Rice tungro bacilliform virus open reading frames II and III are translated from polycistronic pregenomic RNA by leaky scanning

Molecular characterization of recombinant citrus yellow mosaic badnavirus infecting Coorg mandarin exhibiting yellow mosaic disease symptoms in high humid tropic region of Western Ghats

The citrus yellow mosaic badnavirus (CMBV) is one of the most important viruses causing yellowing and declining in different Citrus species. The Coorg mandarin, pomelo and grapefruit showing the yellow mosaic disease symptoms were collected from different famers field during the survey. Further viral pathogenicity was confirmed through grafting on Rangpur lime as root stock. To confirm the identity of the pathogen, total genomic DNA was extracted from Coorg mandarin, Pomelo and grapefruit were subjected to PCR amplification using ORF III specific primers. Further the complete genome of CMBV amplified using different sets of specific primers were cloned and sequenced. The sequence analysis showed that CMBV from the Coorg mandarin showed maximum nt identity of 94.5% with CMBV-AL infecting acid lime. Recombination and GC plot analysis showed that the recombination occurred at in low GC content regions of genome of the CMBV and are derived from the previously reported Badnaviruses infecting different Citrus species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-024-00864-z.

Translation of Plant RNA Viruses

Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5′ cap structure, and 3′ polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.

Two microPeptides are translated from a KSHV polycistronic RNA in human cells by leaky scanning mechanism

Kaposi's sarcoma-associated herpesvirus (KSHV) encodes a 3.0 kb polyadenylated RNA (T3.0) in the opposite strand of the open reading frame 50 (RTA) gene. The T3.0 was mis-annotated as a noncoding RNA but found to be associated with ribosomes and carries at least four translatable sORFs. Two of them, namely vSP-1 and vSP-2, have been characterized. vSP-1 enhances RTA expression by blocking RTA self-ubiquitylation and proteasome-associated degradation. T3.0 RNA is a polycistronic RNA. Furthermore, polycistronic translation has been observed in most of the cases of small peptides (microPeptides) translated from previously annotated noncoding RNAs in eukaryotes. In an effort to elucidate the mechanism underlying polycistronic sORF translation in eukaryotic cells, we found that T3.0 RNA translates vSP-1 and vSP-2 through a leaky scanning mechanism.

Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond

Viruses have compact genomes and usually translate more than one protein from polycistronic RNAs using leaky scanning, frameshifting, stop codon suppression or reinitiation mechanisms. Viral (pre-)genomic RNAs often contain long 5′-leader sequences with short upstream open reading frames (uORFs) and secondary structure elements, which control both translation initiation and replication. In plants, viral RNA and DNA are targeted by RNA interference (RNAi) generating small RNAs that silence viral gene expression, while viral proteins are recognized by innate immunity and autophagy that restrict viral infection. In this review we focus on plant pararetroviruses of the family Caulimoviridae and describe the mechanisms of uORF- and secondary structure-driven ribosome shunting, leaky scanning and reinitiation after translation of short and long uORFs. We discuss conservation of these mechanisms in different genera of Caulimoviridae, including host genome-integrated endogenous viral elements, as well as in other viral families, and highlight a multipurpose use of the highly-structured leader sequence of plant pararetroviruses in regulation of translation, splicing, packaging, and reverse transcription of pregenomic RNA (pgRNA), and in evasion of RNAi. Furthermore, we illustrate how targeting of several host factors by a pararetroviral effector protein can lead to transactivation of viral polycistronic translation and concomitant suppression of antiviral defenses. Thus, activation of the plant protein kinase target of rapamycin (TOR) by the Cauliflower mosaic virus transactivator/viroplasmin (TAV) promotes reinitiation of translation after long ORFs on viral pgRNA and blocks antiviral autophagy and innate immunity responses, while interaction of TAV with the plant RNAi machinery interferes with antiviral silencing.

Unusual genomic features of a badnavirus infecting mulberry

Mulberry badnavirus 1 (MBV1) has been characterized as the aetiological agent of a disease observed on a mulberry tree in Lebanon (accession L34). A small RNA next-generation sequencing library was prepared and analysed from L34 extract, and these data together with genome walking experiments have been used to obtain the full-length virus sequence. Uniquely among badnaviruses, the MBV1 sequence encodes a single ORF containing all the conserved pararetrovirus motifs. Two genome sizes (6 kb and 7 kb) were found to be encapsidated in infected plants, the shortest of which shares 98.95 % sequence identity with the full L34 genome. In the less-than-full-length deleted genome, the translational frame for the replication domains was conserved, but the particle morphology, observed under electron microscopy, was somehow altered. Southern blot hybridization confirmed the coexistence of the two genomic forms in the original L34 accession, as well as the absence of cointegration in the plant genome. Both long and deleted genomes were cloned and proved to be infectious in mulberry. Differently from other similar nuclear-replicating viruses or viroids, the characterization of the MBV1-derived small RNAs showed a reduced amount of the 24-mer class size.

Badnaviruses: The Current Global Scenario

Badnaviruses (Family: Caulimoviridae; Genus: Badnavirus) are non-enveloped bacilliform DNA viruses with a monopartite genome containing about 7.2 to 9.2 kb of dsDNA with three to seven open reading frames. They are transmitted by mealybugs and a few species by aphids in a semi-persistent manner. They are one of the most important plant virus groups and have emerged as serious pathogens affecting the cultivation of several horticultural crops in the tropics, especially banana, black pepper, cocoa, citrus, sugarcane, taro, and yam. Some badnaviruses are also known as endogenous viruses integrated into their host genomes and a few such endogenous viruses can be awakened, e.g., through abiotic stress, giving rise to infective episomal forms. The presence of endogenous badnaviruses poses a new challenge for the fool-proof diagnosis, taxonomy, and management of the diseases. The present review aims to highlight emerging disease problems, virus characteristics, transmission, and diagnosis of badnaviruses.

From the concept of totipotency to biofortified cereals

I was a college teacher when opportunity opened a path into academia. A fascination with totipotency channeled me into research on tissue culture. As I was more interested in contributions to food security than in scientific novelty, I turned my attention to the development of genetic modification technology for cereals. From my cell culture experience, I had reasons not to trust Agrobacterium for that purpose, and I developed direct gene transfer instead. In the early 1990s, I became aware of the problem of micronutrient deficiency, particularly vitamin A deficiency in rice-eating populations. Golden Rice, which contains increased amounts of provitamin A, was probably instrumental for the concept of biofortification to take off. I realized that this rice would remain an academic exercise if product development and product registration were not addressed, and this is what I focused on after my retirement. Although progress is slowly being made, had I known what this pursuit would entail, perhaps I would not have started. Hopefully Golden Rice will reach the needy during my lifetime.

Interactions of Rice tungro bacilliform pararetrovirus and its protein P4 with plant RNA-silencing machinery

Small interfering RNA (siRNA)-directed gene silencing plays a major role in antiviral defense. Virus-derived siRNAs inhibit viral replication in infected cells and potentially move to neighboring cells, immunizing them from incoming virus. Viruses have evolved various ways to evade and suppress siRNA production or action. Here, we show that 21-, 22-, and 24-nucleotide (nt) viral siRNAs together constitute up to 19% of total small RNA population of Oryza sativa plants infected with Rice tungro bacilliform virus (RTBV) and cover both strands of the RTBV DNA genome. However, viral siRNA hotspots are restricted to a short noncoding region between transcription and reverse-transcription start sites. This region generates double-stranded RNA (dsRNA) precursors of siRNAs and, in pregenomic RNA, forms a stable secondary structure likely inaccessible to siRNA-directed cleavage. In transient assays, RTBV protein P4 suppressed cell-to-cell spread of silencing but enhanced cell-autonomous silencing, which correlated with reduced 21-nt siRNA levels and increased 22-nt siRNA levels. Our findings imply that RTBV generates decoy dsRNA that restricts siRNA production to the structured noncoding region and thereby protects other regions of the viral genome from repressive action of siRNAs, while the viral protein P4 interferes with cell-to-cell spread of antiviral silencing.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution

The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called ‘Florendovirus’, members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20–34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.

Endogenous viral elements have been extensively described in animals but their significance in plants is less well understood. Here, Geering et al. describe a new group of endogenous pararetroviruses, called florendoviruses, which have colonized the genomes of many important crop species.

Evasion of short interfering RNA-directed antiviral silencing in Musa acuminata persistently infected with six distinct banana streak pararetroviruses

Vegetatively propagated crop plants often suffer from infections with persistent RNA and DNA viruses. Such viruses appear to evade the plant defenses that normally restrict viral replication and spread. The major antiviral defense mechanism is based on RNA silencing generating viral short interfering RNAs (siRNAs) that can potentially repress viral genes posttranscriptionally through RNA cleavage and transcriptionally through DNA cytosine methylation. Here we examined the RNA silencing machinery of banana plants persistently infected with six pararetroviruses after many years of vegetative propagation. Using deep sequencing, we reconstructed consensus master genomes of the viruses and characterized virus-derived and endogenous small RNAs. Consistent with the presence of endogenous siRNAs that can potentially establish and maintain DNA methylation, the banana genomic DNA was extensively methylated in both healthy and virus-infected plants. A novel class of abundant 20-nucleotide (nt) endogenous small RNAs with 5'-terminal guanosine was identified. In all virus-infected plants, 21- to 24-nt viral siRNAs accumulated at relatively high levels (up to 22% of the total small RNA population) and covered the entire circular viral DNA genomes in both orientations. The hotspots of 21-nt and 22-nt siRNAs occurred within open reading frame (ORF) I and II and the 5' portion of ORF III, while 24-nt siRNAs were more evenly distributed along the viral genome. Despite the presence of abundant viral siRNAs of different size classes, the viral DNA was largely free of cytosine methylation. Thus, the virus is able to evade siRNA-directed DNA methylation and thereby avoid transcriptional silencing. This evasion of silencing likely contributes to the persistence of pararetroviruses in banana plants.

IMPORTANCE

We report that DNA pararetroviruses in Musa acuminata banana plants are able to evade DNA cytosine methylation and transcriptional gene silencing, despite being targeted by the host silencing machinery generating abundant 21- to 24-nucleotide short interfering RNAs. At the same time, the banana genomic DNA is extensively methylated in both healthy and virus-infected plants. Our findings shed light on the siRNA-generating gene silencing machinery of banana and provide a possible explanation why episomal pararetroviruses can persist in plants whereas true retroviruses with an obligatory genome-integration step in their replication cycle do not exist in plants.

Plant pararetroviruses: replication and expression

True retroviruses are not known in plants; however, plant pararetroviruses (caulimoviridae) share many retroviral properties, replicating by transcription in the nucleus followed by reverse transcription in the cytoplasm. Pararetroviruses have circular DNA genomes that do not integrate into the host genome, and display several unique expression strategies. Typical of plant pararetroviral pregenomic RNA is a highly structured leader of about 600nt long that is bypassed by scanning ribosomes. Caulimoviruses and Soymoviruses have a further interesting translation mechanism: at least six of the seven open reading frames are translated via polycistronic translation mediated by a specific transactivator (TAV), which modifies the translation complex. TAV also forms large intracellular inclusion bodies, which are the site of translation and virus assembly.

Further support of genetic conservation in Indian isolates of Rice tungro bacilliform virus by sequence analysis of an isolate from North-Western India

The genomic sequence of an isolate of Rice tungro bacilliform virus (RTBV), collected from the state of Punjab (Pb), a non-endemic tungro region from North-Western India was determined. In silico comparison of the 7931-bp sequence with isolates from Southeast Asia and the three previously characterized Indian isolates, revealed not only similar genome size to other Indian isolates but also high degree of homology both at nucleotide (>93 %) and amino acid (>96 %) levels among them. On the other hand, like the other Indian isolates, RTBV-Pb showed much lower nucleotide (<87 %) and amino acid (<90 % in most of the open reading frames) identities with the Southeast Asian isolates owing to several nucleotide substitutions and indels. In-depth annotation comparisons reinforce the hypothesis that Indian isolates of RTBV have diverged sufficiently from the Southeast Asian ones to form a separate group.

