Advances in imaging RNA in plants

In vivo imaging of tagged mRNA in plant tissues using the bacterial transcriptional antiterminator BglG

RNA transport and localization represent important post-transcriptional mechanisms to determine the subcellular localization of protein synthesis. Plants have the capacity to transport messenger (m)RNA molecules beyond the cell boundaries through plasmodesmata and over long distances in the phloem. RNA viruses exploit these transport pathways to disseminate their infections and represent important model systems to investigate RNA transport in plants. Here, we present an in vivo plant RNA-labeling system based on the Escherichia coli RNA-binding protein BglG. Using the detection of RNA in mobile RNA particles formed by viral movement protein (MP) as a model, we demonstrate the efficiency and specificity of mRNA detection by the BglG system as compared with MS2 and λN systems. Our observations show that MP mRNA is specifically associated with MP in mobile MP particles but hardly with MP localized at plasmodesmata. MP mRNA is clearly absent from MP accumulating along microtubules. We show that the in vivo BglG labeling of the MP particles depends on the presence of the BglG-binding stem-loop aptamers within the MP mRNA and that the aptamers enhance the coprecipitation of BglG by MP, thus demonstrating the presence of an MP:MP mRNA complex. The BglG system also allowed us to monitor the cell-to-cell transport of the MP mRNA, thus linking the observation of mobile MP mRNA granules with intercellular MP mRNA transport. Given its specificity demonstrated here, the BglG system may be widely applicable for studying mRNA transport and localization in plants.

Plant PUF RNA-binding proteins: A wealth of diversity for post-transcriptional gene regulation

PUF proteins are a conserved group of sequence-specific RNA-binding proteins that typically function to negatively regulate mRNA stability and translation. PUFs are well characterized at the molecular, structural and functional levels in Drosophila, Caenorhabditis elegans, budding yeast and human systems. Although usually encoded by small gene families, PUFs are over-represented in the plant genome, with up to 36 genes identified in a single species. PUF gene expansion in plants has resulted in extensive variability in gene expression patterns, diversity in predicted RNA-binding domain structure, and novel combinations of key amino acids involved in modular nucleotide binding. Reports on the characterization of plant PUF structure and function continue to expand, and include RNA target identification, subcellular distribution, crystal structure, and molecular mechanisms. Arabidopsis PUF mutant analysis has provided insight into biological function, and has identified roles related to development and environmental stress tolerance. The diversity of plant PUFs implies an extensive role for this family of proteins in post-transcriptional gene regulation. This diversity also holds the potential for providing novel RNA-binding domains that could be engineered to produce designer PUFs to alter the metabolism of target RNAs in the cell.

Detection of Arbuscular Mycorrhizal Fungal Gene Expression by In Situ Hybridization

The complexity of the obligate symbiotic interaction of arbuscular mycorrhizal (AM) fungi and their host roots requires sophisticated molecular methods. In particular, to capture the dynamic of the interaction, cell-specific methods for gene expression analysis are required. In situ hybridization is a technique that allows to determine the location of transcript accumulation within tissues, being of special interest for these fungi that cannot be genetically modified. The method requires proper fixation and embedding methods as well as specific probes for the hybridization allowing detection of specific transcripts. In this chapter, we present a method to prepare roots, which have established a symbiosis with an arbuscular mycorrhizal fungus for the detection of fungal transcripts. This includes chemical fixation, subsequent embedding in a suitable medium, sectioning and pretreatment of sections, the hybridization procedure itself, as well as the immunological detection of RNA-RNA hybrids.

RNA Imaging with RNase-Inactivated Csy4 in Plants and Filamentous Fungi

Subcellular localizations of RNAs can be imaged in vivo with genetically encoded reporters consisting of a sequence-specific RNA-binding protein (RBP) fused to a fluorescent protein. Several such reporter systems have been described based on RBPs that recognize RNA stem-loops. Here we describe RNA tagging for imaging with an inactive mutant of the bacterial endonuclease Csy4, which has a significantly higher affinity for its cognate stem-loop than alternative systems. This property allows for sensitive imaging with only few tandem copies of the target stem-loop inserted into the RNA of interest.

