Sclerotinia minor Endornavirus 1, a Novel Pathogenicity Debilitation-Associated Mycovirus with a Wide Spectrum of Horizontal Transmissibility

Sclerotinia minor is a phytopathogenic fungus causing sclerotinia blight on many economically important crops. Here, we have characterized the biological and molecular properties of a novel endornavirus, Sclerotinia minor endornavirus 1 (SmEV1), isolated from the hypovirulent strain LC22 of S. minor. The genome of SmEV1 is 12,626 bp long with a single, large open reading frame (ORF), coding for a putative protein of 4020 amino acids. The putative protein contains cysteine-rich region (CRR), viral methyltransferase (MTR), putative DEXDc, viral helicase (Hel), and RNA-dependent RNA polymerase (RdRp) domains. The putative protein and the conserved domains are phylogenetically related to endornaviruses. SmEV1 does not contain a site-specific nick characteristic of most previously described endornaviruses. Hypovirulence and associated traits of strain LC22 and SmEV1 were readily cotransmitted horizontally via hyphal contact to isolates of different vegetative compatibility groups of S. minor. Additionally, SmEV1 in strain LC22 was found capable of being transmitted vertically through sclerotia. Furthermore, mycelium fragments of hypovirulent strain LC22 have a protective activity against attack by S. minor. Taken together, we concluded that SmEV1 is a novel hypovirulence-associated mycovirus with a wide spectrum of transmissibility, and has potential for biological control (virocontrol) of diseases caused by S. minor.

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Phase Variation of Campylobacter jejuni 81-176 Lipooligosaccharide Affects Ganglioside Mimicry and Invasiveness In Vitro

Infection and Immunity ◽

10.1128/iai.70.2.787-793.2002 ◽

2002 ◽

Vol 70 (2) ◽

pp. 787-793 ◽

Cited By ~ 154

Author(s):

Patricia Guerry ◽

Christine M. Szymanski ◽

Martina M. Prendergast ◽

Thomas E. Hickey ◽

Cheryl P. Ewing ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Phase Variation ◽

Outer Core ◽

Gene Encoding ◽

Site Specific ◽

Reading Frame ◽

Specific Mutation ◽

Normal Human ◽

A Site

ABSTRACT The outer cores of the lipooligosaccharides (LOS) of many strains of Campylobacter jejuni mimic human gangliosides in structure. A population of cells of C. jejuni strain 81-176 produced a mixture of LOS cores which consisted primarily of structures mimicking GM2 and GM3 gangliosides, with minor amounts of structures mimicking GD1b and GD2. Genetic analyses of genes involved in the biosynthesis of the outer core of C. jejuni 81-176 revealed the presence of a homopolymeric tract of G residues within a gene encoding CgtA, an N-acetylgalactosaminyltransferase. Variation in the number of G residues within cgtA affected the length of the open reading frame, and these changes in cgtA corresponded to a change in LOS structure from GM2 to GM3 ganglioside mimicry. Site-specific mutation of cgtA in 81-176 resulted in a major LOS core structure that lacked GalNAc and resembled GM3 ganglioside. Compared to wild-type 81-176, the cgtA mutant showed a significant increase in invasion of INT407 cells. In comparison, a site-specific mutation of the neuC1 gene resulted in the loss of sialic acid in the LOS core and reduced resistance to normal human serum but had no affect on invasion of INT407 cells.

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Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

10.21203/rs.3.rs-505029/v1 ◽

2021 ◽

Author(s):

Liying Sun ◽

Ziqian Lian ◽

Subha Das ◽

Jingxian Luo ◽

Ida Bagus Andika

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Amino Acid Sequences ◽

Shanxi Province ◽

Phytopathogenic Fungus ◽

Botryosphaeria Dothidea ◽

Reading Frame ◽

Ring Rot ◽

Ssrna Virus ◽

The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

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Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA.

