RESUMEN
BACKGROUND: Novel protein-coding genes were considered to be born by re-organization of pre-existing genes, such as gene duplication and gene fusion. However, recent progress of genome research revealed that more protein-coding genes than expected were born de novo, that is, gene origination by accumulating mutations in non-genic DNA sequences. Nonetheless, the in-depth process (scenario) for de novo origination is not well understood. RESULTS: We have conceived bioinformatic analysis for sketching a scenario for de novo origination of protein-coding genes. For each de novo protein-coding gene, we firstly identified an edge of a given phylogenetic tree where the gene was born based on parsimony. Then, from a multiple sequence alignment of the de novo gene and its orthologous regions, we constructed ancestral DNA sequences of the gene corresponding to both end nodes of the edge. We finally revealed statistical features observed in evolution between the two ancestral sequences. In the analysis of the Saccharomyces cerevisiae lineage, we have successfully sketched a putative scenario for de novo origination of protein-coding genes. (1) In the beginning was GC-rich genome regions. (2) Neutral mutations were accumulated in the regions. (3) ORFs were extended/combined, and then (4) translation signature (Kozak consensus sequence) was recruited. Interestingly, as the scenario progresses from (2) to (4), the specificity of mutations increases. CONCLUSION: To the best of our knowledge, this is the first report outlining a scenario of de novo origination of protein-coding genes. Our bioinformatic analysis can capture events that occur during a short evolutionary time by directly observing the evolution of the ancestral sequences from non-genic to genic. This property is suitable for the analysis of fast evolving de novo genes.
Asunto(s)
Evolución Molecular , Sistemas de Lectura Abierta , Filogenia , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Biología Computacional/métodos , Mutación , Genoma FúngicoRESUMEN
The whole-genome sequence (WGS) analysis of Aichivirus (AiV) identified in Korea was performed in this study. Using Sanger and Nanopore sequencing, the 8228-nucleotide-long genomic sequence of AiV (OQ121963) was determined and confirmed to belong to genotype A. The full-length genome of OQ121963 consisted of a 7296 nt open reading frame (ORF) that encodes a single polyprotein, and 5' UTR (676 nt) and 3' UTR (256 nt) at 5' and 3' ends, respectively. The ORF consisted of leader protein (L), structural protein P1 (VP0, VP1, and VP3), and nonstructural protein P2 (2A, 2B, and 2C) and P3 (3A, 3B, 3C, and 3D). The secondary structure analysis of the 5' UTR identified only stem-loop C (SL-C) and not SL-A and SL-B. The variable region of the AiV genome was analyzed by MegAlign Pro and reconfirmed by SimPlot analysis using 16 AiV whole genomes known to date. Among the entire regions, structural protein region P1 showed the lowest amino acid identity (96.07%) with reference sequence AB040749 (originated in Japan; genotype A), while the highest amino acid identity (98.26%) was confirmed in the 3D region among nonstructural protein region P2 and P3. Moreover, phylogenetic analysis of the WGS of OQ121963 showed the highest homology (96.96%) with JX564249 (originated in Taiwan; genotype A) and lowest homology (90.14%) with DQ028632 (originated in Brazil; genotype B). Therefore, the complete genome characterization of OQ121963 and phylogenetic analysis of the AiV conducted in this study provide useful information allowing to improve diagnostic tools and epidemiological studies of AiVs.
Asunto(s)
Genoma Viral , Genotipo , Kobuvirus , Sistemas de Lectura Abierta , Filogenia , Secuenciación Completa del Genoma , Genoma Viral/genética , República de Corea , Humanos , Kobuvirus/genética , Kobuvirus/clasificación , Kobuvirus/aislamiento & purificación , Infecciones por Picornaviridae/virología , Infecciones por Picornaviridae/epidemiología , Regiones no Traducidas 5'/genética , Adulto , ARN Viral/genética , Regiones no Traducidas 3'/genéticaRESUMEN
In the complex landscape of cancer biology, the discovery of microproteins has triggered a paradigm shift, thereby, challenging the conventional conceptions of gene regulation. Though overlooked for years, these entities encoded by the small open reading frames (100-150 codons), have a significant impact on various cellular processes. As precision medicine pioneers delve deeper into the genome and proteome, microproteins have come into the limelight. Typically characterized by a single protein domain that directly binds to the target protein complex and regulates their assembly, these microproteins have been shown to play a key role in fundamental biological processes such as RNA processing, DNA repair, and metabolism regulation. Techniques for identification and characterization, such as ribosome profiling and proteogenomic approaches, have unraveled unique mechanisms by which these microproteins regulate cell signaling or pathological processes in most diseases including cancer. However, the functional relevance of these microproteins in cancer remains unclear. In this context, the current review aims to "rethink the essence of these genes" and explore "how these hidden players-microproteins orchestrate the signaling cascades of cancer, both as accelerators and brakes.".
