Elimination of transcriptional interference between tandem genes in plant cells

Plant cells are commonly transformed with two or more tandemly arranged genes, but how orientation affects their expression is not well understood. We investigated the amount of transcriptional interference occurring between two adjacent genes by cloning luciferase and green fluorescent protein (GFP) genes (promoter--coding sequence--terminator) in all possible orientations and expressing the genes in tobacco protoplasts. When two genes are oriented head-to-tail (-->-->), the expression of the downstream gene was reduced 80% by the upstream gene. When two genes are oriented tail-to-tail (--><--), the expression of the upstream gene was reduced 53% by the expression of the downstream gene. There was no interference when the orientation was head-to-head (<---->). Using a chemically inducible gene expression system, we showed that the downstream gene expression was reduced 71% by the induction of an upstream gene. Inserting a mammalian transcription blocker sequence eliminated the interference between the genes in tail-to-tail orientation. The interference in the head-to-tail orientation was eliminated by inserting a 2322-bp lambda phage DNA fragment. The terminators in gene constructs did not prevent the transcriptional interference, and the interference was eliminated by designing the orientation of genes and by placing a transcription blocker or a lambda phage sequence between genes.

Possible emergence of new geminiviruses by frequent recombination

Although exchange of genetic information by recombination plays a role in the evolution of viruses, the extent to which it generates diversity is not clear. We analyzed genomes of geminiviruses for recombination using a new statistical procedure developed to detect gene conversions. Geminiviruses (family, Geminiviridae) are a group of plant viruses characterized by a genome of circular single-stranded DNA (approximately 2700 nucleotides in length) encapsidated in twinned quasi-isometric particles. Complete nucleotide sequences of geminiviruses were aligned, and recombination events were detected by searching pairs of viruses for sequences that are significantly more similar than expected based on random distribution of polymorphic sites. The analyses revealed that recombination is very frequent and occurs between species and within and across genera. Tests identified 420 statistically significant recombinant fragments distributed across the genome. The results suggest that recombination is a significant contributor to geminivirus evolution. The high rate of recombination may be contributing to the recent emergence of new geminivirus diseases.

Identification of replication specificity determinants in two strains of tomato leaf curl virus from New Delhi

We used two strains of tomato leaf curl virus from New Delhi to investigate specificity in replication of their cognate genomes. The strains share 94% sequence identity and are referred to as severe and mild on the basis of symptoms on tomato and tobacco. Replication assays in tobacco protoplasts and plants showed that a single amino acid change, Asn10 to Asp in the N terminus of Rep protein, determines specificity for replication of the two strains based upon its interaction with the origin of replication (ori) sequences. The change of Asp10 to Asn in Rep protein of the mild strain coupled with point mutations at the 3rd and 10th nucleotides of the 13-mer binding site altered its replication ability, resulting in increased levels of virus accumulation. Similarly, changing Asn10 to Asp in Rep protein of the severe strain impaired replication of the virus and altered its severe phenotype in plants. Site-directed mutations made in ori and Asn10 of Rep protein suggested that Asn10 recognizes the third base pair of the putative binding site sequence GGTGTCGGAGTC in the severe strain.

Molecular characterization of a plant mitochondrial chaperone GrpE

Escherichia coli DnaK (Hsp70) cooperates with DnaJ and GrpE in its essential role as a molecular chaperone. Function of mitochondrial Hsp70 (mHsp70) in protein folding and organellar import in eukaryotes is critically dependent on GrpE. We cloned two genes from tobacco (Nicotiana tabacum) BY2 cells based on peptide sequences from a purified protein. The predicted amino acid sequences of both clones resembled that of GrpE from E. coli and its homologues from eukaryotes, and a cDNA clone from Arabidopsis thaliana. One gene (Type 1) encoded a deduced protein that was identical to the purified protein while the other (Type 2) encoded a deduced protein that has 80% sequence identity to Type 1. Both tobacco and Arabidopsis thaliana GrpE homologues bound to DnaK and ATP inhibited this binding. The tobacco GrpE homologue contained a typical N-terminal mitochondrial target presequence of 64 residues and the presequence directed the green fluorescent protein to tobacco mitochondria. The tobacco GrpE homologue also associated with mHsp70 when reintroduced into BY2 protoplasts, and this association was disrupted by ATP. A three-dimensional structure for the tobacco GrpE homologue was modeled based on the X-ray structure of E. coli GrpE complexed with DnaK. The modeled structure has the same overall structure as E. coli GrpE. We propose that the tobacco GrpE homologue interacts with mHsp70 in a manner analogous to E. coli GrpE with DnaK and designate it as tobacco mitochondrial GrpE (NtmGrpE).

A phage single-stranded DNA (ssDNA) binding protein complements ssDNA accumulation of a geminivirus and interferes with viral movement

Geminiviruses are plant viruses with circular single-stranded DNA (ssDNA) genomes encapsidated in double icosahedral particles. Tomato leaf curl geminivirus (ToLCV) requires coat protein (CP) for the accumulation of ssDNA in protoplasts and in plants but not for systemic infection and symptom development in plants. In the absence of CP, infected protoplasts accumulate reduced levels of ssDNA and increased amounts of double-stranded DNA (dsDNA), compared to accumulation in the presence of wild-type virus. To determine whether the gene 5 protein (g5p), a ssDNA binding protein from Escherichia coli phage M13, could restore the accumulation of ssDNA, ToLCV that lacked the CP gene was modified to express g5p or g5p fused to the N-terminal 66 amino acids of CP (CP66:6G:g5). The modified viruses led to the accumulation of wild-type levels of ssDNA and high levels of dsDNA. The accumulation of ssDNA was apparently due to stable binding of g5p to viral ssDNA. The high levels of dsDNA accumulation during infections with the modified viruses suggested a direct role for CP in viral DNA replication. ToLCV that produced the CP66:6G:g5 protein did not spread efficiently in Nicotiana benthamiana plants, and inoculated plants developed only very mild symptoms. In infected protoplasts, the CP66:6G:g5 protein was immunolocalized to nuclei. We propose that the fusion protein interferes with the function of the BV1 movement protein and thereby prevents spread of the infection.

