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1.
Nat Commun ; 11(1): 90, 2020 01 03.
Artigo em Inglês | MEDLINE | ID: mdl-31900416

RESUMO

Detection and quantification of circular RNAs (circRNAs) face several significant challenges, including high false discovery rate, uneven rRNA depletion and RNase R treatment efficiency, and underestimation of back-spliced junction reads. Here, we propose a novel algorithm, CIRIquant, for accurate circRNA quantification and differential expression analysis. By constructing pseudo-circular reference for re-alignment of RNA-seq reads and employing sophisticated statistical models to correct RNase R treatment biases, CIRIquant can provide more accurate expression values for circRNAs with significantly reduced false discovery rate. We further develop a one-stop differential expression analysis pipeline implementing two independent measures, which helps unveil the regulation of competitive splicing between circRNAs and their linear counterparts. We apply CIRIquant to RNA-seq datasets of hepatocellular carcinoma, and characterize two important groups of linear-circular switching and circular transcript usage switching events, which demonstrate the promising ability to explore extensive transcriptomic changes in liver tumorigenesis.


Assuntos
Carcinoma Hepatocelular/genética , Neoplasias Hepáticas/genética , /genética , Algoritmos , Carcinoma Hepatocelular/metabolismo , Humanos , Neoplasias Hepáticas/metabolismo , Processamento de RNA , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , Análise de Sequência de RNA , Transcriptoma
2.
Int J Syst Evol Microbiol ; 70(1): 199-203, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31596197

RESUMO

Two yeast strains, DMKU-WBL1-3 and DMKU GT3-16, were obtained from grease samples collected from grease traps at the Kasetsart University canteen, Thailand. Pairwise sequence analysis indicated that the strains were closely related to Candida cylindracea NRRL Y-17506T, but differed by 11 and 35 nucleotide substitutions in the D1/D2 domain of the large subunit (LSU) rRNA gene and the ITS region, respectively. Based on sequence divergences, the novel species was distinguished from C. cylindracea. The results of phylogenetic analysis based on the concatenated sequences from small subunit rRNA, ITS region and LSU rRNA genes showed that the two strains and C. cylindracea NRRL Y-17506T formed a distinct lineage related to the genus Babjeviella. A novel genus, Limtongozyma, is proposed to accommodate these clade members. Hence, Candida cylindracea NRRL Y-17506T is transferred to this genus and assigned as the type species of the genus. The holotype of Limtongozyma siamensis is DMKU-WBL1-3.


Assuntos
Filogenia , Saccharomycetales/classificação , Candida/classificação , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , RNA Ribossômico/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA , Tailândia
4.
Exp Parasitol ; 209: 107824, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31870927

RESUMO

Giardiasis and cryptosporidiosis are recognized by the WHO as important emerging diseases of the 21st century. Symptoms are similar and include diarrhoea and vomiting, which may be severe, even life-threatening, for the immunocompromised and children under five years of age. Between 2013 and 2017, the Institute for Public Health in Serbia recorded 10 waterborne epidemics that manifested as gastrointestinal disease. Routine testing for enteropathogenic bacteria and viruses did not identify the aetiological agents of these outbreaks. As water is not examined for the presence of protozoa in Serbia, we performed a pilot study to analyse samples from four major rivers and their tributaries using a newly implemented methodology for detection of Giardia and Cryptosporidium, based on the ISO 15553:2006 standard. Using immunofluorescence microscopy, Giardia was detected in 10 out of the 31 samples, Cryptosporidium in five, while two samples were positive for both. Presence of G. duodenalis gDNA was confirmed by amplification of the ß-giardin gene in eight samples, of which one and two, respectively, were identified by RFLP as potentially zoonotic assemblages A and B. The results suggest that surface water in Serbia may be a potential source of infection and call for more in-depth studies using sophisticated molecular tools.


Assuntos
Cryptosporidium/isolamento & purificação , Giardia/isolamento & purificação , Rios/parasitologia , Animais , Cryptosporidium/genética , Proteínas do Citoesqueleto/genética , DNA de Protozoário/química , DNA de Protozoário/isolamento & purificação , Técnicas de Genotipagem , Giardia/classificação , Giardia/genética , Humanos , Complexo Mediador/genética , Microscopia de Fluorescência , Projetos Piloto , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , Proteínas de Protozoários/genética , RNA Ribossômico/genética , Sérvia
5.
BMC Evol Biol ; 19(1): 219, 2019 12 02.
Artigo em Inglês | MEDLINE | ID: mdl-31791235

RESUMO

BACKGROUND: Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building. RESULTS: Here, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree. CONCLUSIONS: Together with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).