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Neoplasias , Humanos , Neoplasias/genética , Neoplasias/metabolismo , Transducción de Señal , Sistemas de Lectura Abierta , Animales , Ribosomas/metabolismo , Ribosomas/genética , MicropéptidosRESUMEN
Mycoviruses with an unprecedented genome organization, featuring the RNA-directed RNA polymerase (RdRp) palm domain coding sequence being split into two distinct genome segments, have been found recently in a few fungi and oomycetes of different lineages and have been proposed to be named "splipalmiviruses". One of these, Oidiodendron maius splipalmivirus 1 (OmSPV1), has been detected in the ericoid mycorrhizal fungus Oidiodendron maius, and it has been proposed to be bisegmented. Here, we complete the genome sequence of this virus by describing a third RNA segment, which is 2000 nt long and whose terminal sequences are identical to those of the other two segments of OmSPV1. This segment contains a single open reading frame that codes for a protein with unknown function and has a low level of sequence identity (47%) to the putative protein encoded by the third segment of another splipalmivirus from Magnaporthe oryzae: Magnaporthe oryzae narnavirus virus 1 (MoNV1). Based on these features, we propose the RNA segment to be the third segment of the OmSPV1 genome.
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Virus Fúngicos , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , ARN Viral , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , ARN Viral/genética , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Proteínas Virales/genética , Secuencia de Bases , Basidiomycota/virología , Basidiomycota/genéticaRESUMEN
Leafcutter ants are dominant herbivores in the Neotropics and rely on a fungus (Leucoagaricus gongylophorus) to transform freshly gathered leaves into a source of nourishment rather than consuming the vegetation directly. Here we report two virus-like particles that were isolated from L. gongylophorus and observed using transmission electron microscopy. RNA sequencing identified two +ssRNA mycovirus strains, Leucoagaricus gongylophorus tymo-like virus 1 (LgTlV1) and Leucoagaricus gongylophorus magoulivirus 1 (LgMV1). Genome annotation of LgTlV1 (7401 nt) showed conserved domains for methyltransferase, endopeptidase, viral RNA helicase, and RNA-dependent RNA polymerase (RdRp). The smaller genome of LgMV1 (2636 nt) contains one open reading frame encoding an RdRp. While we hypothesize these mycoviruses function as symbionts in leafcutter farming systems, further study will be needed to test whether they are mutualists, commensals, or parasites.
Asunto(s)
Hormigas , Virus Fúngicos , Genoma Viral , ARN Viral , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Virus Fúngicos/fisiología , Animales , Hormigas/microbiología , Hormigas/virología , ARN Viral/genética , Filogenia , Sistemas de Lectura Abierta , Simbiosis , ARN Polimerasa Dependiente del ARN/genética , Microscopía Electrónica de Transmisión , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificación , Virus ARN/fisiología , Agaricales/virología , Agaricales/genéticaRESUMEN
The recent emergence of chronic wasting disease (CWD) in Europe has become a new public health risk for monitoring of wild and farmed cervids. This disease, due to prions, has proliferated in North America in a contagious manner. In several mammalian species, polymorphisms in the prion protein gene (PRNP) play a crucial role in the susceptibility to prions and their spread. To obtain a reliable picture of the distribution of PRNP polymorphisms in the two most common cervid species in France, we sequenced the open reading frame (ORF) of this gene in 2114 animals, 1116 roe deer (Capreolus capreolus) and 998 red deer (Cervus elaphus). Selection criteria such as historical origin, spatial distribution and sex ratio have been integrated to establish this sample collection. Except for one heterozygous animal with a non-synonymous mutation at codon 37 (G37A), all the 1116 French roe deer were monomorphic. Red deer showed greater variation with two non-synonymous substitutions (T98A; Q226E), three synonymous substitutions (codons 21, 78 and 136) and a new 24pb deletion (Δ69-77). We found significant regional variations between French regions in the frequency of the identified substitutions. After cloning of the PRNP ORF from animals presenting multiple non-synonymous polymorphisms, we identified six haplotypes and obtained a total of twelve genotypes. As in other European countries, we highlighted the apparent homogeneity of PRNP in the French roe deer and the existence of a greater diversity in the red deer. These results were in line with European phylogeographic studies on these two species.