Non-canonical translation in RNA viruses

Viral protein synthesis is completely dependent upon the translational machinery of the host cell. However, many RNA virus transcripts have marked structural differences from cellular mRNAs that preclude canonical translation initiation, such as the absence of a 5′ cap structure or the presence of highly structured 5′UTRs containing replication and/or packaging signals. Furthermore, whilst the great majority of cellular mRNAs are apparently monocistronic, RNA viruses must often express multiple proteins from their mRNAs. In addition, RNA viruses have very compact genomes and are under intense selective pressure to optimize usage of the available sequence space. Together, these features have driven the evolution of a plethora of non-canonical translational mechanisms in RNA viruses that help them to meet these challenges. Here, we review the mechanisms utilized by RNA viruses of eukaryotes, focusing on internal ribosome entry, leaky scanning, non-AUG initiation, ribosome shunting, reinitiation, ribosomal frameshifting and stop-codon readthrough. The review will highlight recently discovered examples of unusual translational strategies, besides revisiting some classical cases.

Short ORF-dependent ribosome shunting operates in an RNA picorna-like virus and a DNA pararetrovirus that cause rice tungro disease

Rice tungro disease is caused by synergistic interaction of an RNA picorna-like virus Rice tungro spherical virus (RTSV) and a DNA pararetrovirus Rice tungro bacilliform virus (RTBV). It is spread by insects owing to an RTSV-encoded transmission factor. RTBV has evolved a ribosome shunt mechanism to initiate translation of its pregenomic RNA having a long and highly structured leader. We found that a long leader of RTSV genomic RNA remarkably resembles the RTBV leader: both contain several short ORFs (sORFs) and potentially fold into a large stem-loop structure with the first sORF terminating in front of the stem basal helix. Using translation assays in rice protoplasts and wheat germ extracts, we show that, like in RTBV, both initiation and proper termination of the first sORF translation in front of the stem are required for shunt-mediated translation of a reporter ORF placed downstream of the RTSV leader. The base pairing that forms the basal helix is required for shunting, but its sequence can be varied. Shunt efficiency in RTSV is lower than in RTBV. But in addition to shunting the RTSV leader sequence allows relatively efficient linear ribosome migration, which also contributes to translation initiation downstream of the leader. We conclude that RTSV and RTBV have developed a similar, sORF-dependent shunt mechanism possibly to adapt to the host translation system and/or coordinate their life cycles. Given that sORF-dependent shunting also operates in a pararetrovirus Cauliflower mosaic virus and likely in other pararetroviruses that possess a conserved shunt configuration in their leaders it is tempting to propose that RTSV may have acquired shunt cis-elements from RTBV during their co-existence.

Ribosome shunting, first discovered in plant pararetroviruses, is a translation initiation mechanism that combines 5′ end-dependent scanning and internal initiation and allows a bypass of highly-structured leaders of certain viral and cellular mRNAs. Here we demonstrate that a similar shunt mechanism has been developed by the RNA picorna-like virus RTSV and the DNA pararetrovirus RTBV that form a disease complex in rice. Leader sequences of the RTSV genomic RNA and the RTBV pregenomic RNA possess a conserved shunt configuration with a 5′-proximal short ORF (sORF1) terminating in front of a large stem-loop structure. Like in RTBV and a related pararetrovirus Cauliflower mosaic virus, shunt-mediated translation downstream of the RTSV leader depends on initiation and proper termination of sORF1 translation and on formation of the basal helix of the downstream secondary structure. Given that RTBV-like shunt elements with identical sequence motifs are present in all RTSV isolates but absent in related picorna-like viruses, it is likely that RTSV could have acquired these elements after its encounter with RTBV. Alternatively, the RTSV shunt elements could have evolved independently to adapt to the rice translation machinery. Our study highlights on-going genetic exchange and co-adaptation to the host in emerging viral disease complexes.

The large intergenic region of Rice tungro bacilliform virus evolved differentially among geographically distinguished isolates

Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus. The large intergenic region (LIGR) of RTBV having a single transcriptional promoter produces more than genome length pregenomic RNA (pgRNA) which directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis of LIGR, the 11 RTBV isolates sequenced so far were compared with respect to structural organization of promoter and pgRNA 5'-leader. The results revealed only 74.90% identity at LIGR between 'Southeast Asian' (SEA) and 'South Asian' (SA) isolates of RTBV indicating considerable variation between two groups which was also reflected during analysis of promoter and leader sequence. The predicted promoter region of SA isolates exhibited major variations in terms of transcription start site and consensus sequences of cis motifs expecting further exploitation of promoter region of SA isolates. The reduced length of leader sequence along with less numbers and different arrangements of small open reading frames (sORFs) in case of SA isolates might have some alterations in the control of expression of ORF II and III between the two groups. In spite of these variations, the leader sequence of both SEA and SA type isolates showed formation of stable secondary or stem-loop structure having identical features for efficient translation. The conservation of sORF1 at seven nucleotides upstream of stable stem-loop, CU-rich sequence following the sORF1 stop codon and AU-rich shunt landing sequence immediately downstream of the secondary structure suggested conservation of ribosomal shunt mechanism in all RTBV isolates irrespective of their geographical distribution.