Assuntos
Filogenia , Software , Algoritmos , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , Sequência de Bases , Evolução Biológica , Eucariotos/classificação , Eucariotos/genética , Genômica , RNA Ribossômico/genética , Alinhamento de Sequência
6.
Parasit Vectors ; 12(1): 512, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31666097

RESUMO

BACKGROUND: Parasites of deep-sea fishes from the South-East Pacific (SPO) are poorly known. Of c.1030 species of fish found in this area, 100-150 inhabit the deep-sea (deeper than 200 m). Only six articles concerning metazoan parasites of fish from deep-waters of SOP are known, and nine monogenean species have been reported. Currently, ten species are known in Acanthocotyle Monticelli, 1888 (Monogenea) and when stated, all of them are found in shallow waters (10-100 m). Acanthocotyle gurgesiella Ñacari, Sepulveda, Escribano & Oliva, 2018 is the only known species parasitizing deep-sea skates (350-450 m) in the SPO. The aim of this study was the description of two new species of Acanthocotyle from two Rajiformes. METHODS: In September 2017, we examined specimens of two species of deep-sea skates (Rajiformes), Amblyraja frerichsi (Krefft) and Bathyraja peruana McEachran & Myyake, caught at c.1500 m depth off Tocopilla, northern Chile, as a by-catch of the Patagonian tooth fish Dissostichus eleginoides Smitt fishery. Specimens of Acanthocotyle were collected from the skin of the skates. Morphometric (including multivariate analysis of proportional measurements, standardized by total length), morphological and molecular analyses (LSU rRNA and cox1 genes) were performed in order to identify the collected specimens. RESULTS: The three approaches used in this study strongly suggest the presence of two new species in the genus Acanthocotyle: Acanthocotyle imo n. sp. and Acanthocotyle atacamensis n. sp. parasitizing the skin of the thickbody skate Amblyraja frerichsi and the Peruvian skate Bathyraja peruana, respectively. The main morphological differences from the closely related species Acanthocotyle verrilli Goto, 1899 include the number of radial rows of sclerites, the non-discrete vitelline follicles and the number of testes. CONCLUSIONS: The two species of monogeneans described here are the only recorded parasites from their respective host species in the SPO. Assessing host specificity for members of Acanthocotyle requires clarifying the systematics of Rajiformes.


Assuntos
Doenças dos Peixes/parasitologia , Platelmintos/classificação , Infecções por Trematódeos/veterinária , Animais , Teorema de Bayes , Chile , DNA de Helmintos/química , DNA de Helmintos/isolamento & purificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Genes Mitocondriais , Especificidade de Hospedeiro , Funções Verossimilhança , Cadeias de Markov , Método de Monte Carlo , Análise Multivariada , Oceano Pacífico , Filogenia , Platelmintos/anatomia & histologia , Platelmintos/genética , Análise de Componente Principal , RNA Ribossômico/genética , Pele/parasitologia , Infecções por Trematódeos/parasitologia
7.
PLoS Genet ; 15(11): e1008469, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31721758

RESUMO

RNA molecules generated by ribonuclease cleavage sometimes harbor a 2',3'-cyclic phosphate (cP) at their 3'-ends. Those cP-containing RNAs (cP-RNAs) form a hidden layer of transcriptome because standard RNA-seq cannot capture them as a result of cP's prevention of an adapter ligation reaction. Here we provide genome-wide analyses of short cP-RNA transcriptome across multiple mouse tissues. Using cP-RNA-seq that can exclusively sequence cP-RNAs, we identified numerous novel cP-RNA species which are mainly derived from cytoplasmic tRNAs, mRNAs, and rRNAs. Determination of the processing sites of substrate RNAs for cP-RNA generation revealed highly-specific RNA cleavage events between cytidine and adenosine in cP-RNA biogenesis. cP-RNAs were not evenly derived from the overall region of substrate RNAs but rather from specific sites, implying that cP-RNAs are not from random degradation but are produced through a regulated biogenesis pathway. The identified cP-RNAs were abundantly accumulated in mouse tissues, and the expression levels of cP-RNAs showed age-dependent reduction. These analyses of cP-RNA transcriptome unravel a novel, abundant class of non-coding RNAs whose expression could have physiological roles.


