Mobile genetic elements in Drosophila melanogaster (recent experiments)

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 920-928 ◽  
Author(s):  
Georgii P. Georgiev ◽  
Nickolai A. Tchurikov ◽  
Yurii V. Ilyin ◽  
Sofia G. Georgieva ◽  
Lev J. Mizrokhi ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Rna Polymerase Ii ◽  
Mobile Element ◽  
Complete Removal ◽  
Mobile Genetic Elements ◽  
Internal Promoter ◽  
Genetic Elements ◽  
First Case ◽  
Large Numbers ◽  
White Locus

Recent data obtained in the authors' laboratories concerning the behaviour of mobile genetic elements of Drosophila melanogaster are reviewed. It was found that the mobile element jockey represents the typical LINE element. It is efficiently transcribed in D. melanogaster cells in flies and in culture. Transcription is initiated from the +1 nucleotide of jockey and depends on an internal promoter. This is the first case of an internal promoter being used by RNA polymerase II. Several events which take place during the transposition bursts in ctMR2 family of strains were described. Among them are the removal of mobile dispersed genetics (mdg) elements (with solo long terminal repeat (LTR) remaining at the site of excision), complete removal of an mdg element, and reinsertion of the same mdg to the same place either in the presence or in absence of solo LTR sequence. Finally, the formation of deletions was observed. A 462-bp deletion destroying the white locus can be further repaired (w+ reversion). Thus, transposition bursts include many different genetic events. A novel system of prolonged genome destabilization was described. It depends on mobilization of a new mobile element called Stalker. After certain crosses Stalker actively moves for dozens of generations giving rise to large numbers of insertion mutations. Several novel genes were detected using mobilized Stalker. They include a modifier of mdg4 and six enhancers of yellow mutations.Key words: Drosophila melanogaster, mobile elements, transcription.

scholarly journals Mobile genetic element insertions drive antibiotic resistance across pathogens

2019 ◽  
Author(s):  
Matthew G. Durrant ◽  
Michelle M. Li ◽  
Ben Siranosian ◽  
Ami S. Bhatt
Keyword(s):  
Antibiotic Resistance ◽  
De Novo ◽  
Bacterial Species ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Mobile Elements ◽  
Genetic Elements ◽  
Element Insertion ◽  
A Genome ◽  
Mobile Element Insertion

AbstractMobile genetic elements contribute to bacterial adaptation and evolution; however, detecting these elements in a high-throughput and unbiased manner remains challenging. Here, we demonstrate ade novoapproach to identify mobile elements from short-read sequencing data. The method identifies the precise site of mobile element insertion and infers the identity of the inserted sequence. This is an improvement over previous methods that either rely on curated databases of known mobile elements or rely on ‘split-read’ alignments that assume the inserted element exists within the reference genome. We apply our approach to 12,419 sequenced isolates of nine prevalent bacterial pathogens, and we identify hundreds of known and novel mobile genetic elements, including many candidate insertion sequences. We find that the mobile element repertoire and insertion rate vary considerably across species, and that many of the identified mobile elements are biased toward certain target sequences, several of them being highly specific. Mobile element insertion hotspots often cluster near genes involved in mechanisms of antibiotic resistance, and such insertions are associated with antibiotic resistance in laboratory experiments and clinical isolates. Finally, we demonstrate that mutagenesis caused by these mobile elements contributes to antibiotic resistance in a genome-wide association study of mobile element insertions in pathogenicEscherichia coli. In summary, by applying ade novoapproach to precisely identify mobile genetic elements and their insertion sites, we thoroughly characterize the mobile element repertoire and insertion spectrum of nine pathogenic bacterial species and find that mobile element insertions play a significant role in the evolution of clinically relevant phenotypes, such as antibiotic resistance.

scholarly journals CRISPR-interference-based modulation of mobile genetic elements in bacteria

