Nucleotide sequence of bean golden mosaic virus and a model for gene regulation in geminiviruses

Random distribution of nucleotide polymorphism throughout the genome of tomato-infecting begomovirus species occurring in India: implication in PCR based diagnosis

Multiple begomovirus species are known to cause leaf curl disease in tomato in India. In order to develop specific and generic PCR based diagnostics for the tomato-infecting begomoviruses, in this study, we attempted to design primers initially based on the multiple alignment of the complete genome sequence of DNA-A component. However, the specific nucleotide stretches adequate for preparing specific primers could not be obtained. Alternatively, the online Primer-BLAST tool that offers designing of target-specific PCR primers was attempted to prepare specific primers targeting three clones (DNA-A) of tomato-infecting begomovirus species (Tomato leaf curl New Delhi virus, Tomato leaf curl Palampur virus and Tomato leaf curl Joydebpur virus) selected based on their sequence identity and phylogenetic relatedness. The primers derived from Primer-BLAST tool showed high level of cross-reaction among these begomovirus species and therefore were not able to differentiate these target begomovirus species. In order to understand the reason of cross-reactivity further sequence analysis revealed the high occurrence of single nucleotide variations (SNVs) compared to the multi-nucleotide stretches. There was no SNV hot-spot in the genome, rather the SNVs were randomly distributed throughout the genome of these begomovirus species. This pattern of nucleotide diversities among these tomato-infecting begomoviruses seriously implicated on developing specific PCR diagnostics. On the contrary, sequence analysis showed high sequence conservancy, which enabled to develop a generic PCR diagnostic for these begomoviruses. Our study, thus showed that the genome sequence diversity pattern among the tomato-infecting begomoviruses in India poses challenges in developing PCR based specific diagnostics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-022-00785-9.

Insights into Emerging Begomovirus-Deltasatellite Complex Diversity: The First Deltasatellite Infecting Legumes

Begomoviruses and associated DNA satellites are involved in pathosystems that include many cultivated and wild dicot plants and the whitefly vector Bemisia tabaci. A survey of leguminous plants, both crops and wild species, was conducted in Venezuela, an understudied country, to determine the presence of begomoviruses. Molecular analysis identified the presence of bipartite begomoviruses in 37% of the collected plants. Four of the six begomoviruses identified constituted novel species, and two others had not been previously reported in Venezuela. In addition, a novel deltasatellite (cabbage leaf curl deltasatellite, CabLCD) was found to be associated with cabbage leaf curl virus (CabLCV) in several plant species. CabLCD was the first deltasatellite found to infect legumes and the first found in the New World to infect a crop plant. Agroinoculation experiments using Nicotiana benthamiana plants and infectious viral clones confirmed that CabLCV acts as a helper virus for CabLCD. The begomovirus-deltasatellite complex described here is also present in wild legume plants, suggesting the possible role of these plants in the emergence and establishment of begomoviral diseases in the main legume crops in the region. Pathological knowledge of these begomovirus-deltasatellite complexes is fundamental to develop control methods to protect leguminous crops from the diseases they cause.

Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in southern Africa, including the South-west Indian ocean islands

The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.

Begomoviruses Associated with Bean Golden Mosaic Disease in Nicaragua

Begomovirus spp. cause substantial losses in bean crops in tropical and subtropical regions of the Americas. The predominant Begomovirus sp. in Central America associated with golden mosaic symptoms in bean is Bean golden yellow mosaic virus (BGYMV). However, Calopogonium golden mosaic virus was previously found to infect bean crops in the northern region of Costa Rica. The objective of this research was to identify Begomovirus spp. that infect bean plants in different geographical regions of Nicaragua. In all, 126 samples of young bean leaves with symptoms of golden mosaic were collected from eight different regions of Nicaragua. Using DNA hybridization with specific probes, 120 samples tested positive for BGYMV, 14 samples tested positive for Squash yellow mild mottle virus, and 7 samples tested positive for Calopogonium golden mosaic virus. Sequence analysis of polymerase chain reaction-amplified products from three samples (MA-9 Managua, BE-8 Rivas, and SO-9 Granada) also indicated that the symptoms of golden mosaic in bean are associated with viral sequences from three different Begomovirus spp. Management of bean golden mosaic disease must take into account that BGYMV is the predominant virus (95% of the samples) and that 12% of the samples exhibited possible mixed infections or recombination events in the south and central geographical regions of Nicaragua.

