Characterization of DNAbeta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A

Molecular characterization and pathogenicity of a novel monopartite geminivirus infecting tobacco in China

The occurrence of geminiviruses causes significant economic losses in many economically important crops. In this study, a novel geminivirus isolated from tobacco in Sichuan province of China, named tomato leaf curl Chuxiong virus (TLCCxV), was characterized by small RNA-based deep sequencing. The full-length of TLCCxV genome was determined to be 2744 nucleotides (nt) encoding six open reading frames. Phylogenetic and genome-wide pairwise identity analysis revealed that TLCCxV shared less than 91% identities with reported geminiviruses. A TLCCxV infectious clone was constructed and successfully infected Nicotiana benthamiana, N. tabacum, N. glutinosa, Solanum lycopersicum and Petunia hybrida plants. Furthermore, expression of the V2, C1 and C4 proteins through a potato virus X vector caused severe chlorosis or necrosis symptom in N. benthamiana. Taken together, we identified a new geminivirus in tobacco plants, and found that V2, C1 and C4 contribute to symptom development.

Distinct tomato yellow leaf curl Chuxiong virus isolated from whiteflies and plants in China and its symptom determinant and suppressor of post-transcriptional gene silencing

A begomovirus isolated from whiteflies (Bemisia tabaci) and tomato, sweet potato in China was found to be representative of a distinct begomovirus species, for which the name tomato yellow leaf curl Chuxiong virus (TYLCCxV) is proposed. The results of genomic identification and sequence comparison showed that TYLCCxV shares the highest complete nucleotide sequence identity (88.3%) with croton yellow vein mosaic virus (CroYVMV), and may have originated from the recombination between synedrella leaf curl virus (SyLCV) and squash leaf curl Yunnan virus (SLCuYV). Agrobacterium-mediated inoculation showed that TYLCCxV is highly infectious for a range of plant species, producing upward leaf curling, leaf crumpling, chlorosis, distortion, and stunt symptoms in Solanum lycopersicum plants. The results of Southern blot indicated that TYLCCxV is capable of efficiently replicating two heterologous betasatellites. The inoculation of PVX::C4 on Nicotiana benthamiana induced upward leaf curling and stem elongation symptoms, suggesting that TYLCCxV C4 functions as a symptom determinant. TYLCCxV V2 is an important virulence factor that induces downward leaf curling symptoms, elicits systemic necrosis, and suppresses local and systemic GFP silencing in co-agroinfiltrated N. benthamiana and transgenic 16c plants. Considering the multifunctional virulence proteins V2 and C4, the possibility of TYLCCxV causing devastating epidemics on tomato in China is discussed.

A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus

Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.

First report of Ageratum yellow vein virus infecting papaya in Lampung, Indonesia

BACKGROUND

Papaya (Carica papaya) is a tropical fruit of great economic and nutritional importance, loved for its sweet and delicious flesh. However, papaya cultivation faces serious challenges in the form of Begomovirus attacks. Begomoviruses are a group of viruses that pose a serious threat to plants worldwide. Including papaya, Begomovirus has become a significant threat to papaya production in various parts of the world and has been identified in several regions in Indonesia.

METHODS

DNA was extracted from seven samples representing different papaya growing areas using a Plant Genomic DNA Mini Kit. Genomic DNA from the samples was subjected to PCR using universal primers of AC2, AC1, SPG1 and SPG2. The PCR products then sequenced using the dideoxy (Sanger) approach. The obtained sequence then compared to the gene bank using BLAST software available at NCBI. Multiple sequence alignment and phylogenetic tree construction were analyzed using the MEGA11 program.

RESULTS

Detection based on viral nucleic acid in papaya plants in Pesawaran, Lampung Province with seven sampling points using universal primers SPG1/SPG2 showed positive results for Begomovirus infection with visible DNA bands measuring ± 900 bp. Direct nucleotide sequencing using SPG1/SPG2 primers for the AC2 and AC1 genes of the Begomovirus and confirmed by the BLAST program showed that papaya samples were infected with Ageratum yellow vein virus (AYVV). The phylogenetic results show that AYVV from papaya samples has a close relationship with the AYVV group from several other countries, with 98% homology.

CONCLUSION

In the papaya cultivation area in Pesawaran, Lampung province, it was identified as Begomovirus, Ageratum yellow vein virus (AYVV) species and is closely related to the AYVV group from several other countries. Overall, our study further suggests that Ageratum acts as an alternative host and reservoir for Begomovirus.

Two genes encoded by mulberry crinkle leaf virus (MCLV): The V4 gene enhances viral replication, and the V5 gene is needed for MCLV infection in Nicotiana benthamiana

Mulberry crinkle leaf virus (MCLV) is a member of the genus Mulcrilevirus, family Geminiviridae. The expression and functions of the V4 and V5 genes encoded by the MCLV genome remain unknown. Here, we confirmed the expression of V4 and V5 by analyzing the V4 and V5 mRNAs and the promoter activity of individual ORFs upstream sequences. The functions of V4 and V5 were investigated by constructing Agrobacterium-mediated infectious clones of wild-type MCLV variant П (MCLV vII), MCLVwt and MCLV vП mutants, such as MCLVmV4 (start codon of V4 ORF mutated), MCLVdV4 (5'-end partial deletion of V4 ORF sequence) and MCLVmV5 (V5 ORF start codon mutated). Although MCLVwt, MCLVmV4, and MCLVdV4 could infect natural host mulberry and experimental tomato plants systematically, the replication of the MCLVmV4 and MCLVdV4 genomes was obviously reduced compared to MCLVwt in both mulberry and tomato plants. MCLV vП expressing V5 could infect Nicotiana benthamiana plants systematically, but MCLVmV5 could not, implying that V5 is needed for MCLV vП to infect N. benthamiana plants. Taken together, V4 is involved in replication of the MCLV genome in host plants, and V5 potentially might extend the host range. Our findings lay a foundation for in-depth insight into the functions of MCLV-encoded proteins and provide a novel perspective for the subsequent study of MCLV-host plant interactions.

Functional identification of a novel C7 protein of tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is a monopartite geminivirus, and one of the most devastating plant viruses in the world. TYLCV is traditionally known to encode six viral proteins in bidirectional and partially overlapping open reading frames (ORFs). However, recent studies have shown that TYLCV encodes additional small proteins with specific subcellular localizations and potential virulence functions. Here, a novel protein named C7, encoded by a newly-described ORF in the complementary strand, was identified as part of the TYLCV proteome using mass spectrometry. The C7 protein localized to the nucleus and cytoplasm, both in the absence and presence of the virus. C7 was found to interact with two other TYLCV-encoded proteins: with C2 in the nucleus, and with V2 in the cytoplasm, forming conspicuous granules. Mutation of C7 start codon ATG to ACG to block the translation of C7 delayed the onset of viral infection, and the mutant virus caused milder virus symptoms and less accumulations of viral DNAs and proteins. Using the potato virus X (PVX)-based recombinant vector, we found that ectopic overexpression of C7 resulted in more severe mosaic symptoms and promoted a higher accumulation of PVX-encoded coat protein in the late virus infection stage. In addition, C7 was also found to inhibit GFP-induced RNA silencing moderately. This study demonstrates that the novel C7 protein encoded by TYLCV is a pathogenicity factor and a weak RNA silencing suppressor, and that it plays a critical role during TYLCV infection.

ty-5 Confers Broad-Spectrum Resistance to Geminiviruses

The selection of resistant crops is an effective method for controlling geminivirus diseases. ty-5 encodes a messenger RNA surveillance factor Pelota with a single amino acid mutation (PelotaV16G), which confers effective resistance to tomato yellow leaf curl virus (TYLCV). No studies have investigated whether ty-5 confers resistance to other geminiviruses. Here, we demonstrate that the tomato ty-5 line exhibits effective resistance to various geminiviruses. It confers resistance to two representative begomoviruses, tomato yellow leaf curl China virus/tomato yellow leaf curl China betasatellite complex and tomato leaf curl Yunnan virus. The ty-5 line also exhibits partial resistance to a curtovirus beet curly top virus. Importantly, ty-5 confers resistance to TYLCV with a betasatellite. Southern blotting and quantitative polymerase chain reaction analyses showed that significantly less DNA of these geminiviruses accumulated in the ty-5 line than in the susceptible line. Moreover, knockdown of Pelota expression converted a Nicotiana benthamiana plant from a geminivirus-susceptible host to a geminivirus-resistant host. Overall, our findings suggest that ty-5 is an important resistance gene resource for crop breeding to control geminiviruses.

