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1.
Zootaxa ; 5005(3): 276-290, 2021 Jul 27.
Artigo em Inglês | MEDLINE | ID: mdl-34811260

RESUMO

Spongicoloides zhoui sp. nov. (Crustacea: Decapoda: Spongicolidae), a species of deep-sea hexactinellid sponge-associated shrimp, is described based on specimens collected from the Zhenbei Seamount in the South China Sea. The new species is morphologically most similar to the Western Pacific congeneric species Spongicoloides iheyaensis Saito, Tsuchida Yamamoto, 2006 in that the ischium of the third pereiopod is unarmed and the fixed finger of the third pereiopod is armed with small teeth on the distoventral margin. However, S. zhoui sp. nov. can be distinguished from S. iheyaensis in that its female antennal basicerite has three large spines on the distolateral margin. Molecular analyses based on nuclear histone H3, and mitochondrial cytochrome c oxidase subunit I (COI), 12S ribosomal RNA (rRNA), and 16S rRNA gene fragments confirmed the placement of S. zhoui sp. nov. within a clade of Spongicoloides/Spongiocaris species, and their sequence divergences were large enough to justify the recognition of this new species.


Assuntos
Decápodes , Animais , China , Decápodes/genética , Feminino , Mitocôndrias , RNA Ribossômico , RNA Ribossômico 16S
2.
PLoS One ; 16(10): e0258594, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34665841

RESUMO

Sri Lanka is an amphibian hotspot of global significance. Its anuran fauna is dominated by the shrub frogs of the genus Pseudophilautus. Except for one small clade of four species in Peninsular India, these cool-wet adapted frogs, numbering some 59 extant species, are distributed mainly across the montane and lowland rain forests of the island. With species described primarily by morphological means, the diversification has never yet been subjected to a molecular species delimitation analysis, a procedure now routinely applied in taxonomy. Here we test the species boundaries of Pseudophilautus in the context of the phylogenetic species concept (PSC). We use all the putative species for which credible molecular data are available (nDNA-Rag-1; mt-DNA- 12S rRNA, 16S rRNA) to build a well resolved phylogeny, which is subjected to species delimitation analyses. The ABGD, bPTP, mPTP and bGMYC species delimitation methods applied to the 16S rRNA frog barcoding gene (for all species), 12S rRNA and Rag-1 nDNA grouped P. procax and P. abundus; P. hallidayi and P. fergusonianus; P. reticulatus and P. pappilosus; P. pleurotaenia and P. hoipolloi; P. hoffmani and P. asankai; P. silvaticus and P. limbus; P. dilmah and P. hankeni; P. fulvus and P. silus.. Surprisingly, all analyses recovered 14 unidentified potential new species as well. The geophylogeny affirms a distribution across the island's aseasonal 'wet zone' and its three principal hill ranges, suggestive of allopatric speciation playing a dominant role, especially between mountain masses. Among the species that are merged by the delimitation analyses, a pattern leading towards a model of parapatric speciation emerges-ongoing speciation in the presence of gene flow. This delimitation analysis reinforces the species hypotheses, paving the way to a reasonable understanding of Sri Lankan Pseudophilautus, enabling both deeper analyses and conservation efforts of this remarkable diversification. http://zoobank.org/urn:lsid:zoobank.org:pub:DA869B6B-870A-4ED3-BF5D-5AA3F69DDD27.


Assuntos
Anuros/classificação , Código de Barras de DNA Taxonômico/métodos , Proteínas de Homeodomínio/genética , RNA Ribossômico 16S/genética , RNA Ribossômico/genética , Proteínas de Anfíbios/genética , Animais , Anuros/genética , Bases de Dados Genéticas , Índia , Filogenia , Filogeografia , Análise de Sequência de DNA
3.
BMC Genomics ; 22(1): 755, 2021 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-34674653

RESUMO

BACKGROUND: Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance. RESULTS: The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness. CONCLUSIONS: This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.