Molecular Cloning of Coat Protein Gene of an Indian Cotton Leaf Curl Virus (CLCuV-HS2) Isolate and its Phylogenetic Relationship with others Members of Geminiviridae

Cotton leaf curl geminivirus is a whitefly (Bemisia tabaci Genn.) transmitted Begomovirus (Family Geminiviridae) causing a serious disease of cotton in northern India. The very typical symptoms of present isolate (CLCuV-HS2) showed thickened veins, dark green discoloration of the leaves with upward curling and leaf like structure known as enation (one in number), which develops into cup-shaped on the reverse side of leaves. The polymerase chain reaction (PCR) based technique can detect the viral DNA in samples stored upto 3 days after the collection and have wide application for the field diagnosis. The complete nucleotide sequence of the Indian isolate of cotton leaf curl geminivirus (CLCuV-HS2) coat protein (CP) gene component was determined using CP specific primers through PCR amplification from field infected cotton plants growing in Haryana, India. Comparison of the amino acid sequence of the putative CP with some other mono and bipartite geminiviruses revealed a maximum of 97.3% identity with Pakistan cotton leaf curl virus (CLCuV-62). A nuclear localization signal located close to the N-terminal of CP gene was determined.

Pathogenicity of a natural recombinant associated with ageratum yellow vein disease: implications for geminivirus evolution and disease aetiology

Yellow vein disease of Ageratum conyzoides is caused by a viral DNA complex consisting of the genomic component (DNA A) of the monopartite begomovirus Ageratum yellow vein virus (AYVV, family: Geminiviridae) and a small satellite-like DNA beta component. AYVV DNA A is unable to induce symptoms in this host alone but can systemically infect A. conyzoides in which it accumulates to low levels. Here, we demonstrate that the yellow vein phenotype can also be produced by co-inoculating A. conyzoides with AYVV DNA A and recDNA-Abeta17, a naturally occurring recombinant of approximately the same size as DNA beta that contains sequences from both DNA A and DNA beta. Symptoms induced by DNA A and recDNA-Abeta17 in A. conyzoides and Nicotiana glutinosa are qualitatively similar to those associated with DNA A and DNA beta although milder. Recombination between DNA A and DNA beta to produce a chimera resembling recDNA-Abeta17 was observed after whitefly transmission of the disease in A. conyzoides. Hence, such recombination events are likely to occur frequently, implying that recombinants will normally be associated with this type of disease complex in the field. Possible implications of these findings for the evolution of begomoviruses and the aetiology of their diseases are discussed.

Bean golden yellow mosaic virus from Chiapas, Mexico: Characterization, Pseudorecombination with Other Bean-Infecting Geminiviruses and Germ Plasm Screening

ABSTRACT The complete nucleotide (nt) sequences of the cloned DNA-A (2644 nts) and DNA-B (2609 nts) components of Bean golden yellow mosaic virus (BGYMV-MX) from Chiapas, Mexico were determined. The genome organization of BGYMV-MX is similar to that of other Western Hemisphere bipartite geminiviruses (genus Begomovirus). Infectivity of the cloned BGYMV-MX DNA components in common bean (Phaseolus vulgaris) plants was demonstrated by particle bombardment and agroinoculation. BGYMV-MX was identified as a BGYMV (previously type II BGMV) isolate based on sequence analyses, sap-transmissibility, and pseudorecombination experiments with other bean-infecting begomoviruses. On the basis of differences in the DNA-B hypervariable region, symptom phenotype, and properties of infectious pseudorecombinants, BGYMV-MX may represent a distinct strain of BGYMV. Pseudorecombination experiments further established that BGYMV symptom determinants mapped to DNA-B, and that BGYMV-MX was most closely related to BGYMV from Guatemala. A Tomato leaf crumple virus (TLCrV) DNA-A/BGYMV-MX DNA-B pseudorecombinant was infectious in bean, establishing that a viable reassortant can be formed between begomovirus species from different phylogenetic clusters. Bean germ plasm representing the two major gene pools (Andean and Mesoamerican) was screened for response to BGYMV-MX with three methods of inoculation: sap-inoculation, particle bombardment, and agroinoculation. Andean germ plasm was very susceptible and similar results were obtained with all three methods, whereas Mesoamerican germ plasm showed resistance to BGYMV-MX, particularly with agroinoculation.