Functional Characterization of Replication-Associated Proteins Encoded by Alphasatellites Identified in Yunnan Province, China

Alphasatellites, which encode only a replication-associated protein (alpha-Rep), are frequently found to be non-essential satellite components associated with begomovirus/betasatellite complexes, and their presence can modulate disease symptoms and/or viral DNA accumulation during infection. Our previous study has shown that there are three types of alphasatellites associated with begomovirus/betasatellite complexes in Yunnan province in China and they encode three corresponding types of alpha-Rep proteins. However, the biological functions of alpha-Reps remain poorly understood. In this study, we investigated the biological functions of alpha-Reps in post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) using 16c and 16-TGS transgenic Nicotiana benthamiana plants. Results showed that all the three types of alpha-Rep proteins were capable of suppressing the PTGS and reversing the TGS. Among them, the alpha-Rep of Y10DNA1 has the strongest PTGS and TGS suppressor activities. We also found that the alpha-Rep proteins were able to increase the accumulation of their helper virus during coinfection. These results suggest that the alpha-Reps may have a role in overcoming host defense, which provides a possible explanation for the selective advantage provided by the association of alphasatellites with begomovirus/betasatellite complexes.

Identification and Functional Analysis of Four RNA Silencing Suppressors in Begomovirus Croton Yellow Vein Mosaic Virus

Croton yellow vein mosaic virus (CYVMV), a species in the genus Begomovirus, is a prolific monopartite begomovirus in the Indian sub-continent. CYVMV infects multiple crop plants to cause leaf curl disease. Plants have developed host RNA silencing mechanisms to defend the threat of viruses, including CYVMV. We characterized four RNA silencing suppressors, namely, V2, C2, and C4 encoded by CYVMV and betasatellite-encoded C1 protein (βC1) encoded by the cognate betasatellite, croton yellow vein betasatellite (CroYVMB). Their silencing suppressor functions were verified by the ability of restoring the β-glucuronidase (GUS) activity suppressed by RNA silencing. We showed here for the first time that V2 was capable of self-interacting, as well as interacting with the V1 protein, and could be translocalized to the plasmodesmata in the presence of CYVMV. The knockout of either V2 or V1 impaired the intercellular mobility of CYVMV, indicating their novel coordinated roles in the cell-to-cell movement of the virus. As pathogenicity determinants, each of V2, C2, and C4 could induce typical leaf curl symptoms in Nicotiana benthamiana plants even under transient expression. Interestingly, the transcripts and proteins of all four suppressors could be detected in the systemically infected leaves with no correlation to symptom induction. Overall, our work identifies four silencing suppressors encoded by CYVMV and its cognate betasatellite and reveals their subcellular localizations, interaction behavior, and roles in symptom induction and intercellular virus movement.

Selective autophagic receptor NbNBR1 prevents NbRFP1-mediated UPS-dependent degradation of βC1 to promote geminivirus infection

Autophagy is an evolutionarily conserved, lysosomal/vacuolar degradation mechanism that targets cell organelles and macromolecules. Autophagy and autophagy-related genes have been studied for their antiviral and pro-viral roles in virus-infected plants. Here, we demonstrate the pro-viral role of a selective autophagic receptor NbNBR1 in geminivirus-infected Nicotiana benthamiana plants. The βC1 protein encoded by tomato yellow leaf curl China betasatellite (TYLCCNB) that is associated with tomato yellow leaf curl China virus (TYLCCNV) enhanced the expression level of NbNBR1. Then NbNBR1 interacted with βC1 to form cytoplasmic granules. Interaction of NbNBR1 with βC1 could prevent degradation of βC1 by the NbRFP1, an E3 ligase. Overexpression of NbNBR1 in N. benthamiana plants increased βC1 accumulation and promoted virus infection. In contrast, silencing or knocking out NbNBR1 expression in N. benthamiana suppressed βC1 accumulation and inhibited virus infection. A single amino acid substitution in βC1 (βC1K4A) abolished its interaction with NbNBR1, leading to a reduced level of βC1K4A. The TYLCCNV/TYLCCNBK4A mutant virus caused milder disease symptoms and accumulated much less viral genomic DNAs in the infected plants. Collectively, the results presented here show how a viral satellite-encoded protein hijacks host autophagic receptor NbNBR1 to form cytoplasmic granules to protect itself from NbRFP1-mediated degradation and facilitate viral infection.

Dynamic Subcellular Localization, Accumulation, and Interactions of Proteins From Tomato Yellow Leaf Curl China Virus and Its Associated Betasatellite

Geminiviruses contain the largest number of species of plant viruses, and cause devastating crop diseases worldwide. The development of resistance to these viruses will require a clear understanding of viral protein function and interactions. Tomato yellow leaf curl China virus (TYLCCNV) is a typical monopartite geminivirus, which is associated with a tomato yellow leaf curl China betasatellite (TYLCCNB) in the field; the complex infection of TYLCCNV/TYLCCNB leads to serious economic losses in solanaceous plants. The functions of each protein encoded by the TYLCCNV/TYLCCNB complex have not yet been examined in a targeted manner. Here, we show the dynamic subcellular localization and accumulation of six viral proteins encoded by TYLCCNV and the βC1 protein encoded by TYLCCNB in plants over time, and analyzed the effect of TYLCCNV or TYLCCNV/TYLCCNB infection on these parameters. The interaction among the seven viral proteins was also tested in this study: C2 acts as a central player in the viral protein interaction network, since it interacts with C3, C4, V2, and βC1. Self-interactions were also found for C1, C2, and V2. Together, the data presented here provide a template for investigating the function of viral proteins with or without viral infection over time, and points at C2 as a pivotal protein potentially playing a central role in the coordination of the viral life cycle.

Tobacco curly shoot virus C3 protein enhances viral replication and gene expression in Nicotiana benthamiana plants

Geminiviruses are single-stranded DNA viruses that cause devastating diseases in many crops worldwide. The replication enhancer proteins (REn), encoded by the C3 (AC3, and AL3) ORFs of geminiviruses, have critical roles in viral DNA accumulation and symptom development in infected plants. In the current study, we have constructed an infectious clone of the Tobacco curly shoot virus (TbCSV) C3 mutant, TbCSVΔC3, that contains two start codon mutations that abrogated C3 ORF expression, but did not alter the amino acid sequence of the C2 ORF. As predicted, the absence of the C3 protein reduced TbCSV DNA accumulation, and over-expression of the C3 protein enhanced TbCSV DNA accumulation in infected leaves of Nicotiana benthamiana. The C3 mutation reduced the expression levels of both virion- and complementary-sense TbCSV genes whereas over-expression of the C3 protein increased TbCSV gene expression. Furthermore, the expression of the wild-type and site-directed mutants of C3 proteins using the potato virus X (PVX) system showed that Y93A mutation reduced the replication enhancement activity of the C3 protein in N. benthamiana. All the available evidence demonstrates that the C3 protein is tightly coupled with TbCSV DNA accumulation. However, the TbCSVΔC3 mutant was nearly as infectious in N. benthamiana as TbCSVWT and only had slightly delayed and attenuated symptom expression. Our findings demonstrate that TbCSV C3 protein enhances viral replication and gene expression, but has only moderate effects on symptom development in N. benthamiana.

Functional analysis of a novel βV1 gene identified in a geminivirus betasatellite

Betasatellites (DNA β) are circular ssDNA molecules that are associated with monopartite geminiviruses and exert a positive effect on the viral infection. Betasatellites encode one protein, named βC1, on the complementary strand; βC1 functions as a pathogenicity factor and RNA silencing suppressor. In this report, we describe the identification of another betasatellite-encoded protein, βVl, which also contributes to symptom development. The βVl open reading frame can be found on the viral strand of approximately 40% of reported betasatellite sequences, and is conserved in position and sequence. The presence of the βVl transcript was observed in plants infected with Tomato yellow leaf curl China virus (TYTCCNV) along with its associated betasatellite Tomato yellow leaf curl China betasatellite (TYTCCNB). Mutant viruses unable to produce βVl showed reduced virulence and decreased viral load. Ectopic expression of the TYTCCNB-PV1 gene in Nicotiana benthamiana plants from a PVX-based vector resulted in leaf mosaic and chlorosis. We further demonstrated that the βVl protein could elicit hypersensitive response (HR)-type cell death in N. benthamiana leaves. Our results uncover a novel betasatellite-encoded protein that contributes to the virus infection, and this discover gives us a more complete view of the plant-geminivirus interaction landscape.

