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One of the many challenges faced by RNA viruses is the maintenance of their genomes during infections of host cells. Members of the family Tombusviridae are plus-strand RNA viruses with unmodified triphosphorylated genomic 5’-termini. The tombusvirus Carnation Italian ringspot virus was used to investigate how it protects its RNA genome from attack by 5’-end-targeting degradation enzymes. In vivo and in vitro assays were employed to determine the role of genomic RNA structure in conferring protection from the 5’-to-3’ exoribonuclease Xrn. The results revealed that (i) the CIRV RNA genome is more resistant to Xrn than its sg mRNAs, (ii) the genomic 5’UTR folds into a compact RNA structure that effectively and independently prevents Xrn access, (iii) the RNA structure limiting 5’-access is formed by secondary and tertiary interactions that function cooperatively, (iv) the structure is also able to block access of RNA pyrophosphohydrolase to the genomic 5’-terminus, and (v) the RNA structure does not stall an actively digesting Xrn. Based on its proficiency at impeding Xrn 5’-access, we have termed this 5’-terminal structure an X rn- e vading RNA or xeRNA. These and other findings demonstrate that the 5’UTR of the CIRV RNA genome folds into a complex structural conformation that helps to protect its unmodified 5’-terminus from enzymatic decay during infections. IMPORTANCE The plus-strand RNA genomes of plant viruses in the large family Tombusviridae are not 5’-capped. Here we explored how a species in the type genus Tombusvirus protects its genomic 5’-end from cellular nuclease attack. Our results revealed that the 5’-terminal sequence of the CIRV genome folds into a complex RNA structure that limits access of the 5’-to-3’ exoribonuclease Xrn, thereby protecting it from processive degradation. The RNA conformation also impeded access of RNA pyrophosphohydrolase, which converts 5’-triphosphorylated RNA termini into 5’-monophosphorylated forms, the preferred substrate for Xrn. This study represents the first report of a genome-encoded higher-order RNA structure independently conferring resistance to cellular 5’-end-attacking enzymes in an RNA plant virus.
Chaminda D. Gunawardene; Jennifer S. H. Im; K. Andrew White. RNA Structure Protects the 5’-end of an Uncapped Tombusvirus RNA Genome from Xrn Digestion. Journal of Virology 2021, 1 .
AMA StyleChaminda D. Gunawardene, Jennifer S. H. Im, K. Andrew White. RNA Structure Protects the 5’-end of an Uncapped Tombusvirus RNA Genome from Xrn Digestion. Journal of Virology. 2021; ():1.
Chicago/Turabian StyleChaminda D. Gunawardene; Jennifer S. H. Im; K. Andrew White. 2021. "RNA Structure Protects the 5’-end of an Uncapped Tombusvirus RNA Genome from Xrn Digestion." Journal of Virology , no. : 1.
The genomes of RNA viruses contain regulatory elements of varying complexity. Many plus-strand RNA viruses employ largescale intra-genomic RNA-RNA interactions as a means to control viral processes. Here, we describe an elaborate RNA structure formed by multiple distant regions in a tombusvirus genome that activates transcription of a viral subgenomic mRNA. The initial step in assembly of this intramolecular RNA complex involves the folding of a large viral RNA domain, which generates a discontinuous binding pocket. Next, a distally-located protracted stem-loop RNA structure docks, via base-pairing, into the binding site and acts as a linchpin that stabilizes the RNA complex and activates transcription. A multi-step RNA folding pathway is proposed in which rate-limiting steps contribute to a delay in transcription of the capsid protein-encoding viral subgenomic mRNA. This study provides an exceptional example of the complexity of genome-scale viral regulation and offers new insights into the assembly schemes utilized by large intra-genomic RNA structures.
Tamari Chkuaseli; K Andrew White. Activation of viral transcription by stepwise largescale folding of an RNA virus genome. Nucleic Acids Research 2020, 48, 9285 -9300.
AMA StyleTamari Chkuaseli, K Andrew White. Activation of viral transcription by stepwise largescale folding of an RNA virus genome. Nucleic Acids Research. 2020; 48 (16):9285-9300.