Geminiviruses Infecting Tomato Crops in Nicaragua

Geminiviruses transmitted by whiteflies are believed to be responsible for the devastating epidemic in tomato crops in Nicaragua, as well as in other Central American countries. Polymerase chain reaction with degenerate primers was used to amplify partial sequences of the geminivirus coat protein gene from samples of diseased tomato plants collected from the major tomato-growing areas of Nicaragua. The data indicated the presence of geminiviruses in all tested regions of the country. DNA sequence analysis and phylogenetic analysis of the amplified sequences showed that they corresponded to four different geminiviruses related to the other begomoviruses native to the Americas. One of the viruses, which was detected in three regions of Nicaragua, is probably Sinaloa tomato leaf curl virus. The sequences of two of the other detected viruses showed close relationships with several geminiviruses, including Tomato mottle virus, Tomato leaf crumple virus, and Sida golden mosaic virus, all of which previously have been reported from Central America. The fourth virus is closely related at sequence level to a tomato-infecting geminivirus from Honduras, putatively designated Tomato mild mottle virus. This virus seems to be different from the other known American begomoviruses because it groups separately in the phylogenetic analysis.

Biotic, molecular, and phylogenetic characterization of bean calico mosaic virus, a distinct begomovirus species with affiliation in the squash leaf curl virus cluster

ABSTRACT Bean calico mosaic virus (BCMoV), a whitefly-transmitted geminivirus from Sonora, Mexico, was purified, and the genome components were cloned and sequenced. Purified viral fractions and cloned genome components were infectious by biolistic inoculation to bean, completing Koch's postulates for both. The B biotype of the whitefly Bemisia tabaci efficiently transmitted both native virus and progeny virus derived from cloned DNA inoculum. Host ranges of native virus and of progeny virus derived from cloned DNA were identical based upon whitefly and biolistic mediated transmission, respectively. BCMoV has a relatively wide experimental host range among begomoviruses known to infect bean, encompassing genera and species within the Fabaceae, Malvaceae, and Solanaceae. BCMoV has a bipartite genome, as do other New World begomoviruses. BCMoV DNA-A shared highest nucleotide sequence identities with squash leaf curl virus-E strain (SLCV-E) and cabbage leaf curl virus (CaLCV) at 80.1 and 80.7%, respectively. BCMoV DNA-B shared highest nucleotide sequence identity with SLCV-E at 70.7%. The common region (CR) sequences of BCMoV and SLCV-E are 73 to 76% identical; however, modular cis-acting elements within the CR involved in replication origin function and recognition are 100% conserved. Phy-logenetic analysis indicated that BCMoV DNA-A shares a most recent common ancestor with the DNA-A of two viruses that also occur in the Sonoran Desert, SLCV-E and Texas pepper virus (TPV-TAM), and CaLCV from Florida. In contrast, a phylogenetic analysis indicated that BCMoV DNA-B shares a most recent common ancestor with SLCV-E; whereas DNA-B of CaLCV clustered in a separate clade with pepper hausteco virus. Collectively, biological and molecular characteristics indicate that BCMoV is a distinct begomovirus species with the northernmost distribution of any begomovirus isolated from bean in the Americas. Furthermore, the phylogenetic relationships of begomovirus cognate components are not necessarily identical, suggesting that DNA-A and DNA-B of some begomoviruses may have different evolutionary histories.

