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1.
Yi Chuan ; 43(8): 737-746, 2021 Aug 20.
Artigo em Chinês | MEDLINE | ID: mdl-34413014

RESUMO

Existing research has shown that there are a large amount of non-coding RNAs (ncRNAs) in organisms. Short open reading frames (sORFs) abundantly exist in molecular sequences inaccurately annotated as ncRNAs. Several sORFs can be transcribed and translated into evolutionarily conserved micropeptides, which were ignored in previous studies due to short sequence lengths and the limitations of research techniques. To date, sORF-encoded micropeptides with various functions have been found to play important roles in regulating vital biological activities. This article reviews the functional micropeptides which have been found in recent years, introduces the new micropeptide designated as MIAC that we have discovered and describes the related technologies for mining potential micropeptides, thereby providing insights and references for new micropeptide discovery for researchers.


Assuntos
Peptídeos , RNA não Traduzido , Fases de Leitura Aberta/genética , Peptídeos/genética
2.
Arch Virol ; 166(10): 2905-2909, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34383166

RESUMO

Golden trumpet (Allamanda cathartica) plants were observed to exhibit mottling and distortion symptoms on leaves. The genome of an associated begomovirus (Al-K1) was amplified by rolling-circle amplification, cloned, and sequenced. The viral genome consisted of two circular ssDNA molecules, and the organization of the ORFs was similar to those of DNA-A and DNA-B components of bipartite begomoviruses. The size of DNA-A (KC202818) and DNA-B (MG969497) of the begomovirus was 2772 and 2690 nucleotides, respectively. Sequence analysis revealed that the DNA-A and DNA-B components shared the highest sequence identity with duranta leaf curl virus (MN537564, 87.8%) and cotton leaf curl Alabad virus (MH760452, 81.0%), respectively. Interestingly, the Al-K1 isolate shared significantly less nucleotide sequence identity with allamanda leaf curl virus (EF602306, 71.6%), the only monopartite begomovirus reported previously in golden trumpet from China. Al-K1 shared less than 91% sequence identity with other begomoviruses, and hence, according to the latest ICTV guidelines for species demarcation of begomoviruses, Al-K1 is proposed to be a member of a new species, and we propose the name "allamanda leaf mottle distortion virus" (AllLMoDV-[IN-Al_K1-12]) for this virus. AllLMoDV was detected in various golden trumpet samples from different locations by PCR with specific primers based on the genome sequence determined in this study. Our study provides evidence of the occurrence of a new bipartite begomovirus in a perennial ornamental plant in India.


Assuntos
Apocynaceae/virologia , Begomovirus/genética , Doenças das Plantas/virologia , Sequência de Bases , Begomovirus/classificação , DNA Viral/genética , Genoma Viral/genética , Índia , Fases de Leitura Aberta/genética , Filogenia , Folhas de Planta/virologia , Análise de Sequência de DNA , Especificidade da Espécie
3.
Arch Virol ; 166(10): 2943-2953, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34383165

RESUMO

Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.


Assuntos
Anelloviridae/classificação , Mamíferos/virologia , Anelloviridae/genética , Animais , Sequência de Bases , DNA Viral/genética , Bases de Dados Genéticas , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Terminologia como Assunto
4.
Arch Virol ; 166(10): 2881-2885, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34338875

RESUMO

Here, we describe a novel mycovirus, tentatively designated as "Botryosphaeria dothidea mitovirus 3" (BdMV3), isolated from Botryosphaeria dothidea strain FJ, which causes pear ring rot disease in Fujian Province, China. The complete genome nucleotide sequence of BdMV3 is 2538 nt in length and contains a single 2070-nt open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp) of 689 amino acids (aa) using the fungal mitochondrial genetic code. BLASTp analysis revealed that the RdRp of BdMV3 shares 28.91%-69.36% sequence identity (query sequence coverage more than 90%) with those of members of the genus Mitovirus, with the highest sequence identity of 69.36% and 68.79% to the corresponding RdRp aa sequences of Rhizoctonia solani mitovirus 10 and Macrophomina phaseolina mitovirus 4, respectively. Phylogenetic analysis based on RdRp aa sequences indicated that BdMV3 is a new member of the genus Mitovirus in the family Mitoviridae.