Asunto(s)
Ciervos , Sistemas de Lectura Abierta , Animales , Francia , Polimorfismo Genético , Priones/genética , Enfermedad Debilitante Crónica/genética , Proteínas Priónicas/genéticaRESUMEN
Cytoplasmic male sterility (CMS) is important for commercial hybrid seed production. However, it is still not used in eggplant (Solanum melongena L.), and corresponding regulatory genes and mechanisms of action have not been reported. We report CMS line 327A, which was derived from the hybridization between cultivated and wild eggplants. By looking at different stages of anther development under a microscope, we saw that the 327A anther's tapetum layer vacuolized during meiosis, which caused abortion. To investigate the 327A CMS regulatory genes, the mitochondrial genomes of 327A and its maintainer line 327B were assembled de novo. It was found that 15 unique ORFs (Open Reading Frame) were identified in 327A. RT-PCR and RT-QPCAR tests confirmed that orf312a and orf172a, 327A-specific ORFs with a transmembrane domain, were strongly expressed in sterile anthers of 327A. In addition, orf312a has a chimeric structure with the ribosomal protein subunit rpl16. Therefore, orf312a and orf172a can be considered strong candidate genes for CMS. Concurrently, we analyzed the characteristics of CMS to develop a functional molecular marker, CMS312, targeting a future theoretical basis for eggplant CMS three-line molecular breeding.
Asunto(s)
Genoma Mitocondrial , Infertilidad Vegetal , Solanum melongena , Solanum melongena/genética , Infertilidad Vegetal/genética , Sistemas de Lectura Abierta/genética , Regulación de la Expresión Génica de las Plantas , Citoplasma/genética , Citoplasma/metabolismo , Genes de PlantasRESUMEN
Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.
Asunto(s)
Evolución Molecular , Filoviridae , Filogenia , Vertebrados , Animales , Filoviridae/genética , Vertebrados/virología , Vertebrados/genética , Genoma Viral , Humanos , Sistemas de Lectura Abierta , Genómica/métodosRESUMEN
Complete genome sequencing of a virus from a white snakeroot plant (Ageratina altissima (L.) King & H. Rob.) collected in the Great Smoky Mountains National Park, USA, revealed a quadricistronic organization resembling that of umbraviruses. ORFs 1 and 2 are putatively translated via a -1 ribosomal frameshift mechanism as a single polypeptide with a role in viral replication, whereas the 3'-proximal and extensively overlapping ORFs 3 and 4 code for proteins involved in long distance trafficing and cell-to-cell movement within the host. Sequence comparisons and phylogenetic analysis strongly suggested that this virus is a previously undescribed member of the genus Umbravirus (family Tombusviridae), for which the name "white snakeroot virus A" (WSVA) is proposed. In addition, we identified and initiated characterization of its possible helper virus, a putative new member of the genus Luteovirus.
Asunto(s)
Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Enfermedades de las Plantas , Tombusviridae , Secuenciación Completa del Genoma , Genoma Viral/genética , Enfermedades de las Plantas/virología , Tombusviridae/genética , Tombusviridae/aislamiento & purificación , Tombusviridae/clasificación , Proteínas Virales/genética , Secuencia de Bases , BlancoRESUMEN
Mitoviruses are cryptic capsidless viruses belonging to the family Mitoviridae that replicate and are maintained in the mitochondria of fungi. Complete mitovirus-like sequences were recently assembled from plant transcriptome data and plant leaf tissue samples. Passion fruit (Passiflora spp.) is an economically important crop for numerous tropical and subtropical countries worldwide, and many virus-induced diseases impact its production. From a large-scale genomic study targeting viruses infecting Passiflora spp. in Brazil, we detected a de novo-assembled contig with similarity to other plant-associated mitoviruses. The contig is â¼2.6 kb long, with a single open reading frame (ORF) encoding an RNA-dependent RNA polymerase (RdRP). This contig has been named "passion fruit mitovirus-like 1" (PfMv1). An alignment of the predicted amino acid sequence of the RdRP of PfMv1 and those of other plant-associated mitoviruses revealed the presence of the six conserved motifs of mitovirus RdRPs. PfMv1 has 79% coverage and 50.14% identity to Humulus lupulus mitovirus 1. Phylogenetic analysis showed that PfMV1 clustered with other plant-associated mitoviruses in the genus Duamitovirus. Using RT-PCR, we detected a PfMv1-derived fragment, but no corresponding DNA was identified, thus excluding the possibility that this is an endogenized viral-like sequence. This is the first evidence of a replicating mitovirus associated with Passiflora edulis, and it should be classified as a member of a new species, for which we propose the name "Duamitovirus passiflorae".
