The conserved 5' apical hairpin stem loops of bamboo mosaic virus and its satellite RNA contribute to replication competence

Trade-off between local replication and long-distance dissemination during experimental evolution of a satellite RNA

Satellite RNAs (satRNAs) are molecular parasites that depend on their non-homologous helper viruses (HVs) for essential biological functions. While there are multiple molecular and phylogenetic studies on satRNAs, there is no experimental evolution study on how satRNAs may evolve in common infection conditions. In this study, we serially passaged the Bamboo mosaic virus (BaMV) associated-satRNA (satBaMV) under conditions in which satBaMV either coinfects an uninfected host plant, Nicotiana benthamiana, with BaMV or superinfects a transgenic N. benthamiana expressing the full-length BaMV genome. Single-nucleotide polymorphisms (SNPs) of satBaMV populations were analyzed by deep sequencing. Forty-eight SNPs were identified across four different experimental treatments. Most SNPs are treatment-specific, and some are also ephemeral. However, mutations at positions 30, 34, 63, and 82, all located at the 5' untranslated region (UTR), are universal in all treatments. These universal SNPs are configured into several haplotypes and follow different population dynamics. We constructed isogenic satBaMV strains only differing at positions 30 and 82 and conducted competition experiments in protoplasts and host plants. We found that the haplotype that reached high frequency in protoplasts and inoculation leaves also exhibited poor dissemination to systemic leaves and vice versa, thus suggesting an apparent trade-off between local replication and long-distance dissemination. We posit that the trade-off is likely caused by antagonistic pleiotropy at the 5' UTR. Our findings revealed a hitherto under-explored connection between satRNA genome replication and movement within a host plant. The significance of such a connection during satRNA evolution warrants a more thorough investigation.

Dissecting the role of a plant-specific Rab5 small GTPase NbRabF1 in Bamboo mosaic virus infection

NbRabF1, a small GTPase from Nicotiana benthamiana and a homolog of Arabidopsis thaliana Ara6, plays a key role in regulating Bamboo mosaic virus (BaMV) movement by vesicle transport between endosomal membranes. Reducing the expression of NbRabF1 in N. benthamiana by virus-induced gene silencing decreased the accumulation of BaMV, and with smaller infection foci on inoculated leaves, but had no effect in protoplasts. Furthermore, transient expression of NbRabF1 increased the accumulation of BaMV in inoculated leaves. Thus, NbRabF1 may be involved in the cell-to-cell movement of BaMV. The potential acyl modification sites at the second and third amino acid positions of NbRabF1 were crucial for membrane targeting and BaMV accumulation. The localization of mutant forms of NbRabF1 with the GDP-bound (donor site) and GTP-bound (acceptor site) suggested that NbRabF1 might regulate vesicle trafficking between the Golgi apparatus and plasma membrane. Furthermore, GTPase activity could also be involved in BaMV cell-to-cell movement. Overall, in this study, we identified a small GTPase, NbRabF1, from N. benthamiana that interacts with its activation protein NbRabGAP1 and regulates vesicle transport from the Golgi apparatus to the plasma membrane. We suggest that the BaMV movement complex might move from cell to cell through this vesicle trafficking route.

Molecular interactions of plant viral satellites

Plant viral satellites fall under the category of subviral agents. Their genomes are composed of small RNA or DNA molecules a few hundred nucleotides in length and contain an assortment of highly complex and overlapping functions. Each lacks the ability to either replicate or undergo encapsidation or both in the absence of a helper virus (HV). As the number of known satellites increases steadily, our knowledge regarding their sequence conservation strategies, means of replication and specific interactions with host and helper viruses is improving. This review demonstrates that the molecular interactions of these satellites are unique and highly complex, largely influenced by the highly specific host plants and helper viruses that they associate with. Circularized forms of single-stranded RNA are of particular interest, as they have recently been found to play a variety of novel cellular functions. Linear forms of satRNA are also of great significance as they may complement the helper virus genome in exacerbating symptoms, or in certain instances, actively compete against it, thus reducing symptom severity. This review serves to describe the current literature with respect to these molecular mechanisms in detail as well as to discuss recent insights into this emerging field in terms of evolution, classification and symptom development. The review concludes with a discussion of future steps in plant viral satellite research and development.

