A Bipartite Geminivirus with a Highly Divergent Genomic Organization Identified in Olive Trees May Represent a Novel Evolutionary Direction in the Family Geminiviridae

Olea europaea Geminivirus (OEGV) was recently identified in olive in Italy through HTS. In this work, we used HTS to show the presence of an OEGV isolate in Portuguese olive trees and suggest the evolution direction of OEGV. The bipartite genome (DNA-A and DNA-B) of the OEGV-PT is similar to Old World begomoviruses in length, but it lacks a pre-coat protein (AV2), which is a typical feature of New World begomoviruses (NW). DNA-A genome organization is closer to NW, containing four ORFs; three in complementary-sense AC1/Rep, AC2/TrAP, AC3/REn and one in virion-sense AV1/CP, but no AC4, typical of begomoviruses. DNA-B comprises two ORFs; MP in virion sense with higher similarity to the tyrosine phosphorylation site of NW, but in opposite sense to begomoviruses; BC1, with no known conserved domains in the complementary sense and no NSP typical of bipartite begomoviruses. Our results show that OEGV presents the longest common region among the begomoviruses, and the TATA box and four replication-associated iterons in a completely new arrangement. We propose two new putative conserved regions for the geminiviruses CP. Lastly, we highlight unique features that may represent a new evolutionary direction for geminiviruses and suggest that OEGV-PT evolution may have occurred from an ancient OW monopartite Begomovirus that lost V2 and C4, gaining functions on cell-to-cell movement by acquiring a DNA-B component.

The Association between New World Alphasatellites and Bipartite Begomoviruses: Effects on Infection and Vector Transmission

Begomoviruses can be found in association with alphasatellites, which are capable of autonomous replication but are dependent on the helper begomovirus for systemic infection, encapsidation and vector transmission. Previous studies suggest that the presence of NW alphasatellites (genus Clecrusatellite) is associated with more severe symptoms. To better understand this interaction, we investigated the effects of two alphasatellites on infectivity, symptom development, viral DNA accumulation and vector transmission of three begomoviruses in three hosts. In tomato and Nicotiana benthamiana, all combinations were infectious. In Leonurus sibiricus, only the ToYSV/ToYSA combination was infectious. The presence of EuYMA increased symptom severity of EuYMV and ToYSV in N. benthamiana, and the presence of ToYSA was associated with more severe symptoms of ToYSV in N. benthamiana and L. sibiricus. EuYMA increased the accumulation of ToYSV in N. benthamiana but reduced the accumulation of EuYMV in tomato and of ToSRV in N. benthamiana. The presence of ToYSA decreased the accumulation of ToYSV in N. benthamiana and L. sibiricus. ToYSA negatively affected transmission of ToSRV by Bemisia tabaci MEAM1. Together, our results indicate that NW alphasatellites can interact with different begomoviruses, increasing symptom severity and interfering in the transmission of the helper begomovirus. Understanding this interaction is important as it may affect the emergence of diseases caused by begomovirus–alphasatellite complexes in the field.

Begomovirus Caboniensis: a New Bipartite Begomovirus Isolated From Cnidoscolus Urens in Brazil

A novel bipartite begomovirus infecting Cnidoscolus urens (Euphorbiaceae) from Pernambuco State, Brazil has been characterized. The complete DNA-A (2657 to 2692 nt) and DNA-B (2622 nt) components of the viral isolates showed a typical genome organization of New World bipartite begomoviruses. DNA-A of the isolates had the highest percentage of nucleotide identity (88.6–88.9%) with the Cnidoscolus mosaic leaf deformation virus (NC_038982). Based on the current classification criteria for the genus Begomovirus, a new member infecting C. urens was reported, and the name Begomovirus caboniensis was proposed for these viruses, adopting the standardized binomial system.