Chicago/Turabian StyleTamari Chkuaseli; K Andrew White. 2020. "Activation of viral transcription by stepwise largescale folding of an RNA virus genome." Nucleic Acids Research 48, no. 16: 9285-9300.
RNA elements in the untranslated regions of plus-strand RNA viruses can control a variety of viral processes including translation, replication, packaging, and subgenomic mRNA production. The 3′ untranslated region (3′UTR) of Tobacco necrosis virus strain D (TNV-D; genus Betanecrovirus, family Tombusviridae) contains several well studied regulatory RNA elements. Here, we explore a previously unexamined region of the viral 3′UTR, the sequence located upstream of the 3′-cap independent translation enhancer (3′CITE). Our results indicate that (i) a long-range RNA–RNA interaction between an internal RNA element and the 3′UTR facilitates translational readthrough, and may also promote viral RNA synthesis; (ii) a conserved RNA hairpin, SLX, is required for efficient genome accumulation; and (iii) an adenine-rich region upstream of the 3′CITE is dispensable, but can modulate genome accumulation. These findings identified novel regulatory RNA elements in the 3′UTR of the TNV-D genome that are important for virus survival.
Laura R. Newburn; Baodong Wu; K. Andrew White. Investigation of Novel RNA Elements in the 3′UTR of Tobacco Necrosis Virus-D. Viruses 2020, 12, 856 .
AMA StyleLaura R. Newburn, Baodong Wu, K. Andrew White. Investigation of Novel RNA Elements in the 3′UTR of Tobacco Necrosis Virus-D. Viruses. 2020; 12 (8):856.
Chicago/Turabian StyleLaura R. Newburn; Baodong Wu; K. Andrew White. 2020. "Investigation of Novel RNA Elements in the 3′UTR of Tobacco Necrosis Virus-D." Viruses 12, no. 8: 856.
The Red clover necrotic mosaic virus (RCNMV) genome consists of two plus-strand RNA genome segments, RNA1 and RNA2. RNA2 contains a multifunctional RNA structure known as the trans-activator (TA) that (i) promotes subgenomic mRNA transcription from RNA1, (ii) facilitates replication of RNA2, and (iii) mediates particle assembly and copackaging of genome segments. The TA has long been considered a unique RNA element in RCNMV. However, by examining results from RCNMV genome analyses in the ViRAD virus (re-)annotation database, a putative functional RNA element in the polymerase-coding region of RNA1 was identified. Structural and functional analyses revealed that the novel RNA element adopts a TA-like structure (TALS) and, similar to the requirement of the TA for RNA2 replication, the TALS is necessary for the replication of RNA1. Both the TA and TALS possess near-identical asymmetrical internal loops that are critical for efficient replication of their corresponding genome segments, and these structural motifs were found to be functionally interchangeable. Moreover, replacement of the TA in RNA2 with a stabilized form of the TALS directed both RNA2 replication and packaging of both genome segments. Based on their comparable properties and considering evolutionary factors, we propose that the TALS appeared de novo in RNA1 first and, subsequently, the TA arose de novo in RNA2 as a functional mimic of the TALS. This and other related information were used to formulate a plausible evolutionary pathway to describe the genesis of the bi-segmented RCNMV genome. The resulting scenario provides an evolutionary framework to further explore and test possible origins of this segmented RNA plant virus. We have identified a novel RNA element in RNA1 of the segmented positive-strand RNA genome of Red clover necrotic mosaic virus (RCNMV). Its similarity in structure to a known important RNA element in RNA2 suggests that the two RNA structures perform similar viral functions in their respective genome segments, and this was confirmed experimentally. Based on evolutionary considerations, the RNA element in RNA1 is proposed to have appeared earlier in RCNMV genome genesis, with the corresponding element in RNA2 arising subsequently as a functional mimic of the former. This information was integrated into a plausible pathway for the emergence and evolution of this segmented viral genome, thereby providing novel insights into the puzzling history of RCNMV.
