Distinct viral sequence elements are necessary for expression of Tomato golden mosaic virus complementary sense transcripts that direct AL2 and AL3 gene expression

Complementary-sense gene regulation in beet curly top virus-SpCT

A 278-bp region upstream of the beet curly top virus-SpCT (BCTV-SpCT) C2/C3 genes is necessary for promoter activity and exhibits significant sequence similarity to AL2/3 promoter sequences in tomato golden mosaic virus (TGMV). Maximal expression of the downstream C2/3 genes in BCTV-SpCT requires the presence of the C1 protein, which is supported by observations that mutation of the initiator codon for C1 results in decreased C2/C3 expression. This is similar to TGMV and cabbage leaf curl virus, where AL1 is required for maximal AL2/3 expression. Together, these data suggest a common strategy for complementary-sense gene regulation amongst curtoviruses and begomoviruses.

Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection

Histone posttranslational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus Cabbage leaf curl virus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 (EML1) and EML3, which contain Tudor-like Agenet domains predictive of histone PTM binding function. Here, we show that mutant Arabidopsis plants exhibit contrasting hypersusceptible (eml1) and tolerant (eml3) responses to CaLCuV infection and that EML1 deficiency correlates with RNA polymerase II (Pol II) enrichment on viral chromatin and upregulated viral gene expression. Consistent with reader activity, EML1 and EML3 associate with nucleosomes and with CaLCuV chromatin, suggesting a direct impact on pathogenesis. We also demonstrate that EML1 and EML3 bind peptides containing histone H3 lysine 36 (H3K36), a PTM usually associated with active gene expression. The interaction encompasses multiple H3K36 PTMs, including methylation and acetylation, suggesting nuanced regulation. Furthermore, EML1 and EML3 associate with similar regions of viral chromatin, implying possible competition between the two readers. Regions of EML1 and EML3 association correlate with sites of trimethylated H3K36 (H3K36me3) enrichment, consistent with regulation of geminivirus chromatin by direct EML targeting.IMPORTANCE Histone PTMs convey information that regulates chromatin compaction and DNA accessibility. Histone reader proteins bind specific PTMs and translate their effects by modifying chromatin and/or by recruiting effectors that alter chromatin structure or activity. In this study, CaLCuV was used to characterize the activities of two Arabidopsis Agenet domain histone readers, EML1 and EML3. We show that eml1 mutants are hypersusceptible to CaLCuV, whereas eml3 plants are more tolerant of infection than wild-type plants. We also demonstrate that EML1 and EML3 associate with histones and viral chromatin in planta and that both proteins bind peptides containing H3K36, a PTM associated with active gene expression. Consistent with antiviral activity, EML1 suppresses CaLCuV gene expression and reduces Pol II access to viral chromatin. By linking EML1 and EML3 to pathogenesis, these studies have expanded our knowledge of histone reader proteins and uncovered an additional level of viral chromatin regulation.

Arabidopsis Histone Reader EMSY-LIKE 1 Binds H3K36 and Suppresses Geminivirus Infection

Histone posttranslational modifications (PTMs) impart information that regulates chromatin structure and activity. Their effects are mediated by histone reader proteins that bind specific PTMs to modify chromatin and/or recruit appropriate effectors to alter the chromatin landscape. Despite their crucial juxtaposition between information and functional outcome, relatively few plant histone readers have been identified, and nothing is known about their impact on viral chromatin and pathogenesis. We used the geminivirus Cabbage leaf curl virus (CaLCuV) as a model to functionally characterize two recently identified reader proteins, EMSY-LIKE 1 (EML1) and EML3, which contain Tudor-like Agenet domains predictive of histone PTM binding function. Here, we show that mutant Arabidopsis plants exhibit contrasting hypersusceptible (eml1) and tolerant (eml3) responses to CaLCuV infection and that EML1 deficiency correlates with RNA polymerase II (Pol II) enrichment on viral chromatin and upregulated viral gene expression. Consistent with reader activity, EML1 and EML3 associate with nucleosomes and with CaLCuV chromatin, suggesting a direct impact on pathogenesis. We also demonstrate that EML1 and EML3 bind peptides containing histone H3 lysine 36 (H3K36), a PTM usually associated with active gene expression. The interaction encompasses multiple H3K36 PTMs, including methylation and acetylation, suggesting nuanced regulation. Furthermore, EML1 and EML3 associate with similar regions of viral chromatin, implying possible competition between the two readers. Regions of EML1 and EML3 association correlate with sites of trimethylated H3K36 (H3K36me3) enrichment, consistent with regulation of geminivirus chromatin by direct EML targeting.IMPORTANCE Histone PTMs convey information that regulates chromatin compaction and DNA accessibility. Histone reader proteins bind specific PTMs and translate their effects by modifying chromatin and/or by recruiting effectors that alter chromatin structure or activity. In this study, CaLCuV was used to characterize the activities of two Arabidopsis Agenet domain histone readers, EML1 and EML3. We show that eml1 mutants are hypersusceptible to CaLCuV, whereas eml3 plants are more tolerant of infection than wild-type plants. We also demonstrate that EML1 and EML3 associate with histones and viral chromatin in planta and that both proteins bind peptides containing H3K36, a PTM associated with active gene expression. Consistent with antiviral activity, EML1 suppresses CaLCuV gene expression and reduces Pol II access to viral chromatin. By linking EML1 and EML3 to pathogenesis, these studies have expanded our knowledge of histone reader proteins and uncovered an additional level of viral chromatin regulation.

