Functional analysis of the naturally recombinant DNA-A of the bipartite begomovirus Tomato chlorotic mottle virus

Functional role of geminivirus encoded proteins in the host: Past and present

During plant-pathogen interaction, plant exhibits a strong defense system utilizing diverse groups of proteins to suppress the infection and subsequent establishment of the pathogen. However, in response, pathogens trigger an anti-silencing mechanism to overcome the host defense machinery. Among plant viruses, geminiviruses are the second largest virus family with a worldwide distribution and continue to be production constraints to food, feed, and fiber crops. These viruses are spread by a diverse group of insects, predominantly by whiteflies, and are characterized by a single-stranded DNA (ssDNA) genome coding for four to eight proteins that facilitate viral infection. The most effective means to managing these viruses is through an integrated disease management strategy that includes virus-resistant cultivars, vector management, and cultural practices. Dynamic changes in this virus family enable the species to manipulate their genome organization to respond to external changes in the environment. Therefore, the evolutionary nature of geminiviruses leads to new and novel approaches for developing virus-resistant cultivars and it is essential to study molecular ecology and evolution of geminiviruses. This review summarizes the multifunctionality of each geminivirus-encoded protein. These protein-based interactions trigger the abrupt changes in the host methyl cycle and signaling pathways that turn over protein normal production and impair the plant antiviral defense system. Studying these geminivirus interactions localized at cytoplasm-nucleus could reveal a more clear picture of host-pathogen relation. Data collected from this antagonistic relationship among geminivirus, vector, and its host, will provide extensive knowledge on their virulence mode and diversity with climate change.

Current status, breeding strategies and future prospects for managing chilli leaf curl virus disease and associated begomoviruses in Chilli (Capsicum spp.)

Chilli leaf curl virus disease caused by begomoviruses, has emerged as a major threat to global chilli production, causing severe yield losses and economic harm. Begomoviruses are a highly successful and emerging group of plant viruses that are primarily transmitted by whiteflies belonging to the Bemisia tabaci complex. The most effective method for mitigating chilli leaf curl virus disease losses is breeding for host resistance to Begomovirus. This review highlights the current situation of chilli leaf curl virus disease and associated begomoviruses in chilli production, stressing the significant issues that breeders and growers confront. In addition, the various breeding methods used to generate begomovirus resistant chilli cultivars, and also the complicated connections between the host plant, vector and the virus are discussed. This review highlights the importance of resistance breeding, emphasising the importance of multidisciplinary approaches that combine the best of traditional breeding with cutting-edge genomic technologies. subsequently, the article highlights the challenges that must be overcome in order to effectively deploy begomovirus resistant chilli varieties across diverse agroecological zones and farming systems, as well as understanding the pathogen thus providing the opportunities for improving the sustainability and profitability of chilli production.

Geminivirus C5 proteins mediate formation of virus complexes at plasmodesmata for viral intercellular movement

Movement proteins (MPs) encoded by plant viruses deliver viral genomes to plasmodesmata (PD) to ensure intracellular and intercellular transport. However, how the MPs encoded by monopartite geminiviruses are targeted to PD is obscure. Here, we demonstrate that the C5 protein of tomato yellow leaf curl virus (TYLCV) anchors to PD during the viral infection following trafficking from the nucleus along microfilaments in Nicotiana benthamiana. C5 could move between cells and partially complement the traffic of a movement-deficient turnip mosaic virus (TuMV) mutant (TuMV-GFP-P3N-PIPO-m1) into adjacent cells. The TYLCV-C5 null mutant (TYLCV-mC5) attenuates viral pathogenicity and decreases viral DNA and protein accumulation, and ectopic overexpression of C5 enhances viral DNA accumulation. Interaction assays between TYLCV-C5 and the other eight viral proteins described in TYLCV reveal that C5 associates with C2 in the nucleus and with V2 in the cytoplasm and at PD. The V2 protein is mainly localized in the nucleus and cytoplasmic granules when expressed alone; in contrast, V2 forms small punctate granules at PD when co-expressed with C5 or in TYLCV-infected cells. The interaction of V2 and C5 also facilitates their nuclear export. Furthermore, C5-mediated PD localization of V2 is conserved in two other geminiviruses. Therefore, this study solves a long-sought-after functional connection between PD and the geminivirus movement and improves our understanding of geminivirus-encoded MPs and their potential cellular and molecular mechanisms.

Begomoviruses: what is the secret(s) of their success?