Phylogenetic analysis of Rice tungro bacilliform virus ORFs revealed strong correlation between evolution and geographical distribution

A new isolate of Rice tungro bacilliform virus (RTBV) was collected from Chinsura, West Bengal, India. The full genome was sequenced and deposited to GenBank designating the new one as Chinsura isolate. The four open reading frames (ORFs) of the new isolate were compared with those of previously reported 'South-east Asian' (SEA) and 'South Asian' (SA) isolates emphasizing the ORF3, which is the largest and functionally most important gene of RTBV. In the ORFs, Chinsura isolate shared 90.0-100.0% identity at amino acid level with SA isolates, but only 58.76-88.63% identity with SEA isolates for the same. Similarly, the amino acid identity of ORFs between SEA and SA isolates ranged from 58.77 to 88.64, whereas within each group the corresponding value was >96.0%. The phylogenetic analysis based on nucleotide and amino acid sequences of each ORF made two broad clusters of SEA- and SA-types including Chinsura isolate within SA cluster. Moreover, the relative positions and length of functional domains corresponding to movement protein (MP), coat protein (CP), aspartate protease (PR) and reverse transcriptase/ribonuclease H (RT/RNase H) of ORF3 of Chinsura isolate were completely identical with SA isolates. The clustering pattern indicated strong influence of geographical habitat on genomic evolution. Comparison of ORF3 among all the isolates revealed major variations at non-functional regions in between the functional domains and at the hypervariable 3'-terminal end of ORF3, while PR appeared to have evolved differentially in SA isolates expecting further characterization.

Noncanonical translation initiation of the Arabidopsis flowering time and alternative polyadenylation regulator FCA

The RNA binding protein FCA regulates the floral transition and is required for silencing RNAs corresponding to specific noncoding sequences in the Arabidopsis thaliana genome. Through interaction with the canonical RNA 3' processing machinery, FCA affects alternative polyadenylation of many transcripts, including antisense RNAs at the locus encoding the floral repressor FLC. This potential for widespread alteration of gene regulation clearly needs to be tightly regulated, and we have previously shown that FCA expression is autoregulated through poly(A) site choice. Here, we show distinct layers of FCA regulation that involve sequences within the 5' region that regulate noncanonical translation initiation and alter the expression profile. FCA translation in vivo occurs exclusively at a noncanonical CUG codon upstream of the first in-frame AUG. We fully define the upstream flanking sequences essential for its selection, revealing features that distinguish this from other non-AUG start site mechanisms. Bioinformatic analysis identified 10 additional Arabidopsis genes that likely initiate translation at a CUG codon. Our findings reveal further unexpected complexity in the regulation of FCA expression with implications for its roles in regulating flowering time and gene expression and more generally show plant mRNA exceptions to AUG translation initiation.

Facilitated leaky scanning and atypical ribosome shunting direct downstream translation initiation on the tricistronic S1 mRNA of avian reovirus

The S1 mRNA of avian reovirus is functionally tricistronic, encoding three unrelated proteins, p10, p17 and σC, from three sequential, partially overlapping open reading frames (ORFs). The mechanism of translation initiation at the 3'-proximal σC ORF is currently unknown. Transient RNA transfections using Renilla luciferase reporter constructs revealed only a modest reduction in reporter expression upon optimization of either the p10 or p17 start sites. Insertion of multiple upstream AUG (uAUG) codons in a preferred start codon sequence context resulted in a substantial retention of downstream translation initiation on the S1 mRNA, but not on a heterologous mRNA. The S1 mRNA therefore facilitates leaky scanning to promote ribosome access to the σC start codon. Evidence also indicates that σC translation is mediated by a second scanning-independent mechanism capable of bypassing upstream ORFs. This alternate mechanism is cap-dependent and requires a sequence-dependent translation enhancer element that is complementary to 18S rRNA. Downstream translation initiation of the tricistronic S1 mRNA is therefore made possible by two alternate mechanisms, facilitated leaky scanning and an atypical form of ribosome shunting. This dual mechanism of downstream translation initiation ensures sufficient expression of the σC cell attachment protein that is essential for infectious progeny virus production.

Virus versus host cell translation love and hate stories

Regulation of protein synthesis by viruses occurs at all levels of translation. Even prior to protein synthesis itself, the accessibility of the various open reading frames contained in the viral genome is precisely controlled. Eukaryotic viruses resort to a vast array of strategies to divert the translation machinery in their favor, in particular, at initiation of translation. These strategies are not only designed to circumvent strategies common to cell protein synthesis in eukaryotes, but as revealed more recently, they also aim at modifying or damaging cell factors, the virus having the capacity to multiply in the absence of these factors. In addition to unraveling mechanisms that may constitute new targets in view of controlling virus diseases, viruses constitute incomparably useful tools to gain in-depth knowledge on a multitude of cell pathways.

Insights into the translational regulation of biologically active open reading frames of Pelargonium line pattern virus

Pelargonium line pattern virus (PLPV), a proposed member of a prospective genus (Pelarspovirus) within family Tombusviridae, has a positive-sense, single-stranded genomic RNA. According to previous predictions, it contains six open reading frames (ORFs) potentially encoding proteins of 27 (p27), 13 (p13), 87 (p87), 7 (p7), 6 (p6), and 37 kDa (p37). Using a variety of techniques we demonstrate that all predicted ORFs are functional, with the exception of (p13) and (p6). We also characterize a previously unidentified ORF which encodes a 9.7 kDa protein (p9.7) that is essential for viral movement. Furthermore, we present evidence that the single subgenomic RNA (sgRNA) produced by the virus directs synthesis of p7, p9.7 and p37. Remarkably, the translation of these totally unrelated proteins is coordinated via leaky-scanning. This mechanism seems to be favoured by the poor translation context of the start codon of ORF(p7), the non-AUG weak initiation codon of ORF(p9.7) and the lack of additional AUG codons in any reading frame preceding ORF(p37). The results also suggest that precise regulation of protein production from the sgRNA is critical for virus viability. Altogether, the data supports the notion that PLPV belongs to a new genus of plant viruses.

Cross-species functionality of pararetroviral elements driving ribosome shunting

BACKGROUND

Cauliflower mosaic virus (CaMV) and Rice tungro bacilliform virus (RTBV) belong to distinct genera of pararetroviruses infecting dicot and monocot plants, respectively. In both viruses, polycistronic translation of pregenomic (pg) RNA is initiated by shunting ribosomes that bypass a large region of the pgRNA leader with several short (s)ORFs and a stable stem-loop structure. The shunt requires translation of a 5'-proximal sORF terminating near the stem. In CaMV, mutations knocking out this sORF nearly abolish shunting and virus viability.

