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1.
Nucleic Acids Res ; 49(2): 1033-1045, 2021 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-33367793

RESUMO

Diversity-generating retroelements (DGRs) vary protein sequences to the greatest extent known in the natural world. These elements are encoded by constituents of the human microbiome and the microbial 'dark matter'. Variation occurs through adenine-mutagenesis, in which genetic information in RNA is reverse transcribed faithfully to cDNA for all template bases but adenine. We investigated the determinants of adenine-mutagenesis in the prototypical Bordetella bacteriophage DGR through an in vitro system composed of the reverse transcriptase bRT, Avd protein, and a specific RNA. We found that the catalytic efficiency for correct incorporation during reverse transcription by the bRT-Avd complex was strikingly low for all template bases, with the lowest occurring for adenine. Misincorporation across a template adenine was only somewhat lower in efficiency than correct incorporation. We found that the C6, but not the N1 or C2, purine substituent was a key determinant of adenine-mutagenesis. bRT-Avd was insensitive to the C6 amine of adenine but recognized the C6 carbonyl of guanine. We also identified two bRT amino acids predicted to nonspecifically contact incoming dNTPs, R74 and I181, as promoters of adenine-mutagenesis. Our results suggest that the overall low catalytic efficiency of bRT-Avd is intimately tied to its ability to carry out adenine-mutagenesis.


Assuntos
Adenina , Bacteriófagos/genética , Mutagênese , Retroelementos/genética , Adenina/química , Arginina/química , Sequência de Bases , Bordetella/virologia , Catálise , Sistema Livre de Células , Simulação por Computador , DNA Complementar/genética , Glicina/química , Sequenciamento de Nucleotídeos em Larga Escala , Modelos Moleculares , Conformação Proteica , DNA Polimerase Dirigida por RNA/metabolismo , Proteínas Recombinantes/metabolismo
2.
Nat Commun ; 11(1): 5095, 2020 10 09.
Artigo em Inglês | MEDLINE | ID: mdl-33037201

RESUMO

Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome.


Assuntos
Células-Tronco Embrionárias/fisiologia , Heterocromatina/metabolismo , Histonas/metabolismo , Animais , Células Cultivadas , Imunoprecipitação da Cromatina , DNA/metabolismo , DNA Helicases/metabolismo , Heterocromatina/genética , Histonas/genética , Camundongos Knockout , Nucleossomos/genética , Nucleossomos/metabolismo , Células-Tronco Pluripotentes/fisiologia , Retroelementos/genética
3.
Rev. esp. patol. torac ; 32(3): 229-242, oct. 2020. tab, graf
Artigo em Espanhol | IBECS | ID: ibc-ET2-7556

RESUMO

OBJETIVO: Determinar si existen biomarcadores entre los transposones, tanto para diagnóstico como pronóstico de adenocarcinoma, carcinoma epidermoide y carcinoma microcítico de pulmón, así como valorar diferencias y similitudes entre estos tres tipos histológicos. MATERIAL Y MÉTODOS: Se ha secuenciado el RNA total del tejido tumoral y sano adyacente de muestras de adenocarcinoma y carcinoma epidermoide de dieciséis pacientes intervenidos en el Hospital Regional de Málaga. En el caso del carcinoma microcítico, se han utilizado pacientes externos cuyos datos proceden de los repositorios genómicos disponibles para la comunidad científica. Esas secuencias se han analizado con un flujo de trabajo bioinformático específico que conlleva varios pasos: 1º) Preprocesar las lecturas, 2º) Mapearlas sobre el genoma humano de referencia, 3º) Determinar la expresión de los transposones en cada una de las muestras, y 4º) Calcular su expresión diferencial entre el tejido sano y el tumoral de cada paciente. RESULTADOS: En un primer paso, hemos analizado los transposones con expresión diferencial en cada uno de los tipos histológicos estudiados por separado. El análisis del adenocarcinoma, carcinoma microcítico y carcinoma epidermoide de pulmón ha dado como resultado un total de 7, 72 y 12 transposones diferencialmente expresados (TDE), respectivamente. Hemos encontrado transposones comunes a los tres tipos histológicos y otros cuyo comportamiento es específico en cada uno de ellos. CONCLUSIONES: Los transposones se reprograman específicamente cuando una célula normal del pulmón se vuelve cancerosa. Esta reprogramación es una fuente de biomarcadores que podría ayudar al diagnóstico precoz del cáncer


