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Abstract RNA comprises a versatile group of biomolecules that play diverse roles in a wide range of biological processes. From synthesis to degradation, RNAs interact with cognate proteins that assist in processes such as transcription, splicing, modification, trafficking, and the execution of their functions. While numerous valuable techniques exist to study RNA-protein interactions, observing RNAs and their associated proteins simultaneously within cells remains a challenge, despite its potential to provide deeper insights into RNA-protein interactions. In this study, we adapted a modified immunofluorescence (IF) assay combined with RNA fluorescence in situ hybridization (FISH) to successfully visualize the colocalization of potato spindle tuber viroid with RNA polymerase II in the nucleus. This new method that combines IF and FISH will facilitate future studies on RNA and protein colocalization in various plant systems. 

ABSTRACT Viroids are single‐stranded circular noncoding RNAs that mainly infect crops. Upon infection, nuclear‐replicating viroids engage host DNA‐dependent RNA polymerase II for RNA‐templated transcription, which is facilitated by a host protein TFIIIA‐7ZF. The sense‐strand and minus‐strand RNA intermediates are differentially localised to the nucleolus and nucleoplasm regions, respectively. The factors and function underlying the differential localisation of viroid RNAs have not been fully elucidated. The sense‐strand RNA intermediates are cleaved into linear monomers by a yet‐to‐be‐identified RNase III‐type enzyme and ligated to form circular RNA progeny by DNA ligase I (LIG1). The subcellular compartment for the ligation reaction has not been characterised. Here, we show that LIG1 and potato spindle tuber viroid (PSTVd) colocalise near the nucleolar region inNicotiana benthamianaprotoplasts. The colocalised region is also the highly condensed region of sense‐strand PSTVd RNA, indicating that PSTVd RNA and LIG1 form a biomolecular condensate for RNA processing. This finding expands the function of biomolecular condensates to the infection of subviral pathogens. In addition, this knowledge of viroid biogenesis will contribute to exploring thousands of viroid‐like RNAs that have been recently identified. 

Abstract Aphids represent a major threat to crops. Hundreds of different viruses are aphid-borne. Upon aphid attack, plants release volatile organic compounds (VOCs) as airborne alarm signals to turn on the airborne defense (AD) of neighboring plants, thereby repelling aphids as well as reducing aphid fitness and virus transmission. This phenomenon provides a critical community-wide plant protection to fend off aphids, but the underlying molecular basis remains undetermined for a long time. In a recent article, Gong et al. established theNAC2-SAMT1module as the core component regulating the emission of methyl-salicylate (MeSA), a major component of VOCs in aphid-attacked plants. Furthermore, they showed that SABP2 protein is critical for the perception of volatile MeSA signal by converting MeSA to Salicylic Acid (SA), which is the cue to elicit AD against aphids at the community level. Moreover, they showed that multiple viruses use a conserved glycine residue in the ATP-dependent helicase domain in viral proteins to shuttle NAC2 from the nucleus to the cytoplasm for degradation, leading to the attenuation of MeSA emission and AD. These findings illuminate the functional roles of key regulators in the complex MeSA-mediated airborne defense process and a counter-defense mechanism used by viruses, which has profound significance in advancing the knowledge of plant-pathogen interactions as well as providing potential targets for gene editing-based crop breeding. 

We developed a new method for simultaneously visualizing RNAs and proteins in plant cells. This method works well for endogenous as well as infectious RNAs and their cognate binding proteins. 

Long noncoding RNAs (lncRNAs) are commonly defined as transcripts that lack protein-coding capacity and are longer than 200 nucleotides. Since the emergence of next-generation sequencing technologies in this century, thousands of lncRNAs have been identified from nearly all living organisms. Notably, various pathogens also express their own lncRNAs in host cells during infection. In plants, many lncRNAs exhibit dynamic expression patterns in response to environmental stimuli, including pathogen attacks. In contrast to well-established methods in identifying such lncRNAs, the current understanding of lncRNAs’ functional mechanisms is in its infancy. Some lncRNAs serve as precursors for generating small RNAs or serve as target mimics to sequester functional small RNAs, which have been extensively reviewed in the literature. This review focuses on the emerging evidence supporting that certain lncRNAs function as negative or positive regulators of plant immunity. A common theme is that those regulations rely on specific interactions between lncRNAs and key regulatory proteins. Viroids as single-stranded circular noncoding RNAs provide a handle to investigate how RNA local motifs render interaction specificity between lncRNAs and regulatory proteins. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .