A Novel P/V/C Gene in a New Member of theParamyxoviridae Family, Which Causes Lethal Infection in Humans, Horses, and Other Animals

ABSTRACT In 1994, a new member of the family Paramyxoviridaeisolated from fatal cases of respiratory disease in horses and humans was shown to be distantly related to morbilliviruses and provisionally called equine morbillivirus (K. Murray et al., Science 268:94–97, 1995). To facilitate characterization and classification, the virus was purified, viral proteins were identified, and the P/V/C gene was cloned and sequenced. The coding strategy of the gene is similar to that of Sendai and measles viruses, members of the Paramyxovirusand Morbillivirus genera, respectively, in the subfamilyParamyxovirinae. The P/V/C gene contains four open reading frames, three of which, P, C, and V, have Paramyxovirinaecounterparts. The P and C proteins are larger and smaller, respectively, than are cognate proteins in members of the subfamily, and the V protein is made as a result of a single G insertion during transcription. The P/V/C gene has two unique features. (i) A fourth open reading frame is located between those of the C and V proteins and potentially encodes a small basic protein similar to those found in some members of the Rhabdoviridae andFiloviridae families. (ii) There is also a long untranslated 3′ sequence, a feature common in Filoviridaemembers. Sequence comparisons confirm that although the virus is a member of the Paramyxovirinae subfamily, it displays only low levels of homology with paramyxoviruses and morbilliviruses and negligible homologies with rubulaviruses.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

Genetics ◽

10.1093/genetics/143.2.777 ◽

1996 ◽

Vol 143 (2) ◽

pp. 777-788 ◽

Cited By ~ 2

Author(s):

Carole H Sellem ◽

Yves d'Aubenton-Carafa ◽

Michèle Rossignol ◽

Léon Belcour

Keyword(s):

Mitochondrial Genome ◽

Open Reading Frames ◽

Nucleotide Substitutions ◽

Sequence Comparisons ◽

Modular Evolution ◽

Group I ◽

Sequence Variations ◽

Type Strains ◽

Reading Frames ◽

Adjacent Exon

Abstract The mitochondrial genome of 23 wild-type strains belonging to three different species of The mitochondrial genome the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

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The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences

Molecular and Cellular Biology ◽

10.1128/mcb.8.9.3827-3836.1988 ◽

1988 ◽

Vol 8 (9) ◽

pp. 3827-3836

Author(s):

N P Williams ◽

P P Mueller ◽

A G Hinnebusch

Keyword(s):

Translational Control ◽

Normal Growth ◽

Regulatory Elements ◽

Growth Conditions ◽

Open Reading Frames ◽

Regulatory Function ◽

Yeast Saccharomyces Cerevisiae ◽

Reading Frame ◽

Yeast Genes ◽

Reading Frames

Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function.

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Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA 9-11

10.21203/rs.3.rs-520549/v1 ◽

2021 ◽

Author(s):

Yang Sun ◽

Yan qiong Li ◽

Wen han Dong ◽

Ai li Sun ◽

Ning wei Chen ◽

...

Keyword(s):

Rhizoctonia Solani ◽

Rna Virus ◽

Dsrna Virus ◽

Open Reading Frames ◽

The Family ◽

Significant Amino Acid Sequence ◽

Overlapping Open Reading Frames ◽

Significant Amino Acid ◽

Reading Frames

Abstract The complete genome of the dsRNA virus isolated from Rhizoctonia solani AG-1 IA 9–11 (designated as Rhizoctonia solani dsRNA virus 11, RsRV11 ) were determined. The RsRV11 genome was 9,555 bp in length, contained three conserved domains, SMC, PRK and RT-like super family, and encoded two non-overlapping open reading frames (ORFs). ORF1 potentially coded for a 204.12 kDa predicted protein, which shared low but significant amino acid sequence identities with the putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008) ORF1. ORF2 potentially coded for a 132.41 kDa protein which contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). Phylogenetic analysis indicated that RsRV11 was clustered with RsRV-HN008 in a separate clade independent of other virus families. It implies that RsRV11, along with RsRV-HN008 possibly a new fungal virus taxa closed to the family Megabirnaviridae, and RsRV11 is a new member of mycoviruses.