Assuntos
Envelhecimento/genética , Sequência de Bases/genética , RNA/genética , Transcriptoma/genética , Envelhecimento/patologia , Animais , Regulação da Expressão Gênica/genética , Genômica , Humanos , Camundongos , Fosfatos/química , Fosfatos/metabolismo , RNA/química , Clivagem do RNA/genética , RNA Ribossômico/genética , RNA Nucleolar Pequeno/genética , RNA de Transferência/genética , RNA não Traduzido/genética , Análise de Sequência de RNA
8.
Parasitol Res ; 118(12): 3555-3559, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31722067

RESUMO

The aim of this study was to survey the Cryptosporidium species in peafowls (Pavo cristatus) in Henan Province, China. A total of 143 fecal specimens collected from a breeding farm were tested for Cryptosporidium by nested PCR targeting the small subunit rRNA (SSU rRNA), 70-kDa heat shock protein (HSP70), and actin genes of Cryptosporidium followed by sequence analysis. Only one isolate from an asymptomatic host was obtained, and the isolate differed from a new C. xiaoi-like genotype by one nucleotide and from C. xiaoi or C. bovis at the SSU rRNA locus by six nucleotides. Likewise, the actin gene shared 99% identity with the C. xiaoi-like genotype, accompanied by four nucleotide mutations. A complete sequence of the HSP70 gene was obtained, and exhibited 96% similarity with that from C. xiaoi and differed by one nucleotide from that with the C. xiaoi-like genotype. Phylogenetic analysis of the current isolate revealed genetic relatedness to the C. xiaoi-like genotype and distinction from C. xiaoi and C. bovis. Therefore, our results provided the first documentation of avian infection with a C. xiaoi-like genotype in China and further insight into the diversity of Cryptosporidium spp. in avians.


Assuntos
Doenças das Aves/parasitologia , Criptosporidiose/parasitologia , Cryptosporidium/isolamento & purificação , Animais , Doenças das Aves/epidemiologia , China/epidemiologia , Criptosporidiose/epidemiologia , Cryptosporidium/classificação , Cryptosporidium/genética , DNA de Protozoário/genética , Fezes/parasitologia , Galliformes/parasitologia , Genótipo , Filogenia , Reação em Cadeia da Polimerase/veterinária , RNA Ribossômico/genética
9.
Parasitol Res ; 118(12): 3359-3370, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31729575

RESUMO

A new species of naidid oligochaete, Dero rwandae, detected in the bladder and the Wolffian ducts of reed frogs Hyperolius kivuensis from Rwanda, is described. Until now, D. bauchiensis was the only endoparasitic Dero known to infect African frogs infesting the eyes and Harderian glands. To the best of our knowledge, the finding of D. rwandae is the first record of an African Dero species infecting the urinary tract of anurans. In general morphology, the two African Dero parasites resemble each other, but differences in the features of ventral setae morphology exist. Parts of the mitochondrial 16S rRNA locus and the nuclear 18S and 28S rRNA loci were sequenced to assess the phylogenetic relationships to other Dero spp. Among those few species, that are barcoded so far, the closest relative of the new taxon is D. superterrenus, a free-living South American species. The species groups formerly termed subgenera Allodero, Aulophorus and Dero within the genus Dero do not represent distinct evolutionary lineages and the genus is paraphyletic including Branchiodrilus.


Assuntos
Anuros/parasitologia , Oligoquetos/classificação , Doenças Parasitárias em Animais/parasitologia , Bexiga Urinária/parasitologia , Animais , Sequência de Bases , Oligoquetos/genética , Filogenia , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 28S/genética , Ruanda
11.
Nat Genet ; 51(10): 1518-1529, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31570891

RESUMO

RNA modifications are emerging as key determinants of gene expression. However, compelling genetic demonstrations of their relevance to human disease are lacking. Here, we link ribosomal RNA 2'-O-methylation (2'-O-Me) to the etiology of dyskeratosis congenita. We identify nucleophosmin (NPM1) as an essential regulator of 2'-O-Me on rRNA by directly binding C/D box small nucleolar RNAs, thereby modulating translation. We demonstrate the importance of 2'-O-Me-regulated translation for cellular growth, differentiation and hematopoietic stem cell maintenance, and show that Npm1 inactivation in adult hematopoietic stem cells results in bone marrow failure. We identify NPM1 germline mutations in patients with dyskeratosis congenita presenting with bone marrow failure and demonstrate that they are deficient in small nucleolar RNA binding. Mice harboring a dyskeratosis congenita germline Npm1 mutation recapitulate both hematological and nonhematological features of dyskeratosis congenita. Thus, our findings indicate that impaired 2'-O-Me can be etiological to human disease.