Trimolecular Fluorescence Complementation (TriFC) Assay for Visualization of RNA-Protein Interaction in Plants

RNA-protein interactions play important roles in various eukaryotic biological processes. Molecular imaging of subcellular localization of RNA-protein complexes in plants is critical for understanding these interactions. However, methods to image RNA-protein interactions in living plants have not yet been developed until now. Recently, we have developed a trimolecular fluorescence complementation (TriFC) system for in vivo visualization of RNA-protein interaction by transient expression in tobacco leaves. In this method, we combined conventional bimolecular fluorescence complementation (BiFC) system with the MS2 system (phage MS2 coat protein [MCP] and its binding RNA sequence [MS2 sequence]) to tag lncRNA. Target RNA is tagged with 6xMS2, and MCP and RNA-binding protein are fused with YFP fragments. DNA constructs encoding such fusion RNA and proteins are infiltrated into tobacco leaves with Agrobacterium suspensions. RNA-protein interaction in vivo is observed by confocal microscopy.

Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications

Recently, dynamic changes in the location of RNA in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescent labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction into cells and transgenic organisms in a cell type and tissue specific manner by genetic engineering techniques. This Perspective focuses on a possible approach to the development of protein-based RNA probes using Pumilio homology domain (PUM-HD) mutants. The PUM-HD is a domain of an RNA binding protein that allows custom-made modifications to recognize a given eight-base RNA sequence. PUM-HD-based RNA probes have been applied to visualize various RNAs in living cells. Here, the techniques and RNA imaging results obtained using the PUM-HD are introduced.

Pumilio-based RNA in vivo imaging

Subcellular, sequence-specific detection of RNA in vivo is a powerful tool to study the macromolecular transport that occurs through plasmodesmata. The RNA-binding domain of Pumilio proteins can be engineered to bind RNA sequences of choice and fused to fluorescent proteins for RNA imaging. This chapter describes the construction of a Pumilio-based imaging system to track the RNA of Tobacco mosaic virus in vivo, and practical aspects of RNA live-cell imaging.

Identification of phloem-mobile mRNA

Signaling between cells, tissues and organs is essential for multicellular organisms to coordinate and adapt their development and growth to internal and environmental changes. Plants have evolved a plant-specific symplasmic pathway, called plasmodesmata, for efficient intercellular communication, in addition to the receptor-ligand-based apoplasmic pathway. Long-distance signaling between distant organs is enabled via the phloem tube system, where plasmodesmata contribute to phloem loading and unloading for photosynthate allocation. In addition to signaling by small molecules such as metabolites and phytohormones, the transport of proteins, small RNAs and mRNAs is also considered an important mechanism to achieve long-distance signaling in plants. Recent studies on phloem-mobile proteins and small RNAs have revealed their role in crucial physiological processes including flowering, systemic silencing and nutrient allocation. However, the biological role of mRNAs found in the phloem tube is not yet clear, though their mobility over long-distances has been well evidenced. To gain this knowledge, it is important to collect further information on mRNA profiles in the phloem translocation stream. In this review, I summarize the current approaches to identifying the mRNA population in the phloem translocation system, and discuss the possible role of short- and long-distance mRNA transport.

Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis

Alternative splicing (AS) is an important regulatory process that leads to the creation of multiple RNA transcripts from a single gene. Alternative transcripts often carry premature termination codons (PTCs), which trigger nonsense-mediated decay (NMD), a cytoplasmic RNA degradation pathway. However, intron retention, the most prevalent AS event in plants, often leads to PTC-carrying splice variants that are insensitive to NMD; this led us to question the fate of these special RNA variants. Here, we present an innovative approach to monitor and characterize endogenous mRNA splice variants within living plant cells. This method combines standard confocal laser scanning microscopy for molecular beacon detection with a robust statistical pipeline for sample comparison. We demonstrate this technique on the localization of NMD-insensitive splice variants of two Arabidopsis thaliana genes, RS2Z33 and the SEF factor. The experiments reveal that these intron-containing splice variants remain within the nucleus, which allows them to escape the NMD machinery. Moreover, fluorescence recovery after photobleaching experiments in the nucleoplasm show a decreased mobility of intron-retained mRNAs compared with fully spliced RNAs. In addition, differences in mobility were observed for an mRNA dependent on its origin from an intron-free or an intron-containing gene.