Asunto(s)
Genoma Viral , Sistemas de Lectura Abierta , Passiflora , Filogenia , Enfermedades de las Plantas , ARN Polimerasa Dependiente del ARN , Passiflora/virología , Genoma Viral/genética , Enfermedades de las Plantas/virología , Brasil , ARN Polimerasa Dependiente del ARN/genética , Virus ARN/genética , Virus ARN/aislamiento & purificación , Virus ARN/clasificación , Proteínas Virales/genética , ARN Viral/genética , Secuencia de AminoácidosRESUMEN
Recycling of 40S ribosomal subunits following translation termination, entailing release of deacylated tRNA and dissociation of the empty 40S from mRNA, involves yeast Tma20/Tma22 heterodimer and Tma64, counterparts of mammalian MCTS1/DENR and eIF2D. MCTS1/DENR enhance reinitiation (REI) at short upstream open reading frames (uORFs) harboring penultimate codons that confer heightened dependence on these factors in bulk 40S recycling. Tma factors, by contrast, inhibited REI at particular uORFs in extracts; however, their roles at regulatory uORFs in vivo were unknown. We examined effects of eliminating Tma proteins on REI at regulatory uORFs mediating translational control of GCN4 optimized for either promoting (uORF1) or preventing (uORF4) REI. We found that the Tma proteins generally impede REI at native uORF4 and its variants equipped with various penultimate codons regardless of their Tma-dependence in bulk recycling. The Tma factors have no effect on REI at native uORF1 and equipping it with Tma-hyperdependent penultimate codons generally did not confer Tma-dependent REI; nor did converting the uORFs to AUG-stop elements. Thus, effects of the Tma proteins vary depending on the REI potential of the uORF and penultimate codon, but unlike in mammals, are not principally dictated by the Tma-dependence of the codon in bulk 40S recycling.
Asunto(s)
Factores de Transcripción con Cremalleras de Leucina de Carácter Básico , Sistemas de Lectura Abierta , ARN Mensajero , Subunidades Ribosómicas Pequeñas de Eucariotas , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , ARN Mensajero/metabolismo , ARN Mensajero/genética , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/metabolismo , Factores de Transcripción con Cremalleras de Leucina de Carácter Básico/genética , Subunidades Ribosómicas Pequeñas de Eucariotas/metabolismo , Subunidades Ribosómicas Pequeñas de Eucariotas/genética , Iniciación de la Cadena Peptídica Traduccional , Biosíntesis de ProteínasRESUMEN
Sapovirus (SaV) infection is increasing worldwide. Herein, we provided evidence of a significant increase in SaV infection in Japan during 2010-2022, primarily due to the considerable (p = 0.0003) rise of the GI.1 genotype. Furthermore, we found that all major and minor SaV outbreaks in Japan, including the largest SaV outbreak in 2021-2022, were caused by the GI.1 genotype. Therefore, to get insight into the underlying molecular mechanism behind this rising trend of the SaV GI.1 type, we selected 15 SaV GI.1 outbreak strains for complete genome analysis through next-generation sequencing. Phylogenetically, our strains remained clustered in different branches in lineages I and II among the GI.1 genotype. We showed all amino acid (aa) substitutions in different open reading frames (ORFs) in these strains. Importantly, we have demonstrated that the strains involved in the largest SaV outbreak in Japan in 2021-2022 belonged to lineage II and possessed the third ORF. We have identified some unique aa mutations in these major outbreak strains in the NS1 and NS6-NS7 regions that are thought to be associated with viral pathogenicity, cell tropism, and epidemiological competence. Thus, in addition to enriching the database of SaV's complete sequences, this study provides insights into its important mutations.