OBJECTIVE: To determine whether biomarkers exist among transposons for both the diagnosis and prognosis of adenocarcinoma, squamous cell carcinoma and small cell carcinoma of the lung, as well as to evaluate differences and similarities between these three histological types. MATERIAL AND METHODS: The total RNA was sequenced for the tumor tissue and adjacent healthy tissue in adenocarcinoma and squamous cell carcinoma samples from sixteen patients being treated at the Hospital Regional de Málaga. In the case of small cell carcinoma, external patients were used whose data came from genomic repositories available to the scientific community. These sequences were analyzed with a specific bioinformatic workflow which includes several steps: 1) Pre-process readings, 2) Map them on the reference human genome, 3) Determine transposon expression in each of the samples, and 4) Calculate the differential expression between the healthy and tumor tissue in each patient. RESULTS: In the first step, we analyzed the transposons with differential expression in each of the histological types studied separately. The analysis of adenocarcinoma, small cell carcinoma and squamous cell carcinoma of the lung has resulted in a total of 7, 72 and 12 differentially expressed transposons, respectively. We found transposons common to all three histological types and others whose behavior is specific to each type. CONCLUSIONS: Transposons are specifically reprogrammed when a normal lung cell becomes cancerous. This reprogramming is a source of biomarkers that could help with the early diagnosis of cancer


Assuntos
Humanos , Masculino , Feminino , Pessoa de Meia-Idade , Idoso , Retroelementos/genética , Elementos de DNA Transponíveis/genética , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/genética , Carcinoma de Células Escamosas/diagnóstico , Adenocarcinoma/diagnóstico , Carcinoma Pulmonar de Células não Pequenas/diagnóstico , Biomarcadores/análise , Prognóstico , Carcinoma de Células Escamosas/genética , Adenocarcinoma/genética , Carcinoma Pulmonar de Células não Pequenas/epidemiologia , Carcinoma Pulmonar de Células não Pequenas/genética , Biologia Computacional , Diagnóstico Precoce
4.
Trends Plant Sci ; 25(11): 1062-1064, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32863103

RESUMO

The presence of various types of structural variants, including transposons, make up the major part of the genomic differences among plant species. Two recent papers, Domínguez et al. and Alonge et al. explore specifically the impact that retrotransposons and other structural variants had on several tomato phenotypes of agricultural importance.


Assuntos
Lycopersicon esculentum , Elementos de DNA Transponíveis/genética , Genoma de Planta/genética , Genômica , Lycopersicon esculentum/genética , Retroelementos/genética
5.
PLoS Genet ; 16(8): e1008991, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32797042

RESUMO

Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences-collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be "hidden" from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30-10 MYA during the emergence of primate L1Pa7-L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.


Assuntos
Evolução Molecular , Elementos Nucleotídeos Longos e Dispersos/genética , Primatas/genética , Retroelementos/genética , Sequência de Aminoácidos/genética , Animais , Análise Mutacional de DNA , Humanos , Mutação/genética , Proteínas
6.
Nat Commun ; 11(1): 3670, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32728126

RESUMO

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.


