scholarly journals Genome surveillance by HUSH-mediated silencing of intronless mobile elements

Nature ◽  
2021 ◽  
Author(s):  
Marta Seczynska ◽  
Stuart Bloor ◽  
Sergio Martinez Cuesta ◽  
Paul J. Lehner
Keyword(s):  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Silvia Bágeľová Poláková ◽  
Žaneta Lichtner ◽  
Tomáš Szemes ◽  
Martina Smolejová ◽  
Pavol Sulo

AbstractmtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes.


2021 ◽  
pp. 104722
Author(s):  
Muhammad Shafiq ◽  
Jinhu Huang ◽  
Jan Mohammad Shah ◽  
Ilyas Ali ◽  
Sadeeq Ur Rahman ◽  
...  

2021 ◽  
Vol 22 (13) ◽  
pp. 6783
Author(s):  
Renata Orłowska ◽  
Katarzyna A. Pachota ◽  
Wioletta M. Dynkowska ◽  
Agnieszka Niedziela ◽  
Piotr T. Bednarek

A plant genome usually encompasses different families of transposable elements (TEs) that may constitute up to 85% of nuclear DNA. Under stressful conditions, some of them may activate, leading to sequence variation. In vitro plant regeneration may induce either phenotypic or genetic and epigenetic changes. While DNA methylation alternations might be related, i.e., to the Yang cycle problems, DNA pattern changes, especially DNA demethylation, may activate TEs that could result in point mutations in DNA sequence changes. Thus, TEs have the highest input into sequence variation (SV). A set of barley regenerants were derived via in vitro anther culture. High Performance Liquid Chromatography (RP-HPLC), used to study the global DNA methylation of donor plants and their regenerants, showed that the level of DNA methylation increased in regenerants by 1.45% compared to the donors. The Methyl-Sensitive Transposon Display (MSTD) based on methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach demonstrated that, depending on the selected elements belonging to the TEs family analyzed, varying levels of sequence variation were evaluated. DNA sequence contexts may have a different impact on SV generated by distinct mobile elements belonged to various TE families. Based on the presented study, some of the selected mobile elements contribute differently to TE-related SV. The surrounding context of the TEs DNA sequence is possibly important here, and the study explained some part of SV related to those contexts.


1977 ◽  
Vol 19 (6) ◽  
pp. 1537-1544
Author(s):  
E.I. Semenenko ◽  
A.I. Ivanov ◽  
M.A. Markelov ◽  
N.B. Dobrova ◽  
Ye.V. Smurova ◽  
...  

mBio ◽  
2010 ◽  
Vol 1 (4) ◽  
Author(s):  
Kelli L. Palmer ◽  
Michael S. Gilmore

ABSTRACT Clustered, regularly interspaced short palindromic repeats (CRISPR) provide bacteria and archaea with sequence-specific, acquired defense against plasmids and phage. Because mobile elements constitute up to 25% of the genome of multidrug-resistant (MDR) enterococci, it was of interest to examine the codistribution of CRISPR and acquired antibiotic resistance in enterococcal lineages. A database was built from 16 Enterococcus faecalis draft genome sequences to identify commonalities and polymorphisms in the location and content of CRISPR loci. With this data set, we were able to detect identities between CRISPR spacers and sequences from mobile elements, including pheromone-responsive plasmids and phage, suggesting that CRISPR regulates the flux of these elements through the E. faecalis species. Based on conserved locations of CRISPR and CRISPR-cas loci and the discovery of a new CRISPR locus with associated functional genes, CRISPR3-cas, we screened additional E. faecalis strains for CRISPR content, including isolates predating the use of antibiotics. We found a highly significant inverse correlation between the presence of a CRISPR-cas locus and acquired antibiotic resistance in E. faecalis, and examination of an additional eight E. faecium genomes yielded similar results for that species. A mechanism for CRISPR-cas loss in E. faecalis was identified. The inverse relationship between CRISPR-cas and antibiotic resistance suggests that antibiotic use inadvertently selects for enterococcal strains with compromised genome defense. IMPORTANCE For many bacteria, including the opportunistically pathogenic enterococci, antibiotic resistance is mediated by acquisition of new DNA and is frequently encoded on mobile DNA elements such as plasmids and transposons. Certain enterococcal lineages have recently emerged that are characterized by abundant mobile DNA, including numerous viruses (phage), and plasmids and transposons encoding multiple antibiotic resistances. These lineages cause hospital infection outbreaks around the world. The striking influx of mobile DNA into these lineages is in contrast to what would be expected if a self (genome)-defense system was present. Clustered, regularly interspaced short palindromic repeat (CRISPR) defense is a recently discovered mechanism of prokaryotic self-defense that provides a type of acquired immunity. Here, we find that antibiotic resistance and possession of complete CRISPR loci are inversely related and that members of recently emerged high-risk enterococcal lineages lack complete CRISPR loci. Our results suggest that antibiotic therapy inadvertently selects for enterococci with compromised genome defense.