Journey of begomovirus betasatellite molecules: from satellites to indispensable partners

Betasatellites are a group of circular, single-stranded DNA molecules that are frequently found to be associated with monopartite begomoviruses of the family Geminiviridae. Betasatellites require their helper viruses for replication, movement, and encapsidation and they are often essential for induction of typical disease symptoms. The βC1 protein encoded by betasatellites is multifunctional that participates in diverse cellular events. It interferes with several cellular processes like normal development, chloroplasts, and innate immune system of plants. Recent research has indicated βC1 protein interaction with cellular proteins and its involvement in modulation of the host's cell cycle and symptom determination. This article focuses on the functional mechanisms of βC1 and its interactions with other viral and host proteins.

Identification of microRNAs regulated by tobacco curly shoot virus co-infection with its betasatellite in Nicotiana benthamiana

BACKGROUND

MicroRNAs (miRNAs) are a class of 21-24 nucleotide endogenous non-coding small RNAs that play important roles in plant development and defense responses to biotic and abiotic stresses. Tobacco curly shoot virus (TbCSV) is a monopartite begomovirus, cause leaf curling and plant stunting symptoms in many Solanaceae plants. The betasatellite of TbCSV (TbCSB) induces more severe symptoms and enhances virus accumulation when co-infect the plants with TbCSV.

METHODS

In this study, miRNAs regulated by TbCSV and TbCSB co-infection in Nicotiana benthamiana were characterized using high-throughput sequencing technology.

RESULTS

Small RNA sequencing analysis revealed that a total of 13 known miRNAs and 42 novel miRNAs were differentially expressed in TbCSV and TbCSB co-infected N. benthamiana plants. Several potential miRNA-targeted genes were identified through data mining and were involved in both catalytic and metabolic processes, in addition to plant defense mechanisms against virus infections according to Gene Ontology (GO) analyses. In addition, the expressions of several differentially expressed miRNAs and their miRNA-targeted gene were validated through quantitative real time polymerase chain reaction (qRT-PCR) approach.

CONCLUSIONS

A large number of miRNAs are identified, and their target genes, functional annotations also have been explored. Our results provide the information on N. benthamiana miRNAs and would be useful to further understand miRNA regulatory mechanisms after TbCSV and TbCSB co-infection.

Multifaceted role of geminivirus associated betasatellite in pathogenesis

Begomoviruses have emerged as a group of plant pathogens that cause devastating diseases in a wide range of crops in tropical and subtropical regions of the world. Betasatellites, the circular single-stranded DNA molecules with the size of almost half of that of the associated helper begomoviruses, are often essential for the production of typical disease symptoms in several virus-host systems. Association of betasatellites with begomoviruses results in more severe symptoms in the plants and affects the yield of numerous crops leading to huge agroeconomic losses. βC1, the only protein encoded by betasatellites, plays a multifaceted role in the successful establishment of infection. This protein counteracts the innate defence mechanisms of the host, like RNA silencing, ubiquitin-proteasome system and defence responsive hormones. In the last two decades, the molecular aspect of betasatellite pathogenesis has attracted much attention from the researchers worldwide, and reports have shown that βC1 protein aggravates the helper begomovirus disease complex by modulating specific host factors. This review discusses the molecular aspects of the pathogenesis of betasatellites, including various βC1-host factor interactions and their effects on the suppression of defence responses of the plants.

In silico Prediction and Validations of Domains Involved in Gossypium hirsutum SnRK1 Protein Interaction With Cotton Leaf Curl Multan Betasatellite Encoded βC1

Cotton leaf curl disease (CLCuD) caused by viruses of genus Begomovirus is a major constraint to cotton (Gossypium hirsutum) production in many cotton-growing regions of the world. Symptoms of the disease are caused by Cotton leaf curl Multan betasatellite (CLCuMB) that encodes a pathogenicity determinant protein, βC1. Here, we report the identification of interacting regions in βC1 protein by using computational approaches including sequence recognition, and binding site and interface prediction methods. We show the domain-level interactions based on the structural analysis of G. hirsutum SnRK1 protein and its domains with CLCuMB-βC1. To verify and validate the in silico predictions, three different experimental approaches, yeast two hybrid, bimolecular fluorescence complementation and pull down assay were used. Our results showed that ubiquitin-associated domain (UBA) and autoinhibitory sequence (AIS) domains of G. hirsutum-encoded SnRK1 are involved in CLCuMB-βC1 interaction. This is the first comprehensive investigation that combined in silico interaction prediction followed by experimental validation of interaction between CLCuMB-βC1 and a host protein. We demonstrated that data from computational biology could provide binding site information between CLCuD-associated viruses/satellites and new hosts that lack known binding site information for protein-protein interaction studies. Implications of these findings are discussed.

Identification and Analysis of Potential Genes Regulated by an Alphasatellite (TYLCCNA) that Contribute to Host Resistance against Tomato Yellow Leaf Curl China Virus and Its Betasatellite (TYLCCNV/TYLCCNB) Infection in Nicotiana benthamiana

Recently, begomovirus/betasatellite disease complexes were found to be associated with alphasatellites, and their presence modulated disease symptoms and/or viral DNA accumulation in infected plants. However, the biological functions of alphasatellites during begomovirus/betasatellite infections remain unclear. Tomato yellow leaf curl China virus (TYLCCNV) associated with a betasatellite (TYLCCNB) is a widespread monopartite begomovirus in China. In the Yunnan province of China, the TYLCCNV/TYLCCNB disease complex is found in association with an alphasatellite (TYLCCNA). In this study, in order to explain the mechanisms underlying TYLCCNV/TYLCCNB infection and reductions in viral DNA accumulation caused by TYLCCNA, we analyzed the transcriptome profiles of Nicotiana benthamiana seedlings challenged by TYLCCNV/TYLCCNB or TYLCCNV/TYLCCNB/TYLCCNA using RNA sequencing. In total, 2272 and 1207 differentially expressed genes (DEGs) were identified to respond to TYLCCNV/TYLCCNB and TYLCCNV/TYLCCNB/TYLCCNA infections, respectively. Compared with the DEGs in the TYLCCNV/TYLCCNB-infected N. benthamiana seedlings, the number of DEGs in plants co-infected with TYLCCNV/TYLCCNB + TYLCCNA was significantly reduced. Additionally, 36 DEGs were identified to be regulated by TYLCCNA, six of which were further analyzed using the virus-induced gene silencing (VIGS) approach. Silencing of these six TYLCCNA responsive DEGs caused more severe disease symptoms and higher viral DNA accumulation levels, suggesting that TYLCCNA responsive DEGs may attenuate TYLCCNV/TYLCCNB infection.

Iterons Homologous to Helper Geminiviruses Are Essential for Efficient Replication of Betasatellites

Betasatellites associated with geminiviruses can be replicated promiscuously by distinct geminiviruses but exhibit a preference for cognate helper viruses. However, the cis elements responsible for betasatellite origin recognition have not been characterized. In this study, we identified an iteron-like repeated sequence motif, 5'-GAGGACC-3', in a tobacco curly shoot betasatellite (TbCSB) associated with tobacco curly shoot virus (TbCSV). Competitive DNA binding assays revealed that two core repeats (5'-GGACC-3') are required for specific binding to TbCSV Rep; TbCSB iteron mutants accumulated to greatly reduced levels and lost the cognate helper-mediated replication preference. Interestingly, TbCSV also contains identical repeated sequences that are essential for specific Rep binding and in vivo replication. In order to gain insight into the mechanism by which TbCSB has acquired the cognate iterons, we performed a SELEX (systematic evolution of ligands by exponential enrichment) assay to identify the high-affinity Rep binding ligands from a large pool of randomized sequences. Analysis of SELEX winners showed that all of the sequences contained at least one core iteron-like motif, suggesting that TbCSB has evolved to contain cognate iterons for high-affinity Rep binding. Further analyses of various betasatellite sequences revealed a region upstream of the satellite conserved region replete with iterative sequence motifs, including species-specific repeats and a general repeat (5'-GGTAAAT-3'). Remarkably, the species-specific repeats in many betasatellites are homologous to those in their respective cognate helper begomoviruses, whereas the general repeat is widespread in most of the betasatellite molecules analyzed. These data, taken together, suggest that many betasatellites have evolved to acquire homologous iteron-like sequences for efficient replication mediated by cognate helper viruses.IMPORTANCE The geminivirus-encoded replication initiator protein (Rep) binds to repeated sequence elements (also known as iterons) in the origin of replication that serve as essential cis elements for specific viral replication. Betasatellites associated with begomoviruses can be replicated by cognate or noncognate helper viruses, but the cis elements responsible for betasatellite origin recognition have not been characterized. Using a betasatellite (TbCSB) associated with tobacco curly shoot virus (TbCSV) as a model, we identify two tandem repeats (iterons) in the Rep-binding motif (RBM) that are required for specific Rep binding and efficient replication, and we show that identical iteron sequences present in TbCSV are also necessary for Rep binding and the replication of helper viruses. Extensive analysis of begomovirus/betasatellite sequences shows that many betasatellites contain iteron-like elements homologous to those of their respective cognate helper begomoviruses. Our data suggest that many betasatellites have evolved to acquire homologous iteron-like sequences for efficient replication mediated by cognate helper viruses.