2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Ákos Nyerges ◽  
Balázs Bálint ◽  
Judit Cseklye ◽  
István Nagy ◽  
Csaba Pál ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Complete Removal ◽  
Mobile Genetic Elements ◽  
Industrial Biotechnology ◽  
Chromosome Engineering ◽  
Crispr Interference ◽  
Genetic Elements ◽  
Promising Tool ◽  
Single Plasmid

Abstract Spontaneous mutagenesis of synthetic genetic constructs by mobile genetic elements frequently results in the rapid loss of engineered functions. Previous efforts to minimize such mutations required the exceedingly time-consuming manipulation of bacterial chromosomes and the complete removal of insertional sequences (ISes). To this aim, we developed a single plasmid-based system (pCRIS) that applies CRISPR-interference to inhibit the transposition of bacterial ISes. pCRIS expresses multiple guide RNAs to direct inactivated Cas9 (dCas9) to simultaneously silence IS1, IS3, IS5 and IS150 at up to 38 chromosomal loci in Escherichia coli, in vivo. As a result, the transposition rate of all four targeted ISes dropped to negligible levels at both chromosomal and episomal targets. Most notably, pCRIS, while requiring only a single plasmid delivery performed within a single day, provided a reduction of IS-mobility comparable to that seen in genome-scale chromosome engineering projects. The fitness cost of multiple IS-knockdown, detectable in flask-and-shaker systems was readily outweighed by the less frequent inactivation of the transgene, as observed in green fluorescent protein (GFP)-overexpression experiments. In addition, global transcriptomics analysis revealed only minute alterations in the expression of untargeted genes. Finally, the transposition-silencing effect of pCRIS was easily transferable across multiple E. coli strains. The plasticity and robustness of our IS-silencing system make it a promising tool to stabilize bacterial genomes for synthetic biology and industrial biotechnology applications.

Sex and the Spread of Retrotransposon Ty3 in Experimental Populations of Saccharomyces cerevisiae

Genetics ◽  
1996 ◽  
Vol 143 (4) ◽  
pp. 1567-1577 ◽  
Author(s):  
Clifford Zeyl ◽  
Graham Bell ◽  
David M Green
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Selective Sweeps ◽  
Deleterious Mutations ◽  
Genetic Elements ◽  
Initial Frequency ◽  
Experimental Populations ◽  
Asexual Populations ◽  
Yeast Retrotransposon

Abstract Mobile genetic elements may be molecular parasites that reduce the fitness of individuals that bear them by causing predominantly deleterious mutations, but increase in frequency when rare because transposition increases their rates of transmission to the progeny of crosses between infected and uninfected individuals. If this is true, then the initial spread of a mobile element requires sex. We tested this prediction using the yeast retrotransposon Ty3 and a strain of Saccharomyces cerevisiae lacking Ty3. We infected replicate isogenic sexual and asexual populations with a galactose-inducible Ty3 element at an initial frequency of 1%. In two of six asexual populations, active Ty3 elements increased in frequency to 38 and 86%, due to the spread in each population of a competitively superior mutant carrying a new Ty3 insertion. Ty3 frequencies increased above 80% in all sexual populations in which transposition was induced in haplophase or in diplophase. Ty3 did not increase in frequency when active during both haplophase and diplophase, apparently because of selective sweeps during adaptation to galactose. Repressed Ty3 elements spread in sexual populations, by increasing sexual fitness. These results indicate that active Ty3 elements are more likely to become established in sexual populations than in asexual populations.

scholarly journals Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp inKlebsiella pneumoniaepopulations

2017 ◽  
Author(s):  
Margaret M. C. Lam ◽  
Ryan R. Wick ◽  
Kelly L. Wyres ◽  
Claire L. Gorrie ◽  
Louise M. Judd ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Population Genomics ◽  
Bacterial Species ◽  
Critical Role ◽  
Mobile Element ◽  
Mobile Genetic Elements ◽  
Virulence Determinants ◽  
Genome Sequences ◽  
Genetic Elements ◽  
Resistant Strains

ABSTRACTMobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria’s ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in opportunistic pathogenKlebsiella pneumoniae, which are a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants inK. pneumoniaeinclude the polyketide synthesis lociybtandclb(also known aspks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin respectively. These loci are located within an MGE called ICEKp, which is the most common virulence-associated MGE ofK. pneumoniae,providing a mechanism for these virulence factors to spread within the population.Here we apply population genomics to investigate the prevalence, evolution and mobility ofybtandclbinK. pneumoniaepopulations through comparative analysis of 2,498 whole genome sequences. Theybtlocus was detected in 40% ofK. pneumoniaegenomes, particularly amongst those associated with invasive infections. We identified 17 distinctybtlineages and 3clblineages, each associated with one of 14 different structural variants of ICEKp. Comparison with the wider Enterobacteriaceae population showed occasional ICEKpacquisition by other members. Theclblocus was present in 14% of allK. pneumoniaeand 38.4% ofybt+ genomes. Hundreds of independent ICEKpintegration events were detected affecting hundreds of phylogenetically distinctK. pneumoniaelineages, including ≥19 in the globally-disseminated carbapenem-resistant clone CG258. A novel plasmid-encoded form ofybtwas also identified, representing a new mechanism forybtdispersal inK. pneumoniaepopulations. These data show that MGEs carryingybtandclbcirculate freely in theK. pneumoniaepopulation, including among multidrug-resistant strains, and should be considered a target for genomic surveillance along with AMR determinants.AUTHOR SUMMARYKlebsiella pneumoniaeinfections are becoming increasingly difficult to treat with antibiotics. SomeK. pneumoniaestrains also carry extra genes that allow them to synthesise yersiniabactin, an iron-scavenging molecule, which enhances their ability to cause disease. These genes are located on a genetic element that can easily transfer between strains. Here, we screened 2498K. pneumoniaegenome sequences and found substantial diversity in the yersiniabactin genes and the associated genetic elements, including a novel mechanism of transfer, and detected hundreds of distinct yersiniabactin acquisition events betweenK. pneumoniaestrains. We show that these yersiniabactin mobile genetic elements are specifically adapted to theK. pneumoniaepopulation but also occasionally acquired by other bacterial members belonging to the Enterobacteriaceae family such asE. coli.These insights into the movement and genetics of yersiniabactin genes allow tracking of the evolution and spread of yersiniabactin in globalK. pneumoniaepopulations and monitoring for acquisition of yersiniabactin in antibiotic-resistant strains.

scholarly journals Changes in the intralinear level of hybrid dys-genesis manifestation in Drosophila melanogaster in crosses with individuals with tetracycline suppressed internal microflora

2019 ◽  
Vol 25 ◽  
pp. 38-43
Author(s):  
I. D. Gorodnyanski
Keyword(s):  
Drosophila Melanogaster ◽  
Mobile Genetic Elements ◽  
The Body ◽  
Hybrid Dysgenesis ◽  
Control Line ◽  
Specific Interactions ◽  
Wolbachia Pipientis ◽  
Reciprocal Crosses ◽  
Genetic Elements ◽  
Reciprocal Crossing

Aim. To assess the frequency of hybrid dysgenesis in the offspring of reciprocal crosses of individuals of the Oregon-R line, with individuals of the same line, from the organism of which Wolbachia pipientis was eliminated. Methods. The line of Drosophila melanogaster Oregon R (Cambridge), in the genome of which there are MGE hobo, was investiga-ted. This line is infected with wolbachia of the wMel strain. Removal of Wolbachia from the body was implemented using antibiotic tetracycline. The study used the fifth of the generations obtained on a normal handling medium after the removal of Wolbachia. The level of hybrid dysgenesis was studied by the method of extracting gonad flies and assessing their condition. Results. In the progeny from experimental crossing of females from which Wolbachia was eli-minated, with males of the control line, the proportion of females with fully reduced gonads is significantly higher than in the offspring of reciprocal crossing. Conclusions. The results obtained may be a sign of the action of the system of specific interactions of Wolbachia pipientis and Drosophila’s MGE. Keywords: mobile genetic elements, hybrid dysgenesis, Drosophila melanogaster, Wolbachia pipientis.