Assuntos
Ascomicetos/virologia , Genoma Viral/genética , Doenças das Plantas/microbiologia , Pyrus/microbiologia , Vírus de RNA/genética , Sequência de Aminoácidos , China , Micovírus/classificação , Micovírus/genética , Fases de Leitura Aberta/genética , Filogenia , Vírus de RNA/classificação , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética
5.
Virology ; 562: 149-157, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34339929

RESUMO

Six candidate overlapping genes have been detected in SARS-CoV-2, yet current methods struggle to detect overlapping genes that recently originated. However, such genes might encode proteins beneficial to the virus, and provide a model system to understand gene birth. To complement existing detection methods, I first demonstrated that selection pressure to avoid stop codons in alternative reading frames is a driving force in the origin and retention of overlapping genes. I then built a detection method, CodScr, based on this selection pressure. Finally, I combined CodScr with methods that detect other properties of overlapping genes, such as a biased nucleotide and amino acid composition. I detected two novel ORFs (ORF-Sh and ORF-Mh), overlapping the spike and membrane genes respectively, which are under selection pressure and may be beneficial to SARS-CoV-2. ORF-Sh and ORF-Mh are present, as ORF uninterrupted by stop codons, in 100% and 95% of the SARS-CoV-2 genomes, respectively.


Assuntos
Uso do Códon , Homologia de Genes , Fases de Leitura Aberta , SARS-CoV-2/genética , Evolução Molecular , Genoma Viral , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Estatística como Assunto
6.
Arch Virol ; 166(10): 2841-2846, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34357464

RESUMO

Native Australian soldier flies, Inopus spp. (Diptera: Stratiomyidae), are agricultural pests of economic importance to the sugarcane industry. A screen of the salivary gland transcriptome of Inopus flavus (James) revealed the presence of viral RNA belonging to a potentially novel member of the family Dicistroviridae. The complete genome sequence consists of 9793 nucleotides with two open reading frames. The genome includes two potential internal ribosomal entry sites (IRESs): one within the 5' UTR and the other in the intergenic region (IGR). Virus particles purified from infected larvae and visualised by electron microscopy were found to be icosahedral, non-enveloped, and 30 nm in diameter.


Assuntos
Dicistroviridae/classificação , Dípteros/virologia , Saccharum/parasitologia , Sequência de Aminoácidos , Animais , Austrália , Dicistroviridae/genética , Variação Genética , Genoma Viral/genética , Sítios Internos de Entrada Ribossomal/genética , Larva/virologia , Fases de Leitura Aberta/genética , Filogenia , RNA Viral/genética , Glândulas Salivares/virologia , Vírion/ultraestrutura
7.
Arch Virol ; 166(10): 2901-2904, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34363533

RESUMO

The complete genomic sequence of scorzonera virus A (SCoVA) from a Scorzonera austriaca Willd. plant in South Korea was determined by high-throughput sequencing and confirmed by Sanger sequencing. The SCoVA genome contains 9867 nucleotides, excluding the 3'-terminal poly(A) tail. The SCoVA genome structure is typical of potyviruses and contains a single open reading frame encoding a large putative polyprotein of 3168 amino acids. Pairwise comparison analysis of the complete genome and polyprotein sequences of SCoVA with those of other potyviruses showed that they shared the highest nucleotide and amino acid sequences identity (54.47% and 49.57%, respectively) with those of lettuce mosaic virus (GenBank accession number KJ161185). Phylogenetic analysis of the amino acid sequence of the polyprotein confirmed that SCoVA belongs to the genus Potyvirus. These findings suggest that SCoVA should be considered a novel member of the genus Potyvirus, family Potyviridae.


Assuntos
Genoma Viral/genética , Potyvirus/genética , Scorzonera/virologia , Sequência de Aminoácidos , Sequência de Bases , Fases de Leitura Aberta/genética , Filogenia , Poliproteínas/genética , Potyvirus/classificação , Potyvirus/isolamento & purificação , RNA Viral/genética , República da Coreia , Proteínas Virais/genética
8.
Arch Virol ; 166(10): 2779-2787, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34363535

RESUMO

Feline infectious peritonitis (FIP) is a lethal infectious disease of domestic cats caused by feline coronavirus (FCoV) infection. Feline infectious peritonitis virus (FIPV) is a mutant type of FCoV that is characterized by causing fibrinous serositis with effusions in the pleural and abdominal cavities (wet form) and/or granulomatous-necrotizing inflammatory lesions in several organs (dry form). There have been numerous studies on FIP worldwide, whereas information about this disease in Thailand is still limited. Most studies involving molecular surveillance and evaluation of FCoV field strains have examined the genetic diversity of the spike and accessory ORF3c coding regions. Of these, the S gene is more divergent and is responsible for the two FCoV serotypes, while ORF3c harbors mutations that result either in early termination or destruction of the protein. In this study, we investigated the genetic diversity and genetic relationships among the current Thai and global FCoV strains in the accessory and nucleocapsid genes using a virus-specific PCR method. Comparative sequence analysis suggested that the Thai FCoV isolates were most closely related to strains reported in the Netherlands, the USA, and China. In the ORF3ab sequences, some Thai strains were more than 99% identical to the DF-2 prototype strain. Truncation of the 3a gene product was found in Thai FCoV strains of group 2. Amino acid deletions were observed in the N, ORF3c, and ORF7b proteins of Thai FCoV sequences. The accessory gene sequence divergence may be responsible for driving the periodic emergence and continued persistence of FCoVs in Thai domestic cat populations. Our findings provide updated information about the molecular characteristics of the accessory and nucleocapsid genes of FCoV strains in circulation that were not previously documented in this country.


Assuntos
Proteínas do Nucleocapsídeo de Coronavírus/genética , Coronavirus Felino/genética , Peritonite Infecciosa Felina/virologia , Proteínas Virais Reguladoras e Acessórias/genética , Sequência de Aminoácidos , Animais , Gatos , Coronavirus Felino/classificação , Coronavirus Felino/isolamento & purificação , Peritonite Infecciosa Felina/diagnóstico , Variação Genética , Mutação , Fases de Leitura Aberta/genética , Filogenia , RNA Viral/genética , Análise de Sequência , Tailândia/epidemiologia
9.
Arch Virol ; 166(10): 2789-2801, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34370094

RESUMO

Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.


Assuntos
Genoma Viral/genética , Especificidade de Hospedeiro/genética , Nepovirus/genética , Evolução Molecular , Variação Genética , Metagenômica , Nepovirus/classificação , Fases de Leitura Aberta/genética , Filogenia , Filogeografia , Plantas/classificação , Plantas/virologia , RNA Viral/genética , Recombinação Genética
10.
Nat Commun ; 12(1): 5120, 2021 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-34433827

RESUMO

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which infected >200 million people resulting in >4 million deaths. However, temporal landscape of the SARS-CoV-2 translatome and its impact on the human genome remain unexplored. Here, we report a high-resolution atlas of the translatome and transcriptome of SARS-CoV-2 for various time points after infecting human cells. Intriguingly, substantial amount of SARS-CoV-2 translation initiates at a novel translation initiation site (TIS) located in the leader sequence, termed TIS-L. Since TIS-L is included in all the genomic and subgenomic RNAs, the SARS-CoV-2 translatome may be regulated by a sophisticated interplay between TIS-L and downstream TISs. TIS-L functions as a strong translation enhancer for ORF S, and as translation suppressors for most of the other ORFs. Our global temporal atlas provides compelling insight into unique regulation of the SARS-CoV-2 translatome and helps comprehensively evaluate its impact on the human genome.