Laura R. Newburn; K. Andrew White. A trans-activator-like structure in RCNMV RNA1 evokes the origin of the trans-activator in RNA2. PLOS Pathogens 2020, 16, e1008271 .
AMA StyleLaura R. Newburn, K. Andrew White. A trans-activator-like structure in RCNMV RNA1 evokes the origin of the trans-activator in RNA2. PLOS Pathogens. 2020; 16 (1):e1008271.
Chicago/Turabian StyleLaura R. Newburn; K. Andrew White. 2020. "A trans-activator-like structure in RCNMV RNA1 evokes the origin of the trans-activator in RNA2." PLOS Pathogens 16, no. 1: e1008271.
The genomes of RNA viruses contain a variety of RNA sequences and structures that regulate different steps in virus reproduction. Events that are controlled by RNA elements include (i) the translation of viral proteins, (ii) the replication of viral RNA genomes, and (iii) the transcription of viral subgenomic mRNAs. Studies of members of the family Tombusviridae, which possess plus-strand RNA genomes, have revealed novel ways in which the RNA genome structure is utilized to control different viral processes. Recent advances in our understanding of RNA-based viral regulation in select tombusvirids will be presented.
K. Andrew White. Regulation of RNA Virus Processes by Viral Genome Structure. Proceedings 2020, 50, 68 .
AMA StyleK. Andrew White. Regulation of RNA Virus Processes by Viral Genome Structure. Proceedings. 2020; 50 (1):68.
Chicago/Turabian StyleK. Andrew White. 2020. "Regulation of RNA Virus Processes by Viral Genome Structure." Proceedings 50, no. 1: 68.
RNA viruses represent a large and important group of pathogens that infect a broad range of hosts. Segmented RNA viruses are a subclass of this group that encode their genomes in two or more molecules and package all of their RNA segments in a single virus particle. These divided genomes come in different forms, including double-stranded RNA, coding-sense single-stranded RNA, and noncoding single-stranded RNA. Genera that possess these genome types include, respectively, Orbivirus (e.g., Bluetongue virus), Dianthovirus (e.g., Red clover necrotic mosaic virus) and Alphainfluenzavirus (e.g., Influenza A virus). Despite their distinct genomic features and diverse host ranges (i.e., animals, plants, and humans, respectively) each of these viruses uses trans-acting RNA–RNA interactions (tRRIs) to facilitate co-packaging of their segmented genome. The tRRIs occur between different viral genome segments and direct the selective packaging of a complete genome complement. Here we explore the current state of understanding of tRRI-mediated co-packaging in the abovementioned viruses and examine other known and potential functions for this class of RNA–RNA interaction.
Laura R. Newburn; K. Andrew White. Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses. Viruses 2019, 11, 751 .
AMA StyleLaura R. Newburn, K. Andrew White. Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses. Viruses. 2019; 11 (8):751.
Chicago/Turabian StyleLaura R. Newburn; K. Andrew White. 2019. "Trans-Acting RNA–RNA Interactions in Segmented RNA Viruses." Viruses 11, no. 8: 751.
Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5′-to-3′ exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3′-terminal segments within the 3′-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3′-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associated with different plant and animal RNA viruses.
Chaminda D Gunawardene; Laura R Newburn; K Andrew White. A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation. Nucleic Acids Research 2019, 47, 9329 -9342.
AMA StyleChaminda D Gunawardene, Laura R Newburn, K Andrew White. A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation. Nucleic Acids Research. 2019; 47 (17):9329-9342.
Chicago/Turabian StyleChaminda D Gunawardene; Laura R Newburn; K Andrew White. 2019. "A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation." Nucleic Acids Research 47, no. 17: 9329-9342.
