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Host and viral RNA-binding proteins involved in membrane targeting, replication and intercellular movement of plant RNA virus genomes  [PDF]
Masanori Kaido,Tetsuro Okuno
Frontiers in Plant Science , 2014, DOI: 10.3389/fpls.2014.00321
Abstract: Many plant viruses have positive-strand RNA [(+)RNA] as their genome. Therefore, it is not surprising that RNA-binding proteins (RBPs) play important roles during (+)RNA virus infection in host plants. Increasing evidence demonstrates that viral and host RBPs play critical roles in multiple steps of the viral life cycle, including translation and replication of viral genomic RNAs, and their intra- and intercellular movement. Although studies focusing on the RNA-binding activities of viral and host proteins, and their associations with membrane targeting, and intercellular movement of viral genomes have been limited to several viruses, these studies have provided important insights into the molecular mechanisms underlying the replication and movement of viral genomic RNAs. In this review, we briefly overview the currently defined roles of viral and host RBPs whose RNA-binding activity have been confirmed experimentally in association with their membrane targeting, and intercellular movement of plant RNA virus genomes.
RNA-Binding Proteins in Plant Immunity  [PDF]
Virginia Woloshen,Shuai Huang,Xin Li
Journal of Pathogens , 2011, DOI: 10.4061/2011/278697
Abstract: Plant defence responses against pathogen infection are crucial to plant survival. The high degree of regulation of plant immunity occurs both transcriptionally and posttranscriptionally. Once transcribed, target gene RNA must be processed prior to translation. This includes polyadenylation, capping, editing, splicing, and mRNA export. RNA-binding proteins (RBPs) have been implicated at each level of RNA processing. Previous research has primarily focused on structural RNA-binding proteins of yeast and mammals; however, more recent work has characterized a number of plant RBPs and revealed their roles in plant immune responses. This paper provides an update on the known functions of RBPs in plant immune response regulation. Future in-depth analysis of RBPs and other related players will unveil the sophisticated regulatory mechanisms of RNA processing during plant immune responses. 1. Introduction Plants have evolved complex pathogen defence mechanisms partly due to their sessile lifestyle and lack of mobile cells used by mammals. Each plant cell possesses an innate immunity system with which it can defend itself from pathogen attack [1]. Plant defence generally commences by the sensing of molecules or structural features possessed by the invading pathogen. These molecules, from bacteria, oomycetes, and fungi, often have conserved features termed pathogen-associated or microbial-associated molecular patterns (PAMPs or MAMPs). PAMPs are often recognized by transmembrane, pattern recognition receptors (PRRs) usually belonging to the receptor-like kinase (RLK) type, on the plant cell surface. Defence genes are then induced, initiating PAMP-triggered immunity (PTI), and pathogenesis is prevented. However, the pathogen may be able to surpass PTI, by releasing effector molecules, which would lead to effector-triggered susceptibility (ETS). Subsequently, the plants have evolved resistance (R) proteins that can recognize specific effectors and result in effector-triggered immunity (ETI). Recognition of effector molecules is accomplished by R proteins that most often contain nucleotide-binding (NB) and leucine-rich repeat (LRR) domains [1]. Once recognition occurs, a signalling cascade begins, leading to the activation of downstream genes to mount a robust and quick defence response to prevent the spread of pathogens (see Figure 1). Figure 1: RNA processing steps that regulate plant immune responses. Pathogen associated molecular patterns (PAMPs) are recognized by pathogen recognition receptors (PRRs), which induce signaling cascades and lead to PAMP triggered