Interaction between the transcription factor AtTIFY4B and begomovirus AL2 protein impacts pathogenicity

The begomovirus AL2 protein is a transcriptional activator, a silencing suppressor, and inhibitor of basal defense. AL2 forms a complex at the CP promoter, through interaction with a plant-specific DNA-binding protein, Arabidopsis PEAPOD2 (also known as TIFY4B). AtTIFY4B has three domains (PPD, TIFY and CCT_2) conserved between homologs from different plant species. We confirmed that the AL2 protein from Tomato golden mosaic virus and Cabbage leaf curl virus interacts with TIFY4B from Arabidopsis, tomato and Nicotiana benthamiana in the nucleus of plant cells. Bimolecular Fluorescence Complementation demonstrated that the interaction involves both the TIFY and CCT_2 domains. Surprisingly, amino acids 84-150 can prevent AtTIFY4B from localizing to the nucleus, and interaction with AL2 results in some of the protein re-entering the nucleus. When AtTIFY4B is over-expressed, we observe an increase in mean latent period, where systemic symptoms are detected on average, 4 days later than in mock treated plants. This appears to be a consequence of reduced viral DNA titers, possibly related to the role of TIFY4B in cell cycle arrest. Our results point to a potential role for TIFY4B in host defense against geminiviruses. Expression of TIFY4B in N. benthamiana increases in response to geminivirus infection, which would result in suppression of proliferation, reducing viral replication. Geminiviruses may counter this defense response through an interaction between AL2 and TIFY4B, which would inhibit TIY4B function. The consequence of this inhibition would be failure to arrest the cell cycle, providing an environment conducive for geminivirus replication.

Transcript mapping of Cotton leaf curl Burewala virus and its cognate betasatellite, Cotton leaf curl Multan betasatellite

BACKGROUND

Whitefly-transmitted geminiviruses (family Geminiviridae, genus Begomovirus) are major limiting factors for the production of numerous dicotyledonous crops throughout the warmer regions of the world. In the Old World a small number of begomoviruses have genomes consisting of two components whereas the majority have single-component genomes. Most of the monopartite begomoviruses associate with satellite DNA molecules, the most important of which are the betasatellites. Cotton leaf curl disease (CLCuD) is one of the major problems for cotton production on the Indian sub-continent. Across Pakistan, CLCuD is currently associated with a single begomovirus (Cotton leaf curl Burewala virus [CLCuBuV]) and the cotton-specific betasatellite Cotton leaf curl Multan betasatellite (CLCuMuB), both of which have recombinant origins. Surprisingly, CLCuBuV lacks C2, one of the genes present in all previously characterized begomoviruses. Virus-specific transcripts have only been mapped for few begomoviruses, including one monopartite begomovirus that does not associate with betasatellites. Similarly, the transcripts of only two betasatellites have been mapped so far. The study described has investigated whether the recombination/mutation events involved in the evolution of CLCuBuV and its associated CLCuMuB have affected their transcription strategies.

RESULTS

The major transcripts of CLCuBuV and its associated betasatellite (CLCuMuB) from infected Nicotiana benthamiana plants have been determined. Two complementary-sense transcripts of ~1.7 and ~0.7 kb were identified for CLCuBuV. The ~1.7 kb transcript appears similar in position and size to that of several begomoviruses and likely directs the translation of C1 and C4 proteins. Both complementary-sense transcripts can potentially direct the translation of C2 and C3 proteins. A single virion-sense transcript of ~1 kb, suitable for translation of the V1 and V2 genes was identified. A predominant complementary-sense transcript was also confirmed for the betasatellite.