Begomoviruses constitute an extremely successful group of emerging plant viruses transmitted by whiteflies of the Bemisia tabaci complex. Hosts include important vegetable, root, and fiber crops grown in the tropics and subtropics. Factors contributing to the ever-increasing diversity and success of begomoviruses include their predisposition to recombine their genomes, interaction with DNA satellites recruited throughout their evolution, presence of wild plants as a virus reservoir and a source of speciation, and extreme polyphagia and continuous movement of the insect vectors to temperate regions. These features as well as some controversial issues (replication in the insect vector, putative seed transmission, transmission by insects other than B. tabaci, and expansion of the host range to monocotyledonous plants) will be analyzed in this review.

AC5 protein encoded by squash leaf curl China virus is an RNA silencing suppressor and a virulence determinant

Squash leaf curl China virus (SLCCNV) is a bipartite Begomovirus. The function of the protein AC5, which is encoded by SLCCNV, is unknown. Here, we confirmed that the 172-amino acids (aa) long AC5 protein of SLCCNV could suppress single-stranded RNA but not double-stranded RNA-induced post-transcriptional gene silencing (PTGS). Furthermore, we determined that the C-terminal domain (96–172 aa) of the AC5 protein was responsible for RNA silencing suppressor (RSS) activity via deletion mutant analysis. The AC5 protein can reverse GFP silencing and inhibit systemic silencing of GFP by interfering with the systemic spread of the GFP silencing signal. The SLCCNV AC5 protein was localized to both the nucleus and cytoplasm of Nicotiana benthamiana cells. Furthermore, deletion analysis showed that the putative nuclear localization signal (NLS, 102–155 aa) was crucial for the RNA silencing suppression activity of AC5. In addition, the AC5 protein elicited a hypersensitive response and enhanced potoao virus X (PVX) RNA accumulation in infected N. benthamiana plants. Using the infectious clones of the SLCCNV and SLCCNV-AC5 null mutants, mutational analysis confirmed that knockout of the AC5 gene abolished SLCCNV-induced leaf curl symptoms, showing SLCCNV AC5 is also a virulence determinant.

Manipulating resistance to mungbean yellow mosaic virus in greengram (Vigna radiata L): Through CRISPR/Cas9 mediated editing of the viral genome

Clustered regularly interspaced short palindromic repeats (CRISPR) associated protein (CRISPR/Cas9) is an adaptive immune system of bacteria to counter the impending viral pathogen attack. With persistent improvements, CRISPR has become a versatile tool for developing molecular immunity against viruses in plants. In the current report, we utilized the Cas9 endonuclease and dual 20 bp-gRNAs targeting two different locations in single-stranded DNA-A of AC1 (rep protein) and AV1 (coat protein) of mungbean yellow mosaic virus for achieving resistance in greengram. The cotyledonary nodal explants were infected with Agrobacterium strain EHA105 harboring pMDC100-Cas9 with AC1 and AV1 gRNA cassettes and generated transgenic plants. The integration of Cas9 and gRNA cassettes in the transformed plants of greengram were confirmed by PCR and dot blot assays. Agroinfiltrated T2 transgenic lines exhibited minimal mosaic symptoms. A drastic reduction in the accumulation of AC1 and AV1 was observed in T2 transformed lines. The T7EI assay indicated that AC1 fragments were edited at a frequency of 46%, 32%, 20%, and AV1 at 38.15%, 40%, and 21.36% in MYMV infected greengram lines T2-6-2-3, T2-6-4-4, and T2-6-4-7, respectively. The manipulation of resistance to MYMV through the editing of the pathogen genome using the CRISPR/Cas9 tool can be a powerful approach to combat viruses and develop resistance in greengram.

The novel C5 protein from tomato yellow leaf curl virus is a virulence factor and suppressor of gene silencing

Tomato yellow leaf curl virus (TYLCV) is known to encode 6 canonical viral proteins. Our recent study revealed that TYLCV also encodes some additional small proteins with potential virulence functions. The fifth ORF of TYLCV in the complementary sense, which we name C5, is evolutionarily conserved, but little is known about its expression and function during viral infection. Here, we confirmed the expression of the TYLCV C5 by analyzing the promoter activity of its upstream sequences and by detecting the C5 protein in infected cells by using a specific custom-made antibody. Ectopic expression of C5 using a potato virus X (PVX) vector resulted in severe mosaic symptoms and higher virus accumulation levels followed by a burst of reactive oxygen species (ROS) in Nicotiana benthamiana plants. C5 was able to effectively suppress local and systemic post-transcriptional gene silencing (PTGS) induced by single-stranded GFP but not double-stranded GFP, and reversed the transcriptional gene silencing (TGS) of GFP. Furthermore, the mutation of C5 in TYLCV inhibited viral replication and the development of disease symptoms in infected plants. Transgenic overexpression of C5 could complement the virulence of a TYLCV infectious clone encoding a dysfunctional C5. Collectively, this study reveals that TYLCV C5 is a pathogenicity determinant and RNA silencing suppressor, hence expanding our knowledge of the functional repertoire of the TYLCV proteome.