A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation

As a class of parasitic, non-coding RNAs, satellite RNAs (satRNAs) have to compete with their helper virus for limited amounts of viral and/or host resources for efficient replication, by which they usually reduce viral accumulation and symptom expression. Here, we report a cucumber mosaic virus (CMV)-associated satRNA (sat-T1) that ameliorated CMV-induced symptoms, accompanied with a significant reduction in the accumulation of viral genomic RNAs 1 and 2, which encode components of the viral replicase. Intrans replication assays suggest that the reduced accumulation is the outcome of replication competition. The structural basis of sat-T1 responsible for the inhibition of viral RNA accumulation was determined to be a three-way branched secondary structure that contains two biologically important hairpins. One is indispensable for the helper virus inhibition, and the other engages in formation of a tertiary pseudoknot structure that is essential for sat-T1 survival. The secondary structure containing the pseudoknot is the first RNA element with a biological phenotype experimentally identified in CMV satRNAs, and it is structurally conserved in most CMV satRNAs. Thus, this may be a generic method for CMV satRNAs to inhibit the accumulation of the helper virus via the newly-identified RNA structure.

An E3 ubiquitin ligase from Nicotiana benthamiana targets the replicase of Bamboo mosaic virus and restricts its replication

One up-regulated host gene identified previously was found involved in the infection process of Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. The full length cDNA of this gene was cloned by 5' and 3'-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved really interesting new gene (RING) domain and a transmembrane domain. The gene might function as an ubiquitin E3 ligase. We designated this protein in Nicotiana benthamiana as ubiquitin E3 ligase containing RING domain 1 (NbUbE3R1). Further characterization by using Tobacco rattle virus-based virus-induced gene silencing (loss-of-function) revealed that increased BaMV accumulation was in both knockdown plants and protoplasts. The gene might have a defensive role in the replication step of BaMV infection. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed in N. benthamiana plants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/△TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting the accumulation of BaMV. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an up-regulated gene, NbUbE3R1 that plays a role in BaMV replication.

Effects of deletion at the TTTSTTT motif of Hibiscus latent Singapore virus coat protein on viral replication and long-distance movement

Hibiscus latent Singapore virus (HLSV) mutant HLSV-22A could not express coat protein (CP) nor infect plants systemically (Niu et al., 2015). In this study, a serine- and threonine-rich motif TTTSTTT at the C-terminus of HLSV CP was found to be involved in virus replication and systemic movement. Deletion the last amino acid residue in HLSV-22A led to a more rapid virus replication, but with delayed systemic movement. When the RNA structure in TTTSTTT motif was altered, while keeping its amino acids unchanged, mutants HLSV-87A-mmSL and HLSV-22A-mmSL showed no change in viral replication. These results indicated that the unique TTTSTTT motif is associated with virus replication and systemic movement. Deletion but not substitution of amino acid(s) at the C-terminus of TTTSTTT motif of HLSV CP with short internal poly(A) track enhanced virus replication, whereas the virus with a longer internal poly(A) tract of 87 A showed delayed systemic movement (147 words).

SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants

Noncoding RNAs use their sequence and/or structure to mediate function(s). The 5' portion (166 nt) of the 356-nt noncoding satellite RNA C (satC) of Turnip crinkle virus (TCV) was previously modeled to contain a central region with two stem-loops (H6 and H7) and a large connecting hairpin (H2). We now report that in vivo functional selection (SELEX) experiments assessing sequence/structure requirements in H2, H6, and H7 reveal that H6 loop sequence motifs were recovered at nonrandom rates and only some residues are proposed to base-pair with accessible complementary sequences within the 5' central region. In vitro SHAPE of SELEX winners indicates that the central region is heavily base-paired, such that along with the lower stem and H2 region, one extensive hairpin exists composing the entire 5' region. As these SELEX winners are highly fit, these characteristics facilitate satRNA amplification in association with TCV in plants.

Phylogeography and Coevolution of Bamboo Mosaic Virus and Its Associated Satellite RNA

Bamboo mosaic virus (BaMV), a plant potexvirus, has been found only in infected bamboo species. It is frequently associated with a large, linear single-stranded satellite RNA (satBaMV) that encodes a non-structural protein. Decades of collecting across a wide geographic area in Asia have accumulated a sizable number of BaMV and satBaMV isolates. In this study, we reconstructed the BaMV phylogeny and satBaMV phylogeny with partial coat protein gene sequences and partial genomic sequences, respectively. The evolutionary relationships allowed us to infer the phylogeography of BaMV and satBaMV on the Asian continent and its outlying islands. The BaMV phylogeny suggests that the BaMV isolates from Taiwan, unsurprisingly, are most likely derived from China. Interestingly, the newly available satBaMV isolates from China were found to be most closely related to the previously established Clade III, which is found in India. The general pattern of clustering along the China/India and Taiwan divide led us to hypothesize that the Taiwan Strait has been a physical barrier to gene flow in the past evolutionary history of both BaMV and satBaMV. Lastly, cophylogeny analyses revealed a complex association pattern between BaMV and satBaMV isolates from China. In general, closely related BaMV sequences tend to carry closely related satBaMV sequences as well; but instances of mismatching with distantly related satBaMV isolates were also found. We hypothesize plausible scenarios of infection and superinfection of bamboo hosts that may be responsible for the observed association pattern. However, a more systematic sampling throughout the geographic distribution of various bamboo species is needed to unambiguously establish the origin, movement, and evolution of BaMV and satBaMV.