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Complete genome sequence of GII.9 norovirus

Archives of Virology ◽

10.1007/s00705-021-05257-x ◽

2021 ◽

Author(s):

Zilong Zhang ◽

Danlei Liu ◽

Zilei Zhang ◽

Peng Tian ◽

Shenwei Li ◽

...

Keyword(s):

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

High Throughput Sequencing ◽

Open Reading Frames ◽

Viral Sequence ◽

Sequence Comparisons ◽

Rapid Amplification ◽

Genome Level ◽

Reading Frames

AbstractNorovirus is recognized as one of the leading causes of acute gastroenteritis outbreaks. Genotype GII.9 was first detected in Norfolk, VA, USA, in 1997. However, the complete genome sequence of this genotype has not yet been determined. In this study, a complete genome sequence of GII.9[P7] norovirus, SCD1878_GII.9[P7], from a patient was determined using high-throughput sequencing and rapid amplification of cDNA ends (RACE) technology. The complete genome sequence of SCD1878_GII.9[P7] is 7544 nucleotides (nt) in length with a 3’ poly(A) tail and contains three open reading frames. Sequence comparisons indicated that SCD1878_GII.9[P7] shares 92.1%-92.3% nucleotide sequence identity with GII.P7 (AB258331 and AB039777) and 96.7%-97.4% identity with GII.9 (AY038599 and DQ379715). The results suggested that SCD1878_GII.9[P7] is a member of P genotype GII.P7 and G genotype GII.9. This viral sequence fills a gap at the whole-genome level for the GII.9 genotype.

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YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

F1000Research ◽

10.12688/f1000research.6617.2 ◽

2015 ◽

Vol 4 ◽

pp. 155 ◽

Cited By ~ 17

Author(s):

Sandeep Chakraborty ◽

Monica Britton ◽

Jill Wegrzyn ◽

Timothy Butterfield ◽

Pedro José Martínez-García ◽

...

Keyword(s):

Transition Zone ◽

Transcript Abundance ◽

Black Walnut ◽

Open Reading Frames ◽

Rna Seq ◽

Reading Frame ◽

Homologous Genes ◽

Associated Proteins ◽

Molecular Components ◽

Reading Frames

The transcriptome provides a functional footprint of the genome by enumerating the molecular components of cells and tissues. The field of transcript discovery has been revolutionized through high-throughput mRNA sequencing (RNA-seq). Here, we present a methodology that replicates and improves existing methodologies, and implements a workflow for error estimation and correction followed by genome annotation and transcript abundance estimation for RNA-seq derived transcriptome sequences (YeATS - Yet Another Tool Suite for analyzing RNA-seq derived transcriptome). A unique feature of YeATS is the upfront determination of the errors in the sequencing or transcript assembly process by analyzing open reading frames of transcripts. YeATS identifies transcripts that have not been merged, result in broken open reading frames or contain long repeats as erroneous transcripts. We present the YeATS workflow using a representative sample of the transcriptome from the tissue at the heartwood/sapwood transition zone in black walnut. A novel feature of the transcriptome that emerged from our analysis was the identification of a highly abundant transcript that had no known homologous genes (GenBank accession: KT023102). The amino acid composition of the longest open reading frame of this gene classifies this as a putative extensin. Also, we corroborated the transcriptional abundance of proline-rich proteins, dehydrins, senescence-associated proteins, and the DNAJ family of chaperone proteins. Thus, YeATS presents a workflow for analyzing RNA-seq data with several innovative features that differentiate it from existing software.

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Molecular Characterization and Geographic Distribution of a Mymonavirus in the Population of Botrytis cinerea

Viruses ◽

10.3390/v10080432 ◽

2018 ◽

Vol 10 (8) ◽

pp. 432 ◽

Cited By ~ 14

Author(s):

Fangmin Hao ◽

Mingde Wu ◽

Guoqing Li

Keyword(s):