Assuntos
Genoma Mitocondrial , Mariposas , Animais , Mariposas/genética , Nucleotídeos/genética , Filogenia , RNA Ribossômico/genética , RNA de Transferência/genética
4.
J Mol Biol ; 433(21): 167229, 2021 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-34487791

RESUMO

Although RNA-binding proteins (RBPs) are known to be enriched in intrinsic disorder, no previous analysis focused on RBPs interacting with specific RNA types. We fill this gap with a comprehensive analysis of the putative disorder in RBPs binding to six common RNA types: messenger RNA (mRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), non-coding RNA (ncRNA), ribosomal RNA (rRNA), and internal ribosome RNA (irRNA). We also analyze the amount of putative intrinsic disorder in the RNA-binding domains (RBDs) and non-RNA-binding-domain regions (non-RBD regions). Consistent with previous studies, we show that in comparison with human proteome, RBPs are significantly enriched in disorder. However, closer examination finds significant enrichment in predicted disorder for the mRNA-, rRNA- and snRNA-binding proteins, while the proteins that interact with ncRNA and irRNA are not enriched in disorder, and the tRNA-binding proteins are significantly depleted in disorder. We show a consistent pattern of significant disorder enrichment in the non-RBD regions coupled with low levels of disorder in RBDs, which suggests that disorder is relatively rarely utilized in the RNA-binding regions. Our analysis of the non-RBD regions suggests that disorder harbors posttranslational modification sites and is involved in the putative interactions with DNA. Importantly, we utilize experimental data from DisProt and independent data from Pfam to validate the above observations that rely on the disorder predictions. This study provides new insights into the distribution of disorder across proteins that bind different RNA types and the functional role of disorder in the regions where it is enriched.


Assuntos
Proteínas Intrinsicamente Desordenadas/química , RNA Mensageiro/química , RNA Ribossômico/química , RNA Nuclear Pequeno/química , RNA de Transferência/química , RNA não Traduzido/química , Proteínas de Ligação a RNA/química , Acetilação , Sítios de Ligação , Expressão Gênica , Humanos , Proteínas Intrinsicamente Desordenadas/genética , Proteínas Intrinsicamente Desordenadas/metabolismo , Metilação , Fosforilação , Ligação Proteica , Processamento de Proteína Pós-Traducional , Proteoma/genética , Proteoma/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Ribossômico/genética , RNA Ribossômico/metabolismo , RNA Nuclear Pequeno/genética , RNA Nuclear Pequeno/metabolismo , RNA de Transferência/genética , RNA de Transferência/metabolismo , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Ubiquitinação
5.
Methods Enzymol ; 658: 277-310, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34517951

RESUMO

Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNAs. High-throughput pseudouridine profiling of eukaryotic mRNAs from cells has revealed novel sites of modification across the transcriptome. Pseudouridine affects RNA structure and RNA-protein interactions with the potential to influence many steps of mRNA metabolism and thereby affect gene expression. Identifying the mechanisms by which individual pseudouridines sites are modified by pseudouridine synthases (PUS) will facilitate studies on the molecular functions of Ψ. Multiple pseudouridine synthases are expressed in all organisms and might direct pseudouridylation of diverse cellular RNAs, but the RNA targets of many enzymes and their specificity determinants remain to be defined. We developed a high-throughput in vitro pseudouridylation assay followed by sequencing that allows validation of candidate sites identified in cells, assignment of sites as direct targets of PUS and interrogation of the RNA sequence and structural features that direct modification. We also implemented an analysis pipeline to assign Ψ sites from these data, including an updated approach to peak-calling that accounts for noisy signal from low-abundance transcripts.


Assuntos
Pseudouridina , RNA , Pseudouridina/metabolismo , RNA/genética , Processamento Pós-Transcricional do RNA , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Ribossômico/metabolismo , Transcriptoma
6.
Int J Mol Sci ; 22(18)2021 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-34575920

RESUMO

Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.