Cellular RNA Binding Proteins NS1-BP and hnRNP K Regulate Influenza A Virus RNA Splicing  [PDF]
Pei-Ling Tsai,Ni-Ting Chiou,Sharon Kuss,Adolfo García-Sastre,Kristen W. Lynch,Beatriz M. A. Fontoura
PLOS Pathogens , 2013, DOI: 10.1371/journal.ppat.1003460
Abstract: Influenza A virus is a major human pathogen with a genome comprised of eight single-strand, negative-sense, RNA segments. Two viral RNA segments, NS1 and M, undergo alternative splicing and yield several proteins including NS1, NS2, M1 and M2 proteins. However, the mechanisms or players involved in splicing of these viral RNA segments have not been fully studied. Here, by investigating the interacting partners and function of the cellular protein NS1-binding protein (NS1-BP), we revealed novel players in the splicing of the M1 segment. Using a proteomics approach, we identified a complex of RNA binding proteins containing NS1-BP and heterogeneous nuclear ribonucleoproteins (hnRNPs), among which are hnRNPs involved in host pre-mRNA splicing. We found that low levels of NS1-BP specifically impaired proper alternative splicing of the viral M1 mRNA segment to yield the M2 mRNA without affecting splicing of mRNA3, M4, or the NS mRNA segments. Further biochemical analysis by formaldehyde and UV cross-linking demonstrated that NS1-BP did not interact directly with viral M1 mRNA but its interacting partners, hnRNPs A1, K, L, and M, directly bound M1 mRNA. Among these hnRNPs, we identified hnRNP K as a major mediator of M1 mRNA splicing. The M1 mRNA segment generates the matrix protein M1 and the M2 ion channel, which are essential proteins involved in viral trafficking, release into the cytoplasm, and budding. Thus, reduction of NS1-BP and/or hnRNP K levels altered M2/M1 mRNA and protein ratios, decreasing M2 levels and inhibiting virus replication. Thus, NS1-BP-hnRNPK complex is a key mediator of influenza A virus gene expression.
Co-opted Oxysterol-Binding ORP and VAP Proteins Channel Sterols to RNA Virus Replication Sites via Membrane Contact Sites  [PDF]
Daniel Barajas,Kai Xu,Isabel Fernández de Castro Martín,Zsuzsanna Sasvari,Federica Brandizzi,Cristina Risco,Peter D. Nagy
PLOS Pathogens , 2014, DOI: doi/10.1371/journal.ppat.1004388
Abstract: Viruses recruit cellular membranes and subvert cellular proteins involved in lipid biosynthesis to build viral replicase complexes and replication organelles. Among the lipids, sterols are important components of membranes, affecting the shape and curvature of membranes. In this paper, the tombusvirus replication protein is shown to co-opt cellular Oxysterol-binding protein related proteins (ORPs), whose deletion in yeast model host leads to decreased tombusvirus replication. In addition, tombusviruses also subvert Scs2p VAP protein to facilitate the formation of membrane contact sites (MCSs), where membranes are juxtaposed, likely channeling lipids to the replication sites. In all, these events result in redistribution and enrichment of sterols at the sites of viral replication in yeast and plant cells. Using in vitro viral replication assay with artificial vesicles, we show stimulation of tombusvirus replication by sterols. Thus, co-opting cellular ORP and VAP proteins to form MCSs serves the virus need to generate abundant sterol-rich membrane surfaces for tombusvirus replication.