Bacteriophage T7 promoter and RNA polymerase (T7-Pol) are widely used for recombinant protein expression in bacteria. In plants, there exists conflicting results regarding the efficacy of protein expression from T7-Pol-derived mRNAs. To reconcile these contradictory observations, the expression of green fluorescent protein (GFP) from T7 constructs was evaluated in tobacco protoplasts. T7 constructs transcribed by a nuclearly targeted T7-Pol did not express GFP in plant protoplasts, however T7-Pol lacking a nuclear targeting signal was able to translate cytosolically transcribed mRNAs, but only if the messages contained a viral translation enhancer. GFP expression was further evaluated at the plant level by using agroinfiltration-mediated transient expression system. Unlike for cytosolic expression, nuclear T7 transcripts containing a viral translation enhancer element did not express GFP, and modifications designed to stabilize and facilitate export of T7 transcripts to the cytosol did not improve the expression. We conclude that expression of nuclear T7 constructs is not feasible in tobacco cells, but cytosolic transcription provides an alternative means to over-express RNAs directly in the cytosol.
Hyukho Sheen; K. Andrew White. Expression of T7-based constructs in tobacco cells. Biochemical and Biophysical Research Communications 2018, 499, 196 -201.
AMA StyleHyukho Sheen, K. Andrew White. Expression of T7-based constructs in tobacco cells. Biochemical and Biophysical Research Communications. 2018; 499 (2):196-201.
Chicago/Turabian StyleHyukho Sheen; K. Andrew White. 2018. "Expression of T7-based constructs in tobacco cells." Biochemical and Biophysical Research Communications 499, no. 2: 196-201.
Plant viruses that contain positive-strand RNA genomes represent an important class of pathogen. The genomes of these viruses harbor RNA sequences and higher-order RNA structures that are essential for the regulation of viral processes during infections. In recent years, it has become increasingly evident that, in addition to locally positioned RNA structures, long-distance intragenomic interactions, involving nucleotide base pairing over large distances, also contribute significantly to the control of various viral events. Viral processes that are modulated by such interactions include genome replication, translation initiation, translational recoding, and subgenomic mRNA transcription. Here, we review the structure and function of different types of long-distance RNA–RNA interactions, herein termed LDRIs, present in members of the family Tombusviridae and other plus-strand RNA plant viruses.
Tamari Chkuaseli; K. Andrew White. Intragenomic Long-Distance RNA–RNA Interactions in Plus-Strand RNA Plant Viruses. Frontiers in Microbiology 2018, 9, 1 .
AMA StyleTamari Chkuaseli, K. Andrew White. Intragenomic Long-Distance RNA–RNA Interactions in Plus-Strand RNA Plant Viruses. Frontiers in Microbiology. 2018; 9 ():1.
Chicago/Turabian StyleTamari Chkuaseli; K. Andrew White. 2018. "Intragenomic Long-Distance RNA–RNA Interactions in Plus-Strand RNA Plant Viruses." Frontiers in Microbiology 9, no. : 1.
Tobacco necrosis virus, strain D (TNV-D), is a positive-strand RNA virus in the genus Betanecrovirus and family Tombusviridae . The production of its RNA-dependent RNA polymerase, p82, is achieved by translational readthrough. This process is stimulated by an RNA structure that is positioned immediately downstream of the recoding site, termed the readthrough stem-loop (RTSL), and a sequence in the 3′ untranslated region of the TNV-D genome, called the distal readthrough element (DRTE). Notably, a base pairing interaction between the RTSL and the DRTE, spanning ∼3,000 nucleotides, is required for enhancement of readthrough. Here, some of the structural features of the RTSL, as well as RNA sequences and structures that flank either the RTSL or DRTE, were investigated for their involvement in translational readthrough and virus infectivity. The results revealed that (i) the RTSL-DRTE interaction cannot be functionally replaced by stabilizing the RTSL structure, (ii) a novel tertiary RNA structure positioned just 3′ to the RTSL is required for optimal translational readthrough and virus infectivity, and (iii) these same activities also rely on an RNA stem-loop located immediately upstream of the DRTE. Functional counterparts for the RTSL-proximal structure may also be present in other tombusvirids. The identification of additional distinct RNA structures that modulate readthrough suggests that regulation of this process by genomic features may be more complex than previously appreciated. Possible roles for these novel RNA elements are discussed. IMPORTANCE The analysis of factors that affect recoding events in viruses is leading to an ever more complex picture of this important process. In this study, two new atypical RNA elements were shown to contribute to efficient translational readthrough of the TNV-D polymerase and to mediate robust viral genome accumulation in infections. One of the structures, located close to the recoding site, could have functional equivalents in related genera, while the other structure, positioned 3′ proximally in the viral genome, is likely limited to betanecroviruses. Irrespective of their prevalence, the identification of these novel RNA elements adds to the current repertoire of viral genome-based modulators of translational readthrough and provides a notable example of the complexity of regulation of this process.