Assuntos
Brachypodium/genética , Diploide , Evolução Molecular , Genoma de Planta , Poliploidia , Cromossomos de Plantas/genética , Genoma de Cloroplastos , Genômica , Hibridização Genética , Filogenia , Polimorfismo de Nucleotídeo Único , Retroelementos/genética , Especificidade da Espécie
7.
Environ Sci Pollut Res Int ; 27(32): 40749-40756, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32671713

RESUMO

Retrotransposons, as vital regulator of male fertility, are essential for spermatogenesis. Cadmium (Cd) is an environmental toxicant and endocrine disruptor, targeting the reproductive system. Growing evidence shows that Cd exposure can induce male infertility in mammals. In this study, we generated a male C57BL/6 J mice model with consecutive 35 days cadmium chloride (CdCl2) in different concentrations of 0, 0.25, 0.5, 1.0, and 2.0 mg/kg. The results indicated that 1.0 and 2.0 mg/kg CdCl2 significantly affected the body weight. Meanwhile, the highest dose group with 2.0 mg/kg CdCl2 presented low fertility. Furthermore, the expression of retrotransposon mRNA was markedly increased in the higher doses group. We examined methylcytosine (mC) levels of the three active LINE-1 subfamilies TfI, A, and GfII in testis. Conclusively, Cd exposure probably undermines the male mice fertility by disrupting DNA methylation to regulate the retrotransposons. Further studies are required for identifying whether retrotransposon activation has any significant impacts on genome structure, stability, and expression in Cd-induced testicular injury, laying foundation for the treatment for male infertility.


Assuntos
Cádmio , Doenças Testiculares , Animais , Cádmio/toxicidade , Cloreto de Cádmio/toxicidade , Metilação de DNA , Humanos , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Retroelementos/genética , Testículo
8.
Nucleic Acids Res ; 48(16): 9346-9360, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32697302

RESUMO

Long non-coding RNAs (lncRNAs) are attracting widespread attention for their emerging regulatory, transcriptional, epigenetic, structural and various other functions. Comprehensive transcriptome analysis has revealed that retrotransposon elements (REs) are transcribed and enriched in lncRNA sequences. However, the functions of lncRNAs and the molecular roles of the embedded REs are largely unknown. The secondary and tertiary structures of lncRNAs and their embedded REs are likely to have essential functional roles, but experimental determination and reliable computational prediction of large RNA structures have been extremely challenging. We report here the nuclear magnetic resonance (NMR)-based secondary structure determination of the 167-nt inverted short interspersed nuclear element (SINE) B2, which is embedded in antisense Uchl1 lncRNA and upregulates the translation of sense Uchl1 mRNAs. By using NMR 'fingerprints' as a sensitive probe in the domain survey, we successfully divided the full-length inverted SINE B2 into minimal units made of two discrete structured domains and one dynamic domain without altering their original structures after careful boundary adjustments. This approach allowed us to identify a structured domain in nucleotides 31-119 of the inverted SINE B2. This approach will be applicable to determining the structures of other regulatory lncRNAs.


Assuntos
Conformação de Ácido Nucleico , RNA Longo não Codificante/ultraestrutura , Retroelementos/genética , Elementos Nucleotídeos Curtos e Dispersos/genética , Biologia Computacional , Humanos , Espectroscopia de Ressonância Magnética , RNA Antissenso/genética , RNA Antissenso/ultraestrutura , RNA Longo não Codificante/genética , Transcriptoma/genética , Ubiquitina Tiolesterase/genética , Ubiquitina Tiolesterase/ultraestrutura
9.
Nucleic Acids Res ; 48(15): 8431-8444, 2020 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-32667642

RESUMO

Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.


Assuntos
DNA (Citosina-5-)-Metiltransferase 1/genética , Metilação de DNA/genética , Desenvolvimento Embrionário/genética , Genômica , Retroelementos/genética , Animais , Ilhas de CpG/genética , Proteínas de Ligação a DNA/genética , Embrião de Mamíferos , Perfilação da Expressão Gênica , Genoma/genética , Impressão Genômica/genética , Camundongos , Fatores de Transcrição/genética
10.
Cytogenet Genome Res ; 160(5): 272-282, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32516773

RESUMO

Saccharum spontaneum is a wild germplasm resource of the genus Saccharum that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in S. spontaneum. A total of 44 Ty1-copia reverse transcriptase subclones isolated from S. spontaneum showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the S. spontaneum genome.