Characterization of the RNA-binding properties of the triple-gene-block protein 2 of Bamboo mosaic virus
Hsiu-Ting Hsu, Yang-Hao Tseng, Yuan-Lin Chou, Shiaw-Hwa Su, Yau-Heiu Hsu, Ban-Yang Chang
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-50
Abstract: Bamboo mosaic virus (BaMV) is a single-stranded, positive-sense RNA virus. Its genomic RNA has three partially overlapping open reading frames, called triple gene block (TGB), located between the coding sequences for the replicase and capsid protein [1]. The TGB-encoded proteins are referred to as TGBp1, TGBp2 and TGBp3 according to their positions [2] and are required for virus movement in the host plant [3-6]. The TGB proteins are found in several different viral genera. On the basis of amino acid sequence comparisons of the TGB proteins, the TGB-containing viruses have been classified into hordei-like and potex-like viruses [7]. Bamboo mosaic virus is a potex-like virus.The functions of each TGB protein have been investigated. TGBp2 is an integral membrane protein with two transmembrane helices [8] and a topology with both its N- and C-terminal tails exposed to the outer surface of endoplasmic reticulum (ER) and the central loop in the lumen of ER [9,10]. Inhibition of virus movement by mutations disrupting the transmembrane helices of Potato virus X (PVX) TGBp2 indicated that ER association is important for the functioning of TGBp2 (8). Moreover, the PVX TGBp2 is able to induce the formation of granular vesicles derived from the ER, which align on actin filaments [11]. Mutations in the central loop region of PVX TGBp2 eliminate the formation of granular vesicles and inhibit the cell-to-cell movement of virus [12]. In addition, the PVX TGBp2 is able to increase the size exclusion limit of plasmodesmata (PD) [13], probably through its association with host interacting proteins (TIPs) which in accompany with β-1, 3-glucanase regulate callose degradation [14].The membrane-associated TGBp2 is thought to assist the intracellular transport of the viral ribonucleoprotein (RNP) complex to the PD by a subcellular translocation process via cytoskeleton and is assumed to function through protein-protein or protein-RNA interactions [15,16]. The RNA-binding activity of a thio
Tombusvirus P19 RNA silencing suppressor (RSS) activity in mammalian cells correlates with charged amino acids that contribute to direct RNA-binding
Xiang Liu, Laurent Houzet, Kuan-Teh Jeang
Cell & Bioscience , 2012, DOI: 10.1186/2045-3701-2-41
Abstract: We have studied the RSS effect of P19 in mammalian cells, HEK293T, HeLa, and mouse embryonic fibroblasts. We have individually mutated 18 positively charged residues in P19 and found that 6 of these charged residues in P19 reduce its ability to suppress RNA interference. In each case, the reduction of silencing of RNA interference correlated with the reduced ability by these P19 mutants to bind siRNAs (small interfering RNAs).Our findings characterize a class of RNA-binding proteins that function as RSS moieties. We find a tight correlation between positively charged residues in P19 accounting for siRNA-binding and their RSS activity. Because P19’s activity is conserved in plant and animal cells, we conclude that its RSS function unlikely requires cell type-specific co-factors and likely arises from direct RNA-binding.RNA interference (RNAi) is a mechanism of gene regulation that is conserved in a wide range of organisms, from plants to animals [1-3]. RNAi is also reported to function as an antiviral defense against viral infections [4-9]. To counteract host cell RNAi-mediated immunity, viruses have evolved a variety of countermeasures, one of which is to encode RNA silencing suppressor (RSS) proteins [10-14]. Many RSS proteins have been reported; they include tomato bushy stunt virus (TBSV) P19 protein, rice hoja blanca virus NS3 protein, vaccinia virus E3L, influenza A virus NS1 protein, the Ebola virus VP35 protein, HIV-1 Tat protein, amongst others [5,15-23]. Currently, it is incompletely understood how each of these RSS proteins works mechanistically.One of the better characterized RSS is the P19 protein [13,16,24] encoded by TBSV and related tombusviruses [25]. An association between P19 and siRNAs has been demonstrated in infected plants [26]. The crystal structure of P19-siRNA complex reveals that a P19 homodimer tightly binds a single 21-nucleotide (nt) siRNA duplex in a positively charged surface cleft, but that this binding is progressively weaker for a s
Rev Proteins of Human and Simian Immunodeficiency Virus Enhance RNA Encapsidation  [PDF]
Sabine Brandt equal contributor,Maik Bli?enbach equal contributor,Bastian Grewe,Rebecca Konietzny,Thomas Grunwald,Klaus überla
PLOS Pathogens , 2007, DOI: 10.1371/journal.ppat.0030054
Abstract: The main function attributed to the Rev proteins of immunodeficiency viruses is the shuttling of viral RNAs containing the Rev responsive element (RRE) via the CRM-1 export pathway from the nucleus to the cytoplasm. This restricts expression of structural proteins to the late phase of the lentiviral replication cycle. Using Rev-independent gag-pol expression plasmids of HIV-1 and simian immunodeficiency virus and lentiviral vector constructs, we have observed that HIV-1 and simian immunodeficiency virus Rev enhanced RNA encapsidation 20- to 70-fold, correlating well with the effect of Rev on vector titers. In contrast, cytoplasmic vector RNA levels were only marginally affected by Rev. Binding of Rev to the RRE or to a heterologous RNA element was required for Rev-mediated enhancement of RNA encapsidation. In addition to specific interactions of nucleocapsid with the packaging signal at the 5′ end of the genome, the Rev/RRE system provides a second mechanism contributing to preferential encapsidation of genomic lentiviral RNA.