Molecular and Cellular Biology ◽

10.1128/mcb.15.1.298 ◽

1995 ◽

Vol 15 (1) ◽

pp. 298-304 ◽

Cited By ~ 32

Author(s):

S Pande ◽

A Vimaladithan ◽

H Zhao ◽

P J Farabaugh

Keyword(s):

Active Role ◽

Termination Codon ◽

Reading Frame ◽

A Site

Programmed translational frameshifts efficiently alter a translational reading frame by shifting the reading frame during translation. A +1 frameshift has two simultaneous requirements: a translational pause which occurs when either an inefficiently recognized sense or termination codon occupies the A site, and the presence of a special peptidyl-tRNA occupying the P site during the pause. The special nature of the peptidyl-tRNA reflects its ability to slip +1 on the mRNA or to facilitate binding of an incoming aminoacyl-tRNA out of frame in the A site. This second mechanism suggested that in some cases the first +1 frame tRNA could have an active role in frameshifting. We found that overproducing this tRNA can drive frameshifting, surprisingly regardless of whether frameshifting occurs by peptidyl-tRNA slippage or out-of-frame binding of aminoacyl-tRNA. This finding suggests that in both cases, the shift in reading frame occurs coincident with formation of a cognate codon-anticodon interaction in the shifted frame.

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Screening of the Argentinean INTA peanut core collection with a molecular marker associated with resistance to Sclerotinia minor Jaggar

Peanut Science ◽

10.3146/ps19-15.1 ◽

2020 ◽

Vol 47 (1) ◽

pp. 9-16

Author(s):

K.D. Chamberlin ◽

J.J. Baldessari ◽

E.M.C. Mamani ◽

M.V. Moreno

Keyword(s):

Molecular Marker ◽

Core Collection ◽

Field Tests ◽

Field Testing ◽

Blight Resistance ◽

Phenotypic Traits ◽

Sources Of Resistance ◽

Sclerotinia Minor ◽

Sclerotinia Blight ◽

Potential Sources

ABSTRACT Cultivated peanut, the third most important oilseed in the world, is consistently threatened by various diseases and pests. Sclerotinia minor Jagger (S. minor), the causal agent of Sclerotinia blight, is a major threat to peanut production in many countries and can reduce yield by up to 50% in severely infested fields. Host plant resistance will provide the most effective solution to managing Sclerotinia blight, but limited sources of resistance to the disease are available for use in breeding programs. Peanut germplasm collections are available for exploration and identification of new sources of resistance, but traditionally the process is lengthy, requiring years of field testing before those potential sources can be identified. Molecular markers associated with phenotypic traits can speed up the screening of germplasm accessions. The objective of this study was to genotype the peanut core collection of the Instituto Nacional de Tecnología Agropecuaria (INTA) Manfredi, Argentina, with a molecular marker associated with Sclerotinia blight resistance. One hundred and fifty-four (154) accessions from the collection were available and genotyped using the Simple Sequence Repeat (SSR) marker. Accessions from each botanical variety type represented in the core collection were identified as new potential sources of resistance and targeted for further evaluation in field tests for Sclerotinia blight resistance.

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Multi-protein bridging factor 1(Mbf1), Rps3 and Asc1 prevent stalled ribosomes from frameshifting

eLife ◽

10.7554/elife.39637 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 13

Author(s):

Jiyu Wang ◽

Jie Zhou ◽

Qidi Yang ◽

Elizabeth J Grayhack

Keyword(s):

Ribosomal Proteins ◽

Entry Site ◽

Yeast Saccharomyces Cerevisiae ◽

Translation Elongation ◽

Reading Frame ◽

Archaeal Protein ◽

Specific Proteins ◽

A Site ◽

Codon Pairs ◽

Control Complex

Reading frame maintenance is critical for accurate translation. We show that the conserved eukaryotic/archaeal protein Mbf1 acts with ribosomal proteins Rps3/uS3 and eukaryotic Asc1/RACK1 to prevent frameshifting at inhibitory CGA-CGA codon pairs in the yeast Saccharomyces cerevisiae. Mutations in RPS3 that allow frameshifting implicate eukaryotic conserved residues near the mRNA entry site. Mbf1 and Rps3 cooperate to maintain the reading frame of stalled ribosomes, while Asc1 also mediates distinct events that result in recruitment of the ribosome quality control complex and mRNA decay. Frameshifting occurs through a +1 shift with a CGA codon in the P site and involves competition between codons entering the A site, implying that the wobble interaction of the P site codon destabilizes translation elongation. Thus, eukaryotes have evolved unique mechanisms involving both a universally conserved ribosome component and two eukaryotic-specific proteins to maintain the reading frame at ribosome stalls.