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

BACKGROUND

Tobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. It is interesting that TbCSV induced severe upward leaf curling in Nicotiana benthamiana, but in the presence of TbCSB, symptoms changed to be downward leaf curling. However, the mechanism of interactions between viral pathogenicity, host defense, viral-betasatellite interactions and virus-host interactions remains unclear.

METHODS

In this study, RNA-seq was used to analyze differentially expressed genes (DEGs) in N. benthamiana plants infected by TbCSV (Y35A) and TbCSV together with TbCSB (Y35AB) respectively.

RESULTS

Through mapping to N. benthamiana reference genome, 59,814 unigenes were identified. Transcriptome analysis revealed that a total of 4081 and 3196 DEGs were identified in Y35AB vs CK (control check) and Y35A vs CK, respectively. Both GO and KEGG analyses were conducted to classify the DEGs. Ten of the top 15 GO terms were enriched in both DEGs of Y35AB vs CK and Y35A vs CK, and these enriched GO terms mainly classified into three categories including biological process, cellular component and molecular function. KEGG pathway analysis indicated that 118 and 111 pathways were identified in Y35AB vs CK and Y35A vs CK, respectively, of which nine and six pathways were significantly enriched. Three major pathways in Y35AB vs CK involved in metabolic pathways, carbon metabolism and photosynthesis, while those in Y35A vs CK were related to Ribosome, Glyoxylate and dicarboxylate metabolism and DNA replication. We observed that 8 PR genes were significantly up-regulated and 44 LRR-RLK genes were significantly differentially expressed in Y35A treatment or in Y35AB treatment. In addition, 7 and 13 genes were identified to be significantly changed in biosynthesis and signal transduction pathway of brassinosteroid (BR) and jasmonic acid (JA) respectively.

CONCLUSIONS

These results presented here would be particularly useful to further elucidate the response of the host plant against virus infection.

Transcriptome profiling of whitefly guts in response to Tomato yellow leaf curl virus infection

BACKGROUND

Plant viruses in agricultural crops are of great concern worldwide, and over 75% of them are transmitted from infected to healthy plants by insect vectors. Tomato yellow leaf curl virus (TYLCV) is a begomovirus, which is the largest and most economically important group of plant viruses, transmitted by the whitefly Bemisia tabaci. The circulation of TYLCV in the insect involves complex insect-virus interactions, whereas the molecular mechanisms of these interactions remain ambiguous. The insect gut as a barrier for viral entry and dissemination is thought to regulate the vector specificity. However, due to its tiny size, information for the responses of whitefly gut to virus infection is limited.

METHODS

We investigated the transcriptional response of the gut of B. tabaci Middle East-Asia Minor 1 species to TYLCV infection using Illumina sequencing.

RESULTS

A total of 5207 differentially expressed genes (DEGs) between viruliferous and non-viruliferous whitefly guts were identified. Enrichment analyses showed that cargo receptor and ATP-binding cassette (ABC) transporters were enriched in DEGs, and might help the virus to cross gut barrier. TYLCV could perturb cell cycle and DNA repair as a possible result of its replication in the whitefly. Our data also demonstrated that TYLCV can activate whitefly defense responses, such as antimicrobial peptides. Meanwhile, a number of genes involved in intracellular signaling were activated by TYLCV infection.

CONCLUSIONS

Our results reveal the complex insect-virus relationship in whitefly gut and provide substantial molecular information for the role of insect midguts in virus transmission.

Natural infection of croton yellow vein mosaic virus and its cognate betasatellite in germplasm of different Crambe spp in India

Crambe is an important crop grown worldwide for industrial oil and seed meal. Besides the fungal and bacterial diseases, the crop is reported to be infected by tobacco mosaic virus, beet western yellows virus and turnip mosaic virus under experimental condition. Till now, there was no report of natural infection of any begomovirus in this crop. In the present study, a leaf curl disease was observed in germplasm accessions of three species of Crambe (C. abyssinica, C. glabrata and C. hispanica). Based on the symptoms and presence of whitefly population in the field, begomovirus infection was suspected. Molecular characterization through RCA approach, indicated presence of croton yellow vein mosaic virus (CYVMV, KJ747958) and croton yellow vein mosaic betasatellite (CroYVMB, KM229762). Co-agroinoculation of partial dimeric construct of CYVMV with complete dimeric construct of CroYVMB, produced typical leaf curl symptoms in C. abyssinica, whereas, agroinoculation of partial dimeric construct of CYVMV alone could not produce symptoms in the same plant. In contrast, the CYVMV construct alone could produce symptom in Nicotiana benthamiana, a model host for plant virus studies. In N. benthamiana co-inoculation of CroYVMV with CYVMV construct develop more severe symptoms. However, neither the CYVMV construct alone nor the co-inoculation with CroYVMB produce any symptom in Arabidopsis thaliana even with different methods of inoculation. Inoculated Arabidopsis thaliana also did not yield any amplification of the virus as assessed through PCR and rolling circle amplification (RCA). Thus it confirmed that for successful infection in crambe, CYVMV requires betasatellite, while in N. benthamiana, it does not require betasatellite for symptom induction and in Arabidopsis thaliana CYVMV alone or in presence of betasatellite did not replicate and produce any symptom. This study constitutes the first confirmed record of natural infection of a begomovirus in crambe and further confirmed that cognate betasatellite of CYVMV has differential role in infectivity in different hosts.

A molecular insight into papaya leaf curl-a severe viral disease

Papaya leaf curl disease (PaLCuD) caused by papaya leaf curl virus (PaLCuV) not only affects yield but also plant growth and fruit size and quality of papaya and is one of the most damaging and economically important disease. Management of PaLCuV is a challenging task due to diversity of viral strains, the alternate hosts, and the genomic complexities of the viruses. Several management strategies currently used by plant virologists to broadly control or eliminate the viruses have been discussed. In the absence of such strategies in the case of PaLCuV at present, the few available options to control the disease include methods like removal of affected plants from the field, insecticide treatments against the insect vector (Bemisia tabaci), and gene-specific control through transgenic constructs. This review presents the current understanding of papaya leaf curl disease, genomic components including satellite DNA associated with the virus, wide host and vector range, and management of the disease and suggests possible generic resistance strategies.

Mimic Phosphorylation of a βC1 Protein Encoded by TYLCCNB Impairs Its Functions as a Viral Suppressor of RNA Silencing and a Symptom Determinant

Phosphorylation of the βC1 protein encoded by the betasatellite of tomato yellow leaf curl China virus (TYLCCNB-βC1) by SNF1-related protein kinase 1 (SnRK1) plays a critical role in defense of host plants against geminivirus infection in Nicotiana benthamiana However, how phosphorylation of TYLCCNB-βC1 impacts its pathogenic functions during viral infection remains elusive. In this study, we identified two additional tyrosine residues in TYLCCNB-βC1 that are phosphorylated by SnRK1. The effects of TYLCCNB-βC1 phosphorylation on its functions as a viral suppressor of RNA silencing (VSR) and a symptom determinant were investigated via phosphorylation mimic mutants in N. benthamiana plants. Mutations that mimic phosphorylation of TYLCCNB-βC1 at tyrosine 5 and tyrosine 110 attenuated disease symptoms during viral infection. The phosphorylation mimics weakened the ability of TYLCCNB-βC1 to reverse transcriptional gene silencing and to suppress posttranscriptional gene silencing and abolished its interaction with N. benthamiana ASYMMETRIC LEAVES 1 in N. benthamiana leaves. The mimic phosphorylation of TYLCCNB-βC1 had no impact on its protein stability, subcellular localization, or self-association. Our data establish an inhibitory effect of phosphorylation of TYLCCNB-βC1 on its pathogenic functions as a VSR and a symptom determinant and provide a mechanistic explanation of how SnRK1 functions as a host defense factor.IMPORTANCE Tomato yellow leaf curl China virus (TYLCCNV), which causes a severe yellow leaf curl disease in China, is a monopartite geminivirus associated with the betasatellite (TYLCCNB). TYLCCNB encodes a single pathogenicity protein, βC1 (TYLCCNB-βC1), which functions as both a viral suppressor of RNA silencing (VSR) and a symptom determinant. Here, we show that mimicking phosphorylation of TYLCCNB-βC1 weakens its ability to reverse transcriptional gene silencing, to suppress posttranscriptional gene silencing, and to interact with N. benthamiana ASYMMETRIC LEAVES 1. To our knowledge, this is the first report establishing an inhibitory effect of phosphorylation of TYLCCNB-βC1 on its pathogenic functions as both a VSR and a symptom determinant and to provide a mechanistic explanation of how SNF1-related protein kinase 1 acts as a host defense factor. These findings expand the scope of phosphorylation-mediated defense mechanisms and contribute to further understanding of plant defense mechanisms against geminiviruses.