Laura R. Newburn; K. Andrew White. Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D. Journal of Virology 2017, 91, e02443-16 .
AMA StyleLaura R. Newburn, K. Andrew White. Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D. Journal of Virology. 2017; 91 (8):e02443-16.
Chicago/Turabian StyleLaura R. Newburn; K. Andrew White. 2017. "Atypical RNA Elements Modulate Translational Readthrough in Tobacco Necrosis Virus D." Journal of Virology 91, no. 8: e02443-16.
Tombusviruses are small icosahedral viruses that possess plus-sense RNA genomes ∼4.8kb in length. The type member of the genus, tomato bushy stunt virus (TBSV), encodes a 92kDa (p92) RNA-dependent RNA polymerase (RdRp) that is responsible for viral genome replication and subgenomic (sg) mRNA transcription. Several functionally relevant regions in p92 have been identified and characterized, including transmembrane domains, RNA-binding segments, membrane targeting signals, and oligomerization domains. Moreover, conserved tombusvirus-specific motifs in the C-proximal region of the RdRp have been shown to modulate viral genome replication, sg mRNA transcription, and trans-replication of subviral replicons. Interestingly, p92 is initially non-functional, and requires an accessory viral protein, p33, as well as viral RNA, host proteins, and intracellular membranes to become active. These and other host factors, through a well-orchestrated process guided by the viral replication proteins, mediate the assembly of membrane-associated virus replicase complexes (VRCs). Here, we describe what is currently known about the structure and function of the tombusvirus RdRp and how it utilizes host components to build VRCs that synthesize viral RNAs.
Chaminda D. Gunawardene; Logan Donaldson; K. Andrew White. Tombusvirus polymerase: Structure and function. Virus Research 2017, 234, 74 -86.
AMA StyleChaminda D. Gunawardene, Logan Donaldson, K. Andrew White. Tombusvirus polymerase: Structure and function. Virus Research. 2017; 234 ():74-86.
Chicago/Turabian StyleChaminda D. Gunawardene; Logan Donaldson; K. Andrew White. 2017. "Tombusvirus polymerase: Structure and function." Virus Research 234, no. : 74-86.
Tobacco necrosis virus (TNV-D) has a plus-strand RNA genome that is neither 5' capped nor 3' poly-adenylated. Instead, it utilizes a 3' cap-independent translational enhancer (3'CITE) located in its 3' untranslated region (UTR) for translation of its proteins. We have examined the protein expression strategies used by TNV-D and our results indicate that: (i) a base pairing interaction between conserved ACCA and UGGU motifs in the genomic 5'UTR and 3'CITE, respectively, is not required for efficient plant cell infection, (ii) similar potential 5'UTR-3'CITE interactions in the two viral subgenomic mRNAs are not needed for efficient translation of viral proteins in vitro, (iii) a small amount of capsid protein is translated from the viral genome by a largely 3'CITE-independent mechanism, (iv) the larger of two possible forms of capsid protein is efficiently translated, and (v) p7b is translated from subgenomic mRNA1 by a leaky scanning mechanism.
Tamari Chkuaseli; Laura R. Newburn; David Bakhshinyan; K. Andrew White. Protein expression strategies in Tobacco necrosis virus-D. Virology 2015, 486, 54 -62.
AMA StyleTamari Chkuaseli, Laura R. Newburn, David Bakhshinyan, K. Andrew White. Protein expression strategies in Tobacco necrosis virus-D. Virology. 2015; 486 ():54-62.
Chicago/Turabian StyleTamari Chkuaseli; Laura R. Newburn; David Bakhshinyan; K. Andrew White. 2015. "Protein expression strategies in Tobacco necrosis virus-D." Virology 486, no. : 54-62.