METHODOLOGY/PRINCIPAL FINDINGS

Here we show that two distant regions of the CaMV leader that form a minimal shunt configuration comprising the sORF, a bottom part of the stem, and a shunt landing sequence can be replaced by heterologous sequences that form a structurally similar configuration in RTBV without any dramatic effect on shunt-mediated translation and CaMV infectivity. The CaMV-RTBV chimeric leader sequence was largely stable over five viral passages in turnip plants: a few alterations that did eventually occur in the virus progenies are indicative of fine tuning of the chimeric sequence during adaptation to a new host.

CONCLUSIONS/SIGNIFICANCE

Our findings demonstrate cross-species functionality of pararetroviral cis-elements driving ribosome shunting and evolutionary conservation of the shunt mechanism. We are grateful to Matthias Müller and Sandra Pauli for technical assistance. This work was initiated at Friedrich Miescher Institute (Basel, Switzerland). We thank Prof. Thomas Boller for hosting the group at the Institute of Botany.

Translation initiation at an upstream CUG codon regulates the expression of Hibiscus chlorotic ringspot virus coat protein

Viruses depend heavily on host cells for replication and exploit the host translation machinery for its gene expression using various unorthodox translation mechanisms. According to the conventional scanning model, only the 5'-proximal gene in the viral RNA is accessible to the ribosomes whereas other genes are silent. In this study, we use a model plant RNA virus, Hibiscus chlorotic ringspot virus (HCRSV), to investigate various translation mechanisms involved in regulation of the expression of internal genes. The 3'-end 1.2kb region of HCRSV genomic and subgenomic RNAs were shown to encode four polypeptides of 38, 27, 25 and 22.5kDa. Mutagenesis studies revealed that a CUG codon ((2570)CUG) is the initiation codon for p27, the longest of the three co-C-terminal products (p27, p25 and p22.5), and translation of p25 and p22.5 was initiated at (2603)AUG and (2666)AUG, respectively. Translation initiation of the p27 expression at the (2570)CUG codon regulates the expression of p38, the viral coat protein through a leaky scanning mechanism and mutational analysis of an upstream open reading frame (ORF) demonstrated that initiation of the p27 expression at this CUG codon (instead of an AUG) may play a role in maintaining the ratio of p27 and p38. In addition, a previously identified internal ribosome entry site was shown to control the expression of p27 and p38 in the subgenomic RNA 2.

Mechanism of ribosome shunting in Rice tungro bacilliform pararetrovirus

In plant pararetroviruses, pregenomic RNA serves both as a template for replication through reverse transcription and a polysictronic mRNA. This RNA has a complex leader sequence preceding the first large ORF. The leader contains multiple short ORFs and strong secondary structure, both inhibiting ribosome scanning. Translation on this RNA is initiated by shunting, in which scanning ribosomes bypass a large portion of the leader with the inhibitory secondary structure and short ORFs. In Cauliflower mosaic virus (CaMV), the ribosome shunting mechanism involves translation of the 5'-proximal short ORF terminating in front of the secondary structure that appears to force ribosomes to take off and resume scanning at a landing site downstream of the structure. Using two plant protoplast systems and shunt-competent wheat-germ extracts, we demonstrate that in Rice tungro bacilliform virus (RTBV) shunting also depends on the first short ORF followed by strong secondary structure. Swapping of the conserved shunt elements between CaMV and RTBV revealed the importance of nucleotide composition of the landing sequence for efficient shunting. The results suggest that the mechanism of ribosome shunting is evolutionary conserved in plant pararetroviruses.

Translation reinitiation and leaky scanning in plant viruses

While translation of mRNAs in eukaryotic cells in general follows strict rules, viruses infecting these cells break those rules in various ways. Viruses are under high selection pressure to compete with the host, to economize genome size, and to accommodate signals for replication, virus assembly, etc., on their RNAs as well as using them for translation. The cornucopia of extraordinary translation strategies, such as leaky scanning, internal initiation of translation, ribosome shunt, and virus-controlled reinitiation of translation, evolved by viruses continues to surprise and inform our understanding of general translation mechanisms. While internal initiation is treated in another section of this issue, we concentrate on leaky scanning, shunt and reinitiation, with emphasis on plant pararetroviruses.

Regulation of translation via mRNA structure in prokaryotes and eukaryotes

The mechanism of initiation of translation differs between prokaryotes and eukaryotes, and the strategies used for regulation differ accordingly. Translation in prokaryotes is usually regulated by blocking access to the initiation site. This is accomplished via base-paired structures (within the mRNA itself, or between the mRNA and a small trans-acting RNA) or via mRNA-binding proteins. Classic examples of each mechanism are described. The polycistronic structure of mRNAs is an important aspect of translational control in prokaryotes, but polycistronic mRNAs are not usable (and usually not produced) in eukaryotes. Four structural elements in eukaryotic mRNAs are important for regulating translation: (i) the m7G cap; (ii) sequences flanking the AUG start codon; (iii) the position of the AUG codon relative to the 5' end of the mRNA; and (iv) secondary structure within the mRNA leader sequence. The scanning model provides a framework for understanding these effects. The scanning mechanism also explains how small open reading frames near the 5' end of the mRNA can down-regulate translation. This constraint is sometimes abrogated by changing the structure of the mRNA, sometimes with clinical consequences. Examples are described. Some mistaken ideas about regulation of translation that have found their way into textbooks are pointed out and corrected.