Interaction Studies of the Human and Arabidopsis thaliana Med25-ACID Proteins with the Herpes Simplex Virus VP16- and Plant-Specific Dreb2a Transcription Factors  [PDF]
Ximena Aguilar, Jeanette Blomberg, Kristoffer Br?nnstr?m, Anders Olofsson, Jürgen Schleucher, Stefan Bj?rklund
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0098575
Abstract: Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional co-regulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.
Investigating the role of viral integral membrane proteins in promoting the assembly of nepovirus and comovirus replication factories  [PDF]
Hélène Sanfa?on
Frontiers in Plant Science , 2013, DOI: 10.3389/fpls.2012.00313
Abstract: Formation of plant virus membrane-associated replication factories requires the association of viral replication proteins and viral RNA with intracellular membranes, the recruitment of host factors and the modification of membranes to form novel structures that house the replication complex. Many viruses encode integral membrane proteins that act as anchors for the replication complex. These hydrophobic proteins contain transmembrane domains and/or amphipathic helices that associate with the membrane and modify its structure. The comovirus Co-Pro and NTP-binding (NTB, putative helicase) proteins and the cognate nepovirus X2 and NTB proteins are among the best characterized plant virus integral membrane replication proteins and are functionally related to the picornavirus 2B, 2C, and 3A membrane proteins. The identification of membrane association domains and analysis of the membrane topology of these proteins is discussed. The evidence suggesting that these proteins have the ability to induce membrane proliferation, alter the structure and integrity of intracellular membranes, and modulate the induction of symptoms in infected plants is also reviewed. Finally, areas of research that need further investigation are highlighted.
Plant Coilin: Structural Characteristics and RNA-Binding Properties  [PDF]
Valentine Makarov, Daria Rakitina, Anna Protopopova, Igor Yaminsky, Alexander Arutiunian, Andrew J. Love, Michael Taliansky, Natalia Kalinina
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0053571
Abstract: Cajal bodies (CBs) are dynamic subnuclear compartments involved in the biogenesis of ribonucleoproteins. Coilin is a major structural scaffolding protein necessary for CB formation, composition and activity. The predicted secondary structure of Arabidopsis thaliana coilin (Atcoilin) suggests that the protein is composed of three main domains. Analysis of the physical properties of deletion mutants indicates that Atcoilin might consist of an N-terminal globular domain, a central highly disordered domain and a C-terminal domain containing a presumable Tudor-like structure adjacent to a disordered C terminus. Despite the low homology in amino acid sequences, a similar type of domain organization is likely shared by human and animal coilin proteins and coilin-like proteins of various plant species. Atcoilin is able to bind RNA effectively and in a non-specific manner. This activity is provided by three RNA-binding sites: two sets of basic amino acids in the N-terminal domain and one set in the central domain. Interaction with RNA induces the multimerization of the Atcoilin molecule, a consequence of the structural alterations in the N-terminal domain. The interaction with RNA and subsequent multimerization may facilitate coilin’s function as a scaffolding protein. A model of the N-terminal domain is also proposed.
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