In Planta Interaction and Transreplication of Distinct Begomoviruses and their Associated Components

The studies described here were intended to examine the transreplication and interactions abilities of a widespread ToLCNDV, and an emerging begomovirus PeLCV associated with its cognate betasatellite TbLCuB. PeLCV, a monopartite begomovirus, has been characterized from many important crops, vegetables and weeds along with its associated TbLCuB. The DNA-B of bipartite ToLCNDV genome has been successfully transreplicated by the DNA-A of different bipartite begomoviruses, albeit with low frequency. Whether PeLCV can transreplicate DNA-B of ToLCNDV is unknown. To unravel this notion, both these viruses were inoculated to the model Nicotiana benthamiana plants in all possible combinations and the in planta existence of viral components were verified by PCR and Southern blot hybridization. The results demonstrated that PeLCV transreplicated and maintained ToLCNDV DNA-B. Whereas, ToLCNDV DNA-A could not transreplicate TbLCuB. Analyses of Rep proteins structure of ToLCNDV and PeLCV revealed a structural resemblance, whereas putative iteron-binding sequences of PeLCV were compatible with the Rep-binding iterons of ToLCNDV-B. The results suggested that PeLCV and ToLCNDV DNA-B can interact synergistically and can be disastrous under field conditions. © 2021 Friends Science Publishers

Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories

In the Caribbean Basin, malvaceous weeds commonly show striking golden/yellow mosaic symptoms. Leaf samples from Malachra sp. and Abutilon sp. plants with these symptoms were collected in Hispaniola from 2014 to 2020. PCR tests with degenerate primers revealed that all samples were infected with a bipartite begomovirus, and sequence analyses showed that Malachra sp. plants were infected with tobacco leaf curl Cuba virus (TbLCuCV), whereas the Abutilon sp. plants were infected with a new bipartite begomovirus, tentatively named Abutilon golden yellow mosaic virus (AbGYMV). Phylogenetic analyses showed that TbLCuCV and AbGYMV are distinct but closely related species, which are most closely related to bipartite begomoviruses infecting weeds in the Caribbean Basin. Infectious cloned DNA-A and DNA-B components were used to fulfilled Koch’s postulates for these diseases of Malachra sp. and Abutilon sp. In host range studies, TbLCuCV also induced severe symptoms in Nicotiana benthamiana, tobacco and common bean plants; whereas AbGYMV induced few or no symptoms in plants of these species. Pseudorecombinants generated with the infectious clones of these viruses were highly infectious and induced severe symptoms in N. benthamiana and Malachra sp., and both viruses coinfected Malachra sp., and possibly facilitating virus evolution via recombination and pseudorecombination. Together, our results suggest that TbLCuCV primarily infects Malachra sp. in the Caribbean Basin, and occasionally spills over to infect and cause disease in crops; whereas AbGYMV is well-adapted to an Abutilon sp. in the Dominican Republic and has not been reported infecting crops.

BEGOMOVIRUSES AND BETASATELLITES ASSOCIATED WITH CLCuD

Begomoviruses are one of the major types of plant viruses. They are transmitted by whitefly and cause many diseases. The CLCuD is the most damaging disease of cotton. It is the vector of begomoviruses, namely as monpartite or bipartite begomoviruses. Bipartite begomoviruses are consisted of A and B DNA molecuales. Monopatite consist of single genome. It is mainly linked with alphasatellites and betasatellites. Alphasatellites can replicate by using replication protein and not called as true satellites. Betasatellites are called as true satellites as they are linked with alphasatellites. Mainly cause tomato yellow leaf curl disease. Begomoviruses are different from other plant viruses as the basis of RNA genomes. DNA beta satellite is involves in suppressing the expressions of genes in plants. It has a major role in preventing RNA silencing by encoding proteins that binds with DNA and target the nucleus of cell. Affected plants show various symptoms such as leaf curling, enations etc. that cause loss in cotton field by preventing the growth. With the help of PCR, 1.4 kb fragments of DNA have been amplified from DNA template. For cloning the whole begomoviruses genome, a simple method of cloning has been widely used. Cloning is usually done by using the bacteriophage DNA polymerase. The betasatellites have shown association with CLCuD.