Assuntos
Cromossomos de Plantas/genética , Evolução Molecular , Genoma de Planta/genética , Retroelementos/genética , Saccharum/genética , Filogenia
11.
PLoS One ; 15(6): e0235127, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579599

RESUMO

Repeat-induced gene silencing (RIGS) establishes the centromere structure, prevents the spread of transposons and silences transgenes, thereby limiting recombinant protein production. We previously isolated a sequence (B-3-31) that alleviates RIGS from the human genome. Here, we developed an assay system for evaluating the influence of repeat sequences on gene expression, based on in vitro ligation followed by our original gene amplification technology in animal cells. Using this assay, we found that the repeat of B-3-31, three core sequences of replication initiation regions (G5, C12, and D8) and two matrix attachment regions (AR1 and 32-3), activated the co-amplified plasmid-encoded d2EGFP gene in both human and hamster cell lines. This upregulation effect persisted for up to 82 days, which was confirmed to be repeat-induced, and was thus designated as a repeat-induced gene activation (RIGA). In clear contrast, the repeat of three bacterial sequences (lambda-phage, Amp, and ColE1) and three human retroposon sequences (Alu, 5'-untranslated region, and ORF1 of a long interspersed nuclear element) suppressed gene expression, thus reflecting RIGS. RIGS was CpG-independent. We suggest that RIGA might be associated with replication initiation. The discovery of RIGS and RIGA has implications for the repeat in mammalian genome, as well as practical value in recombinant production.


Assuntos
Inativação Gênica , Genoma Humano/genética , Regiões de Interação com a Matriz/genética , Origem de Replicação/genética , Ativação Transcricional , Animais , Sequência de Bases , Células CHO , Linhagem Celular Tumoral , Cricetinae , Cricetulus , Regulação da Expressão Gênica , Proteínas de Fluorescência Verde/genética , Proteínas de Fluorescência Verde/metabolismo , Humanos , Hibridização in Situ Fluorescente/métodos , Plasmídeos/genética , Sequências Repetitivas de Ácido Nucleico/genética , Retroelementos/genética
12.
Nucleic Acids Res ; 48(13): 7197-7217, 2020 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-32558886

RESUMO

The fungus Magnaporthe oryzae causes devastating diseases of crops, including rice and wheat, and in various grasses. Strains from ryegrasses have highly unstable chromosome ends that undergo frequent rearrangements, and this has been associated with the presence of retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons-MoTeRs) inserted in the telomeres. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, mapping, and sequencing of parental and novel telomeric restriction fragments (TRFs), along with MinION sequencing of genomic DNA allowed us to document the precise molecular alterations underlying 109 newly-formed TRFs. These included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by 'plain' telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; MoTeR-independent expansion and contraction of subtelomeric tandem repeats; and a variety of rearrangements initiated through breaks in interstitial telomere tracts that are generated during MoTeR integration. Overall, we estimate that alterations occurred in approximately sixty percent of chromosomes (one in three telomeres) analyzed. Most importantly, we describe an entirely new mechanism by which transposons can promote genomic alterations at exceptionally high frequencies, and in a manner that can promote genome evolution while minimizing collateral damage to overall chromosome architecture and function.


Assuntos
Magnaporthe/genética , Doenças das Plantas/microbiologia , Retroelementos/genética , Telômero/genética , Evolução Molecular
13.
Nat Commun ; 11(1): 3147, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561720

RESUMO

Transposons are known to participate in tissue aging, but their effects on aged stem cells remain unclear. Here, we report that in the Drosophila ovarian germline stem cell (GSC) niche, aging-related reductions in expression of Piwi (a transposon silencer) derepress retrotransposons and cause GSC loss. Suppression of Piwi expression in the young niche mimics the aged niche, causing retrotransposon depression and coincident activation of Toll-mediated signaling, which promotes Glycogen synthase kinase 3 activity to degrade ß-catenin. Disruption of ß-catenin-E-cadherin-mediated GSC anchorage then results in GSC loss. Knocking down gypsy (a highly active retrotransposon) or toll, or inhibiting reverse transcription in the piwi-deficient niche, suppresses GSK3 activity and ß-catenin degradation, restoring GSC-niche attachment. This retrotransposon-mediated impairment of aged stem cell maintenance may have relevance in many tissues, and could represent a viable therapeutic target for aging-related tissue degeneration.