Survey, symptomatology, transmission, host range and characterization of begomovirus associated with yellow mosaic disease of ridge gourd in southern India

Ridge gourd is an important vegetable crop and is affected by several biotic and abiotic factors. Among the different biotic factors, ridge gourd yellow mosaic disease (RgYMD) is new emerging threat for the production of ridge gourd. The incidence of the RgYMD varied from 30 to 100% in southern India with highest disease incidence of 100% observed in Belagavi district of Karnataka state. The infected plants showed chlorosis, mosaic, cupping of leaves, blistering, reduction in leaf size and stunted growth. The varieties/hybrids grown in the farmer's fields were found to be susceptible to the disease. Begomovirus was detected in 61 out 64 samples collected from different areas of southern India. Further, all the samples failed to give amplification for beta and alpha satellites. The transmission studies revealed that single whitefly (Bemisia tabaci) is enough to transmit the virus, however, 100% transmission was observed with 10 whiteflies. The minimum acquisition access period and inoculation access period for transmission of virus by whitefly was 15 min. Among the 56 host plants belonging to diversified families tested for host range, sponge gourd, ash gourd, bottle gourd, pumpkin, cucumber, summer squash, cluster bean, tobacco and datura were shown to be susceptible. Seventy six varieties/hybrids evaluated for identifying the resistance source for RgYMD, all were found highly susceptible. Sequence analysis of DNA-A revealed that the causal virus shared highest nucleotide sequence identity (92.3%) with Tomato leaf curl New Delhi virus (ToLCNDV) infecting sponge gourd from northern India. Sequence and phylogenetic analysis of both DNA-A and DNA-B components showed that the begomovirus associated with RgYMD is found to be strain of ToLCNDV. This is first report of ToLCNDV association with RgYMD from southern India.

Molecular characterization of a novel bipartite begomovirus isolated from Lycianthes biflora in China

A bipartite begomovirus isolate GD was isolated from Lycianthes biflora plants showing yellow mosaic symptoms in Nanxiong, Guangdong Province, China. The apparently full-length DNA-A and DNA-B viral components were cloned after enrichment of circular DNA by rolling circle amplification, restriction digestion, cloning, and DNA sequencing. The DNA-A component (2752nt, KT582302) shares highest (80.2%) nucleotide (nt) sequence identity with tomato leaf curl Sulawesi virus [Indonesia-Sulawesi-Langowan F101-2006] (ToLCSuV- [ID-Sul -LanF09-06], FJ237618), reported in Indonesia as causing yellow leaf curl disease of chilli pepper. The DNA-B component (2704nt, KT582303) shares highest (76.3%) nt sequence identity with pepper yellow leaf curl Indonesia virus-[Indonesia-tomato2-2005] (PepYLCIV-[ID-Tom2-05 AB213599) reported in Indonesia, and associated with yellow leaf curl disease in tomato. Based on the ICTV guidelines for begomoviral species demarcation, the virus is a new, previously undescribed bipartite begomovirus species for which the name "Lycianthes yellow mosaic virus" is proposed.

gb4gv: a genome browser for geminivirus

BACKGROUND

Geminiviruses (family Geminiviridae) are prevalent plant viruses that imperil agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, the NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc.

METHODS

We have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases.

RESULTS

These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser.

DISCUSSION

With the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae.

AVAILABILITY AND IMPLEMENTATION

The database can be found at: http://gb4gv.lafayette.edu.

iTRAQ analysis of the tobacco leaf proteome reveals that RNA-directed DNA methylation (RdDM) has important roles in defense against geminivirus-betasatellite infection

Geminiviruses have caused serious losses in crop production. To investigate the mechanisms underlying host defenses against geminiviruses, an isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic approach was used to explore the expression profiles of proteins in Nicotiana benthamiana (N. benthamiana) leaves in response to tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB) at an early phase. In total, 4155 proteins were identified and 272 proteins were changed differentially in response to TYLCCNV/TYLCCNB infection. Bioinformatics analysis indicated that S-adenosyl-l-methionine cycle II was the most significantly up-regulated biochemical process during TYLCCNV/TYLCCNB infection. The mRNA levels of three proteins in S-adenosyl-l-methionine cycle II were further analyzed by qPCR, each was found significantly up-regulated in TYLCCNV/TYLCCNB-infected N. benthamiana. This result suggested a strong promotion of the biosynthesis of available methyl groups during geminivirus infections. We further tested the potential role of RdDM in N. benthamiana by virus-induced gene silencing (VIGS) and found that a disruption in RdDM resulted in more severe infectious symptoms and higher accumulation of viral DNA after TYLCCNV/TYLCCNB infection. Although the precise functions of these proteins still need to be determined, our proteomic results enhance the understanding of plant antiviral mechanisms.

BIOLOGICAL SIGNIFICANCE

One of the major limitations to crop growth in the worldwide is the prevalence of geminiviruses. They are able to infect food and cash crops and cause serious crop failures and economic losses worldwide, especially in Africa and Asia. Tomato yellow leaf curl China virus (TYLCCNV), which causes severe viral diseases in China, is a monopartite geminivirus associated with the betasatellite (TYLCCNB). However, the mechanisms underlying the TYLCCNV/TYLCCNB defense in plants are still not fully understood at the molecular level. In this study, the combined proteomic, bioinformatic and VIGS analyses revealed that TYLCCNV/TYLCCNB invasion caused complex proteomic alterations in the leaves of N. benthamiana involving the processes of stress and defense, energy production, photosynthesis, protein homeostasis, metabolism, cell structure, signal transduction, transcription, transportation, and cell growth/division. Promotion of available methyl groups via the S-adenosyl-l-methionine cycle II pathway in N. benthamiana appeared crucial for antiviral responses. These findings enhance our understanding in the proteomic aspects of host antiviral defenses against geminiviruses, and also demonstrate that the combination of proteomics with bioinformatics and VIGS analysis is an effective approach to investigate systemic plant responses to geminiviruses and to shed light on plant-virus interactions.

Cotton Leaf Curl Multan Betasatellite DNA as a Tool to Deliver and Express the Human B-Cell Lymphoma 2 (Bcl-2) Gene in Plants

The betasatellite DNA associated with Cotton leaf curl Multan virus (CLCuMB) contains a single complementary-sense ORF, βC1, which is a pathogenicity determinant. CLCuMB was able to replicate in plants in the presence of diverse helper geminiviruses, including Tomato leaf curl virus-Australia (TLCV-Au), Iranian isolate of Tomato yellow leaf curl virus (TYLCV-[Ab]), and Beet curly top virus (BCTV-Svr), and can be used as a plant gene delivery vector. To test the hypothesis that CLCuMB has the potential to act as an animal gene delivery vector, a specific insertion construct was produced by the introduction of a human B-cell lymphoma 2 (Bcl-2) cDNA into a mutant DNA of CLCuMB in which the βC1 was deleted (β∆C1). The recombinant βΔC1-Bcl-2 construct was successfully replicated in tomato and tobacco plants in the presence of TLCV-Au, BCTV-Svr and TYLCV-[Ab]. Real-time PCR and Western blot analyses of plants containing the replicative forms of recombinant βΔC1-Bcl-2 DNA showed that Bcl-2 gene was expressed in an acceptable level in these plants, indicating that β∆C1 can be used as a tool to deliver and express animal genes in plants. This CLCuMB-based system, having its own promoter activity, offers the possibility of production of animal recombinant proteins in plants.

CLCuMuB βC1 Subverts Ubiquitination by Interacting with NbSKP1s to Enhance Geminivirus Infection in Nicotiana benthamiana

Viruses interfere with and usurp host machinery and circumvent defense responses to create a suitable cellular environment for successful infection. This is usually achieved through interactions between viral proteins and host factors. Geminiviruses are a group of plant-infecting DNA viruses, of which some contain a betasatellite, known as DNAβ. Here, we report that Cotton leaf curl Multan virus (CLCuMuV) uses its sole satellite-encoded protein βC1 to regulate the plant ubiquitination pathway for effective infection. We found that CLCuMu betasatellite (CLCuMuB) βC1 interacts with NbSKP1, and interrupts the interaction of NbSKP1s with NbCUL1. Silencing of either NbSKP1s or NbCUL1 enhances the accumulation of CLCuMuV genomic DNA and results in severe disease symptoms in plants. βC1 impairs the integrity of SCFCOI1 and the stabilization of GAI, a substrate of the SCFSYL1 to hinder responses to jasmonates (JA) and gibberellins (GA). Moreover, JA treatment reduces viral accumulation and symptoms. These results suggest that CLCuMuB βC1 inhibits the ubiquitination function of SCF E3 ligases through interacting with NbSKP1s to enhance CLCuMuV infection and symptom induction in plants.

