scholarly journals Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant ‘potex-like’ viruses

2001 ◽  
Vol 82 (1) ◽  
pp. 67-78 ◽  
Author(s):  
Robyn L. J. Howitt ◽  
Ross E. Beever ◽  
Michael N. Pearson ◽  
Richard L. S. Forster
Keyword(s):  
Pathogenic Fungus ◽  
Terminal Region ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Coat Proteins ◽  
Defective Rna ◽  
Genomic Cdna ◽  
Unassigned Genus ◽  
Reading Frames

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus Botrytis cinerea. The mycovirus Botrytis virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3′ terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant ‘tymo-’ and ‘potex-like’ viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in ‘tymo-’ and ‘potex-like’ replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant ‘potex-like’ viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3′-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant ‘potex-like’ virus group.

scholarly journals Molecular Characterization of Divergent Closterovirus Isolates Infecting Ribes Species

Viruses ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 369 ◽  
Author(s):  
Igor Koloniuk ◽  
Thanuja Thekke-Veetil ◽  
Jean-Sébastien Reynard ◽  
Irena Mavrič Pleško ◽  
Jaroslava Přibylová ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Heat Shock Protein 90 ◽  
Open Reading Frames ◽  
Coat Proteins ◽  
Rna Dependent Rna Polymerase ◽  
The Family ◽  
Host Cell Wall ◽  
Reading Frames

Five isolates of a new member of the family Closteroviridae, tentatively named blackcurrant leafroll-associated virus 1 (BcLRaV-1), were identified in the currant. The 17-kb-long genome codes for 10 putative proteins. The replication-associated polyprotein has several functional domains, including papain-like proteases, methyltransferase, Zemlya, helicase, and RNA-dependent RNA polymerase. Additional open reading frames code for a small protein predicted to integrate into the host cell wall, a heat-shock protein 70 homolog, a heat-shock protein 90 homolog, two coat proteins, and three proteins of unknown functions. Phylogenetic analysis showed that BcLRaV-1 is related to members of the genus Closterovirus, whereas recombination analysis provided evidence of intraspecies recombination.

Molecular Characterization of a Novel Partitivirus and a Fusarivirus Co-infected in the Nigrospora Sphaerica Fungus

2021 ◽  
Author(s):  
Jie Zhong ◽  
Ze Zhong Yang ◽  
Xin Yang ◽  
Zhao Jiang Guo ◽  
Wen Xie ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Pathogenic Fungus ◽  
Rna Replication ◽  
Open Reading Frames ◽  
Helicase Domain ◽  
Polya Tail ◽  
Viral Rdrp ◽  
The Family ◽  
Reading Frames

Abstract Here we reported the molecular characterization of two novel mycoviruses co-infected in a plant pathogenic fungus, Nigrospora sphaerica that were designated as Nigrospora sphaerica fusarivirus 1 (NsFV1) and Nigrospora sphaerica partitivirus 1 (NsPV1), respectively. NsFV1 has an undivided genome of 6,147 bp, excluding the polyA tail, and was predicted to contain two nonoverlapping open reading frames (ORF1 and 2). The larger ORF1 encoded a polyprotein containing a conserved RNA-dependent RNA polymerase (RdRp) and a helicase domain that have functions for RNA replication, and the smaller ORF2 encoded a putative protein with an unknown function. The NsPV1 was consists of two genome segments, which were in lengths of 1,796 bp and 1,455 bp, respectively. Each of the two dsRNAs had a single ORF and were deduced to encode proteins with homology to viral RdRp and coat protein (CP), respectively, in the family Partitiviridae. Phylogenetic analysis showed that NsFV1 was placed within the newly proposed family Fusariviridae, while NsPV1 was belonging to the genus Gammapartitivirus in the family Partitiviridae. This was the first description of mycovirses infected the fungus N. sphaerica.

scholarly journals Molecular Characterization of the Movement and Coat Proteins of a New Elm Mottle Virus Isolate Infecting European White Elm (Ulmus laevis Pall.)

2019 ◽  
Vol 8 (1) ◽  
pp. 01-07
Author(s):  
Anne-Mareen Ellen Eisold
Keyword(s):  
Sequence Data ◽  
Open Reading Frames ◽  
Coat Proteins ◽  
Rna Seq ◽  
Genomic Rnas ◽  
Viral Replicase ◽  
Ulmus Laevis ◽  
Reading Frames ◽  
Unknown Isolate

European white elms (Ulmus laevis Pall.) growing in a park in Caputh near Berlin (Germany) were regularly monitored over a period of 18 years showing virus infection-like symptoms such as chloroses, chlorotic ringspots, mottling and dieback. To obtain the evidence for viral infection, RNA-seq using an Illumina Hi Seq2500 was conducted and three contigs were obtained. They match with the three EMoV genomic RNAs and cover the open reading frames for the viral replicase, the polymerase and the movement and coat proteins (MP, CP). The contigs show identities of 95.3–96.4%, 91.9–93.3% and 89.0–92.5% at the nucleotide level with RNA 1, RNA 2 and RNA 3 of reference sequences, respectively. The analyses of the MP and CP showed significant differences in amino acid sequence compositions compared to those of reference EMoV sequences. These results demonstrate the presence of a so far unknown isolate of EMoV. This is the first report of sequence data of EMoV infecting U. laevis.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

scholarly journals Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Chaitanya Erady ◽  
Adam Boxall ◽  
Shraddha Puntambekar ◽  
N. Suhas Jagannathan ◽  
Ruchi Chauhan ◽  
...  
Keyword(s):  
Transcript Level ◽  
Open Reading Frames ◽  
The Cancer Genome Atlas ◽  
Small Subset ◽  
Cancer Tissue ◽  
Post Translational Modifications ◽  
Cancer Genome Atlas ◽  
Systematic Identification ◽  
Reading Frames

AbstractUncharacterized and unannotated open-reading frames, which we refer to as novel open reading frames (nORFs), may sometimes encode peptides that remain unexplored for novel therapeutic opportunities. To our knowledge, no systematic identification and characterization of transcripts encoding nORFs or their translation products in cancer, or in any other physiological process has been performed. We use our curated nORFs database (nORFs.org), together with RNA-Seq data from The Cancer Genome Atlas (TCGA) and Genotype-Expression (GTEx) consortiums, to identify transcripts containing nORFs that are expressed frequently in cancer or matched normal tissue across 22 cancer types. We show nORFs are subject to extensive dysregulation at the transcript level in cancer tissue and that a small subset of nORFs are associated with overall patient survival, suggesting that nORFs may have prognostic value. We also show that nORF products can form protein-like structures with post-translational modifications. Finally, we perform in silico screening for inhibitors against nORF-encoded proteins that are disrupted in stomach and esophageal cancer, showing that they can potentially be targeted by inhibitors. We hope this work will guide and motivate future studies that perform in-depth characterization of nORF functions in cancer and other diseases.

scholarly journals Characterization of Chlamydia trachomatis Plasmid-Encoded Open Reading Frames

2013 ◽  
Vol 195 (17) ◽  
pp. 3819-3826 ◽  
Author(s):  
S. Gong ◽  
Z. Yang ◽  
L. Lei ◽  
L. Shen ◽  
G. Zhong
Keyword(s):  
Chlamydia Trachomatis ◽  
Open Reading Frames ◽  
Reading Frames

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

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.

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

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