Assuntos
COVID-19/virologia , Biossíntese de Proteínas , SARS-CoV-2/genética , Transcriptoma , Regulação Viral da Expressão Gênica , Genoma Humano , Humanos , Fases de Leitura Aberta , RNA Viral/genética , RNA Viral/metabolismo , SARS-CoV-2/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo
11.
PLoS One ; 16(8): e0244468, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34432798

RESUMO

The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.


Assuntos
COVID-19/patologia , SARS-CoV-2/genética , Análise de Sequência de DNA/métodos , COVID-19/virologia , DNA Complementar/química , DNA Complementar/metabolismo , Frequência do Gene , Variação Genética , Genoma Viral , Humanos , Fases de Leitura Aberta/genética , RNA Viral/genética , RNA Viral/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , SARS-CoV-2/isolamento & purificação , Carga Viral
12.
Viruses ; 13(6)2021 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-34199223

RESUMO

Coronavirus accessory proteins are a unique set of proteins whose genes are interspersed among or within the genes encoding structural proteins. Different coronavirus genera, or even different species within the same coronavirus genus, encode varying amounts of accessory proteins, leading to genus- or species-specificity. Though accessory proteins are dispensable for the replication of coronavirus in vitro, they play important roles in regulating innate immunity, viral proliferation, and pathogenicity. The function of accessory proteins on virus infection and pathogenesis is an area of particular interest. In this review, we summarize the current knowledge on accessory proteins of several representative coronaviruses that infect humans or animals, including the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with an emphasis on their roles in interaction between virus and host, mainly involving stress response, innate immunity, autophagy, and apoptosis. The cross-talking among these pathways is also discussed.


Assuntos
Imunidade Inata , SARS-CoV-2/imunologia , SARS-CoV-2/metabolismo , Proteínas Virais Reguladoras e Acessórias/metabolismo , COVID-19/imunologia , COVID-19/virologia , Interações Hospedeiro-Patógeno , Humanos , Evasão da Resposta Imune , Fases de Leitura Aberta , SARS-CoV-2/química , SARS-CoV-2/genética , Proteínas Virais Reguladoras e Acessórias/genética , Replicação Viral
13.
Viruses ; 13(6)2021 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-34200386

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of COVID-19, is a readily transmissible and potentially deadly pathogen which is currently re-defining human susceptibility to pandemic viruses in the modern world. The recent emergence of several genetically distinct descendants known as variants of concern (VOCs) is further challenging public health disease management, due to increased rates of virus transmission and potential constraints on vaccine effectiveness. We report the isolation of SARS-CoV-2 VOCs imported into Australia belonging to the B.1.351 lineage, first described in the Republic of South Africa (RSA), and the B.1.1.7 lineage originally reported in the United Kingdom, and directly compare the replication kinetics of these two VOCs in Vero E6 cells. In this analysis, we also investigated a B.1.1.7 VOC (QLD1516/2021) carrying a 7-nucleotide deletion in the open reading frame 7a (ORF7a) gene, likely truncating and rendering the ORF7a protein of this virus defective. We demonstrate that the replication of the B.1.351 VOC (QLD1520/2020) in Vero E6 cells can be detected earlier than the B.1.1.7 VOCs (QLD1516/2021 and QLD1517/2021), before peaking at 48 h post infection (p.i.), with significantly higher levels of virus progeny. Whilst replication of the ORF7a defective isolate QLD1516/2021 was delayed longer than the other viruses, slightly more viral progeny was produced by the mutant compared to the unmutated isolate QLD1517/2021 at 72 h p.i. Collectively, these findings contribute to our understanding of SARS-CoV-2 replication and evolutionary dynamics, which have important implications in the development of future vaccination, antiviral therapies, and epidemiological control strategies for COVID-19.


