scholarly journals Shaping the Landscape of Eukaryotic Gene Expression: Horizontal Gene Transfer

2021 ◽  
Vol 12 (10) ◽  
pp. 1-2
Author(s):  
Ruby Dhar ◽  
Arun Kumar ◽  
Subhradip Karmakar
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Human Genome ◽  
Genetic Information ◽  
Antibiotic Resistance Genes ◽  
Ion Binding ◽  
Gene Expressions ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Eukaryotic Genomes

Horizontal gene transfer (HGT) in prokaryotes refers to the movement of genes and genetic information between two organisms. This usually results in the spread of antibiotic resistance genes among bacteria. Vertical gene transfer(VGT), on the other hand, refers to the flow of genetic information from parents to offsprings. Until recently, HGT was an exclusive prerogative of the prokaryotes. These are obvious due to the distinct nuclear membrane enclosure of eukaryote genomes that are shielded from outside interferences. VGT can cross species barriers and may even allow the transmission of genes across the kingdoms of life. HGT is now an emerging idea in eukaryotic genomes, challenging previous assertions that HGT is restricted to prokaryotes. It is now accepted that HGT can profoundly influence host metabolic pathways and alter gene expressions even in eukaryotes. HGT, is also fundamentally important during development, origin of human diseases, such as cancer, and neurodegenerative disorders. It may also influence therapeutic outcome by promoting resistant phenotypes.  HGT is recently documented in prokaryote to eukaryote HGT is the tardigrade case though an analysis of a draft tardigrade genome suggested that HGT contributed to up to ~17 % of the gene. Further analysis performed after whole genome pair-wise alignments between human genome as well as 53 vertebrate genomes, it was observed that nearly 1500 human genome regions involving 642 known genes, most of which are enriched with ion binding to be conserved with non-mammals than with most mammals. This indicated horizontal gene transfer is more common than we expected in the human genome. It’s a matter of time or maybe a tip of iceberg to know the full extent and implications of HGT. Surprisingly its seems that the eukaryotic genome has many more ways to update itself to vastly expand its repertoire of expression and usability. HGT is just another feather in the crown.

scholarly journals Horizontally transferred genes in the ctenophore Mnemiopsis leidyi encode enzymes and are expressed during early development

2017 ◽  
Author(s):  
Alexandra M Hernandez ◽  
Joseph F Ryan
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Early Development ◽  
Genetic Information ◽  
Mnemiopsis Leidyi ◽  
Uncharacterized Protein ◽  
Phylogenetic Incongruence ◽  
Wide Range ◽  
Growing Body

Horizontal gene transfer has had major impacts on the biology of a wide range of organisms from antibiotic resistance in bacteria to adaptations to herbivory in arthropods. A growing body of literature shows that horizontal gene transfer (HGT) between non-animals and animals is more commonplace than previously thought. In this study, we present a thorough investigation of HGT in the ctenophore Mnemiopsis leidyi. We applied tests of phylogenetic incongruence to identify nine genes that were likely transferred horizontally early in ctenophore evolution from bacteria and non-metazoan eukaryotes. All but one of these HGTs (an uncharacterized protein) appear to perform enzymatic activities in M. leidyi, supporting previous observations that enzymes are more likely to be retained after HGT events. We found that the majority of these nine horizontally transferred genes were expressed during early development, suggesting that they are active and play a role in the biology of M. leidyi. This is the first report of HGT in ctenophores, and contributes to an ever-growing literature on the prevalence of genetic information flowing between non-animals and animals.

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 SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes

2013 ◽  
Vol 30 (8) ◽  
pp. 1081-1086 ◽  
Author(s):  
K. S. Jaron ◽  
J. C. Moravec ◽  
N. Martinkova
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Eukaryotic Genomes

scholarly journals Identification of a Novel Conjugative Plasmid in Mycobacteria That Requires Both Type IV and Type VII Secretion

mBio ◽  
2014 ◽  
Vol 5 (5) ◽  
Author(s):  
Roy Ummels ◽  
Abdallah M. Abdallah ◽  
Vincent Kuiper ◽  
Anouar Aâjoud ◽  
Marion Sparrius ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Antibiotic Resistance Genes ◽  
Conjugative Plasmid ◽  
Content Type ◽  
Conjugative Plasmids ◽  
Type Vii Secretion ◽  
Type Iv ◽  
Slow Growing

ABSTRACTConjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, includingMycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.IMPORTANCEConjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted thatM. tuberculosisdoes not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred toM. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.

scholarly journals Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Huiquan Liu ◽  
Yanping Fu ◽  
Bo Li ◽  
Xiao Yu ◽  
Jiatao Xie ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Eukaryotic Genomes

scholarly journals Synthetic Fatty Acids Prevent Plasmid-Mediated Horizontal Gene Transfer

mBio ◽  
2015 ◽  
Vol 6 (5) ◽  
Author(s):  
María Getino ◽  
David J. Sanabria-Ríos ◽  
Raúl Fernández-López ◽  
Javier Campos-Gómez ◽  
José M. Sánchez-López ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Aliphatic Chain ◽  
Bacterial Conjugation ◽  
Human Pathogens

ABSTRACT Bacterial conjugation constitutes a major horizontal gene transfer mechanism for the dissemination of antibiotic resistance genes among human pathogens. Antibiotic resistance spread could be halted or diminished by molecules that interfere with the conjugation process. In this work, synthetic 2-alkynoic fatty acids were identified as a novel class of conjugation inhibitors. Their chemical properties were investigated by using the prototype 2-hexadecynoic acid and its derivatives. Essential features of effective inhibitors were the carboxylic group, an optimal long aliphatic chain of 16 carbon atoms, and one unsaturation. Chemical modification of these groups led to inactive or less-active derivatives. Conjugation inhibitors were found to act on the donor cell, affecting a wide number of pathogenic bacterial hosts, including Escherichia, Salmonella, Pseudomonas, and Acinetobacter spp. Conjugation inhibitors were active in inhibiting transfer of IncF, IncW, and IncH plasmids, moderately active against IncI, IncL/M, and IncX plasmids, and inactive against IncP and IncN plasmids. Importantly, the use of 2-hexadecynoic acid avoided the spread of a derepressed IncF plasmid into a recipient population, demonstrating the feasibility of abolishing the dissemination of antimicrobial resistances by blocking bacterial conjugation. IMPORTANCE Diseases caused by multidrug-resistant bacteria are taking an important toll with respect to human morbidity and mortality. The most relevant antibiotic resistance genes come to human pathogens carried by plasmids, mainly using conjugation as a transmission mechanism. Here, we identified and characterized a series of compounds that were active against several plasmid groups of clinical relevance, in a wide variety of bacterial hosts. These inhibitors might be used for fighting antibiotic-resistance dissemination by inhibiting conjugation. Potential inhibitors could be used in specific settings (e.g., farm, fish factory, or even clinical settings) to investigate their effect in the eradication of undesired resistances.

scholarly journals Mobilome and Resistome Reconstruction from Genomes Belonging to Members of the Bifidobacterium Genus

2019 ◽  
Vol 7 (12) ◽  
pp. 638 ◽  
Author(s):  
Walter Mancino ◽  
Gabriele Andrea Lugli ◽  
Douwe van Sinderen ◽  
Marco Ventura ◽  
Francesca Turroni
Keyword(s):  
Antibiotic Resistance ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
In Silico ◽  
Antibiotic Resistance Genes ◽  
Host Health ◽  
Human Animal ◽  
Bacitracin A ◽  
In Silico Analyses ◽  
Growth Experiments

Specific members of the genus Bifidobacterium are among the first colonizers of the human/animal gut, where they act as important intestinal commensals associated with host health. As part of the gut microbiota, bifidobacteria may be exposed to antibiotics, used in particular for intrapartum prophylaxis, especially to prevent Streptococcus infections, or in the very early stages of life after the birth. In the current study, we reconstructed the in silico resistome of the Bifidobacterium genus, analyzing a database composed of 625 bifidobacterial genomes, including partial assembled strains with less than 100 genomic sequences. Furthermore, we screened bifidobacterial genomes for mobile genetic elements, such as transposases and prophage-like elements, in order to investigate the correlation between the bifido-mobilome and the bifido-resistome, also identifying genetic insertion hotspots that appear to be prone to horizontal gene transfer (HGT) events. These insertion hotspots were shown to be widely distributed among analyzed bifidobacterial genomes, and suggest the acquisition of antibiotic resistance genes through HGT events. These data were further corroborated by growth experiments directed to evaluate bacitracin A resistance in Bifidobacterium spp., a property that was predicted by in silico analyses to be part of the HGT-acquired resistome.

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