Asunto(s)
Infecciones por Caliciviridae , Brotes de Enfermedades , Evolución Molecular , Genoma Viral , Genotipo , Sistemas de Lectura Abierta , Filogenia , Sapovirus , Sapovirus/genética , Sapovirus/clasificación , Sapovirus/aislamiento & purificación , Humanos , Infecciones por Caliciviridae/epidemiología , Infecciones por Caliciviridae/virología , Japón/epidemiología , Genoma Viral/genética , Sistemas de Lectura Abierta/genética , Gastroenteritis/virología , Gastroenteritis/epidemiología , Secuenciación de Nucleótidos de Alto Rendimiento , Sustitución de Aminoácidos , Epidemiología Molecular , Secuenciación Completa del Genoma , MutaciónRESUMEN
CircRNAs are an important class of RNAs with diverse cellular functions in human physiology and disease. A thorough knowledge of circRNAs including their biogenesis and subcellular distribution is important to understand their roles in a wide variety of processes. However, the analysis of circRNAs from total RNA sequencing data remains challenging. Therefore, we developed Calcifer, a versatile workflow for circRNA annotation. Using Calcifer, we analysed APEX-Seq data to compare circRNA occurrence between whole cells, nucleus and subnuclear compartments. We generally find that circRNAs show higher abundance in whole cells compared to nuclear samples, consistent with their accumulation in the cytoplasm. The notable exception is the single-exon circRNA circCANX(9), which is unexpectedly enriched in the nucleus. In addition, we observe that circFIRRE prevails over the linear lncRNA FIRRE in both the cytoplasm and the nucleus. Zooming in on the subnuclear compartments, we show that circRNAs are strongly depleted from nuclear speckles, indicating that excess splicing factors in this compartment counteract back-splicing. Our results thereby provide valuable insights into the subnuclear distribution of circRNAs. Regarding circRNA function, we surprisingly find that the majority of all detected circRNAs possess complete open reading frames with potential for cap-independent translation. Overall, we show that Calcifer is an easy-to-use, versatile and sustainable workflow for the annotation of circRNAs which expands the repertoire of circRNA tools and allows to gain new insights into circRNA distribution and function.
Asunto(s)
Núcleo Celular , ARN Circular , ARN Circular/genética , ARN Circular/metabolismo , Humanos , Núcleo Celular/metabolismo , Núcleo Celular/genética , Citoplasma/metabolismo , Citoplasma/genética , Sistemas de Lectura Abierta , Anotación de Secuencia Molecular , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Empalme del ARN , Biología Computacional/métodos , Análisis de Secuencia de ARNRESUMEN
A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.
Asunto(s)
Genoma Viral , Sistemas de Lectura Abierta , Parvovirus , Filogenia , Lobos , Animales , Lobos/virología , Parvovirus/genética , Parvovirus/clasificación , Parvovirus/aislamiento & purificación , Proteínas de la Cápside/genética , Infecciones por Parvoviridae/virología , Infecciones por Parvoviridae/veterinaria , Composición de Base , China , ADN Viral/genéticaRESUMEN
Vibrio parahaemolyticus is a major seafood-borne zoonotic pathogen that causes gastroenteritis in humans and acute hepatopancreatic necrosis disease (AHPND) in shrimp. In this study, we isolated and characterized Vibrio phage vB_VpM-pA2SJ1, which infects clinical and AHPND-associated strains of V. parahaemolyticus. The phage genome is a linear dsDNA 51,054 bp in length with a G + C content of 43.7%, and it contains 89 open reading frames. Genome comparisons revealed basal similarity to other Vibrio phages, particularly Vibrio phage vB_VpP_1, with 84.2% identity and 46% coverage. Phylogenetic analysis based on the whole genome, the terminase large subunit, and the major capsid protein revealed that phage vB_VpM-pA2SJ1 did not cluster with other known phage families, thus indicating its uniqueness.