Assuntos
Disceratose Congênita/genética , Epigenômica/métodos , Mutação em Linhagem Germinativa , Proteínas Nucleares/genética , Processamento Pós-Transcricional do RNA , RNA Mensageiro/genética , RNA Ribossômico/genética , Animais , Disceratose Congênita/patologia , Perfilação da Expressão Gênica , Células-Tronco Hematopoéticas , Masculino , Metilação , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Proteínas Nucleares/química , RNA Nucleolar Pequeno , Transcriptoma
12.
Parasit Vectors ; 12(1): 495, 2019 Oct 22.
Artigo em Inglês | MEDLINE | ID: mdl-31640746

RESUMO

BACKGROUND: Our study aimed to assess the diversity of the species of Anaplasmataceae in Senegal that infect animals and ticks in three areas: near Keur Momar Sarr (northern region), Dielmo and Diop (Sine Saloum, central region of Senegal), and in Casamance (southern region of Senegal). METHODS: A total of 204 ticks and 433 blood samples were collected from ruminants, horses, donkeys and dogs. Ticks were identified morphologically and by molecular characterization targeting the 12S rRNA gene. Molecular characterization of species of Anaplasmataceae infecting Senegalese ticks and animals was conducted using the 23S rRNA, 16S rRNA, rpoB and groEL genes. RESULTS: Ticks were identified as Rhipicephalus evertsi evertsi (84.3%), Hyalomma rufipes (8.3%), Hyalomma impeltatum (4.9%), R. bursa (1.5%) and R. muhsamae (0.9%). The overall prevalence of Anaplasmataceae infection in ticks was 0.9%, whereas 41.1% of the sampled animals were found infected by one of the species belonging to this family. We identified the pathogen Anaplasma ovis in 55.9% of sheep, A. marginale and A. centrale in 19.4% and 8.1%, respectively, of cattle, as well as a putative new species of Anaplasmataceae. Two Anaplasma species commonly infecting ruminants were identified. Anaplasma cf. platys, closely related to A. platys was identified in 19.8% of sheep, 27.7% of goats and 22.6% of cattle, whereas a putative new species, named here provisionally "Candidatus Anaplasma africae", was identified in 3.7% of sheep, 10.3% of goats and 8.1% of cattle. Ehrlichia canis and Anaplasma platys were identified only from dogs sampled in the Keur Momar Sarr area. Ehrlichia canis was identified in 18.8% of dogs and two R. e. evertsi ticks removed from the same sheep. Anaplasma platys was identified in 15.6% of dogs. Neither of the dogs sampled from Casamance region nor the horses and donkeys sampled from Keur Momar Sarr area were found infected by an Anaplasmataceae species. CONCLUSIONS: This study presents a summary of Anaplasmataceae species that infect animals and ticks in three areas from the northern, central and southern regions of Senegal. To our knowledge, our findings demonstrate for the first time the presence of multiple Anaplasmataceae species that infect ticks and domestic animals in Senegal. We recorded two potentially new species commonly infecting ruminants named here provisionally as Anaplasma cf. platys and "Candidatus Anaplasma africae". However, E. canis was the only species identified and amplified from ticks. None of the other Anaplasmataceae species identified in animals were identified in the tick species collected from animals.


Assuntos
Infecções por Anaplasmataceae/veterinária , Anaplasmataceae/classificação , Anaplasmataceae/genética , Animais Domésticos/microbiologia , Carrapatos/microbiologia , Infecções por Anaplasmataceae/microbiologia , Animais , Animais Domésticos/parasitologia , Bovinos , Chaperonina 60/genética , DNA Ribossômico/sangue , DNA Ribossômico/química , DNA Ribossômico/isolamento & purificação , RNA Polimerases Dirigidas por DNA/genética , Doenças do Cão/microbiologia , Doenças do Cão/parasitologia , Cães , Equidae/microbiologia , Equidae/parasitologia , Feminino , Variação Genética , Cabras , Doenças dos Cavalos/microbiologia , Doenças dos Cavalos/parasitologia , Cavalos , Masculino , Filogenia , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Ruminantes/microbiologia , Ruminantes/parasitologia , Senegal , Alinhamento de Sequência/veterinária , Ovinos , Infestações por Carrapato/complicações , Infestações por Carrapato/veterinária
14.
Nucleic Acids Res ; 47(19): 10267-10281, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31665743

RESUMO

Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m4C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m4C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.