Variability in Geminivirus Isolates Associated with Phaseolus spp. in Brazil

ABSTRACT Bean golden mosaic geminivirus (BGMV) is the single most devastating virus of common beans in the tropical and subtropical Americas and the Caribbean Basin. The BGMV from Brazil, named BGMV-BZ, is considered distinct from BGMV-PR isolates from Puerto Rico, Guatemala, and the Dominican Republic because of DNA sequence data, the ability to form pseudorecombinants, and mechanical transmissibility properties. In bean-growing areas of Brazil, samples were collected from beans, lima beans, and the weed Leonurus sibiricus displaying typical symptoms of infection by geminiviruses. Viral DNA fragments comprising part of the rep gene, the common region, and part of the cp gene were amplified by polymerase chain reaction, cloned, and sequenced. The bean samples had geminivirus with sequences nearly identical to that of BGMV-BZ collected in Goiânia, state of Goiás, in 1986. The sample from lima bean contained a new species of geminivirus that induces symptoms similar to those induced by BGMV-BZ and was named lima bean golden mosaic virus (LBGMV-BR). While all sequences from bean samples clustered with BGMV-BZ, the sequence from the lima bean isolate stood alone. A mixed infection with abutilon mosaic geminivirus was also found in a single sample from the state of São Paulo. DNA sequence comparisons indicate that the virus isolate from L. sibiricus represents a new geminivirus species, designated here as leonurus mosaic virus.

Sinaloa Tomato Leaf Curl Geminivirus: Biological and Molecular Evidence for a New Subgroup III Virus

ABSTRACT The biological and molecular properties of Sinaloa tomato leaf curl virus (STLCV) were investigated in line with the hypothesis that STLCV is a previously uncharacterized, whitefly-transmitted geminivirus from North America. STLCV causes yellow leaf curl symptoms in tomato and yellow-green foliar mottle in pepper. Five species belonging to two plant families were STLCV experimental hosts. STLCV had a persistent relationship with its whitefly vector, Bemisia tabaci. Polymerase chain reaction fragments of STLCV common region (CR) sequences of the A or B genomic components and the viral coat protein gene (AV1) were molecularly cloned and sequenced. The STLCV A- and B-component CR sequences (174 nucleotides each) shared 97.9% identity and contained identical cis elements putatively involved in transcriptional regulation and an origin of replication (the AC cleavage site within the loop of the hairpin structure and two direct repeat sequences thought to constitute the Rep binding motif), which collectively are diagnostic for subgroup III geminiviruses. The STLCV CR sequence shared 23.1 to 77.6% identity with CR sequences of representative geminiviridae, indicating the STLCV CR sequence is unique. Molecular phylogenetic analysis of CR or AV1 sequences of STLCV and the respective sequences of 31 familial members supported the placement of STLCV as a unique bipartite, subgroup III virus most closely related to other viruses from the Western Hemisphere. STLCV is provisionally described as a new species within the genus Begomovirus, family Geminiviridae.

The nucleotide sequence and genome structure of mung bean yellow mosaic geminivirus

Complete nucleotide sequences of the infectious cloned DNA components (DNA 1 and DNA 2) of mung bean yellow mosaic virus (MYMV) were determined. MYMV DNA 1 and DNA 2 consists of 2,723 and 2,675 nucleotides respectively. DNA 1 and DNA 2 have little sequence similarity except for a region of approximately 200 bases which is almost identical in the two molecules. Analysis of open reading frames revealed nine potential coding regions for proteins of mol. wt. > 10,000, six in DNA 1 and three in DNA 2. The nucleotide sequence of MYMV DNA was compared with that of bean golden mosaic virus (BGMV), tomato golden mosaic virus (TGMV) and African cassava mosaic virus (ACMV). The 200-base region common to the two DNAs of each virus had little sequence similarity, except for a highly conserved 33-36 base sequence potentially capable of forming a stable hairpin structure. The potential coding regions in the MYMV DNAs had counterparts in the BGMV, TGMV and ACMV, suggesting an overall similarity in genome organization, except for absence of 1L3 in MYMV DNA 1. The most highly conserved ORFs, MYMV 1R1, BGMV 1R1, TGMV 1R1 and ACMV 1R1, are the putative genes for the coat proteins of MYMV, BGMV, TGMV and ACMV, respectively. MYMV 1L1 has also a high degree of sequence similarity with BGMV 1L1, TGMV 1L1 and ACMV 1L1.