2012 ◽  
Vol 312-313 ◽  
pp. 93-117 ◽  
Author(s):  
Fabien Deschamps ◽  
Marguerite Godard ◽  
Stéphane Guillot ◽  
Catherine Chauvel ◽  
Muriel Andreani ◽  
...  

2015 ◽  
Vol 112 (23) ◽  
pp. 7273-7278 ◽  
Author(s):  
Michael S. Gilmore ◽  
Marcus Rauch ◽  
Matthew M. Ramsey ◽  
Paul R. Himes ◽  
Sriram Varahan ◽  
...  

Multidrug-resistantEnterococcus faecalispossess numerous mobile elements that encode virulence and antibiotic resistance traits as well as new metabolic pathways, often constituting over one-quarter of the genome. It was of interest to determine how this large accretion of mobile elements affects competitive growth in the gastrointestinal (GI) tract consortium. We unexpectedly observed that the prototype clinical isolate strain V583 was actively killed by GI tract flora, whereas commensal enterococci flourished. It was found that killing of V583 resulted from lethal cross-talk between accumulated mobile elements and that this cross-talk was induced by a heptapeptide pheromone produced by nativeE. faecalispresent in the fecal consortium. These results highlight two important aspects of the evolution of multidrug-resistant enterococci: (i) the accretion of mobile elements inE. faecalisV583 renders it incompatible with commensal strains, and (ii) because of this incompatibility, multidrug-resistant strains sharing features found in V583 cannot coexist with commensal strains. The accumulation of mobile elements in hospital isolates of enterococci can include those that are inherently incompatible with native flora, highlighting the importance of maintaining commensal populations as means of preventing colonization and subsequent infection by multidrug-resistant strains.


Ethnomusic ◽  
2018 ◽  
Vol 14 (1) ◽  
pp. 142-177
Author(s):  
Jarema Pavliv ◽  

In the offered article, a comparative analysis of two performing versions of the wedding ceremonial dance “Hutsulka”, dominant in the Eastern Carpathians region of Ukraine has been made, with outstanding violinists-capellists, which, based on traditions and their own virtuoso style, developed this dance genre due to the accumulation of stable and mobile elements of melo-, rhythm- and form-making, as well as the establishment of aesthetics of regional styles. The material for the study was the audio version of the “Hutsulka” recorded on the basis of the performance of two violinists representing the region of Kosmach- Brusturiv villages tradition – Kyrylo Lyndiuk (“Vityshyn”, 1929–2003) (recorded by prof. Bogdan Lukaniuk in 1991) and Ivan Sokoliuk (born in 1944; Musician's own recording of 2017) – and transcribed by the author of the article. The performance of “Hutsulka” by each violinist is characteristic of common and distinctive features concerning the formation of the variative composition, the thematic material (respectively, 29 and 43 themes of kolomyika, kozachok and voloshka bases), tonality and rhythmic structuring, individual interpretation of ornamentation, which is collectively connected with artistic orientation on certain artistic and performing directions, presented by iconic musicians-predecessors. The formal features of the Hutsulka composition depends on scenery where it is performed (1); the tonality outline determined by established regional tradition (2), and rhythmic outline, by the overall style, varyation technics, updating and ornamentation of rhythmic formulas, characteristic of the personal manner and style of the performer (3). Ornamentation, as the essence of the performing style of any Hutsul musician, in K. “Vityshyn” is characterized by intense interweaving of short melismatic legal groups and non-legal figurations within melodic line and texture. I. Sokoliuk 166 enriches the linear movement with prolonged melismatic groups and rhythm- intonational and figurational turns that decorate it and amplify the expression of dance overall sonority. In performing aesthetics of K. Lyndiuk prevails an acute articulation of melodic expressiveness with accented and often pointed rhythmic patterns that provides representative-temperamental virtuosity. For strategic performance aesthetics of I. Sokoliuk, rich in virtuosic expressiveness, is characterized by choral and transparent ringing articulation in the context of “stratum”-development creation of the whole large-scale virtuoso composition. Each version reveals individual compositional, improvised, techno-performing, emotional as well as aesthetic mind of their creators. All these qualities, formed by both musicians in a single tradition and expressed in related kolomyika and kozachok-voloshka tunes, present the decision of developmental, composite, rhythmic, intonational, articulation, tempo and many other aspects of style, characteristic of folk violinists – soloists and capellists, inherent to each of them, in their performing manner, evident in “Hutsulka” rendering.


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