scholarly journals Consecuencias de la transferencia horizontal de genes en la evolución genómica eucarionte [Consequences of horizontal gene transfer in eukaryotic genomic evolution]

2020 ◽  
Author(s):  
José Darío Martínez-Ezquerro
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Global Economy ◽  
Genetic Material ◽  
Evolutionary Process ◽  
Indirect Evidence ◽  
Genomic Evolution ◽  
P Gene ◽  
Lines Of Descent ◽  
La Red

Gene exchange between prokaryotes has long been recognized as an important biological process, to the extent that it has been proposed that a more suitable metaphor to describe the evolutionary process, at least in prokaryotes, should be that of "the web of life", where lines of descent not only diverge but also communicate and even fuse with each other, resulting in a reticulated pattern. This pattern partially describes and outlines the actual complexity because, with the exception of some ancestral horizontal gene transfer (HGT) events, it relegates most eukaryotes.In this work, I summarize the evidence on how such lines of descent diverge, communicate, and merge with each other, in both prokaryotes and eukaryotes, involving deep branches and recent divergences. In fact, both direct and indirect evidence shows the existence of active HGT mechanisms in eukaryotes, indicating that horizontal transfer of genetic material is an ongoing evolutionary process in these organisms, as important as it is in the case of prokaryotes. Some of the consequences in eukaryotic genomic evolution that this phenomenon implies include, as in prokaryotes, the acquisition of novel functions, reacquisition of lost genes, and incorporation of adaptive advantages.HGT involves not only phagocytic single-celled eukaryotes but all eukaryotes —protists, plants, fungi, and animals, including humans. This lateral transfer of genetic material occurs through homologous HGT mechanisms that also exist in bacteria: conjugation, transduction, endogenization, and transformation. Given the evidence, I suggest a global economy of genetic material among all current organisms: viruses, prokaryotes, and eukaryotes; fading the notion of barriers between species, as a result of the continuous horizontal circulation and use of available genetic material.Finally, I propose an ecological classification focused on the various interactions with which foreign genetic material is obtained, to facilitate the understanding of HGT as an ecological and evolutionary phenomenon, natural and global, that affects all organisms and involves all reservoirs of genetic material. **Resumen**Desde hace tiempo, se reconoce al intercambio de genes entre procariontes como un proceso biológico importante, al grado de que se ha propuesto que una metáfora más adecuada para describir el proceso evolutivo, al menos procarionte, debería ser la de “la red de la vida” en donde las líneas de la descendencia no sólo divergen sino también se comunican e incluso se fusionan unas con otras, dando como resultado un patrón reticulado. Este patrón describe y esquematiza parcialmente la complejidad real debido a que, con excepción de algunos eventos de transferencia horizontal de genes (THG) ancestrales, relega a la mayoría de los eucariontes.En este trabajo sintetizo la evidencia sobre cómo dichas líneas de descendencia divergen, se comunican y fusionan unas con otras, tanto en procariontes como en eucariontes, involucrando ramas profundas y divergencias recientes. De hecho, diversas evidencias tanto directas como indirectas, muestran la existencia de mecanismos de THG activos en los eucariontes, indicando que la transferencia horizontal de material genético es un proceso evolutivo actual en estos organismos, tan importante como lo es en el caso de los procariontes. Algunas de las consecuencias en la evolución genómica eucarionte que este fenómeno implica incluyen, al igual que en los procariontes, la adquisición de funciones novedosas, readquisición de genes perdidos e incorporación de ventajas adaptativas.La THG involucra no sólo a eucariontes unicelulares principalmente fagocíticos sino a todos los eucariontes —protistas, plantas, hongos y animales, incluyendo a los humanos. Esta transferencia lateral de material genético occure mediante mecanismos homólogos de THG que también existen en bacterias: conjugación, transducción, endogenización y transformación. Dada la evidencia, planteo una economía global del material genético entre todos los organismos actuales —virus, procariontes y eucariontes; desvaneciendo la noción de barreras entre las especies, resultado de la continua circulación horizontal y aprovechamiento del material genético disponible. Finalmente, propongo una clasificación ecológica centrada en las diversas interacciones con las que se obtiene el material genético foráneo, para facilitar el entendimiento de la THG como un fenómeno ecológico y evolutivo, natural y global, que afecta a todos los organismos e involucra a todos los reservorios de material genético.