Interfering Satellite RNAs of Bamboo mosaic virus

Satellite RNAs (satRNAs) are sub-viral agents that may interact with their cognate helper virus (HV) and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV), the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms. In this review, we summarize the molecular mechanisms underlying the interaction of interfering satBaMV and BaMV. Like other satRNAs, satBaMV mimics the secondary structures of 5'- and 3'-untranslated regions (UTRs) of BaMV as a molecular pretender. However, a conserved apical hairpin stem loop (AHSL) in the 5'-UTR of satBaMV was found as the key determinant for downregulating BaMV replication. In particular, two unique nucleotides (C⁶⁰ and C⁸³) in the AHSL of satBaMVs determine the satBaMV interference ability by competing for the replication machinery. Thus, transgenic plants expressing interfering satBaMV could confer resistance to BaMV, and interfering satBaMV could be used as biological-control agent. Unlike two major anti-viral mechanisms, RNA silencing and salicylic acid-mediated immunity, our findings in plants by in vivo competition assay and RNA deep sequencing suggested replication competition is involved in this transgenic satBaMV-mediated BaMV interference. We propose how a single nucleotide of satBaMV can make a great change in BaMV pathogenicity and the underlying mechanism.

Satellite RNA pathogens of plants: impacts and origins-an RNA silencing perspective

Viral satellite RNAs (satRNAs) are among the smallest RNA pathogens in plants. They have little or no protein-coding capacity but can have a major impact on the host plants through trilateral interactions with helper viruses and host plants. Studies around the 1980s revealed much of what we know about satRNAs: they can affect helper virus accumulation, modulate helper virus-induced disease symptoms, and induce their own symptoms with the assistance of helper viruses which depend on specific nucleotide sequences of their genome and host species. The molecular basis of these satRNA-caused impacts and the origin of satRNAs have yet to be fully understood and revealed, but recent understanding of the antiviral RNA silencing pathways and advancement in RNA and DNA sequencing technologies have provided new avenues and opportunities to examine these unanswered questions. These RNA silencing-based studies have revealed the existence of cross silencing between some satRNAs and helper viruses, the downregulation of helper virus-encoded suppressor (VSR) of RNA silencing or inhibition/enhancement of VSR activity by satRNAs, the silencing of host-encoded genes by satRNA-derived small interfering RNA (siRNAs), and the presence of satRNA-like small RNAs in uninfected host plants. These findings have provided alternative RNA silencing-based models to explain the pathogenicity and origin of satRNAs. WIREs RNA 2016, 7:5-16. doi: 10.1002/wrna.1311 For further resources related to this article, please visit the WIREs website.

Biologically-supported structural model for a viral satellite RNA

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.

The molecular basis for flexibility in the flexible filamentous plant viruses

Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.

Genetic diversity and evolution of satellite RNAs associated with the bamboo mosaic virus

Satellite RNAs (satRNAs) are subviral agents that depend on cognate helper viruses for genome replication and encapsidation. Their negative impacts on helper viruses have been exploited to control plant viral diseases. SatBaMV is a commonly found satRNA associated with Bamboo mosaic virus (BaMV) that infects diverse bamboo species in the field. To investigate the genetic diversity and evolution of satRNAs, we examined seven satBaMV populations derived from five bamboo species and cultivars from Taiwan, China, and India and one from the greenhouse. We found 3 distinct clades among the seven populations. Clade I is consisted of all satBaMV isolates, except for those from Dendrocalamus latiflorus in Taiwan and Bambusa vulgaris in India, which belong to Clades II and III, respectively. Interestingly, nucleotide diversity was lower for Clade I than II and III. However, the nucleotide diversity did not seem to depend on bamboo species or geographic location. Our population genetic analyses revealed the presence of excessive low-frequency polymorphic sites, which suggests that the satBaMV population was under purifying selection and/or population expansion. Further analysis of P20, the only satBaMV gene that encodes a non-structural protein involved in the long-distance movement of satBaMV, showed evidence of purifying selection. Taken together, our results suggest that purifying selection against defective P20 protein is responsible at least in part for the evolution of the satBaMV genome.