Satellite RNAs (satRNAs) are a class of small parasitic RNA replicon that associate with different viruses, including plus-strand RNA viruses. Because satRNAs do not encode a polymerase or capsid subunit, they rely on a companion virus to provide these proteins for their RNA replication and packaging. SatRNAs recruit these and other required factors via their RNA sequences and structures. Here, through a combination of chemical probing analysis of RNA structure, phylogenetic structural comparisons, and viability assays of satRNA mutants in infected cells, the biological importance of a deduced higher-order structure for a 619 nt long tombusvirus satRNA was assessed. Functionally-relevant secondary and tertiary RNA structures were identified throughout the length of the satRNA. Notably, a 3′-terminal segment was found to adopt two mutually-exclusive RNA secondary structures, both of which were required for efficient satRNA accumulation. Accordingly, these alternative conformations likely function as a type of RNA switch. The RNA switch was also found to engage in a required long-range kissing-loop interaction with an upstream sequence. Collectively, these results establish a high level of conformational complexity within this small parasitic RNA and provide a valuable structural framework for detailed mechanistic studies.
Peter Ashton; Baodong Wu; Jessica D'angelo; Jorg Grigull; K. Andrew White. Biologically-supported structural model for a viral satellite RNA. Nucleic Acids Research 2015, 43, 9965 -9977.
AMA StylePeter Ashton, Baodong Wu, Jessica D'angelo, Jorg Grigull, K. Andrew White. Biologically-supported structural model for a viral satellite RNA. Nucleic Acids Research. 2015; 43 (20):9965-9977.
Chicago/Turabian StylePeter Ashton; Baodong Wu; Jessica D'angelo; Jorg Grigull; K. Andrew White. 2015. "Biologically-supported structural model for a viral satellite RNA." Nucleic Acids Research 43, no. 20: 9965-9977.
Plant viruses that contain plus-sensed single-stranded RNA genomes are highly abundant in nature. As the equivalents of large mRNAs, these viral genomes utilize a wide variety of gene expression strategies for the production of their encoded proteins. The potyviruses, which are among the most agriculturally important members in this category, contain a single large open reading frame (ORF) coding for a polyprotein that is processed into functional units. For many years, the products derived from the full-length polyprotein were thought to be the only functional viral proteins. However, this notion was dispelled when an additional essential viral ORF, PIPO, was discovered encoded in an alternative reading frame. Since then, the PIPO protein—P3N-PIPO, which mediates virus movement in plants—has been intensively studied, but its mode of expression remained elusive until now. Two articles, one in this issue of EMBO Reports, now report that slippage of the viral polymerase during viral genome replication is responsible for shifting PIPO into a translated reading frame, thereby allowing for production of P3N-PIPO 1,2. This mechanism of gene expression represents a novel strategy for plant viruses.
K Andrew White. The polymerase slips and PIPO exists. EMBO reports 2015, 16, 885 -886.
AMA StyleK Andrew White. The polymerase slips and PIPO exists. EMBO reports. 2015; 16 (8):885-886.
Chicago/Turabian StyleK Andrew White. 2015. "The polymerase slips and PIPO exists." EMBO reports 16, no. 8: 885-886.
The genomes of RNA viruses contain local structural elements and long-range interactions that control various steps in virus replication. While many individual RNA elements have been characterized, it remains less clear how the structure and activity of such elements are integrated and regulated within the complex context of complete viral genomes. Recent technical advances, particularly the development of high-throughput solution structure mapping methods, have made secondary structural analysis of entire viral RNA genomes feasible. As a consequence, whole-genome structural models have been deduced for a number of plus-strand RNA viruses and retroviruses and these structures have provided intriguing functional and evolutionary insights into global genome architecture.
Beth L Nicholson; K Andrew White. Exploring the architecture of viral RNA genomes. Current Opinion in Virology 2015, 12, 66 -74.
AMA StyleBeth L Nicholson, K Andrew White. Exploring the architecture of viral RNA genomes. Current Opinion in Virology. 2015; 12 ():66-74.