Effective Translation of the Second Cistron in Two Drosophila Dicistronic Transcripts Is Determined by the Absence of In-frame AUG Codons in the First Cistron

The novel dicistronic transcript encoded by the Drosophila melanogaster stoned gene was recognized as being unusual in that the protein encoded by the first open reading frame, stoned-A (STNA), contains no internal methionine residues in a protein of 93 kDa. The dicistronic nature of the stoned locus and the lack of methionine residues in STNA is conserved across dipteran species. A second methionine-free cistron, encoding Snapin, was identified in Drosophila and also found to be dicistronic, the second open reading frame (ORF) encoding a methyltransferase. We have replaced the methyltransferase cistron with green fluorescent protein (GFP) and used this dicistronic construct to show that the GFP cistron is translated in Drosophila S2 cells. The insertion of in-frame AUG codons into the snapin ORF attenuates the translation of GFP, and the level of attenuation correlates with the number of inserted AUGs. Increasing the efficiency of translation-initiation of the Snapin cistron also attenuates the translation of GFP. This indicates that failure to initiate translation at the first AUG allows ribosomes to scan through the Snapin ORF and to initiate translation of the second cistron, unless new AUG codons are inserted. These data are used to interpret the expression of the stoned locus and in particular, to explain the altered stoned protein levels in the stoned-temperature-sensitive mutant allele, which replaces a lysine with a methionine codon early in the first, stonedA, cistron.

Pushing the limits of the scanning mechanism for initiation of translation

Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5' end plays a dominant role in identifying the start codon. This "position effect" is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream site. The position effect is evident also in cases where a silent internal AUG codon is activated upon being relocated closer to the 5' end. Two mechanisms for escaping the first-AUG rule--reinitiation and context-dependent leaky scanning--enable downstream AUG codons to be accessed in some mRNAs. Although these mechanisms are not new, many new examples of their use have emerged. Via these escape pathways, the scanning mechanism operates even in extreme cases, such as a plant virus mRNA in which translation initiates from three start sites over a distance of 900 nt. This depends on careful structural arrangements, however, which are rarely present in cellular mRNAs. Understanding the rules for initiation of translation enables understanding of human diseases in which the expression of a critical gene is reduced by mutations that add upstream AUG codons or change the context around the AUG(START) codon. The opposite problem occurs in the case of hereditary thrombocythemia: translational efficiency is increased by mutations that remove or restructure a small upstream open reading frame in thrombopoietin mRNA, and the resulting overproduction of the cytokine causes the disease. This and other examples support the idea that 5' leader sequences are sometimes structured deliberately in a way that constrains scanning in order to prevent harmful overproduction of potent regulatory proteins. The accumulated evidence reveals how the scanning mechanism dictates the pattern of transcription--forcing production of monocistronic mRNAs--and the pattern of translation of eukaryotic cellular and viral genes.

Tissue-specific silencing of a transgene in rice

In a transgenic rice line, a beta-glucuronidase reporter gene under the control of the rice tungro bacilliform virus promoter became gradually methylated, and gene activity was lost concomitantly. Methylation was observed only in the homozygous offspring and was initially restricted to the promoter region and accompanied by loss of expression in the vascular bundle tissue only. This expression pattern was similar to that of a promoter with a deletion of a vascular bundle expression element. The gene activity could be reestablished by treatment with 5-azacytidine. Methylation per se did not inhibit the binding to the promoter region of protein factors which also bound to the unmethylated sequence. Instead, promoter methylation enabled the alternative binding of a protein with specificity for sequence and methylation. In further generations of homozygous offspring the methylation spread into the transcribed region and gene activity was completely repressed also in nonvascular cells. The results indicate that different stages are involved in DNA methylation-correlated gene inactivation, and that at least one of them may involve the attraction of a sequence and methylation-specific DNA-binding protein.

Contribution of downstream promoter elements to transcriptional regulation of the rice tungro bacilliform virus promoter

Downstream sequences influence activity of the rice tungro bacilliform virus (RTBV) promoter in protoplasts derived from cultured rice cells. We previously identified a DNA element located between positions +50 and +90 relative to the transcription start site to which rice nuclear proteins bind. In this study, using DNA UV crosslinking assays, we show that two rice nuclear proteins bind specifically to this DNA element. We demonstrate that the DNA element enhances RTBV promoter activity in a copy number-dependent manner when transferred to a position upstream of the promoter. In addition, using electrophoretic mobility shift assays, we show that at least two novel nuclear proteins from rice cell suspension cultures bind to a subregion (from +50 to +59) of the DNA element and that a protein from rice root, but not shoot, nuclear extracts interacts with a perfect palindromic sequence motif located within the sequence +45 to +59. Furthermore, a position-dependent GAGA motif, present in three copies within downstream promoter sequences from +1 to +50, is involved in the regulation of RTBV promoter activity.

Viral strategies of translation initiation: ribosomal shunt and reinitiation

Due to the compactness of their genomes, viruses are well suited to the study of basic expression mechanisms, including details of transcription, RNA processing, transport, and translation. In fact, most basic principles of these processes were first described in viral systems. Furthermore, viruses seem not to respect basic rules, and cases of "abnormal" expression strategies are quiet common, although such strategies are usually also finally observed in rare cases of cellular gene expression. Concerning translation, viruses most often violate Kozak's original rule that eukaryotic translation starts from a capped monocistronic mRNA and involves linear scanning to find the first suitable start codon. Thus, many viral cases have been described where translation is initiated from noncapped RNA, using an internal ribosome entry site. This review centers on other viral translation strategies, namely shunting and virus-controlled reinitiation as first described in plant pararetroviruses (Caulimoviridae). In shunting, major parts of a complex leader are bypassed and not melted by scanning ribosomes. In the Caulimoviridae, this process is coupled to reinitiation after translation of a small open reading frame; in other cases, it is possibly initiated upon pausing of the scanning ribosome. Most of the Caulimoviridae produce polycistronic mRNAs. Two basic mechanisms are used for their translation. Alternative translation of the downstream open reading frames in the bacilliform Caulimoviridae occurs by a leaky scanning mechanism, and reinitiation of polycistronic translation in many of the icosahedral Caulimoviridae is enabled by the action of a viral transactivator. Both of these processes are discussed here in detail and compared to related processes in other viruses and cells.