CONCLUSIONS

Overall, the transcription of CLCuBuV and the recombinant CLCuMuB is equivalent to earlier mapped begomoviruses/betasatellites. The recombination events that featured in the origins of these components had no detectable effects on transcription. The transcripts spanning the mutated C2 gene showed no evidence for involvement of splicing in restoring the ability to express intact C2 protein.

Characterization of sequence elements from Malvastrum yellow vein betasatellite regulating promoter activity and DNA replication

BACKGROUND

Many monopartite begomoviruses are associated with betasatellites, but only several promoters from which were isolated and studied. In this study, the βC1 promoter from Malvastrum yellow vein betasatellite (MYVB) was characterized and important sequence elements were identified to modulate promoter activity and replication of MYVB.

RESULTS

A 991 nucleotide (nt) fragment upstream of the translation start site of the βC1 open reading frame of MYVB and a series of deletions within this fragment were constructed and fused to the β-glucuronidase (GUS) and green fluorescent protein (GFP) reporter genes, respectively. Agrobacterium-mediated transient expression assays showed that the 991 nt fragment was functional and that a 28 nt region (between -390 nt and -418 nt), which includes a 5'UTR Py-rich stretch motif, was important for promoter activity. Replication assays using Nicotiana benthamiana leaf discs and whole plants showed that deletion of the 5'UTR Py-rich stretch impaired viral satellite replication in the presence of the helper virus. Transgenic assays demonstrated that the 991 nt fragment conferred a constitutive expression pattern in transgenic tobacco plants and that a 214 nt fragment at the 3'-end of this sequence was sufficient to drive this expression pattern.

CONCLUSION

Our results showed that the βC1 promoter of MYVB displayed a constitutive expression pattern and a 5'UTR Py-rich stretch motif regulated both βC1 promoter activity and MYVB replication.

Sequences within the Spinach curly top virus virion sense promoter are necessary for vascular-specific expression of virion sense genes

Sequences necessary for activity of the Spinach curly top virus virion sense promoter have been identified within an 84 bp region upstream of two transcription start sites located at nt 252 and 292. RNAs initiating at these sites are expressed at equivalent levels in SCTV-infected Arabidopsis and from promoter-reporter constructs. The promoter is capable of directing expression of all three virion sense genes, although not to the same degree. While CP and V3 expression are similar, expression of V2 is elevated. The promoter is active in transient leaf infusion assays in the absence of C2. In Nicotiana benthamiana plants the promoter is active in vascular tissue and under no conditions did we detect promoter activity in the mesophyll. This is in contrast to begomoviruses where the virion sense promoter is dependent on AL2, a positional homolog of C2, and the promoter is functional in both vascular and mesophyll tissue.

Suppression of methylation-mediated transcriptional gene silencing by βC1-SAHH protein interaction during geminivirus-betasatellite infection

DNA methylation is a fundamental epigenetic modification that regulates gene expression and represses endogenous transposons and invading DNA viruses. As a counter-defense, the geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a betasatellite called DNA β. This study presents evidence that suppression of methylation-mediated TGS by the sole betasatellite-encoded protein, βC1, is crucial to the association of Tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB). We show that TYLCCNB complements Beet curly top virus (BCTV) L2^- mutants deficient for methylation inhibition and TGS suppression, and that cytosine methylation levels in BCTV and TYLCCNV genomes, as well as the host genome, are substantially reduced by TYLCCNB or βC1 expression. We also demonstrate that while TYLCCNB or βC1 expression can reverse TGS, TYLCCNV by itself is ineffective. Thus its AC2/AL2 protein, known to have suppression activity in other geminiviruses, is likely a natural mutant in this respect. A yeast two-hybrid screen of candidate proteins, followed by bimolecular fluorescence complementation analysis, revealed that βC1 interacts with S-adenosyl homocysteine hydrolase (SAHH), a methyl cycle enzyme required for TGS. We further demonstrate that βC1 protein inhibits SAHH activity in vitro. That βC1 and other geminivirus proteins target the methyl cycle suggests that limiting its product, S-adenosyl methionine, may be a common viral strategy for methylation interference. We propose that inhibition of methylation and TGS by βC1 stabilizes geminivirus/betasatellite complexes.

Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses, and geminiviruses respond by elaborating proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a satellite called DNA β (betasatellite), which depends on the helper virus for replication and spread within and between hosts. In return, the sole betasatellite encoded protein, βC1, encodes a pathogenicity factor that enhances viral replication and is responsible for inducing disease symptoms. Geminivirus/betasatellite complexes are common and cause significant losses of food and fiber crops. Here, we explore the molecular basis of the association between Tomato yellow leaf curl China virus (TYLCCNV) and its betasatellite (TYLCCNB). We show that TYLCCNV by itself is unable to reverse TGS. However, co-inoculation of TYLCCNB, or expression of βC1 protein, results in reduced methylation of both the helper virus and host genome, and reversal of TGS directed against a transgene and an endogenous locus. We also present evidence that βC1 accomplishes this by interacting with and inhibiting the activity of S-adenosyl homocysteine hydrolase (SAHH), an enzyme needed to maintain the methyl cycle that generates the methyltransferase co-factor S-adenosyl methionine. Thus, we propose that inhibition of methylation-mediated TGS by βC1 drives geminivirus/betasatellite association.

Regulation of Tomato golden mosaic virus AL2 and AL3 gene expression by a conserved upstream open reading frame

A translational regulatory mechanism for Tomato golden mosaic virus (TGMV) complementary-sense gene expression has been characterized. TGMV transcribes two mRNAs, AL-1935 and AL-1629 transcripts, both of which contain the AL2 and AL3 open reading frames. However, AL2 is only expressed from AL-1629 whereas AL3 is expressed from both. Three AUG translation initiation codons are located upstream of both the AL2 and AL3 coding regions, within the 5'-untranslated region (UTR) of the AL-1935 transcript. Translation can initiate at the first AUG, specifying the C-terminal 122 amino acids of the AL1 protein (cAL1). Initiation of translation at this AUG is inhibitory for the downstream expression of both AL2 and AL3. This is most likely due to the terminator codon of cAL1 being positioned after the AUG initiation codon for the AL2 ORF. The mechanism by which AL3 is expressed from AL-1935 is currently unknown but a gap between the cAL1 termination codon and the start of AL3 suggests that it may involve reinitiation and/or internal initiation. In contrast, expression of AL3 from AL-1629 most likely occurs via leaky ribosome scanning since the AL3 initiation codon occurs before the terminator codon of AL2. Mutation of the AUG encoding cAL1 in the curtovirus, Spinach curly top virus, leads to increased infectivity as measured by a shorter latent period. Together this suggests that geminiviruses use a post-translational regulatory mechanism to regulate the synthesis of viral proteins important for replication and suppression of host defenses.

Geminiviruses

Plant pathogenic geminiviruses have been proliferating worldwide and have, therefore, attracted considerable scientific interest during the past three decades. Current knowledge concerning their virion and genome structure, their molecular biology of replication, recombination, transcription, and silencing, as well as their transport through plants and dynamic competition with host responses are summarized. The topics are chosen to provide a comprehensive introduction for animal virologists, emphasizing similarities and differences to the closest functional relatives, polyomaviruses and circoviruses.

Identification of sequence elements regulating promoter activity and replication of a monopartite begomovirus-associated DNA beta satellite

DNA beta is a circular single-stranded satellite DNA associated with certain monopartite begomoviruses (family Geminiviridae) which causes economically important diseases such as cotton leaf curl disease. DNA beta contains a single gene, betaC1, which encodes a pathogenicity protein responsible for symptom production. Transient expression studies in Nicotiana tabacum using the beta-glucuronidase reporter gene driven by a betaC1 promoter-deletion series of the DNA beta associated with cotton leaf curl Multan virus identified a 68 nt region (between -139 and -207) which is important for betaC1 transcription. This 68 nt region contains a G-box (CACGTG) located 143 nt upstream of the betaC1 start codon. Mutation of the G-box resulted in a significant reduction in betaC1 promoter activity and DNA beta replication efficiency. In addition, the G-box motif was found to bind specifically to a protein(s) in nuclear extracts prepared from tobacco leaf tissues. Our results indicate that interaction of the G-box motif with host nuclear factors is important for efficient gene expression and replication of DNA beta.

Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen

Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these - MSV-A - causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the 'grass-adapted' MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.