Insights into the multifunctional roles of geminivirus-encoded proteins in pathogenesis

Geminiviruses are a major threat to agriculture in tropical and subtropical regions of the world. Geminiviruses have small genome with limited coding capacity. Despite this limitation, these viruses have mastered hijacking the host cellular metabolism for their survival. To compensate for the small size of their genome, geminiviruses encode multifunctional proteins. In addition, geminiviruses associate themselves with satellite DNA molecules which also encode proteins that support the virus in establishing successful infection. Geminiviral proteins recruit multiple host factors, suppress the host defense, and manipulate host metabolism to establish infection. We have updated the knowledge accumulated about the proteins of geminiviruses and their satellites in the context of pathogenesis in a single review. We also discuss their interactions with host factors to provide a mechanistic understanding of the infection process.

The C5 protein encoded by Ageratum leaf curl Sichuan virus is a virulence factor and contributes to the virus infection

Earlier reports have indicated that begomoviruses encode four proteins (AC1/C1, AC2/C2, AC3/C3, and AC4/C4 proteins) using complementary-sense DNA as the template. In recent years, several reports have shown that some begomoviruses also encode an AC5/C5 protein from the complementary DNA strand, and these AC5/C5 proteins play different roles in virus infections. Here, we provide evidence showing that Ageratum leaf curl Sichuan virus (ALCScV), a monopartite begomovirus, also encodes a C5 protein that is important for disease symptom formation and can affect viral replication. Infection of Nicotiana benthamiana plants with a potato virus X (PVX)-based vector carrying the ALCScV C5 gene resulted in more severe disease symptoms and higher virus accumulation levels. ALCScV C5 protein can be found in the cytoplasm and the nucleus. Furthermore, this protein is also a suppressor of posttranscriptional gene silencing. Mutational analysis showed that knockout of C5 gene expression significantly reduced ALCScV-induced disease symptoms and virus accumulation, while expression of the C5 gene using the PVX-based vector enhanced ALCScV accumulation in coinfected N. benthamiana plants.

Maintenance of Cotton Leaf Curl Multan Betasatellite by Tomato Leaf Curl New Delhi Virus-Analysis by Mutation

Viruses of the genus Begomovirus (family Geminiviridae) are economically important phytopathogens that are transmitted plant-to-plant by the whitefly Bemisia tabaci. Most Old World (OW) begomoviruses are monopartite and many of these interact with symptoms and host range determining betasatellites. Tomato leaf curl New Delhi virus (ToLCNDV) is one of only a few OW begomoviruses with a bipartite genome (components known as DNA A and DNA B). Four genes [AV2, coat protein (CP), transcriptional-activator protein (TrAP), and AC4] of ToLCNDV were mutated and the effects of the mutations on infectivity, symptoms and the ability to maintain Cotton leaf curl Multan betasatellite (CLCuMuB) were investigated. Infectivity and virus/betasatellite DNA titer were assessed by Southern blot hybridization, PCR, and quantitative PCR. The results showed TrAP of ToLCNDV to be essential for maintenance of CLCuMuB and AV2 to be important only in the presence of the DNA B. AC4 was found to be important for the maintenance of CLCuMuB in the presence of, but indispensable in the absence of, the DNA B. Rather than being required for maintenance, the CP was shown to possibly interfere with maintenance of the betasatellite. The findings show that the interaction between a bipartite begomovirus and a betasatellite is more complex than just trans-replication. Clearly, multiple levels of interactions are present and such associations can cause additional significant losses to crops although the interaction may not be stable.