Assuntos
Proteínas Argonauta/metabolismo , Senescência Celular , Proteínas de Drosophila/metabolismo , Drosophila melanogaster , Células Germinativas/metabolismo , Animais , Proteínas Argonauta/genética , Caderinas/metabolismo , Proteínas de Drosophila/genética , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Feminino , Inativação Gênica , Quinase 3 da Glicogênio Sintase/metabolismo , Ovário/citologia , Ovário/metabolismo , Retroelementos/genética , Transdução de Sinais , Nicho de Células-Tronco/fisiologia , Células-Tronco/metabolismo , Receptores Toll-Like/metabolismo , beta Catenina/metabolismo
14.
Int J Food Microbiol ; 325: 108647, 2020 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-32361480

RESUMO

Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.


Assuntos
Retroelementos/genética , Saccharomycetales/genética , Fermento Seco/genética , Sítios de Ligação , Primers do DNA/genética , Ecossistema , Variação Genética/genética , Filogenia , Polimorfismo Genético/genética , Saccharomycetales/classificação
15.
Artigo em Inglês | MEDLINE | ID: mdl-32378983

RESUMO

Ionizing radiation in environment comes from various natural and anthropogenic sources. The effect of radioactivity released after the CNPP (Chernobyl Nuclear Power Plant) on plant systems remains of great interest. Even now, more than three decades after the nuclear accident, the long-lived radionuclides represent a strong stress factor. Herein, the emphasis has been placed on analysis of genetic variability represented by activation of LTR (Long Terminal Repeat)-retrotransposons. Polymorphism in LTR-retrotransposon insertions has been investigated throughout the genome of two flax varieties, Kyivskyi and Bethune. For this purpose, two retrotransposon-based marker techniques, IRAP (Inter-Retrotransposon Amplified Polymorphism) and iPBS (inter-Primer Binding Site), have been employed. The hypothesis that chronic radioactive stress may induce mechanism of retransposition has been supported by the activation of FL9, FL11 and FL12 LTR-retrotransposons in flax seeds harvested from radioactive environment. Out of two retrotransposon-based approaches, IRAP appears to be more suitable for identification of LTR-retrotransposon polymorphism. Even though the LTR-retrotransposon polymorphism was identified, the results suggest the high level of plant adaptation in the radioactive Chernobyl area. However, it is not really surprising that plants developed an effective strategy to survive in radio-contaminated environment over the past 30 years.


Assuntos
Acidente Nuclear de Chernobyl , Linho/genética , Genoma de Planta , Polimorfismo Genético , Retroelementos/genética , Sequências Repetidas Terminais , Sítios de Ligação , DNA de Plantas/genética , Linho/crescimento & desenvolvimento , Linho/efeitos da radiação , Marcadores Genéticos , Modelos Teóricos , Radiação Ionizante , Ucrânia
16.
Exp Mol Pathol ; 114: 104433, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32243892