Botrytis Cinerea ◽

Sclerotinia Sclerotiorum ◽

Cdna Sequence ◽

Rna Virus ◽

Open Reading Frames ◽

Phytopathogenic Fungus ◽

Rna Dependent Rna Polymerase ◽

Rdrp Domain ◽

The Family ◽

Reading Frames

Here, we characterized a negative single-stranded (−ss)RNA mycovirus, Botrytis cinerea mymonavirus 1 (BcMyV1), isolated from the phytopathogenic fungus Botrytis cinerea. The genome of BcMyV1 is 7863 nt in length, possessing three open reading frames (ORF1–3). The ORF1 encodes a large polypeptide containing a conserved mononegaviral RNA-dependent RNA polymerase (RdRp) domain showing homology to the protein L of mymonaviruses, whereas the possible functions of the remaining two ORFs are still unknown. The internal cDNA sequence (10-7829) of BcMyV1 was 97.9% identical to the full-length cDNA sequence of Sclerotinia sclerotiorum negative stranded RNA virus 7 (SsNSRV7), a virus-like contig obtained from Sclerotinia sclerotiorum metatranscriptomes, indicating BcMyV1 should be a strain of SsNSRV7. Phylogenetic analysis based on RdRp domains showed that BcMyV1 was clustered with the viruses in the family Mymonaviridae, suggesting it is a member of Mymonaviridae. BcMyV1 may be widely distributed in regions where B. cinerea occurs in China and even over the world, although it infected only 0.8% of tested B. cinerea strains.

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An Umbra-related Virus Found in Vasconcellea X Heilbornii (Caricaceae)

10.21203/rs.3.rs-196384/v1 ◽

2021 ◽

Author(s):

Juan F Cornejo-Franco ◽

Francisco Flores ◽

Dimitre Mollov ◽

diego fernando quito-avila

Keyword(s):

Phylogenetic Analysis ◽

New Genus ◽

Complete Sequence ◽

Open Reading Frames ◽

Rna Dependent Rna Polymerase ◽

Sequence Comparisons ◽

Genomic Features ◽

Overlapping Open Reading Frames ◽

Reading Frames

Abstract The complete sequence of a new viral RNA from babaco (Vasconcellea x heilbornii) was determined. The genome consisted of 4,584 nucleotides organized in two non-overlapping open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5’ terminus and a 1,843 -nt-long NCR at the 3’ terminus. Sequence comparisons of ORF 2 revealed homology to the RNA-dependent-RNA-polymerase (RdRp) of several umbra- and umbra-related viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported from papaya, citrus, opuntia, maize and sugarcane hosts. This clade shares a most recent ancestor with the umbraviruses but has different genomic features. The creation of a new genus, within the Tombusviridae, is proposed for the classification of these novel viruses.

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Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine

Genome Announcements ◽

10.1128/genomea.00995-17 ◽

2017 ◽

Vol 5 (37) ◽

Cited By ~ 9

Author(s):

Yeonhwa Jo ◽

Myung-Kyu Song ◽

Hoseong Choi ◽

Jae-Seong Park ◽

Jae-Wung Lee ◽

...

Keyword(s):

Genome Sequence ◽

Rna Virus ◽

Open Reading Frames ◽

Grapevine Virus ◽

The Family ◽

Putative Member ◽

Reading Frames

ABSTRACT Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae.

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Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

Phytopathology ◽

10.1094/phyto-09-20-0420-r ◽

2020 ◽

Author(s):

Armelle Marais ◽

Sergio Murolo ◽

Chantal Faure ◽

Yoann Brans ◽

Clement Larue ◽

...

Keyword(s):

High Throughput Sequencing ◽

Molecular Detection ◽

Phylogenetic Analyses ◽

Epidemiological Studies ◽

Mosaic Disease ◽

Open Reading Frames ◽

Sequence Comparisons ◽

High Incidence ◽

The Usa ◽

Reading Frames

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted and sequenced on an Illumina NextSeq500 (2x150 or 2x 75 nt). In each source, we identified a single contig of about 7.2 kilobases that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5% with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons show that this virus is a novel species for which we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak), as well in chestnut trees presenting typical ChMD symptoms in the field (100% and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut SRA transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the USA, as well as ChMV detection in C. dentata from the USA. Preliminary epidemiological studies, performed in France and in Central Eastern Italy, showed that ChMV has a high incidence in some commercial orchards, with a low within-orchard genetic diversity.

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