Chicago/Turabian StyleBeth L Nicholson; K Andrew White. 2015. "Exploring the architecture of viral RNA genomes." Current Opinion in Virology 12, no. : 66-74.
Positive-strand RNA viruses are the most common type of plant virus. Many aspects of the reproductive cycle of this group of viruses have been studied over the years and this has led to the accumulation of a significant amount of insightful information. In particular, the identification and characterization of cis-acting RNA elements within these viral genomes have revealed important roles in many fundamental viral processes such as virus disassembly, translation, genome replication, subgenomic mRNA transcription, and packaging. These functional cis-acting RNA elements include primary sequences, secondary and tertiary structures, as well as long-range RNA-RNA interactions, and they typically function by interacting with viral or host proteins. This review provides a general overview and update on some of the many roles played by cis-acting RNA elements in positive-strand RNA plant viruses.
Laura R. Newburn; K. Andrew White. Cis-acting RNA elements in positive-strand RNA plant virus genomes. Virology 2015, 479-480, 434 -443.
AMA StyleLaura R. Newburn, K. Andrew White. Cis-acting RNA elements in positive-strand RNA plant virus genomes. Virology. 2015; 479-480 ():434-443.
Chicago/Turabian StyleLaura R. Newburn; K. Andrew White. 2015. "Cis-acting RNA elements in positive-strand RNA plant virus genomes." Virology 479-480, no. : 434-443.
The replication of plus-strand RNA virus genomes is mediated by virally encoded RNA-dependent RNA polymerases (RdRps). We have investigated the role of the C-proximal region in the RdRp of tomato bushy stunt virus (TBSV) in mediating viral RNA synthesis. TBSV is the prototype species in the genusTombusvirus, familyTombusviridae, and its RdRp is responsible for replicating the viral genome, transcribing two subgenomic mRNAs, and supporting replication of defective interfering RNAs. Comparative sequence analysis of the RdRps of tombusvirids identified three highly conserved motifs in their C-proximal regions, and these sequences were subsequently targeted for mutational analysis in TBSV. The results revealed that these motifs are important for (i) synthesizing viral genomic RNA and subgenomic mRNAs, (ii) facilitating plus- and/or minus-strand synthesis, and (iii) modulatingtrans-replication of a defective interfering RNA. These motifs were also found to be conserved in other plant viruses as well as in a fungal and insect virus. The collective findings are discussed in relation to viral RNA synthesis and taxonomy.IMPORTANCELittle is currently known about the structure and function of the viral polymerases that replicate the genomes of RNA plant viruses. Tombusviruses, the prototype of the tombusvirids, have been used as model plus-strand RNA plant viruses for understanding many of the steps in the infectious process; however, their polymerases remain poorly characterized. To help address this issue, the function of the C-terminal region of the polymerase of a tombusvirus was investigated. Three conserved motifs were identified and targeted for mutational analysis. The results revealed that these polymerase motifs are important for determining what type of viral RNA is produced, facilitating different steps in viral RNA production, and amplifying subgenomic RNA replicons. Accordingly, the C-terminal region of the tombusvirus polymerase is needed for a variety of fundamental activities. Furthermore, as these motifs are also present in distantly related viruses, the significance of these results extends beyond tombusvirids.
Chaminda D. Gunawardene; Karolina Jaluba; K. Andrew White. Conserved Motifs in a Tombusvirus Polymerase Modulate Genome Replication, Subgenomic Transcription, and Amplification of Defective Interfering RNAs. Journal of Virology 2015, 89, 3236 -3246.
AMA StyleChaminda D. Gunawardene, Karolina Jaluba, K. Andrew White. Conserved Motifs in a Tombusvirus Polymerase Modulate Genome Replication, Subgenomic Transcription, and Amplification of Defective Interfering RNAs. Journal of Virology. 2015; 89 (6):3236-3246.
Chicago/Turabian StyleChaminda D. Gunawardene; Karolina Jaluba; K. Andrew White. 2015. "Conserved Motifs in a Tombusvirus Polymerase Modulate Genome Replication, Subgenomic Transcription, and Amplification of Defective Interfering RNAs." Journal of Virology 89, no. 6: 3236-3246.