Cloning and sequence analysis of an infectious clone of Citrus yellow mosaic virus that can infect sweet orange via Agrobacterium-mediated inoculation

Citrus yellow mosaic virus (CYMV), a member of the family Caulimoviridae, genus Badnavirus, causes citrus mosaic disease, a disease that occurs commonly in India. The CYMV genome has been cloned and its complete nucleotide sequence determined. Its DNA genome is 7559 bp in length and contains six putative open reading frames (ORFs), all on the plus-strand of the genome and each capable of encoding proteins with a molecular mass of greater than 10 kDa. ORF 3, the largest ORF, encodes a putative polyprotein for functions involved in virus movement, assembly and replication. The other ORFs encode proteins whose exact functions are not completely understood. The genome also contains a plant tRNA(met)-binding site, which may serve as a primer for minus-strand DNA synthesis, in its intergenic region. Phylogenetic analysis of the badnaviruses revealed that CYMV is most closely related to Cacao swollen shoot virus. It was demonstrated that a construct containing 1.4 copies of the cloned CYMV genome could infect sweet orange via Agrobacterium-mediated inoculation.

Polyadenylation in rice tungro bacilliform virus: cis-acting signals and regulation

The polyadenylation signal of rice tungro bacilliform virus (RTBV) was characterized by mutational and deletion analysis. The cis-acting signals required to direct polyadenylation conformed to what is known for plant poly(A) signals in general and were very similar to those of the related cauliflower mosaic virus. Processing was directed by a canonical AAUAAA poly(A) signal, an upstream UG-rich region considerably enhanced processing efficiency, and sequences downstream of the cleavage site were not required. When present at the end of a transcription unit, the cis-acting signals for 3'-end processing were highly efficient in both monocot (rice) and dicot (Nicotiana plumbaginifolia) protoplasts. In a promoter-proximal position, as in the viral genome, the signal was also efficiently processed in rice protoplasts, giving rise to an abundant "short-stop" (SS-) RNA. The proportion of SS-RNA was considerably lower in N. plumbaginifolia protoplasts. In infected plants, SS-RNA was hardly detectable, suggesting either that SS-RNA is unstable in infected plants or that read-through of the promoter-proximal poly(A) site is very efficient. SS-RNA is readily detectable in transgenic rice plants (A. Klöti, C. Henrich, S. Bieri, X. He, G. Chen, P. K. Burkhardt, J. Wünn, P. Lucca, T. Hohn, I. Potrylus, and J. Fütterer, 1999. Plant Mol. Biol. 40:249-266), thus the absence of SS-RNA in infected plants can be attributed to poly(A) site bypass in the viral context to ensure production of the full-length pregenomic viral RNA. RTBV poly(A) site suppression thus depends both on context and the expression system; our results suggest that the circular viral minichromosome directs assembly of a transcription-processing complex with specific properties to effect read-through of the promoter-proximal poly(A) signal.

Genetic Diversity Among Banana streak virus Isolates from Australia

ABSTRACT Banana streak virus (BSV) is an important pathogen of bananas and plantains (Musa spp.) throughout the world. We have cloned and sequenced part of the genomes of four isolates of BSV from Australia, designated BSV-RD, BSV-Cav, BSV-Mys, and BSV-GF. These isolates originated from banana cvs. Red Dacca, Williams, Mysore, and Goldfinger, respectively. All clones contained a sequence covering part of open reading frame III and the intergenic region of the badnavirus genome. The sequences were compared with those of other badnaviruses, including BSV-Onne, a previously characterized isolate from Nigeria. The BSV-RD sequence was virtually identical to that of BSV-Onne, differing by only two nucleotides over 1,292 bp. However, BSV-Cav, -Mys, and -GF were divergent in nucleotide sequence. Phylogenetic analyses using conserved sequences in the ribonuclease H domain revealed that all BSV isolates were more closely related to each other than to any other badnavirus. BSV-Cav was most closely related to BSV-Onne, and there was 95.1% identity between the two amino acid sequences. Other relationships between the BSV isolates were less similar, with sequence identities ranging from 66.4 to 78.2%, which is a magnitude comparable to the distance between some of the recognized badnavirus species. Immunocapture-polymerase chain reaction assays have been developed, allowing specific detection and differentiation of the four isolates of BSV.

The rice tungro bacilliform virus gene II product interacts with the coat protein domain of the viral gene III polyprotein

Rice tungro bacilliform virus (RTBV) is a plant pararetrovirus whose DNA genome contains four genes encoding three proteins and a large polyprotein. The function of most of the viral proteins is still unknown. To investigate the role of the gene II product (P2), we searched for interactions between this protein and other RTBV proteins. P2 was shown to interact with the coat protein (CP) domain of the viral gene III polyprotein (P3) both in the yeast two-hybrid system and in vitro. Domains involved in the P2-CP association have been identified and mapped on both proteins. To determine the importance of this interaction for viral multiplication, the infectivity of RTBV gene II mutants was investigated by agroinoculation of rice plants. The results showed that virus viability correlates with the ability of P2 to interact with the CP domain of P3. This study suggests that P2 could participate in RTBV capsid assembly.

A gene cluster encoded by panicum mosaic virus is associated with virus movement

A subgenomic RNA (sgRNA) of about 1500 nucleotides has been detected in millet plants and protoplasts infected with panicum mosaic virus (PMV). This sgRNA expressed p8, p6.6, p15, and the 26-kDa capsid protein (CP) genes during in vitro translation assays, as determined by using mutants inactivated for expression of each open reading frame. Abolishing expression of p8 and p6.6, the two 5'-proximal genes on the sgRNA, did not affect the replication of PMV in millet protoplasts, but obstructed spread in plants. As predicted for a typical cell-to-cell movement protein, p8 localized to the cell wall fraction of PMV-infected millet plants. The introduction of premature stop codons downstream of the PMV p15 start codon (p15*) abolished infectivity in planta, but did not impair replication in protoplasts. However, a delayed systemic infection in millet plants was supported by the p15aug(-) start codon mutant, which may reflect very low levels of expression from a suboptimal start codon context and/or leaky scanning to a second inframe AUG codon to express the C-terminal portion of the 15-kDa protein. PMV CP mutants had little effect on sgRNA accumulation, but were correlated with a reduction of the gRNA and the decreased expression of the 8-kDa protein in protoplasts as well as abolishment of cell-to-cell spread in plants. These results imply that the successful establishment of a PMV systemic infection in millet host plants appears to be dependent on the concerted expression of the p8, p6.6, p15, and CP genes.