The minimal sequence essential for replication and movement of Cotton leaf curl Multan betasatellite DNA by a helper virus in plant cells

Betasatellites are single-stranded circular DNAs associated with a number of monopartite begomoviruses. Betasatellites rely on the helper begomoviruses for replication and movement in plant tissues and plant-to-plant transmission by vectors. Their genomes are approximately half the size of the helper viruses and consist of three main regions including the βC1 gene, an adenine-rich (A-rich) region, and the satellite conserved region (SCR). In this study, we investigated the minimal sequences required for Cotton leaf curl Multan betasatellite (CLCuMB) replication and movement. Mutational analysis of CLCuMB DNA genome indicated that βC1 gene and A-rich region were not required for trans-replication and movement of CLCuMB in host plants by a helper virus. Deletion of βC1 gene and a fragment (135 nt in length) upstream of this gene impaired CLCuMB replication. However, CLCuMB mutant with deletion of βC1 gene and a further 163 nucleotides replicated at a lower level as compared to the wild-type betasatellite. This suggests that there are essential elements in the fragment upstream of βC1 gene, which are required for the replication of CLCuMB rather than the size limitation of CLCuMB DNA.

Characterization of Non-coding DNA Satellites Associated with Sweepoviruses (Genus Begomovirus, Geminiviridae) - Definition of a Distinct Class of Begomovirus-Associated Satellites

Begomoviruses (family Geminiviridae) are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas). Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus-satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus), with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem–loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem–loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.

A Novel DNA Motif Contributes to Selective Replication of a Geminivirus-Associated Betasatellite by a Helper Virus-Encoded Replication-Related Protein

Rolling-circle replication of single-stranded genomes of plant geminiviruses is initiated by sequence-specific DNA binding of the viral replication-related protein (Rep) to its cognate genome at the replication origin. Monopartite begomovirus-associated betasatellites can be trans replicated by both cognate and some noncognate helper viruses, but the molecular basis of replication promiscuity of betasatellites remains uncharacterized. Earlier studies showed that when tomato yellow leaf curl China virus (TYLCCNV) or tobacco curly shoot virus (TbCSV) is coinoculated with both cognate and noncognate betasatellites, the cognate betasatellite dominates over the noncognate one at the late stages of infection. In this study, we constructed reciprocal chimeric betasatellites between tomato yellow leaf curl China betasatellite and tobacco curly shoot betasatellite and assayed their competitiveness against wild-type betasatellite when coinoculated with TYLCCNV or TbCSV onto plants. We mapped a region immediately upstream of the conserved rolling-circle cruciform structure of betasatellite origin that confers the cognate Rep-mediated replication advantage over the noncognate satellite. DNase I protection and in vitro binding assays further identified a novel sequence element termed Rep-binding motif (RBM), which specifically binds to the cognate Rep protein and to the noncognate Rep, albeit at lower affinity. Furthermore, we showed that RBM-Rep binding affinity is correlated with betasatellite replication efficiency in protoplasts. Our data suggest that although strict specificity of Rep-mediated replication does not exist, betasatellites have adapted to their cognate Reps for efficient replication during coevolution.

IMPORTANCE

Begomoviruses are numerous circular DNA viruses that cause devastating diseases of crops worldwide. Monopartite begomoviruses are frequently associated with betasatellites which are essential for induction of typical disease symptoms. Coexistence of two distinct betasatellites with one helper virus is rare in nature. Our previous research showed that begomoviruses can trans replicate cognate betasatellites to higher levels than noncognate ones. However, the molecular mechanisms of betasatellites selective replication remain largely unknown. We investigated the interaction between the begomovirus replication-associated protein and betasatellite DNA. We found that the replication-associated protein specifically binds to a motif in betasatellites, with higher affinity for the cognate motif than the noncognate motif. This preference for cognate motif binding determines the selective replication of betasatellites. We also demonstrated that this motif is essential for betasatellite replication. These findings shed new light on the promiscuous yet selective replication of betasatellites by helper geminiviruses.

Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae)

Monopartite begomoviruses (Geminiviridae), which are whitefly-transmitted single-stranded DNA viruses known for causing devastating crop diseases, are often associated with satellite DNAs. Since begomovirus acquisition or exchange of satellite DNAs may lead to adaptation to new plant hosts and emergence of new disease complexes, it is important to investigate the diversity and distribution of these molecules. This study reports begomovirus-associated satellite DNAs identified during a vector-enabled metagenomic (VEM) survey of begomoviruses using whiteflies collected in various locations (California (USA), Guatemala, Israel, Puerto Rico, and Spain). Protein-encoding satellite DNAs, including alphasatellites and betasatellites, were identified in Israel, Puerto Rico, and Guatemala. Novel alphasatellites were detected in samples from Guatemala and Puerto Rico, resulting in the description of a phylogenetic clade (DNA-3-type alphasatellites) dominated by New World sequences. In addition, a diversity of small (~640-750 nucleotides) satellite DNAs similar to satellites associated with begomoviruses infecting Ipomoea spp. were detected in Puerto Rico and Spain. A third class of satellite molecules, named gammasatellites, is proposed to encompass the increasing number of reported small (<1 kilobase), non-coding begomovirus-associated satellite DNAs. This VEM-based survey indicates that, although recently recovered begomovirus genomes are variations of known genetic themes, satellite DNAs hold unexplored genetic diversity.

MicroRNA profiling of the whitefly Bemisia tabaci Middle East-Aisa Minor I following the acquisition of Tomato yellow leaf curl China virus

Background

The begomoviruses are the largest and most economically important group of plant viruses exclusively vectored by whitefly (Bemisia tabaci) in a circulative, persistent manner. During this process, begomoviruses and whitefly vectors have developed close relationships and complex interactions. However, the molecular mechanisms underlying these interactions remain largely unknown, and the microRNA profiles for viruliferous and nonviruliferous whiteflies have not been studied.

Methods

Sequences of Argonaute 1(Ago1) and Dicer 1 (Dcr1) genes were cloned from B. tabaci MEAM1 cDNAs. Subsequently, deep sequencing of small RNA libraries from uninfected and Tomato yellow leaf curl China virus (TYLCCNV)-infected whiteflies was performed. The conserved and novel miRNAs were identified using the release of miRBase Version 19.0 and the prediction software miRDeep2, respectively. The sequencing results of selected deregulated and novel miRNAs were further confirmed using quantitative reverse transcription-PCR. Moreover, the previously published B. tabaci MEAM1 transcriptome database and the miRNA target prediction algorithm miRanda 3.1 were utilized to predict potential targets for miRNAs. Gene Ontology (GO) analysis was also used to classify the potential enriched functional groups of their putative targets.

Results

Ago1 and Dcr1orthologs with conserved domains were identified from B. tabaci MEAM1. BLASTn searches and sequence analysis identified 112 and 136 conserved miRNAs from nonviruliferous and viruliferous whitefly libraries respectively, and a comparison of the conserved miRNAs of viruliferous and nonviruliferous whiteflies revealed 15 up- and 9 down-regulated conserved miRNAs. 7 novel miRNA candidates with secondary pre-miRNA hairpin structures were also identified. Potential targets of conserved and novel miRNAs were predicted using GO analysis, for the targets of up- and down-regulated miRNAs, eight and nine GO terms were significantly enriched.

Conclusions

We identified Ago1 and Dcr1 orthologs from whiteflies, which indicated that miRNA-mediated silencing is present in whiteflies. Our comparative analysis of miRNAs from TYLCCNV viruliferous and nonviruliferous whiteflies revealed the relevance of deregulated miRNAs for the post-transcriptional gene regulation in these whiteflies. The potential targets of all expressed miRNAs were also predicted. These results will help to acquire a better understanding of the molecular mechanism underlying the complex interactions between begomoviruses and whiteflies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0469-7) contains supplementary material, which is available to authorized users.

Molecular identification of tobacco leaf curl disease in Sichuan province of China

BACKGROUND

Tobacco leaf curl disease (TLCD) is caused by begomoviruses in Geminiviridae, and infected plants exhibit leaf thickening, downward leaf curling, vein swelling as well as stunting symptoms. It is one of the economically important diseases in tropical and subtropical tobacco-growing areas. Seven monopartite begomoviruses have been identified causing TLCD in China.