Assuntos
Fases de Leitura Aberta/genética , SARS-CoV-2/genética , SARS-CoV-2/fisiologia , Proteínas Virais/genética , Replicação Viral , Adulto , Animais , Austrália , COVID-19/prevenção & controle , COVID-19/transmissão , COVID-19/virologia , Chlorocebus aethiops , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cinética , Pessoa de Meia-Idade , Mutação , Nasofaringe/virologia , Filogenia , SARS-CoV-2/classificação , África do Sul , Reino Unido , Células Vero
14.
Viruses ; 13(6)2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-34199948

RESUMO

Bat species worldwide are receiving increased attention for the discovery of emerging viruses, cross-species transmission, and zoonoses, as well as for characterizing virus infections specific to bats. In a previous study, we investigated the presence of coronaviruses in faecal samples from bats at different locations in Denmark, and made phylogenies based on short, partial ORF1b sequences. In this study, selected samples containing bat coronaviruses from three different bat species were analysed, using a non-targeted approach of next-generation sequencing. From the resulting metagenomics data, we assembled full-genome sequences of seven distinct alphacoronaviruses, three astroviruses, and a polyomavirus, as well as partial genome sequences of rotavirus H and caliciviruses, from the different bat species. Comparisons to published sequences indicate that the bat alphacoronaviruses belong to three different subgenera-i.e., Pedacovirus, Nyctacovirus, and Myotacovirus-that the astroviruses may be new species in the genus Mamastrovirus, and that the polyomavirus could also be a new species, but unassigned to a genus. Furthermore, several viruses of invertebrates-including two Rhopalosiphum padi (aphid) viruses and a Kadipiro virus-present in the faecal material were assembled. Interestingly, this is the first detection in Europe of a Kadipiro virus.


Assuntos
Alphacoronavirus/genética , Astroviridae/genética , Quirópteros/virologia , Genoma Viral , Sequenciamento Completo do Genoma , Alphacoronavirus/classificação , Alphacoronavirus/isolamento & purificação , Animais , Astroviridae/classificação , Astroviridae/isolamento & purificação , Dinamarca , Fezes/virologia , Genômica/métodos , Fases de Leitura Aberta , Filogenia
15.
Arch Virol ; 166(10): 2859-2863, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34291341

RESUMO

Sclerotinia sclerotiorum ourmiavirus 17 (SsOV17) was isolated from the hypovirulent strain GF3 of Sclerotinia sclerotiorum. The genome of SsOV17 is 2,802 nt in length and contains a single long open reading frame (ORF) flanked by a short structured 5'-untranslated region (5'-UTR) (28 nt) and a long 3'-UTR (788 nt), respectively. The ORF encodes a protein with 663 amino acids and a predicted molecular mass of 75.0 kDa. A BLASTp search indicated that the protein encoded by SsOV17 is closely related to the putative RNA-dependent RNA polymerase (RdRp) of Sclerotinia sclerotiorum ourmiavirus 13 (71% identity). A multiple sequence alignment indicated that eight conserved amino acid motifs were present in the RdRp conserved region of SsOV17. Phylogenetic analysis demonstrated that SsOV17 clustered with members of the genus Botoulivirus.


Assuntos
Ascomicetos/virologia , Micovírus/classificação , Doenças das Plantas/microbiologia , Vírus de RNA/classificação , Motivos de Aminoácidos , Ascomicetos/patogenicidade , Brassica napus/microbiologia , Micovírus/genética , Micovírus/isolamento & purificação , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Vírus de RNA/genética , Vírus de RNA/isolamento & purificação , RNA Viral/genética , RNA Polimerase Dependente de RNA/genética , Regiões não Traduzidas/genética
16.
Arch Virol ; 166(10): 2865-2868, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34292374