Assuntos
Perfilação da Expressão Gênica , MicroRNAs/genética , RNA Ribossômico/genética , RNA não Traduzido/genética , Transcriptoma , Regiões 5' não Traduzidas , Animais , Linhagem Celular Tumoral , Regulação da Expressão Gênica , Loci Gênicos , Humanos , Camundongos , Transporte de RNA , RNA Ribossômico 5,8S/genética , Ribonucleoproteínas/genética
7.
Nat Commun ; 12(1): 5638, 2021 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-34561441

RESUMO

In bacteria, ribosome kinetics are considered rate-limiting for protein synthesis and cell growth. Enhanced ribosome kinetics may augment bacterial growth and biomanufacturing through improvements to overall protein yield, but whether this can be achieved by ribosome-specific modifications remains unknown. Here, we evolve 16S ribosomal RNAs (rRNAs) from Escherichia coli, Pseudomonas aeruginosa, and Vibrio cholerae towards enhanced protein synthesis rates. We find that rRNA sequence origin significantly impacted evolutionary trajectory and generated rRNA mutants with augmented protein synthesis rates in both natural and engineered contexts, including the incorporation of noncanonical amino acids. Moreover, discovered consensus mutations can be ported onto phylogenetically divergent rRNAs, imparting improved translational activities. Finally, we show that increased translation rates in vivo coincide with only moderately reduced translational fidelity, but do not enhance bacterial population growth. Together, these findings provide a versatile platform for development of unnatural ribosomal functions in vivo.


Assuntos
Biossíntese de Proteínas , RNA Ribossômico/metabolismo , Proteínas Recombinantes/metabolismo , Proteínas Ribossômicas/metabolismo , Ribossomos/metabolismo , Sequência de Bases , Evolução Molecular Direcionada/métodos , Escherichia coli/genética , Escherichia coli/metabolismo , Cinética , Espectrometria de Massas/métodos , Modelos Moleculares , Mutação , Conformação de Ácido Nucleico , Proteoma/metabolismo , RNA Ribossômico/química , RNA Ribossômico/genética , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Proteínas Ribossômicas/genética , Ribossomos/genética
8.
Biochemistry (Mosc) ; 86(8): 913-925, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34488569

RESUMO

Once it was believed that ribosomal RNA encodes proteins, and GTP hydrolysis supplies the energy for protein synthesis. Everything has changed, when Alexander Spirin joined the science. It turned out that proteins are encoded by a completely different RNA, and GTP hydrolysis only accelerates the process already provided with energy. It was Spirin who first put forward the idea of a Brownian ratchet and explained how and why molecular machines could arise in the RNA world.


Assuntos
Guanosina Trifosfato/metabolismo , Biossíntese de Proteínas , RNA Ribossômico/metabolismo , Bioquímica/história , Catálise , DNA Bacteriano/análise , RNA Polimerases Dirigidas por DNA/química , História do Século XX , Hidrólise , Modelos Moleculares , Dobramento de Proteína , RNA/biossíntese , Ribossomos/fisiologia , U.R.S.S.
9.
Biochemistry (Mosc) ; 86(8): 926-941, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34488570

RESUMO

Resolving first crystal structures of prokaryotic and eukaryotic ribosomes by our group has been based on the knowledge accumulated over the decades of studies, starting with the first electron microscopy images of the ribosome obtained by J. Pallade in 1955. In 1983, A. Spirin, then a Director of the Protein Research Institute of the USSR Academy of Sciences, initiated the first study aimed at solving the structure of ribosomes using X-ray structural analysis. In 1999, our group in collaboration with H. Noller published the first crystal structure of entire bacterial ribosome in a complex with its major functional ligands, such as messenger RNA and three transport RNAs at the A, P, and E sites. In 2011, our laboratory published the first atomic-resolution structure of eukaryotic ribosome solved by the X-ray diffraction analysis that confirmed the conserved nature of the main ribosomal functional components, such as the decoding and peptidyl transferase centers, was confirmed, and eukaryote-specific elements of the ribosome were described. Using X-ray structural analysis, we investigated general principles of protein biosynthesis inhibition in eukaryotic ribosomes, along with the mechanisms of antibiotic resistance. Structural differences between bacterial and eukaryotic ribosomes that determine the differences in their inhibition were established. These and subsequent atomic-resolution structures of the functional ribosome demonstrated for the first time the details of binding of messenger and transport RNAs, which was the first step towards understanding how the ribosome structure ultimately determines its functions.