Positive-strand RNA viruses are important human, animal and plant pathogens that are defined by their single-stranded positive-sense RNA genomes. In recent years, it has become increasingly evident that interactions that occur between distantly positioned RNA sequences within these genomes can mediate important viral activities. These long-range intragenomic RNA-RNA interactions involve direct nucleotide base pairing and can span distances of thousands of nucleotides. In this Review, we discuss recent insights into the structure and function of these intriguing genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.
Beth L. Nicholson; K. Andrew White. Functional long-range RNA–RNA interactions in positive-strand RNA viruses. Nature Reviews Microbiology 2014, 12, 493 -504.
AMA StyleBeth L. Nicholson, K. Andrew White. Functional long-range RNA–RNA interactions in positive-strand RNA viruses. Nature Reviews Microbiology. 2014; 12 (7):493-504.
Chicago/Turabian StyleBeth L. Nicholson; K. Andrew White. 2014. "Functional long-range RNA–RNA interactions in positive-strand RNA viruses." Nature Reviews Microbiology 12, no. 7: 493-504.
Defective RNAs (D RNAs) are small RNA replicons derived from viral RNA genomes. No D RNAs have been found associated with members of the plus-strand RNA virus genus Aureusvirus (family Tombusviridae). Accordingly, we sought to construct a D RNA for the aureusvirus Cucumber leaf spot virus (CLSV) using the known structure of tombusvirus defective interfering RNAs as a guide. An efficiently accumulating CLSV D RNA was generated that contained four non-contiguous regions of the viral genome and this replicon was used as a tool to studying viral cis-acting RNA elements. The results of structural and functional analyses indicated that CLSV contains counterparts for several of the major RNA elements found in tombusviruses. However, although similar, the CLSV D RNA and its components are distinct and provide insights into RNA-based specificity and mechanisms of function
Pui Kei K. Lee; K. Andrew White. Construction and characterization of an aureusvirus defective RNA. Virology 2014, 452-453, 67 -74.
AMA StylePui Kei K. Lee, K. Andrew White. Construction and characterization of an aureusvirus defective RNA. Virology. 2014; 452-453 ():67-74.
Chicago/Turabian StylePui Kei K. Lee; K. Andrew White. 2014. "Construction and characterization of an aureusvirus defective RNA." Virology 452-453, no. : 67-74.
The plus-strand RNA genome of Tobacco necrosis virus-D (TNV-D) expresses its polymerase via translational readthrough. The RNA signals involved in this readthrough process were characterized in vitro using a wheat germ extract translation system and in vivo via protoplast infections. The results indicate that (i) TNV-D requires a long-range RNA-RNA interaction between an extended stem-loop (SL) structure proximal to the readthrough site and a sequence in the 3'-untranslated region of its genome; (ii) stability of the extended SL structure is important for its function; (iii) TNV-D readthrough elements are compatible with UAG and UGA, but not UAA; (iv) a readthrough defect can be rescued by a heterologous readthrough element in vitro, but not in vivo; and (v) readthrough elements can also mediate translational frameshifting. These results provide new information on determinants of readthrough in TNV-D and further support the concept of a common general mechanism for readthrough in Tombusviridae
Laura R. Newburn; Beth L. Nicholson; Michael Yosefi; Peter A. Cimino; K. Andrew White. Translational readthrough in Tobacco necrosis virus-D. Virology 2014, 450-451, 258 -265.
AMA StyleLaura R. Newburn, Beth L. Nicholson, Michael Yosefi, Peter A. Cimino, K. Andrew White. Translational readthrough in Tobacco necrosis virus-D. Virology. 2014; 450-451 ():258-265.
Chicago/Turabian StyleLaura R. Newburn; Beth L. Nicholson; Michael Yosefi; Peter A. Cimino; K. Andrew White. 2014. "Translational readthrough in Tobacco necrosis virus-D." Virology 450-451, no. : 258-265.