RESUMO

Combination antiretroviral therapy (cART) has greatly improved the prognosis of patients with human immunodeficiency virus type-1 (HIV-1) infection. However, cardiovascular disease (CVD) remains a serious issue even in the post-cART era. Viral protein R (Vpr), an accessory gene product of HIV-1, exerts pleiotropic activities such as the induction of DNA damage signals, apoptosis by mitochondrial membrane depolarization, G2/M-phase cell cycle abnormalities, and retrotransposition. Importantly, some of these cellular responses are induced by the trans-acting activity of Vpr. Recently, we established an enzyme-linked immunosorbent assay to detect Vpr and reported that about 22% of blood samples from 100 HIV-1-positive patients were positive for Vpr. Here, we investigated the biological effects of recombinant Vpr (rVpr) in vivo. We observed that repeated injections of rVpr increased the copy number of long interspersed element-1 (L1) in the heart genome in mice. rVpr also increased the number of cells positive for senescence-associated ß-galactosidase (SA-ß-gal) and fibrosis in the heart. Notably, co-administration of a reverse transcriptase inhibitor reduced the number of rVpr-induced SA-ß-gal-positive cells and fibrosis concomitantly with the attenuation of L1 retrotransposition. Interestingly, a Vpr mutant defective for mitochondrial dysfunction also induced heart senescence and increased L1 copy number. Together with a recent report that L1 retrotransposition functions as a molecular basis of senescence, our current data suggest that rVpr-induced L1 retrotransposition is linked with senescence in heart tissue. We would propose that Vpr in the bloodstream may be one of risk factors for CVD, and that its monitoring will lead to well understanding of the heterogeneity and multifactorial mechanisms of CVD in HIV-1 patients.


Assuntos
Senescência Celular/genética , Infecções por HIV/genética , Retroelementos/genética , Produtos do Gene vpr do Vírus da Imunodeficiência Humana/genética , Animais , Infecções por HIV/virologia , HIV-1/patogenicidade , Coração/fisiopatologia , Coração/virologia , Humanos , Camundongos
17.
PLoS One ; 15(4): e0231323, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32287287

RESUMO

Following allopolyploidization, nascent polyploid wheat species react with massive genomic rearrangements, including deletion of transposable element-containing sequences. While such massive rearrangements are considered to be a prominent process in wheat genome evolution and speciation, their structure, extent, and underlying mechanisms remain poorly understood. In this study, we retrieved ~3500 insertions of a specific variant of Fatima, one of the most dynamic gypsy long-terminal repeat retrotransposons in wheat from the recently available high-quality genome drafts of Triticum aestivum (bread wheat) and Triticum turgidum ssp. dicoccoides or wild emmer, the allotetraploid mother of all modern wheats. The dynamic nature of Fatima facilitated the identification of large (i.e., up to ~ 1 million bases) Fatima-containing insertions/deletions (indels) upon comparison of bread wheat and wild emmer genomes. We characterized 11 such indels using computer-assisted analysis followed by PCR validation, and found that they might have occurred via unequal intra-strand recombination or double-strand break (DSB) events. Additionally, we observed one case of introgression of novel DNA fragments from an unknown source into the wheat genome. Our data thus indicate that massive large-scale DNA rearrangements might play a prominent role in wheat speciation.


Assuntos
Evolução Molecular , Rearranjo Gênico , Genoma de Planta , Triticum/genética , Quebras de DNA de Cadeia Dupla , Variações do Número de Cópias de DNA , Deleção de Genes , Mutagênese Insercional , Recombinação Genética , Retroelementos/genética
18.
Proc Natl Acad Sci U S A ; 117(18): 9973-9980, 2020 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-32303657

RESUMO

When transitioning from the environment, pathogenic microorganisms must adapt rapidly to survive in hostile host conditions. This is especially true for environmental fungi that cause opportunistic infections in immunocompromised patients since these microbes are not well adapted human pathogens. Cryptococcus species are yeastlike fungi that cause lethal infections, especially in HIV-infected patients. Using Cryptococcus deneoformans in a murine model of infection, we examined contributors to drug resistance and demonstrated that transposon mutagenesis drives the development of 5-fluoroorotic acid (5FOA) resistance. Inactivation of target genes URA3 or URA5 primarily reflected the insertion of two transposable elements (TEs): the T1 DNA transposon and the TCN12 retrotransposon. Consistent with in vivo results, increased rates of mutagenesis and resistance to 5FOA and the antifungal drugs rapamycin/FK506 (rap/FK506) and 5-fluorocytosine (5FC) were found when Cryptococcus was incubated at 37° compared to 30° in vitro, a condition that mimics the temperature shift that occurs during the environment-to-host transition. Inactivation of the RNA interference (RNAi) pathway, which suppresses TE movement in many organisms, was not sufficient to elevate TE movement at 30° to the level observed at 37°. We propose that temperature-dependent TE mobilization in Cryptococcus is an important mechanism that enhances microbial adaptation and promotes pathogenesis and drug resistance in the human host.