Assuntos
Cristalografia por Raios X , Biossíntese de Proteínas , RNA Ribossômico/química , Ribossomos/química , Animais , Drosophila melanogaster , Eucariotos , Células Eucarióticas/metabolismo , Humanos , Ligantes , Conformação Molecular , RNA Mensageiro/química , Proteínas Ribossômicas/metabolismo , Saccharomyces cerevisiae , Tetrahymena thermophila , U.R.S.S.
10.
Cancer Sci ; 112(11): 4515-4525, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34490691

RESUMO

We aimed to identify whether Rho GTPase activating proteins (RhoGAPs) were downregulated in cervical cancers and might be targeted to reduce the growth of cervical cancer using the GEO database and immunohistochemical analysis to identified changes in transcription and protein levels. We analyzed their proliferation, clone formation ability, and their growth as subcutaneous tumors in mice. To detect ARHGAP30 localization in cells, immunofluorescence assays were conducted. Mass spectrometry combined with immunoprecipitation experiments were used to identify binding proteins. Protein interactions were validated with co-immunoprecipitation assays. Western-blot and q-PCR were applied to analyze candidate binding proteins that were associated with ribosome biogenesis. Puromycin incorporation assay was used to detect the global protein synthesis rate. We identified that ARHGAP30 was the only downregulated RhoGAP and was related to the survival of cervical cancer patients. Overexpression of ARHGAP30 in cervical cancer cells inhibited cell proliferation and migration. ARHGAP30 immunoprecipitated proteins were enriched in the ribosome biogenesis process. ARHGAP30 was located in the nucleous and interacted with nucleolin (NCL). Overexpression of ARHGAP30 inhibited rRNA synthesis and global protein synthesis. ARHGAP30 overexpression induced the ubiquitination of NCL and decreased its protein level in Hela cells. The function of ARHGAP30 on cervical cancer cell ribosome biogenesis and proliferation was independent of its RhoGAP activity as assessed with a RhoGAP-deficient plasmid of ARHGAP30R55A . Overall, the findings revealed that ARHGAP30 was frequently downregulated and associated with shorter survival of cervical cancer patients. ARHGAP30 may suppress growth of cervical cancer by reducing ribosome biogenesis and protein synthesis through promoting ubiquitination of NCL.


Assuntos
Proliferação de Células , Proteínas Ativadoras de GTPase/metabolismo , Ribossomos/metabolismo , Neoplasias do Colo do Útero/metabolismo , Animais , Linhagem Celular Tumoral , Nucléolo Celular/metabolismo , Regulação para Baixo , Feminino , Células HeLa , Humanos , Imunoprecipitação , Espectrometria de Massas , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Nus , Proteínas de Neoplasias/metabolismo , Fosfoproteínas/metabolismo , Biossíntese de Proteínas , RNA Ribossômico/biossíntese , Proteínas de Ligação a RNA/metabolismo , Ensaio Tumoral de Célula-Tronco , Ubiquitinação , Neoplasias do Colo do Útero/mortalidade , Neoplasias do Colo do Útero/patologia
11.
PLoS Comput Biol ; 17(8): e1009304, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34370725

RESUMO

Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and pipelines have been developed, to date, for the identification and assembly of viral genomes. Assembly pipelines often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases. In the current report, we present a group of deposited sequences that encompass ribosomal RNA (rRNA) contamination. We highlight the detrimental role of chimeric next generation sequencing reads, between host rRNA sequences and viral sequences, in virus genome assembly and we present the hindrances these reads may pose to current methodologies. We have further developed a refining pipeline, the Zero Waste Algorithm (ZWA) that assists in the assembly of low abundance viral genomes. ZWA performs context-depended trimming of chimeric reads, precisely removing their rRNA moiety. These, otherwise discarded, reads were fed to the assembly pipeline and assisted in the construction of larger and cleaner contigs making a substantial impact on current assembly methodologies. ZWA pipeline may significantly enhance virus genome assembly from low abundance samples and virus metagenomics approaches in which a small number of reads determine genome quality and integrity.


