽  
Hanhong Bae
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genetic Material ◽  
Biological Species ◽  
Economic Importance ◽  
Comprehensive Analysis ◽  
Current Perspective ◽  
Novel Traits ◽  
The Impact ◽  
Insight Into

Horizontal gene transfer (HGT), an important evolutionary mechanism observed in prokaryotes, is the transmission of genetic material across phylogenetically distant species. In recent years, the availability of complete genomes has facilitated the comprehensive analysis of HGT and highlighted its emerging role in the adaptation and evolution of eukaryotes. Endophytes represent an ecologically favored association, which highlights its beneficial attributes to the environment, in agriculture and in healthcare. The HGT phenomenon in endophytes, which features an important biological mechanism for their evolutionary adaptation within the host plant and simultaneously confers “novel traits” to the associated microbes, is not yet completely understood. With a focus on the emerging implications of HGT events in the evolution of biological species, the present review discusses the occurrence of HGT in endophytes and its socio-economic importance in the current perspective. To our knowledge, this review is the first report that provides a comprehensive insight into the impact of HGT in the adaptation and evolution of endophytes.

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