RESUMO

A putative new virus with sequence similarity to members of the genus Cavemovirus in the family Caulimoviridae was identified in wild chicory (Cichorium intybus) by next-generation sequencing (NGS). The putative new virus was tentatively named "chicory mosaic cavemovirus" (ChiMV), and its genome was determined to be 7,775 nucleotides (nt) long with the typical genome organization of cavemoviruses. ORF1 encodes a putative coat protein/movement polyprotein (1,278 aa), ORF2 encodes a putative replicase (650 aa), and ORF3 encodes a putative transactivator factor (384 aa). The first two putative proteins have 46.2% and 68.7% amino acid sequence identity to the CP/MP protein (YP_004347414) and replicase (YP_004347415), respectively, of sweet potato collusive virus (SPCV). ORF3 encodes a protein with 38.5% amino acid sequence identity to the putative transactivator factor (NP_056849) of cassava vein mosaic virus (CsVMV). The new putative viral genome and those of three cavemoviruses (epiphyllum virus 4 [EpV-4], SPCV, and CsVMV) differ by 24-27% in the nt sequence of the replicase gene, which exceeds the species demarcation cutoff (>20%) for the family.


Assuntos
Caulimoviridae/genética , Chicória/virologia , Sequência de Aminoácidos , Caulimoviridae/classificação , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , Folhas de Planta/virologia , RNA Viral/genética , Especificidade da Espécie , Proteínas Virais/genética
17.
Arch Virol ; 166(10): 2875-2879, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34297223

RESUMO

Wheat plants showing yellowing and mosaic in leaves and stunting were collected from wheat fields in Henan Province, China. Analysis of these plants by transmission electron microscopy showed that they contained two types of filamentous virus-like particles with a length of 200-500 nm and 1000-1300 nm, respectively. RNA-seq revealed a coinfection with wheat yellow mosaic virus (WYMV) and an unknown wheat-infecting virus. The genome of the unknown virus is 8,410 nucleotides long, excluding its 3' poly(A) tail. It has six open reading frames (ORFs). ORF1 encodes a putative viral replication-associated protein (Rep), and ORFs 2, 3, and 4 encode the triple gene block (TGB) proteins. ORFs 5 and 6 encode the capsid protein (CP) and a protein with unknown function, respectively. Phylogenetic analysis showed that this novel virus is evolutionarily related to members of the subfamily Quinvirinae, family Betaflexiviridae. It is, however, distinct from the viruses in the currently established genera. Based on the species and genus demarcation criteria set by the International Committee on Taxonomy of Viruses (ICTV), we tentatively name this novel virus "wheat yellow stunt-associated betaflexivirus" (WYSaBV), and we propose it to be a member of a new genus in the family Betaflexiviridae.


Assuntos
Flexiviridae/genética , Triticum/virologia , China , Flexiviridae/classificação , Flexiviridae/patogenicidade , Flexiviridae/ultraestrutura , Genoma Viral/genética , Fases de Leitura Aberta/genética , Filogenia , Doenças das Plantas/virologia , Folhas de Planta/virologia , RNA Viral/genética , Especificidade da Espécie , Proteínas Virais/genética , Vírion/ultraestrutura
18.
Gene ; 799: 145852, 2021 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-34274480