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Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1901310116 ◽

2019 ◽

Vol 116 (16) ◽

pp. 7813-7818 ◽

Cited By ~ 18

Author(s):

Jie Zhou ◽

Laura Lancaster ◽

John Paul Donohue ◽

Harry F. Noller

Keyword(s):

Crystal Structure ◽

Elongation Factor ◽

Intermediate Complex ◽

Reading Frame ◽

Hybrid State ◽

Head Domain ◽

30S Subunit ◽

A Site ◽

Insight Into ◽

Factor G

The elongation factor G (EF-G)–catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon–anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.

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Oxazolidinone Antibiotics Target the P Site on Escherichiacoli Ribosomes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.46.4.1080-1085.2002 ◽

2002 ◽

Vol 46 (4) ◽

pp. 1080-1085 ◽

Cited By ~ 87

Author(s):

Hiroyuki Aoki ◽

Lizhu Ke ◽

Susan M. Poppe ◽

Toni J. Poel ◽

Elizabeth A. Weaver ◽

...

Keyword(s):

Antimicrobial Agents ◽

Wide Spectrum ◽

Anaerobic Bacteria ◽

Elongation Factor ◽

Peptide Bond ◽

23S Rrna ◽

Peptide Bonds ◽

A Site ◽

Domain V ◽

Trna Binding

ABSTRACT The oxazolidinones are a novel class of antimicrobial agents that target protein synthesis in a wide spectrum of gram-positive and anaerobic bacteria. The oxazolidinone PNU-100766 (linezolid) inhibits the binding of fMet-tRNA to 70S ribosomes. Mutations to oxazolidinone resistance in Halobacterium halobium, Staphylococcus aureus, and Escherichia coli map at or near domain V of the 23S rRNA, suggesting that the oxazolidinones may target the peptidyl transferase region responsible for binding fMet-tRNA. This study demonstrates that the potency of oxazolidinones corresponds to increased inhibition of fMet-tRNA binding. The inhibition of fMet-tRNA binding is competitive with respect to the fMet-tRNA concentration, suggesting that the P site is affected. The fMet-tRNA reacts with puromycin to form peptide bonds in the presence of elongation factor P (EF-P), which is needed for optimum specificity and efficiency of peptide bond synthesis. Oxazolidinone inhibition of the P site was evaluated by first binding fMet-tRNA to the A site, followed by translocation to the P site with EF-G. All three of the oxazolidinones used in this study inhibited translocation of fMet-tRNA. We propose that the oxazolidinones target the ribosomal P site and pleiotropically affect fMet-tRNA binding, EF-P stimulated synthesis of peptide bonds, and, most markedly, EF-G-mediated translocation of fMet-tRNA into the P site.

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ORF Ι of Mycovirus SsNSRV-1 is Associated with Debilitating Symptoms of Sclerotinia sclerotiorum

Viruses ◽

10.3390/v12040456 ◽

2020 ◽

Vol 12 (4) ◽

pp. 456

Author(s):

Zhixiao Gao ◽

Junyan Wu ◽

Daohong Jiang ◽

Jiatao Xie ◽

Jiasen Cheng ◽

...

Keyword(s):

Sclerotinia Sclerotiorum ◽

Protein Biosynthesis ◽

Secretory Proteins ◽

Viral Mrna ◽

Fungal Host ◽

Reading Frame ◽

Mutant Strains ◽

Hypovirulent Strain ◽

Viral Proliferation ◽

Host Genes

We previously identified Sclerotinia sclerotiorum negative-stranded virus 1 (SsNSRV-1), the first (−) ssRNA mycovirus, associated with hypovirulence of its fungal host Sclerotinia sclerotiorum. In this study, functional analysis of Open Reading Frame Ι (ORF Ι) of SsNSRV-1 was performed. The integration and expression of ORF Ι led to defects in hyphal tips, vegetative growth, and virulence of the mutant strains of S. sclerotiorum. Further, differentially expressed genes (DEGs) responding to the expression of ORF Ι were identified by transcriptome analysis. In all, 686 DEGs consisted of 267 up-regulated genes and 419 down-regulated genes. DEGs reprogramed by ORF Ι were relevant to secretory proteins, pathogenicity, transcription, transmembrane transport, protein biosynthesis, modification, and metabolism. Alternative splicing was also detected in all mutant strains, but not in hypovirulent strain AH98, which was co-infected by SsNSRV-1 and Sclerotinia sclerotiorum hypovirus 1 (SsHV-1). Thus, the integrity of SsNSRV-1 genome may be necessary to protect viral mRNA from splicing and inactivation by the host. Taken together, the results suggested that protein ORF Ι could regulate the transcription, translation, and modification of host genes in order to facilitate viral proliferation and reduce the virulence of the host. Therefore, ORF Ι may be a potential gene used for the prevention of S. sclerotiorum.