FINDINGS

In this study, two begomoviruses were identified, characterized and polygenetically analyzed to be responsible for TLCD in Sichuan province, China. The complete genomes of two isolates SC230 and SC379 from diseased tobacco samples were cloned and sequenced to be 2738 nucleotides (nts) and 2748 nts in size, respectively. Sequence alignment indicated that SC230 and SC379 were most closely related to Tomato yellow leaf curl China virus (TYLCCNV-CN[CN:Sc226:Mal:12]) and Papaya leaf curl China virus (PaLCuCNV-CN[CN:Gx30:Lyc:03]), with a sequence identity of 99.2 and 99.2 %, respectively. The infection rate of TYLCCNV and PaLCuCNV was 100 and 34.78 %, respectively and the co-infection rate was 34.78 % in fields. Betasatellites of SC230 and SC379 share the highest sequence identity with Tomato yellow leaf curl China betasatellite (TYLCCNB-CN[CN:Sc176:Malva:12]) and TYLCCNB-CN[CN:Yn149:Tom:09], with a sequence identity of 95.2 and 97.2 % respectively. Sequence identity between betasatellites of SC230 and SC379 was 89.6 %. And TYLCCNB was detected in all the samples.

CONCLUSION

Co-infection of TYLCCNV and PaLCuCNV was identified in tobacco plants with typical symptoms of TLCD from Sichuan province in China, and this is the first report of PaLCuCNV infecting tobacco in China. TYLCCNV/TYLCCNB disease complex is widespread in tobacco-growing areas in Panzhihua city of Sichuan.

Determinants of Disease Phenotype Differences Caused by Closely-Related Isolates of Begomovirus Betasatellites Inoculated with the Same Species of Helper Virus

Tomato yellow leaf curl China virus (TYLCCNV) is a monopartite begomovirus associated with different betasatellites. In this study, we investigate two different isolates of Tomato yellow leaf curl China betasatellite (TYLCCNB) to determine what features of the viral genome are required for induction of characteristic phenotypic differences between closely-related betasatellite. When co-agroinoculated with TYLCCNV into Nicotiana spp. and tomato plants, TYLCCNB-Y25 induced only leaf curling on all hosts, while TYLCCNB-Y10 also induced enations, vein yellowing, and shoot distortions. Further assays showed that βC1 of TYLCCNB-Y25 differs from that of TYLCCNB-Y10 in symptom induction and transcriptional modulating. Hybrid satellites were constructed in which the βC1 gene or 200 nt partial promoter-like fragment upstream of the βC1 were exchanged. Infectivity assays showed that a TYLCCNB-Y25 hybrid with the intact TYLCCNB-Y10 βC1 gene was able to induce vein yellowing, shoot distortions, and a reduced size and number of enations. A TYLCCNB-Y10 hybrid with the intact TYLCCNB-Y25 βC1 gene produced only leaf curling. In contrast, the TYLCCNB-Y25 and TYLCCNB-Y10 hybrids with swapped partial promoter-like regions had little effect on the phenotypes induced by wild-type betasatellites. Further experiments showed that the TYLCCNB-Y25 hybrid carrying the C-terminal region of TYLCCNB-Y10 βC1 induced TYLCCNB-Y10-like symptoms. These findings indicate that the βC1 protein is the major symptom determinant and that the C-terminal region of βC1 plays an important role in symptom induction.

Genetic variability of Cotton leaf curl betasatellite in Northern India

Cotton is an important crop and its production is affected by various disease pathogens. Monopartite begomovirus associated betasatellites cause Cotton leaf curl disease (CLCuD) in Northern India. In order to access the occurrence and genetic variability of Cotton leaf curl betasatellites, an extensive field survey was conducted in states of Rajasthan, Punjab and Haryana. We selected the betasatellite sequence for analysis as they are reported as important for disease severity and sequence variability. Based on the field observations, the disease incidence ranged from 30% to 80% during the survey. Full genome and DNA β were amplified from various samples while no amplicon was obtained in some samples. The nucleotide sequence homology ranged from 90.0% to 98.7% with Cotton leaf curl virus (CLCuV), 55.2-55.5% with Bhendi yellow vein mosaic virus, 55.8% with Okra leaf curl virus and 51.70% with Tomato leaf curl virus isolates. The lowest similarity (47.8%) was found in CLCuV-Sudan isolate. Phylogenetic analysis showed that analyzed isolates formed a close cluster with various CLCuV isolates reported earlier. The analysis results show sequence variation in Cotton leaf curl betasatellite which could be the result of recombination. The results obtained by genome amplification and sequence variability indicate that some new variants are circulating and causing leaf curl disease in Rajasthan, Punjab and Haryana.

Specific cells in the primary salivary glands of the whitefly Bemisia tabaci control retention and transmission of begomoviruses

The majority of plant viruses are vectored by arthropods via persistent-circulative or noncirculative transmission. Previous studies have shown that specific binding sites for noncirculative viruses reside within the stylet or foregut of insect vectors, whereas the transmission mechanisms of circulative viruses remain ambiguous. Here we report the critical roles of whitefly primary salivary glands (PSGs) in the circulative transmission of two begomoviruses. The Middle East Asia Minor 1 (MEAM1) species of the whitefly Bemisia tabaci complex efficiently transmits both Tomato yellow leaf curl China virus (TYLCCNV) and Tomato yellow leaf curl virus (TYLCV), whereas the Mediterranean (MED) species transmits TYLCV but not TYLCCNV. PCR and fluorescence in situ hybridization experiments showed that TYLCCNV efficiently penetrates the PSGs of MEAM1 but not MED whiteflies. When a fragment of the coat protein of TYLCCNV was exchanged with that of TYLCV, mutated TYLCCNV accumulated in the PSGs of MED whiteflies, while mutant TYLCV was nearly undetectable. Confocal microscopy revealed that virion transport in PSGs follows specific paths to reach secretory cells in the central region, and the accumulation of virions in the secretory region of PSGs was correlated with successful virus transmission. Our findings demonstrate that whitefly PSGs, in particular the cells around the secretory region, control the specificity of begomovirus transmission.

IMPORTANCE

Over 75% of plant viruses are transmitted by insects. However, the mechanisms of virus transmission by insect vectors remain largely unknown. Begomoviruses and whiteflies are a complex of viruses and vectors which threaten many crops worldwide. We investigated the transmission of two begomoviruses by two whitefly species. We show that specific cells of the whitefly primary salivary glands control viral transmission specificity and that virion transport in the glands follows specific paths to reach secretory cells in the central region and then to reach the salivary duct. Our results indicate that the secretory cells in the central region of primary salivary glands determine the recognition and transmission of begomoviruses. These findings set a foundation for future research not only on circulative plant virus transmission but also on other human and animal viruses transmitted by arthropod vectors.

RNAi mediated gene silencing against betasatellite associated with Croton yellow vein mosaic begomovirus

Plant viruses encode suppressors of posttranscriptional gene silencing, an adaptive antiviral defense responses that confines virus infection. Previously, we identified single-stranded DNA satellite (also known as DNA-β) of ~1,350 nucleotides in length associated with Croton yellow vein mosaic begomovirus (CYVMV) in croton plants. The expression of genes from DNA-β requires the begomovirus for packaged, replication, insect transmission and movement in plants. The present study demonstrates the effect of the βC1 gene on the silencing pathway as analysed by using both transgenic systems and transient Agrobacterium tumefaciens based delivery. Plants that carry an intron-hairpin construct covering the βC1 gene accumulated cognate small-interfering RNAs and remained symptom-free after exposure to CYVMV and its satellite. These results suggest that βC1 interferes with silencing mechanism.