Tomato yellow leaf curl virus from Sardinia is a whitefly-transmitted monopartite geminivirus

The genome of an isolate of tomato yellow leaf curl virus from Sardinia, Italy (TYLCV-S), a geminivirus transmitted by the whitefly Bemisia tabaci, has been cloned and sequenced. The single circular DNA molecule comprises 2770 nucleotides. Genome organisation closely resembles that of the DNA A component of the whitefly-transmitted geminiviruses with a bipartite genome. A 1.8 mer of the TYLCV-S genome in a binary vector of Agrobacterium tumefaciens is infectious upon agroinoculation of tomato plants. Typical tomato yellow leaf curl disease symptoms developed about three weeks after inoculation. The disease was transmitted by the natural vector B.tabaci from agroinfected plants to test plants, reproducing in this way the full biological cycle and proving that the genome of TYLCV-S consists of only one circular single-stranded DNA molecule. Contrary to the other whitefly-transmitted geminiviruses described so far, there is no evidence for the existence nor the necessity of a second component (B DNA) in the TYLCV-S genome.

Wheat dwarf virus vectors replicate and express foreign genes in cells of monocotyledonous plants

Wheat dwarf virus (WDV) is a geminivirus that infects monocotyledonous plants. To exploit the potential of WDV as a replicative gene vector, we developed a transient replication and expression system based on the transfection of protoplasts derived from Triticum monococcum suspension culture cells. Cloned genomic copies of various WDV isolates as well as mutants constructed in vitro were introduced into the protoplasts and assayed for their ability to replicate. As a result, regions of the WDV genome necessary or dispensable for the viral DNA replication could be defined. In addition, the gene encoding the viral capsid protein was replaced by three different bacterial marker genes, neomycin phosphotransferase, chloramphenicol acetyltransferase, and beta-galactosidase. The beta-galactosidase gene doubled the size of the WDV genome. The replication of the recombinant WDV genomes and the expression of these genes were monitored in suspension culture cells of T. monococcum. The potential of replicative expression vectors based on the WDV genome is discussed.

Computer analysis between nucleotide and amino acid sequences of bean golden mosaic virus and those of maize streak, wheat dwarf, chloris striate mosaic, and beet curly top viruses

Bean golden mosaic virus (BGMV) DNA 1 and 2 have little sequence homology with maize streak virus (MSV), wheat dwarf virus (WDV), and chloris striate mosaic virus (CSMV) DNAs. BGMV DNA 1 and beet curly top virus (BCTV) DNA are closely related, whereas BGMV DNA 2 and BCTV DNA are not related. Direct amino acid homologies of predicted proteins between BGMV ORFs and MSV ORFs, WDV ORFs or CSMV ORFs were 40-50%. BGMV 1L1 and BCTV L1, and BGMV IL3 and BCTV L4 were highly conserved. The sequence TAATATTAC was detected in the loops of hairpin structures of 5 gemini-viruses.

Comparative analysis of alternating purine-pyrimidine tracts and potential Z-DNA sequences in DNA plant viruses

The DNAs of several plant viruses were analyzed for the presence of alternating purine-pyrimidine sequences that can potentially undergo B to Z transition. The DNA of the caulimoviruses (plant retroviruses) was compared with that of the geminiviruses, with the cDNA of an RNA plant virus, and with several computer-generated random sequences. Our analysis indicates that potential Z-DNA sites tend to be restricted in the DNA of the caulimoviruses, whereas the same does not occur significantly in the other viral DNAs examined. This result is discussed in relation to the mode of replication of the caulimoviral DNA and offers additional evidence of the existence of selection processes regulating the frequency and distribution of the Z-DNA sites in the different genomes.

Molecular variation in vector-borne plant viruses: epidemiological significance

Patterns of variation are examined in four groups of plant viruses, with special reference to their particle proteins and to changes in vector transmissibility and specificity. In the nepoviruses and potyviruses, non-circulative transmission, by nematodes and aphids respectively, seems dependent on structural features on the surface of the virus particles. The N-terminal part of the particle protein may play the key role in potyviruses. Similarly in the luteoviruses, and possibly in the geminiviruses, specificity of circulative transmission by aphids, whiteflies and leafhoppers is linked to the antigenic specificity of the virus particles. Among naturally occurring isolates of the same virus, variation seems often to be discontinuous, and is predominantly of two sorts. Minor variations, characterized by loss of an epitope or substitutions of a few amino acids, can be associated with loss of transmissibility in luteoviruses and potyviruses, or have no effect. Major variations are associated with differences in vector specificity and seem likely to involve radical genetic changes that have evolved over long periods. The adaptation of virus particle proteins for transmission by vectors probably results in conservation of the genes that encode them, and in greater conservation of some parts of these genes than of others.