Assuntos
Antifúngicos/farmacologia , Cryptococcus neoformans/efeitos dos fármacos , Micoses/genética , Retroelementos/genética , Animais , Antifúngicos/efeitos adversos , Cryptococcus neoformans/patogenicidade , Farmacorresistência Fúngica/genética , Interações Hospedeiro-Patógeno/genética , Humanos , Camundongos , Mutagênese/genética , Micoses/microbiologia , Ácido Orótico/efeitos adversos , Ácido Orótico/análogos & derivados , Ácido Orótico/farmacologia , Sirolimo/farmacologia , Tacrolimo/farmacologia , Virulência/genética
19.
PLoS Genet ; 16(4): e1008599, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32271759

RESUMO

In 1993, Denise Barlow proposed that genomic imprinting might have arisen from a host defense mechanism designed to inactivate retrotransposons. Although there were few examples at hand, she suggested that there should be maternal-specific and paternal-specific factors involved, with cognate imprinting boxes that they recognized; furthermore, the system should build on conserved biochemical factors, including DNA methylation, and maternal control should predominate for imprints. Here, we revisit this hypothesis in the light of recent advances in our understanding of host defense and DNA methylation and in particular, the link with Krüppel-associated box-zinc finger (KRAB-ZF) proteins.


Assuntos
Inativação Gênica , Impressão Genômica , Modelos Genéticos , Retroelementos/genética , Animais , DNA (Citosina-5-)-Metiltransferases/metabolismo , Metilação de DNA , Humanos , Fatores de Transcrição Kruppel-Like/metabolismo , RNA Interferente Pequeno/metabolismo , Proteínas Repressoras/metabolismo
20.
Biochem Biophys Res Commun ; 525(3): 570-575, 2020 05 07.
Artigo em Inglês | MEDLINE | ID: mdl-32115149

RESUMO

Retrotransposon activation occurs in a variety of neurological disorders including multiple sclerosis and Alzheimer's Disease. While the origins of disease-related retrotransposon activation have remained mostly unidentified, this phenomenon may well contribute to disease progression by inducing inflammation, disrupting transcription and, potentially, genomic insertion. Here, we report that the inhibition of mitochondrial respiratory chain complex I by pharmacological agents widely used to model Parkinson's disease leads to a significant increase in expression of the ORF1 protein of the long interspersed nucleotide element 1 (LINE1) retrotransposon in human dopaminergic LUHMES cells. These findings were recapitulated in midbrain lysates from accordingly treated wild-type mice that mimic Parkinson's disease. Retrotransposon activation was paralleled by a loss of DNA cytosine methylation, providing a potential mechanism of retrotransposon mobilization. Loss of DNA methylation as well as retrotransposon activation were suppressed by the mitochondrial antioxidant phenothiazine, indicating that the well-established production of oxidants by inhibited complex I was causing these effects. Retrotransposon activation in some brain disorders may be less of a primary disease trigger rather than a consequence of mitochondrial distress, which is very common in neurodegenerative diseases.


Assuntos
Mitocôndrias/genética , Neurônios/metabolismo , Retroelementos/genética , Animais , Linhagem Celular , Metilação de DNA/genética , Complexo I de Transporte de Elétrons/antagonistas & inibidores , Complexo I de Transporte de Elétrons/metabolismo , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Masculino , Mesencéfalo/citologia , Camundongos Endogâmicos C57BL
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