Assuntos
Metiltransferases/genética , Mitocôndrias/genética , Ribossomos Mitocondriais/química , RNA Ribossômico/genética , Citidina/genética , Humanos , Metilação , Mitocôndrias/química , Fosforilação Oxidativa , Biossíntese de Proteínas/genética , Dobramento de RNA/genética , Processamento Pós-Transcricional do RNA/genética , RNA Ribossômico/química
15.
Nucleic Acids Res ; 47(19): 10414-10425, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31665744

RESUMO

Bacteria harbor a number GTPases that function in the assembly of the ribosome and are essential for growth. RbgA is one of these GTPases and is required for the assembly of the 50S subunit in most bacteria. Homologs of this protein are also implicated in the assembly of the large subunit of the mitochondrial and eukaryotic ribosome. We present here the cryo-electron microscopy structure of RbgA bound to a Bacillus subtilis 50S subunit assembly intermediate (45SRbgA particle) that accumulates in cells upon RbgA depletion. Binding of RbgA at the P site of the immature particle stabilizes functionally important rRNA helices in the A and P-sites, prior to the completion of the maturation process of the subunit. The structure also reveals the location of the highly conserved N-terminal end of RbgA containing the catalytic residue Histidine 9. The derived model supports a mechanism of GTP hydrolysis, and it shows that upon interaction of RbgA with the 45SRbgA particle, Histidine 9 positions itself near the nucleotide potentially acting as the catalytic residue with minimal rearrangements. This structure represents the first visualization of the conformational changes induced by an assembly factor in a bacterial subunit intermediate.


Assuntos
GTP Fosfo-Hidrolases/química , RNA Ribossômico/química , Proteínas Ribossômicas/química , Bacillus subtilis/química , Bacillus subtilis/genética , Microscopia Crioeletrônica , GTP Fosfo-Hidrolases/ultraestrutura , Hidrólise , Modelos Moleculares , Conformação Proteica , RNA Ribossômico/genética , RNA Ribossômico/ultraestrutura , Proteínas Ribossômicas/ultraestrutura , Subunidades Ribossômicas Maiores de Bactérias/química , Subunidades Ribossômicas Maiores de Bactérias/genética , Subunidades Ribossômicas Maiores de Bactérias/ultraestrutura , Ribossomos/genética , Ribossomos/ultraestrutura
16.
Genes (Basel) ; 10(10)2019 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-31569787

RESUMO

Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastoderma edule) and lagoon (Cerastoderma glaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C. edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b-RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management.


Assuntos
Cardiidae/genética , Polimorfismo de Nucleotídeo Único , Animais , Cardiidae/classificação , Cardiidae/parasitologia , Código de Barras de DNA Taxonômico/normas , Resistência à Doença/genética , Hibridização Genética , RNA Ribossômico/genética , Rhizaria/patogenicidade
17.
Turkiye Parazitol Derg ; 43(3): 111-117, 2019 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-31502772

RESUMO

Objective: The aim of the study was to determine the prevalence of Blastocystis subspecies in water samples collected from Ordu province. Methods: Seventy-five surface water samples and 25 drinking water samples were collected from Ordu and its boroughs. The samples were flocculated by aluminum sulphate and concentrated by sucrose gradient method. Small subunit ribosomal RNA (SSU rRNA) gene was amplified by polymerase chain reaction (PCR). Sequence analysis was performed on the positive PCR products and the base sequences were aligned using Bioedit. Phylogeny trees were drawn and Blastocystis subspecies were identified. Results: Four out of the 100 water samples were positive for Blastocystis spp. No positivity was found in the drinking water. Blastocystis ST-1 subspecies was detected in Bülbül River, Kacali River and Bolaman Stream. Blastocystis ST-3 subspecies were found in Karabalçik River. The lowest genetic distance was found between ST-1 subspecies and the samples from Bülbül River, Kacali River and Bolaman Stream. The nucleotide similarities between them were 98.8%, 76.6 and 98.8%, respectively. The lowest genetic distance was found between Karabalçik River and ST-3 subspecies and the nucleotide similarity between them was 99.1%. Conclusion: This is the first study on the presence of Blastocystis spp. in the surface water and drinking water samples in Ordu province of the Black Sea area in Turkey.


