P1-independent replication and local movement of Rice yellow mottle virus in host and non-host plant species

Nummert, Grete; Sõmera, Merike; Uffert, Gabriela; Abner, Erik; Truve, Erkki

doi:10.1016/j.virol.2016.12.007

Cited by 8 publications

(18 citation statements)

References 26 publications

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“…This protein is involved in viral accumulation and post-transcriptional gene silencing by suppressing the mechanisms of host RNA silencing ( Siré et al, 2008 ; Lacombe et al, 2010 ). P1 is dispensable for the local movement and replication of RYMV but is essential for systemic infection ( Brugidou et al, 1995 ; Bonneau et al, 1998 ; Nummert et al, 2017 ). At the 5' terminus of ORF1 is a viral genome-linked protein (VPg) instead of a cap while the 3' end of the viral genome is not polyadenylated ( Hull, 1977 ; Yassi et al, 1994 ).…”

Section: Rymv Genome Structure Gene Function and Diversitymentioning

confidence: 99%

“…To facilitate the active passage of virus particles to neighboring cells, the plasmodesmata must be modified with the help of host proteins. ORF1 and ORF3 play a key role in the modification of plasmodesmata ( Bonneau et al, 1998 ; Nummert et al, 2017 ). Generally, two hypotheses explain plasmodesmata modification during viral transport ( Schoelz et al, 2011 ; Reagan and Burch-Smith, 2020 ): the size exclusion limit and the removal of desmotubules and endoplasmic reticulum membranes ( Schoelz et al, 2011 ; Reagan and Burch-Smith, 2020 ).…”

Section: Rymv-host Plant Interactionmentioning

confidence: 99%

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Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

et al. 2021

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Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.

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Section: Rymv Genome Structure Gene Function and Diversitymentioning

confidence: 99%

Section: Rymv-host Plant Interactionmentioning

confidence: 99%

Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

et al. 2021

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“…To our knowledge, we here report the first 3D structure revealing ZnF features within a plant VSR protein, with very few similarities with other proteins in the databases. P1 protein is essential for RYMV systemic spread in rice tissues (Bonneau et al, 1998;Siré et al, 2008) and also plays an important role in viral replication despite being not strictly essential in this early step of RYMV infection (Bonneau et al, 1998;Nummert et al, 2017). Indeed, a mutation of P1 translation initiation codon rendering P1 undetectable in infected rice tissues almost abolished RYMV particles accumulation in infected and systemic leaves.…”

Section: Discussionmentioning

confidence: 99%

An original structural fold underlies the multitask P1, a silencing suppressor encoded by the Rice yellow mottle virus

Poignavent

Hoh

Terral

et al. 2020

Preprint

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The Rice Yellow Mottle sobemovirus (RYMV) belongs to the most damaging pathogens devastating rice fields in Africa. P1, a key protein for RYMV, was reported as a potent RNAi suppressor counteracting RNA silencing in plant reporter systems. Here we describe the complete 3D structure and dynamics of P1. Its N-terminal region contains ZnF1, a structural CCCC-type zinc finger strongly affine to zinc and a prominent short helix, rendering this region poorly amenable to structural changes. P1 C-terminal region contains ZnF2, an atypical HCHC-type ZnF that does not belong to any existing class of Zn finger proteins. ZnF2 appeared much less affine to zinc and more sensitive to oxidizing environments than ZnF1, and may serve as a sensor of plant redox status. We also identified key residues essential for RYMV infectivity and spread in rice tissues through their participation in P1 oligomerization and folding.Altogether, our results provide the first complete structure of a rice antiviral silencing suppressor and highlight P1 structural properties that may serve RYMV functions to infect and invade the host plant.

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“…Therefore, before conducting RNA isolation, users must be clear about its end use(s). Here, we list a few published examples of different downstream applications of RNA isolated by the CiAR method: (1) RT‐qPCR (Oñate‐Sánchez & Vicente‐Carbajosa, 2008; Verdonk and Sullivan, 2013; Ambreetha, Chinnadurai, Marimuthu, & Balachandar, 2018; Arruabarrena et al., 2016; de Vries et al., 2020; Krithika et al., 2016; Lortzing et al., 2017; Mbaluto, Ahmad, Fu, Martínez‐Medina, & van Dam, 2020; Priyanka et al., 2019; Sõmera et al., 2019; Touw et al., 2020; Wang, Severing, Koornneef, & Aarts, 2020), (2) RT‐PCR (Kirkin et al., 2018; Nummert, Sõmera, Uffert, Abner, & Truve, 2017), (3) RACE‐PCR (Zhou, Wilkens, Hanelt, & von Schwartzenberg, 2020), (4) direct PCR for detection of DNA virus (Arruabarrena et al., 2016), (5) DNA barcoding and preparation of RNA‐based libraries (Sõmera et al., 2019), and (6) cDNA labeling and microarray hybridization (Lortzing et al., 2017).…”

Section: Commentarymentioning

confidence: 99%

Citrate‐Citric Acid RNA Isolation (CiAR) for Fast, Low‐Cost, and Reliable RNA Extraction from Multiple Plant Species and Tissues

Oñate-Sánchez

Verdonk

2021

Current Protocols

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RNA isolation is routinely carried out in many laboratories for different downstream applications. Although protocols for this can vary between labs depending on the specific plant species and tissues under study and the preferences of their researchers, these protocols usually include the use of volatile organic and toxic chemicals. As an alternative, several companies offer less hazardous RNA extraction kits, but these kits significantly increase the cost per sample and are thus not affordable for every lab, especially when a large number of samples is to be processed. We have previously described a fast and efficient method for RNA isolation from plant vegetative tissues that requires only two home-made, simple, inexpensive, and nontoxic buffers. Both buffers have low concentrations of citric acid and its sodium salt. The first buffer also contains a detergent to help with nucleic acid solubilization while keeping RNases inactive. The second buffer has sodium chloride at high molarity to separate protein from nucleic acids. RNA is precipitated, and contaminating DNA can then be optionally removed. Here, we describe and expand on this approach, which we call the citrate-citric acid RNA isolation, or CiAR, method. We provide a detailed description of the protocol, describe a modification to make it compatible with non-vegetative tissues, and compile and extend the number of species and tissues to which it can be applied.

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P1-independent replication and local movement of Rice yellow mottle virus in host and non-host plant species

Cited by 8 publications

References 26 publications

Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance

An original structural fold underlies the multitask P1, a silencing suppressor encoded by the Rice yellow mottle virus

Citrate‐Citric Acid RNA Isolation (CiAR) for Fast, Low‐Cost, and Reliable RNA Extraction from Multiple Plant Species and Tissues

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