Two key arginine residues in the coat protein of Bamboo mosaic virus differentially affect the accumulation of viral genomic and subgenomic RNAs

The interactions between viral RNAs and coat proteins (CPs) are critical for the efficient completion of infection cycles of RNA viruses. However, the specificity of the interactions between CPs and genomic or subgenomic RNAs remains poorly understood. In this study, Bamboo mosaic virus (BaMV) was used to analyse such interactions. Using reversible formaldehyde cross-linking and mass spectrometry, two regions in CP, each containing a basic amino acid (R99 and R227, respectively), were identified to bind directly to the 5' untranslated region of BaMV genomic RNA. Analyses of the alanine mutations of R99 and R227 revealed that the secondary structures of CP were not affected significantly, whereas the accumulation of BaMV genomic, but not subgenomic, RNA was severely decreased at 24 h post-inoculation in the inoculated protoplasts. In the absence of CP, the accumulation levels of genomic and subgenomic RNAs were decreased to 1.1%-1.5% and 33%-40% of that of the wild-type (wt), respectively, in inoculated leaves at 5 days post-inoculation (dpi). In contrast, in the presence of mutant CPs, the genomic RNAs remained about 1% of that of wt, whereas the subgenomic RNAs accumulated to at least 87%, suggesting that CP might increase the accumulation of subgenomic RNAs. The mutations also restricted viral movement and virion formation in Nicotiana benthamiana leaves at 5 dpi. These results demonstrate that R99 and R227 of CP play crucial roles in the accumulation, movement and virion formation of BaMV RNAs, and indicate that genomic and subgenomic RNAs interact differently with BaMV CP.

Viral and nonviral elements in potexvirus replication and movement and in antiviral responses

In Potato virus X, a member of the genus Potexvirus, special sequences and structures at the 5' and 3' ends of the nontranslated region function as cis-acting elements for viral replication. These elements greatly affect interactions between viral RNAs and those between viral RNAs and host factors. The potexvirus genome encodes five open-reading frames. Viral replicase, which is required for the synthesis of viral RNA, binds viral RNA elements and host factors to form a viral replication complex at the host cellular membrane. The coat protein (CP) and three viral movement proteins (TGB1, TGB2, and TGB3) have critical roles in mediating cell-to-cell viral movement through plasmodesmata by virion formation or by nonvirion ribonucleoprotein (RNP) complex formation with viral movement proteins (TGBs). The RNP complex, like TGB1-CP-viral RNA, is associated with viral replicase and used for immediate reinitiation of viral replication in newly invaded cells. Higher plants have defense mechanisms against potexviruses such as Rx-mediated resistance and RNA silencing. The CP acts as an avirulence effector for plant defense mechanisms, while TGB1 functions as a viral suppressor of RNA silencing, which is the mechanism of innate immune resistance. Here, we describe recent findings concerning the involvement of viral and host factors in potexvirus replication and in antiviral responses to potexvirus infection.

Transgenic resistance to Bamboo mosaic virus by expression of interfering satellite RNA

Plant genetic engineering has broadened the options for plant virus resistance and is mostly based on pathogen-derived resistance. Previously, we have shown that interfering satellite RNA (satRNA) of Bamboo mosaic virus (satBaMV) greatly reduces Bamboo mosaic virus (BaMV) accumulation and BaMV-induced symptoms in co-inoculated plants. Here, we generated a nonviral source of virus-resistant transgenic Nicotiana benthamiana and Arabidopsis thaliana by introducing interfering satBaMV. Asymptomatic transgenic N. benthamiana lines were highly resistant to BaMV virion and viral RNA infection, and the expression of the transgene BSL6 was higher in asymptomatic than mildly symptomatic lines. In addition, BaMV- and satBaMV-specific small RNAs were detectable only after BaMV challenge, and their levels were associated with genomic viral RNA or satRNA levels. By transcriptomic analysis, the salicylic acid (SA) signalling pathway was not induced in satBaMV transgenic A. thaliana in mock conditions, suggesting that two major antiviral mechanisms, RNA silencing and SA-mediated resistance, are not involved directly in transgenic satBaMV-mediated BaMV interference. In contrast, resistance is associated with the level of the interfering satBaMV transgene. We propose satBaMV-mediated BaMV interference in transgenic plants by competition for replicase with BaMV.