Expression of the Totivirus Helminthosporium victoriae 190S virus RNA-dependent RNA polymerase from its downstream open reading frame in dicistronic constructs

The undivided double-stranded RNA (dsRNA) genome of Helminthosporium victoriae 190S virus (Hv190SV) (genus Totivirus) consists of two large overlapping open reading frames (ORFs). The 5'-proximal ORF encodes a capsid protein (CP), and the downstream, 3'-proximal ORF encodes an RNA-dependent RNA polymerase (RDRP). Unlike the RDRPs of some other totiviruses, which are expressed as a CP-RDRP (Gag-Pol-like) fusion protein, the Hv190SV RDRP is detected only as a separate, nonfused polypeptide. In this study, we examined the expression of the RDRP ORF fused in frame to the coding sequence of the green fluorescent protein (GFP) in bacteria and Schizosaccharomyces pombe cells. The GFP fusions were readily detected in bacteria transformed with the monocistronic construct RDRP:GFP; expression of the downstream RDRP:GFP from the dicistronic construct CP-RDRP:GFP could not be detected. However, fluorescence microscopy and Western blot analysis indicated that RDRP:GFP was expressed at low levels from its downstream ORF in the dicistronic construct in S. pombe cells. No evidence that the RDRP ORF was expressed from a transcript shorter than the full-length dicistronic mRNA was found. A coupled termination-reinitiation mechanism that requires host or eukaryotic cell factors is proposed for the expression of Hv190SV RDRP.

A short open reading frame terminating in front of a stable hairpin is the conserved feature in pregenomic RNA leaders of plant pararetroviruses

In plant pararetroviruses, pregenomic RNA (pgRNA) directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis, the 14 plant pararetroviruses sequenced so far were compared with respect to structural organization of their pgRNA 5'-leader. The results revealed that the pgRNA of all these viruses carries a long leader sequence containing several short ORFs and having the potential to form a large stem-loop structure; both features are known to be inhibitory for downstream translation. Formation of the structure brings the first long ORF into the close spatial vicinity of a 5'-proximal short ORF that terminates 5 to 10 nt upstream of the stable structural element. The first long ORF on the pgRNA is translated by a ribosome shunt mechanism discovered in cauliflower mosaic (CaMV) and rice tungro bacilliform viruses, representing the two major groups of plant pararetroviruses. Both the short ORF and the structure have been implicated in the shunt process for CaMV pgRNA translation. The conservation of these elements among all plant pararetroviruses suggests conservation of the ribosome shunt mechanism. For some of the less well-studied viruses, the localization of the conserved elements also allowed predictions of the pgRNA promoter region and the translation start site of the first long ORF.

Upstream and downstream sequence elements determine the specificity of the rice tungro bacilliform virus promoter and influence RNA production after transcription initiation

The contribution of sequences upstream and downstream of the transcription start site to the strength and specificity of the promoter of rice tungro bacilliform virus was analysed in transgenic rice plants. The promoter is strongly stimulated by downstream sequences which include an intron and is active in all vascular and epidermal cells. Expression in the vascular tissue requires a promoter element located between -100 and -164 to which protein(s) from rice nuclear extracts bind. Elimination of this region leads to specificity for the epidermis. Due to the presence of a polyadenylation signal in the intron, short-stop RNA is produced from the promoter in addition to full-length primary transcript and its spliced derivatives. The ratio between short-stop RNA and full-length or spliced RNA is determined by upstream promoter sequences, suggesting the assembly of RNA polymerase complexes with different processivity on this promoter.

Cloning and sequence analysis of banana streak virus DNA

Banana streak virus (BSV), a member of the Badnavirus group of plant viruses, causes severe problems in banana cultivation, reducing fruit yield and restricting plant breeding and the movement of germplasm. Current detection methods are relatively insensitive. In order to develop a PCR-based diagnostic method that is both reliable and sensitive, the genome of a Nigerian isolate of BSV has been sequenced and shown to comprise 7389 bp and to be organized in a manner characteristic of badnaviruses. Comparison of this sequence with those of other badnaviruses showed that BSV is a distinct virus. PCR with primers based on sequence data indicated that BSV sequences are present in the banana genome.

The 105-kDa polyprotein of southern bean mosaic virus is translated by scanning ribosomes

The cowpea strain of southern bean mosaic virus (SBMV-C) is a positive-sense RNA virus. Three open reading frames (ORF-1, ORF2, and ORF3) are expressed from the genomic RNA. The ORF1 and ORF2 initiation codons are located at nucleotide (nt) positions 49 and 570, respectively. ORF1 is expressed by a 5' end-dependent scanning mechanism, but it is not known how ribosomes gain access to the ORF2 initiation codon. In experiments described here, it was demonstrated that the translation of ORF2 was sensitive to cap analog in a cell-free extract. In vitro and in vivo studies showed that the addition of one or more AUG codons between the 5' end of the SBMV-C RNA and the ORF2 initiation codon reduced ORF2 expression and that elimination of the ORF1 initiation codon increased ORF2 expression. Altering the sequence context of the ORF1 initiation codon to one more favorable for translation initiation also reduced ORF2 expression in vivo. Nucleotide deletions and insertions between SBMV-C nt 218-520 did not abolish ORF2 expression. In most cases, these mutations resulted in reduced expression of both ORF1 and ORF2. These results are consistent with translation of ORF2 by leaky scanning.