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Applications of CRISPR/Cas9 for the Treatment of Duchenne Muscular Dystrophy

Journal of Personalized Medicine ◽

10.3390/jpm8040038 ◽

2018 ◽

Vol 8 (4) ◽

pp. 38 ◽

Cited By ~ 15

Author(s):

Kenji Lim ◽

Chantal Yoon ◽

Toshifumi Yokota

Keyword(s):

Duchenne Muscular Dystrophy ◽

Muscular Dystrophy ◽

Wide Spectrum ◽

Membrane Integrity ◽

Dystrophin Gene ◽

Muscle Membrane ◽

Reading Frame ◽

Long Term Treatment

Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disease prevalent in 1 in 3500 to 5000 males worldwide. As a result of mutations that interrupt the reading frame of the dystrophin gene (DMD), DMD is characterized by a loss of dystrophin protein that leads to decreased muscle membrane integrity, which increases susceptibility to degeneration. CRISPR/Cas9 technology has garnered interest as an avenue for DMD therapy due to its potential for permanent exon skipping, which can restore the disrupted DMD reading frame in DMD and lead to dystrophin restoration. An RNA-guided DNA endonuclease system, CRISPR/Cas9 allows for the targeted editing of specific sequences in the genome. The efficacy and safety of CRISPR/Cas9 as a therapy for DMD has been evaluated by numerous studies in vitro and in vivo, with varying rates of success. Despite the potential of CRISPR/Cas9-mediated gene editing for the long-term treatment of DMD, its translation into the clinic is currently challenged by issues such as off-targeting, immune response activation, and sub-optimal in vivo delivery. Its nature as being mostly a personalized form of therapy also limits applicability to DMD patients, who exhibit a wide spectrum of mutations. This review summarizes the various CRISPR/Cas9 strategies that have been tested in vitro and in vivo for the treatment of DMD. Perspectives on the approach will be provided, and the challenges faced by CRISPR/Cas9 in its road to the clinic will be briefly discussed.

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Sodium Nitroprusside Infusion for the Treatment of Schizophrenia

Schizophrenia Bulletin Open ◽

10.1093/schizbullopen/sgaa047 ◽

2020 ◽

Vol 1 (1) ◽

Author(s):

Mark Weiser ◽

Daisy Zamora ◽

Linda Levi ◽

Valentin Matei ◽

Ilan Gonen ◽

...

Keyword(s):

Sodium Nitroprusside ◽

Wide Spectrum ◽

Controlled Trial ◽

Study Groups ◽

Current Evidence ◽

Double Blind ◽

Syndrome Scale ◽

Meta Analyses ◽

A Site ◽

Negative Syndrome

Abstract One previous small single-center clinical trial showed that a single intravenous administration of sodium nitroprusside added-on to antipsychotics improved a wide spectrum of schizophrenia (SCZ) symptoms more than placebo, and the improvement persisted for 4 weeks after infusion even though no additional drug was given. Our study attempted to replicate these data in a 4-week, add-on, double-blind, randomized, placebo-controlled trial on 20 patients performed in a site in Romania and a site in Moldova. This study’s sample size and protocol were identical to the previous trial, including patients with a diagnosis of SCZ, within the first 5 years after diagnosis. Patients recruited needed to have a baseline total positive and negative syndrome scale (PANSS) score of 60 or above. Ten participants received a single dose of 0.5 µg/kg/min intravenous sodium nitroprusside over 4 hours, and 10 participants received matching placebo infusion, added-on to antipsychotics. The primary outcomes were the PANSS total score and the PANSS negative subscale. There were no significant between-group differences in PANSS total scores or negative subscale scores during the infusion on daily evaluations for the next 7 days nor on weekly evaluations at weeks 2, 3, and 4. No significant differences were found between the 2 study groups in adverse events. Meta-analyses including all 5 published randomized controlled trials on the topic, representing 155 subjects, do not show a statistically significant benefit of sodium nitroprusside. We conclude that the current evidence does not support the efficacy of sodium nitroprusside in the treatment of SCZ.

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