Suppression of RNA silencing by a plant DNA virus satellite requires a host calmodulin-like protein to repress RDR6 expression

In plants, RNA silencing plays a key role in antiviral defense. To counteract host defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different effector molecules in the RNA silencing pathway. Evidence has shown that plants also encode endogenous suppressors of RNA silencing (ESRs) that function in proper regulation of RNA silencing. The possibility that these cellular proteins can be subverted by viruses to thwart host defense is intriguing but has not been fully explored. Here we report that the Nicotiana benthamiana calmodulin-like protein Nbrgs-CaM is required for the functions of the VSR βC1, the sole protein encoded by the DNA satellite associated with the geminivirus Tomato yellow leaf curl China virus (TYLCCNV). Nbrgs-CaM expression is up-regulated by the βC1. Transgenic plants over-expressing Nbrgs-CaM displayed developmental abnormities reminiscent of βC1-associated morphological alterations. Nbrgs-CaM suppressed RNA silencing in an Agrobacterium infiltration assay and, when over-expressed, blocked TYLCCNV-induced gene silencing. Genetic evidence showed that Nbrgs-CaM mediated the βC1 functions in silencing suppression and symptom modulation, and was required for efficient virus infection. Moreover, the tobacco and tomato orthologs of Nbrgs-CaM also possessed ESR activity, and were induced by betasatellite to promote virus infection in these Solanaceae hosts. We further demonstrated that βC1-induced Nbrgs-CaM suppressed the production of secondary siRNAs, likely through repressing RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) expression. RDR6-deficient N. benthamiana plants were defective in antiviral response and were hypersensitive to TYLCCNV infection. More significantly, TYLCCNV could overcome host range restrictions to infect Arabidopsis thaliana when the plants carried a RDR6 mutation. These findings demonstrate a distinct mechanism of VSR for suppressing PTGS through usurpation of a host ESR, and highlight an essential role for RDR6 in RNA silencing defense response against geminivirus infection.

Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia

Over the past three decades diseases caused by whitefly-transmitted geminiviruses (begomoviruses) have emerged to be important constraints to the production of solanaceous crops, particularly tomato (Solanum lycopersicum) and peppers (Capsicum spp.), in many tropical and subtropical regions of the world. The most studied of these is Tomato yellow leaf curl virus (TYLCV), which has spread to many other areas from its likely origin in the Mediterranean basin region. The virus is usually associated with the polyphagous and virus-vectoring-efficient B-biotype of its vector whitefly (Bemisia tabaci). However, in Southeast and East Asia, a wide variety of distinct local begomovirus species have been identified from tomato and pepper crops over this period, and TYLCV was detected in Japan only in about 1996, China in 2006 and Korea in 2008, despite B-biotype whiteflies being present in several of the countries of the region since at least the early 1990s. Continental Southeast Asia appears to be a major center of diversity for begomoviruses and some species may have spread across the region; Tomato yellow leaf curl Thailand virus (TYLCTHV) appears to have spread from the Thailand-Myanmar region into southern China and is now displacing the local tomato-infecting species in Taiwan, and Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) appears to have spread from the Thailand-Vietnam region to Java, Indonesia. Since many of the native tomato- or pepper-infecting begomoviruses and associated satellite DNAs have also been detected in local weed species, it seems likely that their ancestors originated in these weed hosts, but with the expansion and intensification of tomato and pepper production in the region, there was selection for recombinant or mutant forms with greater virulence on tomato and/or pepper. Expansion and intensification of these crops may also have resulted in increased populations of local, and if present, B- or Q-biotype whiteflies, aiding the increase and spread of local begomovirus species.

A naturally occurring defective DNA satellite associated with a monopartite begomovirus: evidence for recombination between alphasatellite and betasatellite

Monopartite begomoviruses and their associated satellites form unique disease complexes that have emerged as a serious threat to agriculture worldwide. It is well known that frequent recombination contributes to the diversification and evolution of geminiviruses. In this study, we identified a novel defective satellite molecule (RecSat) in association with Tobacco leaf curl Yunnan virus (TbLCYNV) in a naturally infected tobacco plant. Sequence analysis showed that Recsat comprises 754 nucleotides in size and is a chimera involving alphasatellite and betasatellite sequences, containing both betasatellite-conserved region and alphasatellite stem-loop structure. Recombination analysis revealed that RecSat has arisen from three independent recombination events likely involving Tomato yellow leaf curl China betasatellite, Ageratum yellow vein China betasatellite and Tobacco curly shoot alphasatellite. Co-inoculation of RecSat with TbLCYNV induced symptoms indistinguishable from those induced by TbLCYNV alone in Nicotiana benthamiana. Southern blot hybridization showed that RecSat could be trans-replicated stably in N. benthamiana plants by TbLCYNV, and impaired the accumulation of helper virus and co-inoculated alphasatellite. Our results provide the first evidence for recombination between two distinct types of satellites among geminivirus complex and highlight recombination as a driving force for geminivirus evolution.

A recombinant begomovirus resulting from exchange of the C4 gene

A begomovirus isolated from Malvastrum coromandelianum and tomato originating from Yunnan province (China) was shown to be representative of a new begomovirus species, for which the name tomato leaf curl Yunnan virus (TLCYnV) is proposed. TLCYnV has high levels of sequence identity to tomato yellow leaf curl China virus (TYLCCNV) across the whole genome, except for sequences encompassing the C4 gene. Agrobacterium-mediated inoculation showed TLCYnV to be highly infectious to a range of plant species but poorly infectious to M. coromandelianum. In contrast to TYLCCNV, TLCYnV was shown to infect tomato in the absence of a betasatellite. In field-collected samples, TLCYnV was identified most frequently in tomato in which it was not associated with a betasatellite. Transgenic expression in Nicotiana benthamiana showed that the C4 protein of TYLCCNV did not induce developmental abnormalities, whereas the C4 of TLCYnV induced severe developmental abnormalities, reminiscent of virus symptoms. The genome of TLCYnV was shown to be significantly less methylated in plants than that of TYLCCNV and the C4 protein of TLCYnV was shown to suppress post-transcriptional gene silencing and transcriptional gene silencing more effectively than the C4 of TYLCCNV. The results indicate that TLCYnV evolved from TYLCCNV by recombination, acquiring a more virulent C4, allowing it to dispense with the requirement for a betasatellite. The implications of these findings in relation to the evolution of monopartite begomoviruses are discussed.

A new, previously undescribed monopartite begomovirus infecting Premna serratifolia in Vietnam

The complete genome sequence of a monopartite begomovirus isolate infecting Creek Premna (Premna serratifolia L.) plants that exhibited leaf curl, vein swelling, and enation symptoms in Nha Trang, Vietnam, was cloned and sequenced. It comprises 2,753 nucleotides (JQ793786) and has a typical organization of begomoviruses DNA-A with AV1 and AV2 open reading frames (ORFs) in the viral-sense strand and AC1, AC2, AC3, AC4 and AC5 ORFs in the complementary-sense strand. The full-length genome sequence of the isolate (clone VN7) shared the highest level of nucleotide sequence identity (83 %) with the isolate IN:Pusa:Tb:10 of tobacco leaf curl Pusa virus (HQ180391). The phylogenetic relationship of VN7 to other begomoviruses was also investigated. VN7 grouped most closely with a clade containing begomoviruses from China, India and Japan. According to the current taxonomic criteria for the genus Begomovirus, family Geminiviridae, the isolate VN7 represents a new species, herein named "Premna leaf curl virus" (PrLCV).

Molecular characterization of a novel monopartite begomovirus isolated from Pouzolzia zeylanica in China

The complete genome sequence of a monopartite begomovirus isolate TY01 was obtained from diseased Pouzolzia zeylanica plants exhibiting golden mosaic symptoms in Baise, Guangxi Province, China. It consisted of 2723 nucleotides (nt) and encoded two ORFs (CP and AV2) in the virion-sense DNA and five ORFs (AC1-AC5) in the complementary-sense DNA. Compared with the DNA-A sequences of other begomoviruses, it has the highest (78.5 %) nucleotide sequence identity with ageratum yellow vein virus (AYVV) isolate AFSP6D from Thailand, which is less than the 89 % identity in the complete genome that has been defined as the threshold value for demarcation of species in the genus Begomovirus, family Geminiviridae. Phylogenetic analysis showed that TY01 was grouped in a separate clade from the other 28 begomovirus isolates. These results indicate that isolate TY01 is a member of a novel Begomovirus species, for which the name "Pouzolzia golden mosaic virus" (PGMV) is proposed.

Advances in understanding begomovirus satellites

Begomoviruses are numerous and geographically widespread viruses that cause devastating diseases in many crops. Monopartite begomoviruses are frequently associated with betasatellites or alphasatellites. Both betasatellite and alphasatellite DNA genomes are approximately half the size of begomovirus DNA genomes. Betasatellites are essential for induction of typical disease symptoms. The βC1 genes encoded by the betasatellites have important roles in symptom induction, in suppression of transcriptional and posttranscriptional gene silencing, and they can affect jasmonic acid responsive genes. Host plants of begomoviruses have evolved diverse innate defense mechanisms against the βC1 protein to counter these challenges. Alphasatellites have been identified mainly in monopartite begomoviruses that associate with betasatellites and have no known contributions to pathogenesis of begomovirus-betasatellite disease complexes. Applications of current molecular tools are facilitating viral diagnosis and the discovery of novel species of geminiviruses and satellite DNAs and are also advancing our understanding of the global diversity and evolution of satellite DNAs.