Assuntos
Infecções por Blastocystis/epidemiologia , Blastocystis/isolamento & purificação , Água Potável/parasitologia , Rios/parasitologia , Sequência de Bases , Mar Negro , Blastocystis/classificação , Blastocystis/genética , Humanos , Filogenia , Reação em Cadeia da Polimerase , Prevalência , RNA Ribossômico/genética , Alinhamento de Sequência , Turquia/epidemiologia
18.
Nucleic Acids Res ; 47(19): 10340-10356, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31504769

RESUMO

Mitochondrial tRNA processing defects were associated with human diseases but their pathophysiology remains elusively. The hypertension-associated m.4401A>G mutation resided at a spacer between mitochondrial tRNAMet and tRNAGln genes. An in vitro processing experiment revealed that the m.4401A>G mutation caused 59% and 69% decreases in the 5' end processing efficiency of tRNAGln and tRNAMet precursors, catalyzed by RNase P, respectively. Using human umbilical vein endothelial cells-derived cybrids, we demonstrated that the m.4401A>G mutation caused the decreases of all 8 tRNAs and ND6 and increases of longer and uncleaved precursors from the Light-strand transcript. Conversely, the m.4401A>G mutation yielded the reduced levels of tRNAMet level but did not change the levels of other 13 tRNAs, 12 mRNAs including ND1, 12S rRNA and 16S rRNA from the Heavy-strand transcript. These implicated the asymmetrical processing mechanisms of H-strand and L-strand polycistronic transcripts. The tRNA processing defects play the determined roles in the impairing mitochondrial translation, respiratory deficiency, diminishing membrane potential, increasing production of reactive oxygen species and altering autophagy. Furthermore, the m.4401A>G mutation altered the angiogenesis, evidenced by aberrant wound regeneration and weaken tube formation in mutant cybrids. Our findings provide new insights into the pathophysiology of hypertension arising from mitochondrial tRNA processing defects.


Assuntos
DNA Mitocondrial/genética , Hipertensão/genética , RNA de Transferência de Metionina/genética , Transcrição Genética , Células Endoteliais da Veia Umbilical Humana , Humanos , Mutação/genética , NADH Desidrogenase/genética , Processamento Pós-Transcricional do RNA/genética , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , RNA de Transferência de Glutamina/genética
19.
Nucleic Acids Res ; 47(19): 10357-10372, 2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31504794

RESUMO

Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine-binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.


Assuntos
Proteínas de Ciclo Celular/genética , Proteínas de Ligação a DNA/genética , Histona Acetiltransferases/genética , Proteínas Nucleares/genética , Fatores de Transcrição/genética , Acetilação , Carcinogênese/genética , Cromatina/genética , Metilação de DNA/genética , DNA Ribossômico/genética , Histonas/genética , Humanos , RNA Polimerase I/genética , RNA Ribossômico/biossíntese , RNA Ribossômico/genética , Transcrição Genética
20.
RNA ; 25(12): 1714-1730, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31506380

RESUMO

The origin of the genetic code remains enigmatic five decades after it was elucidated, although there is growing evidence that the code coevolved progressively with the ribosome. A number of primordial codes were proposed as ancestors of the modern genetic code, including comma-free codes such as the RRY, RNY, or GNC codes (R = G or A, Y = C or T, N = any nucleotide), and the X circular code, an error-correcting code that also allows identification and maintenance of the reading frame. It was demonstrated previously that motifs of the X circular code are significantly enriched in the protein-coding genes of most organisms, from bacteria to eukaryotes. Here, we show that imprints of this code also exist in the ribosomal RNA (rRNA). In a large-scale study involving 133 organisms representative of the three domains of life, we identified 32 universal X motifs that are conserved in the rRNA of >90% of the organisms. Intriguingly, most of the universal X motifs are located in rRNA regions involved in important ribosome functions, notably in the peptidyl transferase center and the decoding center that form the original "proto-ribosome." Building on the existing accretion models for ribosome evolution, we propose that error-correcting circular codes represented an important step in the emergence of the modern genetic code. Thus, circular codes would have allowed the simultaneous coding of amino acids and synchronization of the reading frame in primitive translation systems, prior to the emergence of more sophisticated start codon recognition and translation initiation mechanisms.


Assuntos
Evolução Molecular , Código Genético , Motivos de Nucleotídeos , Biossíntese de Proteínas , Ribossomos/genética , Ribossomos/metabolismo , Modelos Biológicos , Modelos Moleculares , Conformação Molecular , Conformação de Ácido Nucleico , RNA Ribossômico/química , RNA Ribossômico/genética , Ribossomos/química , Relação Estrutura-Atividade
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