Genetic analysis of the tomato golden mosaic virus. II. The product of the AL1 coding sequence is required for replication

Tomato golden mosaic virus (TGMV) belongs to the geminivirus subgroup that is characterized by a split genome consisting of two single-stranded circular DNAs. The TGMV A genome component encodes the virus coat protein as well as all of the functions necessary for viral DNA replication. Analysis of the nucleotide sequence indicates that the TGMV A component has, in addition to the coat protein encoding ORF, four overlapping open reading frames (ORFs) with the potential to encode proteins of greater than 10 kD. We have investigated the functions of these putative proteins in both symptom formation and DNA replication by creating mutations in each of the ORFs. Our results show that the AL4 ORF, which is encoded within the N-terminal region of ORF AL1, is not essential for normal virus infection. In contrast, we find that disruption of the AL3 ORF results in delay and attenuation of symptom formation. We also report that the products of the AL1 and AL2 ORFs are absolutely required for symptom formation. Studies of DNA replication show that only the AL1 open reading frame is essential for viral DNA synthesis. The significance of these results for the development of vectors from the geminiviruses is discussed.

Potential gene products of bean golden mosaic virus have higher sequence homologies to those of tomato golden mosaic virus than to those of cassava latent virus

Comparison of the nucleotide sequences of the DNAs of bean golden mosaic virus (BGMV), tomato golden mosaic virus (TGMV) and cassava latent virus (CLV) revealed a fairly close relationship between BGMV DNA1, TGMV DNA1, and CLV DNA1 and a comparatively distant relationship between BGMV DNA2, TGMV DNA2, and CLV DNA2. The 200-base region common to the two DNAs of each virus had little sequence homology, except for a highly conserved 33-36 base sequence potentially capable of forming a stable hairpin structure. All the potential coding regions in the BGMV DNAs had counterparts in the TGMV and CLV DNAs suggesting an overall similarity in genome organization but two potential coding regions in the BGMV DNAs had no counterparts in the TGMV DNAs. The most highly conserved ORFs, BGMV 1R1, TGMV 1R1, and CLV 1R1, are the putative genes for the coat proteins of BGMV, TGMV, and CLV. BGMV 1R1 has 91.9% and 71.6% homology with respect to TGMV and CLV. The ORFs (BGMV 1L1; CLV 1L1; TGMV 1L1) and the two smaller overlapping ORFs (BGMV 1L2, 1L3; TGMV 1L2, 1L3; CLV 1L5, 1L3) are conserved in the three viruses. BGMV 2R1 and BGMV 2L1 have higher homology with respect to TGMV but not with respect to 2R1 and 2L1 in CLV. From this study we conclude that BGMV is more closely related to TGMV than CLV.

Infectivity and complete nucleotide sequence of the genome of a South African isolate of maize streak virus

The complete infectious genome of a South African isolate of the geminivirus maize streak (MSV-S) has been cloned, characterized, and sequenced. Using an A. tumefaciens Ti plasmid delivery system, the cloned -2.7 kb single circular MSV component was shown to be necessary and sufficient for infection of maize. Based on sequence analysis of the infectious clone, MSV-S is highly homologous to the previously characterized Kenyan and Nigerian isolates. While the genomic organization of MSV-S has elements in common with each of these previously characterized isolates, it is identical to neither and its analysis addresses the discrepancies between them. The result is a somewhat simplified and unified picture of the viral genome, the structural organization of which is essentially identical to that of wheat dwarf virus.

Independent encapsidation of tomato golden mosaic virus A component DNA in transgenic plants

Tomato golden mosaic virus (TGMV), a member of the geminivirus group, has a genome consisting of two DNA molecules designated the A and B components. Both are required for infectivity in healthy plants, although the former has been shown to replicate independently in transgenic plants containing tandem direct repeats of the A genome component. In the studies presented here, petunia plants transgenic for either both components (A×B hybrids) or the A component alone were examined for the presence of virus particles and encapsidated, single stranded viral DNA. The results of DNase protection experiments and direct observation of extracts from transgenic plants by electron microscopy indicate that single stranded TGMV DNA is in both cases packaged into paired particles identical to those obtained from virus-infected plants. DNase-treated virions isolated from A×B hybrid petunia are infectious when inoculated onto healthy Nicotiana benthamiana. Likewise, virions obtained from transgenic A petunia are infectious for plants transgenic for the B component.Our observations of TGMV replication in transgenic plants indicate that TGMV A DNA encodes all viral functions necessary for the replication and encapsidation of viral DNA. The possible role of the B component in TGMV replication is discussed.