Assuntos
Genoma Viral , Metagenômica , Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA Ribossômico/genética , RNA Viral/genética
12.
BMC Bioinformatics ; 22(1): 400, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34384346

RESUMO

BACKGROUND: The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron. RESULTS: To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa. CONCLUSION: Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.


Assuntos
Bases de Dados de Ácidos Nucleicos , RNA Ribossômico , DNA Ribossômico , Filogenia , RNA Ribossômico 16S/genética , RNA Ribossômico 18S/genética , Análise de Sequência de RNA
13.
Biomed Res Int ; 2021: 6637617, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34395621

RESUMO

Staphylococcus aureus is a major human pathogen present on a third of the healthy population. The bacterium possesses an extensive arsenal of virulence factors. The pathogenicity is linked with S. aureus high plasticity and its exceptional ability to incorporate foreign genetic material. The aim of the present study was to perform molecular characterization of Staphylococcus aureus strains isolated from the clinical environment of the CHU-Z Abomey-Calavi/Sô-Ava. Isolation of Staphylococcus aureus bacterium was performed on Chapman agar. Toxin production by isolated S. aureus strains was investigated using the radial immunoprecipitation technique. A colorimetric assay was used to evaluate Staphylococcus aureus lipase (SA-Lipase) production. Finally, the expression of antibiotic resistance genes and genes encoding toxins production was investigated. Our data suggest that none of the isolated Staphylococcus aureus strains expressed the investigated toxin genes. Interestingly, SA-Lipase was produced by 14.28% of our isolated S. aureus strains. The mecA gene was present in 57.14% of the isolated strains, while PVL and TSST-1 genes were identified in 2.85 and 7.14% of S. aureus, respectively. Significant genetic diversity was observed along the hospital environment S. aureus strains. The present study reveals the level of virulence of S. aureus strains isolated in the different units of CHU-Z Abomey Calavi/Sô-Ava through the production of lipase, PVL, and epidermolysins. The molecular study has favored a genetic characterization within the isolated strains.


Assuntos
Infecções Estafilocócicas/microbiologia , Staphylococcus aureus/isolamento & purificação , Staphylococcus aureus/patogenicidade , Fatores de Virulência/genética , Proteínas de Bactérias/genética , Toxinas Bacterianas/genética , Benin , Enterotoxinas/genética , Exotoxinas/genética , Hospitais Universitários , Humanos , Leucocidinas/genética , Lipase/genética , Proteínas de Ligação às Penicilinas/genética , RNA Bacteriano/genética , RNA Ribossômico/genética , RNA Ribossômico 16S/genética , Staphylococcus aureus/genética , Superantígenos/genética , Virulência
15.
Gene ; 804: 145871, 2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34363887

RESUMO

Chrysotila dentata is an ecologically important marine alga contributing to the coccolith formation. In this study, a complete chloroplast (cp DNA) genome of Chrysotila dentata was sequenced by using Illumina Hiseq and was analyzed with the help of a bioinformatics tool CPGAVAS2. The circular chloroplast genome of Chrysotila dentata has a size of 109,017 bp with two inverted repeats (IRs) regions (4513 bp each) which is a common feature in most land plants and algal species. The Chrysotila dentata cp genome consists of 61 identified protein-coding genes, 30 tRNA genes and 6 rRNAs with 21 microsatellites. The phylogenetic relationship with other select algal species revealed a close phylogeny of Chrysotila dentata with Phaeocystis antarctica. This is the first report of the cp genome analysis of genus Chrysotila and the results from this study will be helpful for understanding the genetic structure and function of chloroplast in other species of Chrysotila.