The dynamic pathway of nuclear RNA in eukaryotes

The passage of mRNA molecules from the site of synthesis, through the nucleoplasm and the nuclear pore, en route to the cytoplasm, might appear straightforward. Nonetheless, several decades of detailed examination of this pathway, from high resolution electron microscopy in fixed specimens, through the development of immuno-detection techniques and fluorescence toolkits, to the current era of live-cell imaging, show this to be an eventful journey. In addition to mRNAs, several species of noncoding RNAs travel and function in the nucleus, some being retained within throughout their lifetime. This review will highlight the nucleoplasmic paths taken by mRNAs and noncoding RNAs in eukaryotic cells with special focus on live-cell data and in concurrence with the biophysical nature of the nucleus.

In vivo visualization of RNA in plants cells using the λN₂₂ system and a GATEWAY-compatible vector series for candidate RNAs

The past decade has seen a tremendous increase in RNA research, which has demonstrated that RNAs are involved in many more processes than were previously thought. The dynamics of RNA synthesis towards their regulated activity requires the interplay of RNAs with numerous RNA binding proteins (RBPs). The localization of RNA, a mechanism for controlling translation in a spatial and temporal fashion, requires processing and assembly of RNA into transport granules in the nucleus, transport towards cytoplasmic destinations and regulation of its activity. Compared with animal model systems little is known about RNA dynamics and motility in plants. Commonly used methods to study RNA transport and localization are time-consuming, and require expensive equipment and a high level of experimental skill. Here, we introduce the λN₂₂ RNA stem-loop binding system for the in vivo visualization of RNA in plant cells. The λN₂₂ system consists of two components: the λN₂₂ RNA binding peptide and the corresponding box-B stem loops. We generated fusions of λN₂₂ to different fluorophores and a GATEWAY vector series for the simple fusion of any target RNA 5' or 3' to box-B stem loops. We show that the λN₂₂ system can be used to detect RNAs in transient expression assays, and that it offers advantages compared with the previously described MS2 system. Furthermore, the λN₂₂ system can be used in combination with the MS2 system to visualize different RNAs simultaneously in the same cell. The toolbox of vectors generated for both systems is easy to use and promises significant progress in our understanding of RNA transport and localization in plant cells.

RNA transport during TMV cell-to-cell movement

Studies during the last 25 years have provided increasing evidence for the ability of plants to support the cell-to-cell and systemic transport of RNA molecules and that this process plays a role in plant development and in the systemic orchestration of cellular responses against pathogens and other environmental challenges. Since RNA viruses exploit the cellular RNA transport machineries for spreading their genomes between cells they represent convenient models to investigate the underlying mechanisms. In this regard, the intercellular spread of Tobacco mosaic virus (TMV) has been studied for many years. The RNA of TMV moves cell-to-cell in a non-encapsidated form in a process depending on virus-encoded movement protein (MP). Here, we discuss the current state of the art in studies using TMV and its MP as a model for RNA transport. While the ability of plants to transport viral and cellular RNA molecules is consistent with RNA transport phenomena in other systems, further studies are needed to increase our ability to visualize viral RNA (vRNA) in vivo and to distinguish RNA-transport related processes from those involved in antiviral defense.

Tracking the green invaders: advances in imaging virus infection in plants

Bioimaging contributes significantly to our understanding of plant virus infections. In the present review, we describe technical advances that enable imaging of the infection process at previously unobtainable levels. We highlight how such new advances in subcellular imaging are contributing to a detailed dissection of all stages of the viral infection process. Specifically, we focus on: (i) the increasingly detailed localizations of viral proteins enabled by a diversifying palette of cellular markers; (ii) approaches using fluorescence microscopy for the functional analysis of proteins in vivo; (iii) the imaging of viral RNAs; (iv) methods that bridge the gap between optical and electron microscopy; and (v) methods that are blurring the distinction between imaging and structural biology. We describe the advantages and disadvantages of such techniques and place them in the broader perspective of their utility in analysing plant virus infection.