Asunto(s)
Bacteriófagos , Composición de Base , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Vibrio parahaemolyticus , Vibrio parahaemolyticus/virología , Vibrio parahaemolyticus/genética , Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación , Bacteriófagos/clasificación , Animales , Penaeidae/virología , Penaeidae/microbiología , Vibriosis/microbiología , Vibriosis/virología , Vibriosis/veterinaria , Hepatopáncreas/virología , Hepatopáncreas/microbiología , Hepatopáncreas/patología , ADN Viral/genéticaRESUMEN
Conidiobolus sensu lato, a genus within the family Ancylistaceae, encompasses a diverse range of fungal species that are widely distributed in plant debris and soil. In this study, we identified three double-stranded RNA (dsRNA) viruses coinfecting a strain of Conidiobolus taihushanensis. These viruses were identified as Conidiobolus taihushanensis totivirus 1 (CtTV1), Conidiobolus nonsegmented RNA virus 1-2 (CNRV1-2), and Conidiobolus taihushanensis virus 1 (CtV1). Through high-throughput sequencing and RNA-ligase-mediated rapid amplification of cDNA ends (RLM-RACE), we determined their complete genome sequences. The genome of CtTV1 is 6,921 nucleotides in length, containing two open reading frames (ORFs). ORF1 encodes a 1,124-amino-acid capsid protein (CP) with a molecular weight of 125.07 kDa, and ORF2 encodes a 780-amino-acid RNA-dependent RNA polymerase (RdRp) with a molecular weight of 88.05 kDa. CNRV1-2, approximately 3.0 kb in length, also contains two ORFs, which are predicted to encode a 186-amino-acid hypothetical protein (HP) and a 758-amino-acid RdRp. CtV1 has a smaller genome consisting of 3,081 base pairs (bp) with two ORFs: one encoding a 244-amino-acid HP (26.85 kDa) and the other encoding a 707-amino-acid RdRp (80.64 kDa). Phylogenetic analysis based on RdRp sequences revealed that CtTV1 shows the highest similarity to Phytophthora pluvialis RNA virus 1, with 38.79% sequence identity, and clusters with members of the family Orthototiviridae, and it is most closely related to Utsjoki toti-like virus. In contrast, CtV1 formed a unique branch and might represent a new genus. The genome sequence of CNRV1-2 is 99.74% identical to that of the previously described Conidiobolus non-segmented RNA virus 1 (CNRV1). Our findings indicate that CtTV1 and CtV1 are distinct novel viruses, while CNRV1-2 appears to be a variant of CNRV1. This study enhances our understanding of the genetic diversity and evolutionary relationships among mycoviruses associated with C. taihushanensis.
Asunto(s)
Conidiobolus , Virus ARN Bicatenario , Genoma Viral , Sistemas de Lectura Abierta , Filogenia , Genoma Viral/genética , Virus ARN Bicatenario/genética , Virus ARN Bicatenario/clasificación , Virus ARN Bicatenario/aislamiento & purificación , Conidiobolus/genética , ARN Viral/genética , ARN Polimerasa Dependiente del ARN/genética , Enfermedades de las Plantas/virología , Enfermedades de las Plantas/microbiología , Virus Fúngicos/genética , Virus Fúngicos/clasificación , Virus Fúngicos/aislamiento & purificación , Proteínas Virales/genética , ARN Bicatenario/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Genómica/métodos , Virus ARN/genética , Virus ARN/clasificación , Virus ARN/aislamiento & purificaciónRESUMEN
Grapevine leafroll-associated virus 3 (GLRaV-3) is a formidable threat to the stability of the global grape and wine industries. It is the primary etiological agent of grapevine leafroll disease (GLD) and significantly impairs vine health, fruit quality, and yield. GLRaV-3 is a member of the genus Ampelovirus, Closteroviridae family. Viral genes within the 3' proximal unique gene blocks (UGB) remain highly variable and poorly understood. The UGBs of Closteroviridae viruses include diverse open reading frames (ORFs) that have been shown to contribute to viral functions such as the suppression of the host RNA silencing defense response and systemic viral spread. This study investigates the role of GLRaV-3 ORF8, ORF9, and ORF10, which encode the proteins p21, p20A, and p20B, respectively. These genes represent largely unexplored facets of the GLRaV-3 genome. Here, we visualize the subcellular localization of wildtype and mutagenized GLRaV-3 ORFs 8, 9, and 10, transiently expressed in Nicotiana benthamiana. Our results indicate that p21 localizes to the cytosol, p20A associates with microtubules, and p20B is trafficked into the nucleus to carry out the suppression of host RNA silencing. The findings presented herein provide a foundation for future research aimed at the characterization of the functions of these ORFs. In the long run, it would also facilitate the development of innovative strategies to understand GLRaV-3, mitigate its spread, and impacts on grapevines and the global wine industry.