The AC2 Protein of a Bipartite Geminivirus Stimulates the Transcription of the BV1 Gene through Abscisic Acid Responsive Promoter Elements

Geminiviruses possess single-stranded, circular DNA genomes and control the transcription of their late genes, including BV1 of many bipartite begomoviruses, through transcriptional activation by the early expressing AC2 protein. DNA binding by AC2 is not sequence-specific; hence, the specificity of AC2 activation is thought to be conferred by plant transcription factors (TFs) recruited by AC2 in infected cells. However, the exact TFs AC2 recruits are not known for most viruses. Here, we report a systematic examination of the BV1 promoter (PBV1) of the mungbean yellow mosaic virus (MYMV) for conserved promoter motifs. We found that MYMV PBV1 contains three abscisic acid (ABA)-responsive elements (ABREs) within its first 70 nucleotides. Deleting these ABREs, or mutating them all via site-directed mutagenesis, abolished the capacity of PBV1 to respond to AC2-mediated transcriptional activation. Furthermore, ABRE and other related ABA-responsive elements were prevalent in more than a dozen Old World begomoviruses we inspected. Together, these findings suggest that ABA-responsive TFs may be recruited by AC2 to BV1 promoters of these viruses to confer specificity to AC2 activation. These observations are expected to guide the search for the actual TF(s), furthering our understanding of the mechanisms of AC2 action.

Ty-2 and Ty-3a Conferred Resistance are Insufficient Against Tomato Yellow Leaf Curl Kanchanaburi Virus from Southeast Asia in Single or Mixed Infections of Tomato

Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus that originated in the eastern Mediterranean, has spread worldwide, becoming a serious threat to tomato (Solanum lycopersicum L.) production. Southeast Asia is considered one of the hotspots for begomovirus diversity, and a wide variety of local begomovirus species distinct from TYLCV have been identified. In this study, the protection effect of introgressions of single TYLCV Ty resistance genes, Ty-2 and Ty-3a, in tomato was examined against inoculations of the bipartite begomoviruses Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) and Pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated from Indonesia. Our findings suggest that Ty-2 in the heterozygous state was found to be ineffective against PepYLCIV and TYLCKaV, whereas Ty-3a in the heterozygous state was effective against PepYLCIV and partially effective against TYLCKaV. Quantification of viral DNAs showed correlation between symptom expression and viral DNA accumulation. Moreover, mixed infections of TYLCKaV and PepYLCIV caused notably severe symptoms in tomato plants harboring Ty-3a. In cases of mixed infection, quantifying viral DNAs showed a relatively high accumulation of PepYLCIV, indicating that Ty-3a loses its effectiveness against PepYLCIV when TYLCKaV is also present. This study demonstrates the lack of effectiveness of Ty resistance genes against single and mixed infections of distinct local begomoviruses from Southeast Asia.

The AC2 Protein of a Bipartite Geminivirus Stimulates the Transcription of the BV1 Gene Through Abscisic Acid Responsive Promoter Elements

Geminiviruses possess single-stranded, circular DNA genomes, and control the transcription of their late genes, including BV1 of many bipartite begomoviruses, through transcriptional activation by the early expressing AC2 protein. DNA binding by AC2 is not sequence-specific, hence the specificity of AC2 activation is thought to be conferred by plant transcription factors (TFs) recruited by AC2 in infected cells. However, the exact TFs AC2 recruits are not known for most viruses. Here we report a systematic examination of the BV1 promoter (PBV1) of mungbean yellow mosaic virus (MYMV) for conserved promoter motifs. We found that MYMV PBV1 contains three abscisic acid (ABA)-responsive elements (ABREs) within its first 70 nucleotides. Deleting these ABREs, or mutating them all via site-directed mutagenesis, abolished the capacity of PBV1 to respond to AC2-mediated transcriptional activation. Furthermore, ABRE and other related ABA-responsive elements were prevalent in more than a dozen Old World begomoviruses we inspected. Together these findings suggest that ABA-responsive TFs may be recruited by AC2 to BV1 promoters of these viruses to confer specificity to AC2 activation. These observations are expected to guide the search for the actual TF(s), furthering our understanding of the mechanism of AC2 action.