The AC5 protein encoded by Mungbean yellow mosaic India virus is a pathogenicity determinant that suppresses RNA silencing-based antiviral defenses

It is generally accepted that begomoviruses in the family Geminiviridae encode four proteins (from AC1/C1 to AC4/C4) using the complementary-sense DNA as template. Although AC5/C5 coding sequences are increasingly annotated in databases for many begomoviruses, the evolutionary relationships and functions of this putative protein in viral infection are obscure. Here, we demonstrate several important functions of the AC5 protein of a bipartite begomovirus, Mungbean yellow mosaic India virus (MYMIV). Mutational analyses and transgenic expression showed that AC5 plays a critical role in MYMIV infection. Ectopic expression of AC5 from a Potato virus X (PVX) vector resulted in severe mosaic symptoms followed by a hypersensitive-like response in Nicotiana benthamiana. Furthermore, MYMIV AC5 effectively suppressed post-transcriptional gene silencing induced by single-stranded but not double-stranded RNA. AC5 was also able to reverse transcriptional gene silencing of a green fluorescent protein transgene by reducing methylation of promoter sequences, probably through repressing expression of a CHH cytosine methyltransferase (DOMAINS REARRANGED METHYLTRANSFERASE2) in N. benthamiana. Our results demonstrate that MYMIV AC5 is a pathogenicity determinant and a potent RNA silencing suppressor that employs novel mechanisms to suppress antiviral defenses, and suggest that the AC5 function may be conserved among many begomoviruses.

Isolation and molecular characterization of a distinct begomovirus and its associated betasatellite infecting Hedyotis uncinella (Hook. et Arn.) in Vietnam

A begomovirus isolate VN1 associated with symptomatic Hedyotis uncinella Hook. et Arn. from Vietnam was characterized. The virus, which we provisionally name H. uncinella yellow mosaic virus (HUYMV), has a monopartite genome of 2,749 nucleotides (nts). Pairwise comparisons of DNA-A sequences showed that HUYMV had a maximum nt sequence identity with Soybean crinkle leaf virus (SbLCV) and Premna leaf curl virus (PLCuV) at 82.1 and 81.9 %, respectively, which are less than the 89 % identity in the complete genome, which has been used as the threshold value for demarcation of species in the genus Begomovirus, the family Geminiviridae. One recombination event was detected for HUYMV, which involves an unknown begomovirus as the major parent and Tomato leaf curl Philippines virus (ToLCPV) as the minor parent, with nt 2163 and nt 2452 as the beginning and ending breakpoints, respectively. A betasatellite was found to be associated with HUYMV. The betasatellite showed the highest nt sequence identity (70 %) with Tomato leaf curl Philippine betasatellite--[Philippines:Laguna2:2006]. The name H. uncinella yellow mosaic betasatellite [Vietnam: Binh Dinh: 2013] was proposed for the betasatellite.

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.

Tomato dwarf leaf virus, a New World begomovirus infecting tomato in Argentina

Begomovirus infection is becoming a threat in fresh-market tomato in Argentina, where mixed infections with begomoviruses are common. The complete sequence of a begomovirus isolate infecting tomato sampled in Salta was molecularly characterized. Phylogenetic analysis showed that this virus isolate is closely related to previously reported Brazilian, Bolivian and Argentinean begomoviruses. The associated symptoms in Nicotiana benthamiana and Solanum lycopersicum were determined by biolistic delivery of infectious DNA-A and DNA-B clones. This begomovirus isolate induced leaf mottling, rugosity and dwarfing, and growth retardation in tomato. Based on these symptoms, we propose the name of tomato dwarf leaf virus (ToDLV) for this new begomovirus.

Transreplication of a Tomato yellow leaf curl Thailand virus DNA-B and replication of a DNAbeta component by Tomato leaf curl Vietnam virus and Tomato yellow leaf curl Vietnam virus

The genomes of two tomato-infecting begomoviruses from Vietnam were cloned and sequenced. A new variant of Tomato leaf curl Vietnam virus (ToLCVV) consisting of a DNA-A component and associated with a DNAbeta molecule as well as an additional begomovirus tentatively named Tomato yellow leaf curl Vietnam virus (TYLCVV) consisting also of a DNA-A component were identified. To verify if monopartite viruses occurring in Vietnam and Thailand are able to transreplicate the DNA-B component of Tomato yellow leaf curl Thailand virus-[Asian Institute of Technology] (TYLCTHV-[AIT]) infectivity assays were performed via agroinoculation and mechanically. As result, the DNA-B component of TYLCTHV-[AIT] was transreplicated by different DNA-A components of viruses from Vietnam and Thailand in Nicotiana benthamiana and Solanum lycopersicum. Moreover, the TYLCTHV-[AIT] DNA-B component facilitated the mechanical transmission of monopartite viruses by rub-inoculation as well as by particle bombardment in N. benthamiana and tomato plants. Finally, defective DNAs ranging from 735 to 1457 nucleotides were generated in N. benthamiana from those combinations containing TYLCTHV-[AIT] DNA-B component.