scholarly journals CRISPR-interference based modulation of mobile genetic elements in bacteria

2018 ◽  
Author(s):  
Ákos Nyerges ◽  
Balázs Bálint ◽  
Judit Cseklye ◽  
István Nagy ◽  
Csaba Pál ◽  
...  
Keyword(s):  
Complete Removal ◽  
Mobile Genetic Elements ◽  
Industrial Biotechnology ◽  
Chromosome Engineering ◽  
Crispr Interference ◽  
Genetic Elements ◽  
Promising Tool ◽  
Single Plasmid ◽  
Bacterial Chromosomes

ABSTRACTSpontaneous mutagenesis of synthetic genetic constructs by mobile genetic elements frequently results in the rapid loss of advantageous functions. Previous efforts to minimize such mutations required the exceedingly time-consuming manipulation of bacterial chromosomes and the complete removal of insertional sequences (ISes). To this aim, we developed a single plasmid-based system (pCRIS) that applies CRISPR-interference to inhibit the transposition of bacterial ISes. pCRIS expresses multiple guide RNAs to direct inactivated Cas9 (dCas9) to simultaneously silence IS1, IS3, IS5, and IS150at up to 38 chromosomal loci inEscherichia coli,in vivo. As a result, the transposition rate of all four targeted ISes dropped to negligible levels at both chromosomal and episomal targets, increasing the half-life of exogenous protein expression. Most notably, pCRIS, while requiring only a single plasmid delivery performed within a single day, provided a reduction of IS-mobility comparable to that seen in genome-scale chromosome engineering projects. Global transcriptomics analysis revealed nevertheless only minute alterations in the expression of untargeted genes. Finally, the transposition-silencing effect of pCRIS was easily transferable across multipleE. colistrains. The plasticity and robustness of our IS-silencing system make it a promising tool to stabilize bacterial genomes for synthetic biology and industrial biotechnology applications.

scholarly journals Effect of suppression of internal microflora by tetracycline on the level of manifestation of the hybrid dysgenesis of Drosophila melanogaster

2018 ◽  
Vol 22 ◽  
pp. 34-39
Author(s):  
I. D. Gorodnyanski ◽  
L. I. Vorobyova
Keyword(s):  
Drosophila Melanogaster ◽  
Mobile Genetic Elements ◽  
The Body ◽  
Hybrid Dysgenesis ◽  
Specific Interactions ◽  
Host Organism ◽  
Wolbachia Pipientis ◽  
Genetic Elements

Aim. The main goal of this article was to assess changes in the frequency of the development of hybrid dysgenesis in the Oregon-R line of Drosophila melanogaster, observed under the influence of tetracycline. Methods. The line of Drosophila melanogaster Oregon R (Cambridge), in the genome of which there are full-sized and functionally active copies of the MGE hobo, was investigated. Also, this line is infected with wolbachia of the wMel strain. Removal of Wolbachia from the body was implemented using antibiotic tetracycline. The level of hybrid dysgenesis was studied by the method of extracting gonad flies and assessing their condition. Results. This article presents the results of studying the effect of suppression of the internal microflora of Drosophila melanogaster – in particular, the parasitic bacterium Wolbachia pipientis - on the level of manifestation of hybrid dysgenesis. After exposure to tetracycline, a significant increase in the proportion of dysgenic individuals within the line was observed. Conclusions. The results obtained may be associated with a violation of the system of specific interactions of the host organism and internal microflora. Keywords: mobile genetic elements, hybrid dysgenesis, Drosophila melanogaster, Wolbachia pipientis.

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