Editing of the Sendai virus P/C mRNA by G insertion occurs during mRNA synthesis via a virus-encoded activity

Vidal, S; Curran, Joseph; Kolakofsky, Daniel

doi:10.1128/jvi.64.1.239-246.1990

Cited by 154 publications

(79 citation statements)

References 36 publications

(24 reference statements)

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“…The ultimate immunoevasion strategy may be virally-encoded nucleotides (Bryson et al, 2015;Murphy et al, 2013;Weigele et al, 2017). Host and virallyencoded RNA editing already bedevils calling of accurate whole genome sequences in both positive-and negative-strand RNA viruses (Park et al, 2015;Pelet et al, 1991;Piontkivska et al, 2017;Vidal et al, 1990). Adenosine-based modifications of viral genomes have shown effects on viral and host biology, but detecting them requires additional modifications to most sequencing protocols (Gokhale and Horner, 2017;Gonzales-van Horn and Sarnow, 2017;Kennedy et al, 2016Kennedy et al, , 2017.…”

Section: Easier Faster Better Broader Protocolsmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.

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Section: Easier Faster Better Broader Protocolsmentioning

confidence: 99%

A decade of RNA virus metagenomics is (not) enough

2018

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“…To identify the RNA editing site, reference V or D protein sequence is aligned to the protein sequence deduced from genomic sequence to locate the frame-shifting region. In measles virus, Sendai virus, bPIV-3, hPIV-3, the sequence string AAAAAGGG immediately upstream the editing site is conserved and is screened to identify the RNA editing site (4,5). A single G residue is added into the complementary DNA sequence of measles virus at the editing site and the reading frame shifts from +1 to +2; in hPIV-3, bPIV-3 and Sendai virus, two G residues are inserted at the editing site.…”

Section: Rna Editingmentioning

confidence: 99%

“…Sendai virus is the best studied virus in the paramyxovirus family. The P gene gives rise to a maximum of six different proteins by means of RNA editing, overlapping frames and ribosomal shunting (5,22,23,12). The V protein is produced from the edited mRNA.…”

Section: Parainfluenza Viruses and Sendai Virusmentioning

confidence: 99%

VIGOR extended to annotate genomes for additional 12 different viruses

Wang

Sundaram

Stockwell

2012

Nucleic Acids Research

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A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately identified based on sequence similarity and signature residues. VIGOR produces four output files: a gene prediction file, a complementary DNA file, an alignment file, and a gene feature table file. The gene feature table can be used to create GenBank submission. VIGOR takes a single input: viral genomic sequences in FASTA format. VIGOR has been extended to predict genes for 12 viruses: measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus and Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus and Sendai virus. VIGOR accurately detects the complex gene features like ribonucleicacid editing, stop codon leakage and ribosomal shunting. Precisely identifying the mat_peptide cleavage for some viruses is a built-in feature of VIGOR. The gene predictions for these viruses have been evaluated by testing from 27 to 240 genomes from GenBank.

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“…1). In all cases one mRNA is an exact copy of the gene, whereas the other is modified by the addition of either one or two Gs, within a short run of Gs (Thomas at al., 1988 ;Cattaneo at at, 1989 ;Vidal et at, 1990a) . The G additions are thought to take place by the viral polymerase reiteratively copying a template C residue during mRNA synthesis, by a stuttering mechanism (Vidal et at, 1990b ;Pelet et al, 1991).…”

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confidence: 99%

Characterization of the Sendai virus V protein with an anti-peptide antiserum

et al. 1991

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The Sendai virus V protein, which is a fusion of the P and V ORFs of the P gene, was characterized with antisera to a portion of the V ORF and compared to the P protein. The only property found in common with P is that V is also highly phosphorylated, and this is so even when these proteins are expressed independently of the other viral proteins. Otherwise, V was not found in virions, was not strongly associated with viral nucleocapsids like P, and anti-V had no effect on viral RNA synthesis in vitro under conditions where anti-P was highly inhibitory. The available evidence suggests that V may play a role in RNA synthesis, but it is not an essential one like that of the P protein.

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Editing of the Sendai virus P/C mRNA by G insertion occurs during mRNA synthesis via a virus-encoded activity

Cited by 154 publications

References 36 publications

A decade of RNA virus metagenomics is (not) enough

A decade of RNA virus metagenomics is (not) enough

VIGOR extended to annotate genomes for additional 12 different viruses

Characterization of the Sendai virus V protein with an anti-peptide antiserum

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