Assuntos
Cloroplastos/genética , Haptófitas/genética , Biologia Computacional/métodos , Evolução Molecular , Genes de Plantas , Genoma , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequências Repetidas Invertidas/genética , Repetições de Microssatélites/genética , Filogenia , RNA Ribossômico/genética , Análise de Sequência de DNA/métodos , Sequenciamento Completo do Genoma/métodos
16.
EMBO Rep ; 22(10): e52435, 2021 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-34409714

RESUMO

Ribosome biogenesis is an essential cellular process that requires integration of extracellular cues, such as metabolic state, with intracellular signalling, transcriptional regulation and chromatin accessibility at the ribosomal DNA. Here, we demonstrate that the recently identified histone modification, methylation of H2AQ105 (H2AQ105me), is an integral part of a dynamic chromatin network at the rDNA locus. Its deposition depends on a functional mTor signalling pathway and acetylation of histone H3 at position K56, thus integrating metabolic and proliferative signals. Furthermore, we identify a first epigenetic reader of this modification, the ribonucleoprotein Nhp2, which specifically recognizes H2AQ105me. Based on functional and proteomic data, we suggest that Nhp2 functions as an adapter to bridge rDNA chromatin with components of the small subunit processome to efficiently coordinate transcription of rRNA with its post-transcriptional processing. We support this by showing that an H2AQ105A mutant has a mild defect in early processing of rRNA.


Assuntos
Proteômica , Transcrição Genética , Nucléolo Celular/metabolismo , Histonas/genética , Histonas/metabolismo , RNA Ribossômico/genética
17.
Nucleic Acids Res ; 49(16): 9574-9593, 2021 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-34403481

RESUMO

Sequence variation in a widespread, recurrent, structured RNA 3D motif, the Sarcin/Ricin (S/R), was studied to address three related questions: First, how do the stabilities of structured RNA 3D motifs, composed of non-Watson-Crick (non-WC) basepairs, compare to WC-paired helices of similar length and sequence? Second, what are the effects on the stabilities of such motifs of isosteric and non-isosteric base substitutions in the non-WC pairs? And third, is there selection for particular base combinations in non-WC basepairs, depending on the temperature regime to which an organism adapts? A survey of large and small subunit rRNAs from organisms adapted to different temperatures revealed the presence of systematic sequence variations at many non-WC paired sites of S/R motifs. UV melting analysis and enzymatic digestion assays of oligonucleotides containing the motif suggest that more stable motifs tend to be more rigid. We further found that the base substitutions at non-Watson-Crick pairing sites can significantly affect the thermodynamic stabilities of S/R motifs and these effects are highly context specific indicating the importance of base-stacking and base-phosphate interactions on motif stability. This study highlights the significance of non-canonical base pairs and their contributions to modulating the stability and flexibility of RNA molecules.


Assuntos
Motivos de Nucleotídeos/genética , RNA Ribossômico/ultraestrutura , RNA/ultraestrutura , Pareamento de Bases/genética , Cristalografia por Raios X , Ligação de Hidrogênio/efeitos dos fármacos , Conformação de Ácido Nucleico/efeitos dos fármacos , RNA/efeitos dos fármacos , RNA/genética , RNA Ribossômico/efeitos dos fármacos , RNA Ribossômico/genética , Ricina/farmacologia
18.
Malar J ; 20(1): 338, 2021 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-34362388