Functional analysis of bipartite begomovirus coat protein promoter sequences

We demonstrate that the AL2 gene of Cabbage leaf curl virus (CaLCuV) activates the CP promoter in mesophyll and acts to derepress the promoter in vascular tissue, similar to that observed for Tomato golden mosaic virus (TGMV). Binding studies indicate that sequences mediating repression and activation of the TGMV and CaLCuV CP promoter specifically bind different nuclear factors common to Nicotiana benthamiana, spinach and tomato. However, chromatin immunoprecipitation demonstrates that TGMV AL2 can interact with both sequences independently. Binding of nuclear protein(s) from different crop species to viral sequences conserved in both bipartite and monopartite begomoviruses, including TGMV, CaLCuV, Pepper golden mosaic virus and Tomato yellow leaf curl virus suggests that bipartite begomoviruses bind common host factors to regulate the CP promoter. This is consistent with a model in which AL2 interacts with different components of the cellular transcription machinery that bind viral sequences important for repression and activation of begomovirus CP promoters.

Early and late gene expression in pepper huasteco yellow vein virus

Viral infections usually take place in an orderly manner and can be divided into at least two phases: an early and a late stage. In geminiviruses, plant viruses with a circular, single-stranded DNA genome, expression of viral genes involves complex regulation strategies that suggest the existence of a pattern of temporal gene expression. In this work, the transcription of pepper huasteco yellow vein virus (PHYVV) genes was studied. Green fluorescent protein replacements and RT-PCR analyses were used to monitor PHYVV gene expression chronologically in suspension cells and plant tissue. A model is proposed to describe the order of geminivirus gene expression, where the genes that encode Rep, TrAP and REn are expressed during an early stage of infection. The genes that encode the coat protein and the nuclear shuttle protein are expressed during the late stage of infection.

A conserved binding site within the Tomato golden mosaic virus AL-1629 promoter is necessary for expression of viral genes important for pathogenesis

We have identified a nine base pair sequence in Tomato golden mosaic virus that is required for binding of nuclear proteins from tobacco and Arabidopsis to viral DNA. The sequence is located within the promoter for a 0.7 kb complementary sense mRNA (AL-1629). Mutation of the binding site results in a two- to six-fold reduction in the accumulation of AL-1629 mRNA, leading to reduced AL2 and AL3 gene expression. Viral sequences located immediately adjacent to the core binding site appear to influence AL2 and AL3 expression, but retain some binding affinity to a soluble host protein(s). The ability of a nuclear protein(s) to bind sequences within the AL-1629 promoter correlates with efficient viral DNA replication, as mutation of these sequences results in reduced viral DNA levels. Analysis of begomo- and curtoviruses indicates extensive conservation of this binding site, which suggests a common mechanism regulating expression of two viral genes involved in replication and suppression of host defense responses.

AL1-dependent repression of transcription enhances expression of Tomato golden mosaic virus AL2 and AL3

Studies using Nicotiana benthamiana protoplasts have determined that repression of upstream transcription by AL1 protein enhances AL2 and AL3 expression in Tomato golden mosaic virus (TGMV). Mutations resulting in the inability of TGMV AL1 protein to associate with its cognate binding site, result in a decrease in both AL2 and AL3 expression. Reduced expression correlates with an increase in transcription from the AL62 start site, and decreased transcription from downstream initiation sites (AL1935 and AL1629) present within the AL1 coding region. The results demonstrate that, in a tobacco protoplast system, repression of AL62 transcription, regulated through binding of AL1 protein to sequences in the origin of replication, is required prior to AL2 and AL3 gene expression from the AL1935 and AL1629 viral transcripts. This provides a mechanism to regulate expression of AL2, which is involved in suppression of host defense responses and is required for late gene expression.

PSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interactions

Plant functional proteomics research is increasingly dependent upon vectors that facilitate high-throughput gene cloning and expression of fusions to autofluorescent proteins. Here, we describe the pSITE family of plasmids, a new set of Agrobacterium binary vectors, suitable for the stable integration or transient expression of various autofluorescent protein fusions in plant cells. The pSITE vectors permit single-step Gateway-mediated recombination cloning for construction of binary vectors that can be used directly in transient expression studies or for the selection of transgenic plants on media containing kanamycin. These vectors can be used to express native proteins or fusions to monmeric red fluorescent protein or the enhanced green fluorescent protein and its cyan and yellow-shifted spectral variants. We have validated the vectors for use in transient expression assays and for the generation of transgenic plants. Additionally, we have generated markers for fluorescent highlighting of actin filaments, chromatin, endoplasmic reticulum, and nucleoli. Finally, we show that pSITE vectors can be used for targeted gene expression in virus-infected cells, which should facilitate high-throughput characterization of protein dynamics in host-virus interactions.