scholarly journals Horizontal Gene Transfer Involving Chloroplasts

2021 ◽  
Vol 22 (9) ◽  
pp. 4484
Author(s):  
Ewa Filip ◽  
Lidia Skuza
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Driving Force ◽  
Genetic Material ◽  
Adaptive Significance ◽  
Chloroplast Genomes ◽  
Organelle Genomes ◽  
Number Of Genes ◽  
Cellular Compartments

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

scholarly journals Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

2014 ◽  
Vol 83 (4) ◽  
pp. 317-323 ◽  
Author(s):  
Maria Virginia Sanchez-Puerta
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Plant Mitochondria ◽  
Genetic Material ◽  
Single Copy ◽  
Convincing Evidence ◽  
Cell Contact ◽  
Plant Mtdna ◽  
Nuclear Genomes ◽  
Foreign Genes

This review focuses on plant-to-plant horizontal gene transfer (HGT) involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA) of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting) facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

scholarly journals Trasposon Mediated Horizontal Gene Transfer (T-HGT) of Circulating Tumor DNA Reshapes MM Clonal Architecture

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 3065-3065
Author(s):  
Munevver Cinar ◽  
Steven Flygare ◽  
Marina Mosunjac ◽  
Ganji Nagaraju ◽  
Dongkyoo Park ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Drug Sensitivity ◽  
Genetic Material ◽  
Host Cells ◽  
Response To Treatment ◽  
Hierarchical Architecture ◽  
Tumor Evolution ◽  
Sequencing Analysis

Spatial genetic heterogeneity is a characteristic phenomenon that influences multiple myeloma's (MM) phenotype and drug sensitivity (Rasche L. et al and Bolli N et al.). Hence, the branch model of tumor evolution is not sufficient to explain the disorganized architecture observed in MM. In this study, we investigated whether MM ctDNA horizontal gene transfer (HGT) affect tumor genetic architecture and drug sensitivity, resembling what is seen in prokaryotes, and elucidated the mechanisms involved in the mobilization of genetic material from one cell to another. We identified that plasma from patients with MM transmits drug sensitivity or resistance to cells in culture. This transmission of drug sensitivity is mediated by ctDNA transfer of oncogenes to a host cell. Importantly, in vitro and in vivo demonstrated that ctDNA mainly targets cells resembling the cell of origin (tropism). Karyotype spreads and whole genome sequencing demonstrated that once patients ctDNA encounters host cells, it migrates into the nucleus where it ultimately integrates into the cell's genome. Integration to the genome was confirmed to be targeted to myeloma cells. Further sequencing analysis of multiple MM samples identified ctDNA tropism and integration is dependent on the 5' and 3' end presence of transposable elements (TE), particularly of the MIR and ALUsq family. These results were further validated by TE mediated delivery of GFP into MM cells in vitro and HSVTK in tumors of mouse xenografts. In conclusion, this data indicates for the first time that TE mediates MM ctDNA HGT into homologous tumor cells shaping the hierarchical architecture of tumor clones and affecting tumor response to treatment. Therapeutically, this unique quality of ctDNA can be exploited for targeted gene therapeutic approaches in MM and potentially other cancers. Disclosures Bernal-Mizrachi: Kodikas Therapeutic Solutions, Inc: Equity Ownership; TAKEDA: Research Funding; Winship Cancer Institute: Employment, Patents & Royalties.