RESUMO

BACKGROUND: Plasmodium vivax is transmitted by members of the Anopheles Hyrcanus Group that includes six species in the Republic of Korea: Anopheles sinensis sensu stricto (s.s.), Anopheles pullus, Anopheles kleini, Anopheles belenrae, Anopheles lesteri, and Anopheles sineroides. Individual Anopheles species within the Hyrcanus Group demonstrate differences in their geographical distributions, vector competence and insecticide resistance, making it crucial for accurate species identification. Conventional species identification conducted using individual genotyping (or barcoding) based on species-specific molecular markers requires extensive time commitment and financial resources. RESULTS: A population-based quantitative sequencing (QS) protocol developed in this study provided a rapid estimate of species composition ratios among pooled mosquitoes as a cost-effective alternative to individual genotyping. This can be accomplished by using species- or group-specific nucleotide sequences of the mitochondrial cytochrome C oxidase subunit I (COI) and the ribosomal RNA internal transcribed spacer 2 (ITS2) region as species identification alleles in a two-step prediction protocol. Standard genomic DNA fragments of COI and ITS2 genes were amplified from each Anopheles species using group-specific universal primer sets. Following sequencing of the COI or ITS2 amplicons generated from sets of standard DNA mixtures, equations were generated via linear regression to predict species-specific nucleotide sequence frequencies at different positions. Species composition ratios between An. sineroides, An. pullus and An. lesteri were estimated from QS of the COI amplicons based on the mC.260A, mC.122C and mC.525C alleles at the first step, followed by the prediction of species composition ratios between An. sinensis, An. kleini and An. belenrae based on QS of the ITS2 amplicons using the rI.370G and rI.389T alleles. The COI copy number was not significantly different between species, suggesting the reliability of COI-based prediction. In contrast, ITS2 showed a slightly but significantly higher copy number in An. belenrae, requiring an adjustment of its predicted composition ratio. A blind test proved that predicted species composition ratios either from pooled DNA specimens or pooled mosquito specimens were not statistically different from the actual values, demonstrating that the QS-based prediction is accurate and reliable. CONCLUSIONS: This two-step prediction protocol will facilitate rapid estimation of the species composition ratios in field-collected Anopheles Hyrcanus Group populations and is particularly useful for studying the vector ecology of Anopheles population and epidemiology of malaria.


Assuntos
Anopheles/parasitologia , Mosquitos Vetores/parasitologia , Animais , Anopheles/classificação , Anopheles/genética , Análise Custo-Benefício , DNA/genética , DNA/isolamento & purificação , Complexo IV da Cadeia de Transporte de Elétrons/genética , Modelos Lineares , Mosquitos Vetores/classificação , Mosquitos Vetores/genética , Filogenia , RNA Ribossômico/genética , República da Coreia , Alinhamento de Sequência , Especificidade da Espécie
19.
Dev Cell ; 56(16): 2269-2270, 2021 08 23.
Artigo em Inglês | MEDLINE | ID: mdl-34428395

RESUMO

Instead of causing immediate sterility, loss of the C. elegans PIWI protein PRG-1 leads to accumulated infertility after tens of generations. In this issue of Developmental Cell, Wahba et al. show that this correlates with aberrant RNA interference pathway-dependent feed forward amplification of ribosomal siRNAs-the proposed accumulative sterility factor.


Assuntos
Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Animais , Proteínas Argonauta/genética , Proteínas Argonauta/metabolismo , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Interferência de RNA , RNA Ribossômico , RNA Interferente Pequeno/genética
20.
Nucleic Acids Res ; 49(16): 9194-9210, 2021 09 20.
Artigo em Inglês | MEDLINE | ID: mdl-34365510

RESUMO

Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed the association of NRDE proteins with pre-rRNAs and the silencing of pre-rRNAs. In the presence of risiRNAs, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNAs inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the RNAi-targeted site. Meanwhile, exosomes mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results established a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.


Assuntos
RNA Ribossômico/metabolismo , RNA Interferente Pequeno/metabolismo , Elongação da Transcrição Genética , Animais , Caenorhabditis elegans , Nucléolo Celular/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , Exossomos/genética , Exossomos/metabolismo , Inativação Gênica , Mutação , RNA Ribossômico/genética , RNA Interferente Pequeno/genética
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