RESUMO

Cerebellins (CBLN1-4), together with C1qTNF proteins, belong to the CBLN subfamily of C1q proteins. Cerebellin-1 (CBLN1) is active in synapse formation and functions at the parallel fiber-Purkinje cell synapses. Cerebellins form tripartite complexes with neurexins and the glutamate-receptor-related proteins GluD1 and GluD2, playing a role as trans-synaptic cell-adhesion molecules that critically contribute to both synapse formation and functioning and brain development. In this study, I present a molecular characterization of the four porcine CBLN genes. Experimental data and in silico analyses collectively describes the gene structure, chromosomal localization, and expression of CBLN1-4. Two cDNAs encoding the cerebellins CBLN1 and CBLN3 were RT-PCR cloned and sequenced. The nucleotide sequence of the CBLN1 clone contains an open reading frame of 582 nucleotides and encodes a protein of 193 amino acids. The deduced amino acid of the porcine CBLN1 protein was 99% identical to both mouse CBLN1 and to human CBLN1. The deduced CBLN1 protein contains a putative signal sequence of 21 residues, two conserved cysteine residues, and C1q domain. The nucleotide sequence of the CBLN3 cDNA clone comprises an open reading frame of 618 nucleotides and encodes a protein of 205 amino acids. The deduced amino acid sequence of the porcine CBLN3 protein was 88% identical to mouse CBLN3 and 94% identical to human CBLN3. The amino terminal ends of both the CBLN1 and CBLN3 proteins contain three possible N-linked glycosylation sites. The genomic organization of both porcine CBLN1 and CBLN3 is very similar to those of their human counterparts. The expression analyses demonstrated that CBLN1 and CBLN3 transcripts are predominantly expressed in the cerebellum. The sequences of the porcine precerebellin genes and cDNAs were submitted to DDBJ/EMBL/GenBank under the following accession numbers: CBLN1 gene (GenBank ID: FJ621565), CBLN1 cDNA (GenBank ID: EF577504), CBLN3 gene (GenBank ID: FJ621566), CBLN3 cDNA (GenBank ID: EF577505) and CBLN4 cDNA (GenBank ID: FJ196070).


Assuntos
Encéfalo/embriologia , Regulação da Expressão Gênica no Desenvolvimento , Proteínas do Tecido Nervoso/genética , Animais , Encéfalo/fisiologia , Clonagem Molecular , Feminino , Glicosilação , Família Multigênica , Proteínas do Tecido Nervoso/metabolismo , Fases de Leitura Aberta , Precursores de Proteínas/genética , Suínos
19.
Int J Mol Sci ; 22(14)2021 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-34298953

RESUMO

A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.


Assuntos
DNA Viral , Genoma Viral , Guanosina , Fases de Leitura Aberta , Pantoea/virologia , Siphoviridae , Proteínas Virais , DNA Viral/genética , DNA Viral/metabolismo , Guanosina/análogos & derivados , Guanosina/química , Guanosina/metabolismo , Siphoviridae/genética , Siphoviridae/metabolismo , Proteínas Virais/genética , Proteínas Virais/metabolismo
20.
Biochim Biophys Acta Proteins Proteom ; 1869(10): 140693, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34237472

RESUMO

The SARS-CoV-2 virus causes the coronavirus disease 19 emerged in 2020. The pandemic triggered a turmoil in public health and is having a tremendous social and economic impact around the globe. Upon entry into host cells, the SARS-CoV-2 virus hijacks cellular machineries to produce and maintain its own proteins, spreading the infection. Although the disease is known for prominent respiratory symptoms, accumulating evidence is also demonstrating the involvement of the central nervous system, with possible mid- and long-term neurological consequences. In this study, we conducted a detailed bioinformatic analysis of the SARS-CoV-2 proteome aggregation propensity by using several complementary computational tools. Our study identified 10 aggregation prone proteins in the reference SARS-CoV-2 strain: the non-structural proteins Nsp4, Nsp6 and Nsp7 as well as ORF3a, ORF6, ORF7a, ORF7b, ORF10, CovE and CovM. By searching for the available mutants of each protein, we have found that most proteins are conserved, while ORF3a and ORF7b are variable and characterized by the occurrence of a large number of mutants with increased aggregation propensity. The geographical distribution of the mutants revealed interesting differences in the localization of aggregation-prone mutants of each protein. Aggregation-prone mutants of ORF7b were found in 7 European countries, whereas those of ORF3a in only 2. Aggregation-prone sequences of ORF7b, but not of ORF3a, were identified in Australia, India, Nepal, China, and Thailand. Our results are important for future analysis of a possible correlation between higher transmissibility and infection, as well as the presence of neurological symptoms with aggregation propensity of SARS-CoV-2 proteins.


Assuntos
Proteoma , SARS-CoV-2/metabolismo , Proteínas Virais/metabolismo , Mutação , Fases de Leitura Aberta , Ligação Proteica , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade , Replicação Viral
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