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Nicotiana , Proteínas Virales , Nicotiana/genética , Nicotiana/virología , Nicotiana/metabolismo , Proteínas Virales/metabolismo , Proteínas Virales/genética , Enfermedades de las Plantas/virología , Enfermedades de las Plantas/genética , Sistemas de Lectura Abierta/genética , Vitis/genética , Vitis/virología , Vitis/metabolismo , Closteroviridae/genética , Closteroviridae/metabolismoRESUMEN
Rainbow trout (Oncorhynchus mykiss, Walbaum, 1792) is an important economic cold-water fish that is susceptible to heat stress. To date, the heat stress response in rainbow trout is more widely understood at the transcriptional level, while little research has been conducted at the translational level. To reveal the translational regulation of heat stress in rainbow trout, in this study, we performed a ribosome profiling assay of rainbow trout liver under normal and heat stress conditions. Comparative analysis of the RNA-seq data with the ribosome profiling data showed that the folding changes in gene expression at the transcriptional level are moderately correlated with those at the translational level. In total, 1213 genes were significantly altered at the translational level. However, only 32.8% of the genes were common between both levels, demonstrating that heat stress is coordinated across both transcriptional and translational levels. Moreover, 809 genes exhibited significant differences in translational efficiency (TE), with the TE of these genes being considerably affected by factors such as the GC content, coding sequence length, and upstream open reading frame (uORF) presence. In addition, 3468 potential uORFs in 2676 genes were identified, which can potentially affect the TE of the main open reading frames. In this study, Ribo-seq and RNA-seq were used for the first time to elucidate the coordinated regulation of transcription and translation in rainbow trout under heat stress. These findings are expected to contribute novel data and theoretical insights to the international literature on the thermal stress response in fish.
Asunto(s)
Respuesta al Choque Térmico , Hígado , Oncorhynchus mykiss , Biosíntesis de Proteínas , Ribosomas , Análisis de Secuencia de ARN , Animales , Oncorhynchus mykiss/genética , Respuesta al Choque Térmico/genética , Ribosomas/metabolismo , Ribosomas/genética , Biosíntesis de Proteínas/genética , Hígado/metabolismo , Regulación de la Expresión Génica , Transcripción Genética , Perfilación de la Expresión Génica , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Sistemas de Lectura Abierta/genética , Transcriptoma , Perfilado de RibosomasRESUMEN
Saussurea inversa is a perennial herb used in traditional Chinese medicine and is effective against rheumatoid arthritis. In this study, we sequenced the complete mitochondrial (mt) genome of S. inversa (GenBank accession number: ON584565.1). The circular mt genome of S. inversa was 335,372 bp in length, containing 62 genes, including 33 mRNAs, 22 tRNAs, 6 rRNAs, and 1 pseudogene, along with 1626 open reading frames. The GC content was 45.14%. Predictive analysis revealed substantial RNA editing, with ccmFn being the most abundantly edited gene, showing 36 sites. Gene migration between the mt and chloroplast (cp) genomes of S. inversa was observed through the detection of homologous gene fragments. Phylogenetic analysis revealed that S. inversa was clustered with Arctium tomentosum (Asteraceae). Our findings provide extensive information regarding the mt genome of S. inversa and help lay the foundation for future studies on its genetic variations, phylogeny, and breeding via the analysis of the mt genome.
Asunto(s)
Genoma Mitocondrial , Filogenia , Saussurea , Genoma Mitocondrial/genética , Saussurea/genética , Edición de ARN/genética , ARN de Transferencia/genética , Composición de Base/genética , Sistemas de Lectura Abierta/genética , Genoma del CloroplastoRESUMEN
Loss of function mutations in the checkpoint kinase gene CHEK2 are associated with increased risk of breast and other cancers. Most of the 3,188 unique amino acid changes that can result from non-synonymous single nucleotide variants (SNVs) of CHEK2, however, have not been tested for their impact on the function of the CHEK2-enocded protein (CHK2). One successful approach to testing the function of variants has been to test for their ability to complement mutations in the yeast ortholog of CHEK2, RAD53. This approach has been used to provide functional information on over 100 CHEK2 SNVs and the results align with functional assays in human cells and known pathogenicity. Here we tested all but two of the 4,887 possible SNVs in the CHEK2 open reading frame for their ability to complement RAD53 mutants using a high throughput technique of deep mutational scanning (DMS). Among the non-synonymous changes, 770 were damaging to protein function while 2,417 were tolerated. The results correlate well with previous structure and function data and provide a first or additional functional assay for all the variants of uncertain significance identified in clinical databases. Combined, this approach can be used to help predict the pathogenicity of CHEK2 variants of uncertain significance that are found in susceptibility screening and could be applied to other cancer risk genes.