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 Effect of the environment on horizontal gene transfer between bacteria and archaea

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3865 ◽  
Author(s):  
Clara A. Fuchsman ◽  
Roy Eric Collins ◽  
Gabrielle Rocap ◽  
William J. Brazelton
Keyword(s):  
High Temperature ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genome Size ◽  
Thermophilic Bacteria ◽  
Genetic Material ◽  
Strongly Correlated ◽  
Temperature Conditions ◽  
Large Numbers ◽  
Reciprocal Blast

BackgroundHorizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).ResultsWe investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.ConclusionsAnaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria.In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.

scholarly journals Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 569 ◽  
Author(s):  
Phale ◽  
Shah ◽  
Malhotra
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Food Web ◽  
Microbial Communities ◽  
Metabolic Pathways ◽  
Anthropogenic Activities ◽  
Genetic Material ◽  
Genomic Islands ◽  
Biochemical Pathways ◽  
Integrative Conjugative Elements

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

scholarly journals Mitochondrial genomes of two parasitic Cuscuta species show little evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

2021 ◽  
Author(s):  
Benjamin M. Anderson ◽  
Kirsten Krause ◽  
Gitte Petersen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genetic Material ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Sexual Exchange ◽  
Intimate Association ◽  
Nuclear Genomes ◽  
Candidate Regions ◽  
Complete Mitochondrial Genomes

Background: The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results: The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with ten missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions: The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of our Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

scholarly journals Gene exchange networks define species-like units in marine prokaryotes

2020 ◽  
Author(s):  
R. Stepanauskas ◽  
J.M. Brown ◽  
U. Mai ◽  
O. Bezuidt ◽  
M. Pachiadaki ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Dynamic Environment ◽  
Evolutionary Process ◽  
Gene Exchange ◽  
Marine Microorganisms ◽  
Nucleotide Difference ◽  
Tropical Ocean ◽  
Exchange Networks ◽  
Taxonomic Marker

SUMMARYAlthough horizontal gene transfer is recognized as a major evolutionary process in Bacteria and Archaea, its general patterns remain elusive, due to difficulties tracking genes at relevant resolution and scale within complex microbiomes. To circumvent these challenges, we analyzed a randomized sample of >12,000 genomes of individual cells of Bacteria and Archaea in the tropical and subtropical ocean - a well-mixed, global environment. We found that marine microorganisms form gene exchange networks (GENs) within which transfers of both flexible and core genes are frequent, including the rRNA operon that is commonly used as a conservative taxonomic marker. The data revealed efficient gene exchange among genomes with <28% nucleotide difference, indicating that GENs are much broader lineages than the nominal microbial species, which are currently delineated at 4-6% nucleotide difference. The 42 largest GENs accounted for 90% of cells in the tropical ocean microbiome. Frequent gene exchange within GENs helps explain how marine microorganisms maintain millions of rare genes and adapt to a dynamic environment despite extreme genome streamlining of their individual cells. Our study suggests that sharing of pangenomes through horizontal gene transfer is a defining feature of fundamental evolutionary units in marine planktonic microorganisms and, potentially, other microbiomes.

scholarly journals CryoEM structure of the Vibrio cholerae Type IV competence pilus secretin PilQ

2020 ◽  
Author(s):  
Sara J. Weaver ◽  
Matthew H. Sazinsky ◽  
Triana N. Dalia ◽  
Ankur B. Dalia ◽  
Grant J. Jensen
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Vibrio Cholerae ◽  
Natural Transformation ◽  
Structural Information ◽  
Genetic Material ◽  
Surface Binding ◽  
Exogenous Dna ◽  
Type Iv

AbstractNatural 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, the Type IV competence pilus 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. A lack of structural information has hindered our understanding of this process, however. Here, we solved the first ever high-resolution structure of a Type IV competence pilus secretin. A functional tagged allele of VcPilQ purified from native V. cholerae cells was used to determine the cryoEM structure of the PilQ secretin in amphipol to ∼2.7 Å. This structure highlights for the first time key differences in the architecture of the Type IV competence pilus secretin from the Type II and Type III Secretin System secretins. Based on our cryoEM structure, we designed a series of mutants to interrogate the mechanism of PilQ. These experiments provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation. We prove that it is possible to reduce pilus biogenesis and natural transformation by sealing the gate, suggesting VcPilQ as a new drug target.

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.

Sign in / Sign up

Export Citation Format

Share Document