Total nucleotide sequences of the infectious cloned DNAs of bean golden mosaic virus

Complete nucleotide sequences of the infectious cloned DNA components (DNA A and B) of bean bolden mosaic virus were determined. The DNA A (2585 nucleotides) and DNA B (2647 nucleotides) have little sequence homology with each other, but both A and B contain a common region of 205 nucleotides. A possible large hairpin structure is detected in the common region. Nucleotide sequences of DNAs A and B revealed the presence of 8 potential coding regions for proteins (m.w. greater than 10,000). Among them, four open reading frames (ORFs 1-4) encode proteins of m.w. 30,000 or greater, and are individually coded in virion DNA A and B senses (+) and their complementary senses (-), respectively. The other four ORFs 5-8 are in virion DNA B(+) and its complementary sense (-). All of the ORFs 1-4 have regulatory signals for RNA synthesis (TATAA/T) in the region 5' upstream from a potential start codon ATG.

The nucleotide sequence of tobacco vein mottling virus RNA

The nucleotide sequence of the RNA of tobacco vein mottling virus, a member of the potyvirus group, was determined. The RNA was found to be 9471 residues in length, excluding a 3'-terminal poly(A) tail. The first three AUG codons from the 5'-terminus were followed by in-frame termination codons. The fourth, at position 206, was the beginning of an open reading frame of 9015 residues which could encode a polyprotein of 340 kDa. No other long open reading frames were present in the sequence or its complement. This AUG was present in the sequence AGGCCAUG, which is similar to the consensus initiation sequence shared by most eukaryotic mRNAs. The chemically-determined amino acid compositions of the helper component and coat proteins were similar to those predicted from the nucleotide sequence. Amino acid sequencing of coat protein from which an amino-terminal peptide had been removed allowed exact location of the coat protein cistron. A consensus sequence of V-(R or K)-F-Q was found on the N-terminal sides of proposed cleavage sites for proteolytic processing of the polyprotein.

DNA and RNA polymerase activities of nuclei and hypotonic extracts of nuclei isolated from tomato golden mosaic virus infected tobacco leaves

Nuclei and hypotonically leached extracts of nuclei prepared from tomato golden mosaic virus (TGMV)-infected Nicotiana benthamiana leaves have been used in in vitro DNA and RNA polymerisation reactions. The synthesis of virus-specific DNA was resistant to aphidicolin, sensitive to N-ethylmaleimide and dideoxy TTP, and stimulated by KC1 and ATP. Variably virion (+) and complementary (-) strand DNA of both the A and B genomic components were synthesised. Virus-specific RNA was synthesised in reactions which were initiated prior to nuclei isolation and leaching. From inhibitor studies and salt requirements RNA synthesis appeared to be catalysed by a DNA-dependent RNA polymerase type II enzyme. Both components of the TGMV genome were transcribed in a bidirectional fashion with a prevalence in some experiments of transcripts derived from DNA component A.

Bidirectional transcription of maize streak virus DNA and identification of the coat protein gene

Three RNA transcripts encoded by maize streak virus DNA were detected in polyadenylated RNA from virus-infected maize leaves. Two of the transcripts, a major 0.9 kb and a minor 1.05 kb RNA, were mapped on the virion (+) sense DNA and the other minor transcript of 1.2 kb was mapped on the complementary (-) sense DNA, demonstrating that transcription of MSV DNA was bidirectional. The two virion sense transcripts were 3' coterminal at nucleotide 1114 but had 5' termini at nucleotides 2682 and 163 respectively. Virus-specific polyadenylated RNA translated in vitro to produce a 28,000 MW polypeptide, specifically immunoprecipitable by antiserum raised against whole virus. The mRNA for this protein was mapped by hybrid-arrested translation to the long open reading frame in virion sense DNA whose potential amino acid composition, calculated from nucleotide sequence data, closely agreed with that determined experimentally for the coat protein.