Distribution and diversity of geminiviruses in trinidad and tobago

ABSTRACT Seven crop and eight weed species from 12 agricultural locations in Trinidad and Tobago were assayed for the presence of whitefly-transmitted geminiviruses (WTGs) by using dot blot hybridization and polymerase chain reaction (PCR) amplification of the N-terminal coat protein sequence with degenerate primers. The amplified fragments were cloned and analyzed by restriction enzyme digestion to determine fragment length polymorphism among the cloned fragments. Representative clones were then sequenced and subjected to phylogenetic analysis to determine the sequence similarity to known WTGs. WTGs were found in every location sampled and in 10 of the 15 species investigated: Lycopersicon esculentum(tomato), Capsicum annuum (pepper), Capsicum frutescens (sweet pepper), Abelmoschus esculentus (okra), Phaseolus vulgaris (beans), Alternanthera tenella, Desmodium frutescens, Euphorbia heterophylla, Malva alceifolia, and Sida acuta. The geminiviruses infecting these plants were closely related to potato yellow mosaic virus from Venezuela (PYMV-VE) and tomato leaf curl virus from Panama (ToLCV-PA). However, in pepper, sweet pepper, okra, Alternanthera tenella, Euphorbia heterophylla, Des-modium frutescens, and in one sample of tomato, a PYMV-VE-related virus was found in mixed infections with a virus related to pepper huasteco virus. Full-length infectious DNA-A and DNA-B of a tomato-infecting geminivirus from Trinidad and Tobago were cloned and sequenced. DNA-A appears to be a recombinant derived from PYMV-VE or ToLCV-PA, and Sida golden mosaic from Honduras. The implications of these findings in the control of WTGs are discussed.

The role of AV2 ("precoat") and coat protein in viral replication and movement in tomato leaf curl geminivirus

We analyzed various mutants of tomato leaf curl virus-India to investigate the role of ORFs AV3, AV2, and coat protein (CP) in viral replication, movement, and symptom development. The results of these studies indicate that ORF AV3 does not encode a protein. Plants inoculated with infectious DNA which contained deletions in AV2 developed very mild symptoms and accumulated only low levels of both single-stranded (ss) and double-stranded (ds) viral DNA, whereas inoculated protoplasts accumulated both ss and dsDNA to wild-type levels, showing that AV2 is required for efficient viral movement. However, both plants and protoplasts inoculated with substitution, frameshift, and other similar mutations in AV2 accumulated low levels of viral DNA. The low levels of accumulation of DNA of these mutants were apparently not due to a defect in AV2 synthesis. Mutations in the CP caused a marked decrease in ssDNA accumulation in plants and protoplasts while increasing dsDNA accumulation in protoplasts. Mutations in both AV2 and CP behaved like AV2 mutants in plants and like CP mutants in protoplasts. The results demonstrated that multiple functions provided by AV2, BV1, BC1 are essential for viral movement, and that changes in A-component virion-sense mRNA structure or translation affect viral replication.

Classification and identification of geminiviruses using sequence comparisons

The genomes and ORFs of 36 geminiviruses were compared to obtain phylogenetic trees and frequency distributions of all possible pairwise comparisons with an objective to classify geminiviruses. Such comparisons show that geminiviruses form two distinct clusters of leafhopper-transmitted viruses that infect monocots (subgroup I) and whitefly-transmitted viruses that infect dicots (subgroup III), irrespective of the part of the genome considered. Of the two leafhopper-transmitted viruses that infect dicots, tobacco yellow dwarf virus has a sequence most similar to subgroup I viruses, and that of beet curly top virus differed depending upon the ORF considered. The distributions of identities within subgroups are significantly different suggesting that the taxonomic status of a particular isolate within a subgroup can be quantified. All the recognized strains of any one virus have greater than 90% sequence identity. It was observed that the 200 nucleotide intercistronic regions of geminiviruses are more variable than the remainder of the genome. The amino acid sequences of the coat protein (CP) of subgroup III viruses are more conserved than the remainder of the genome. However, a short N-terminal region (60-70 amino acids) of the CP is more variable than the rest of the CP sequence and is a close representation of the genome. PCR primers based on conserved sequences can be used to clone and sequence the N-terminal sequences of the CP of the geminiviruses; this sequence is sufficient to classify a virus isolate. A possible taxonomic structure for geminiviruses is proposed after considering the sequence comparisons and biological properties.

Tomato leaf curl geminivirus from India has a bipartite genome and coat protein is not essential for infectivity

Genomes of two isolates of tomato leaf curl geminivirus from India (ToLCV-India) have been sequenced. ToLCV-India contains A and B components, both of which are required for systemic movement and symptom development. The two isolates have 94% sequence identify but one isolate gave mild symptoms in Nicotiana benthamiana and tomato. The genome organization of ToLCV-India is similar to other whitefly-transmitted geminiviruses (WTGs) with bipartite genomes. However, it contains an additional ORF, AV3, that has not been reported for other WTGs. Its coat protein (CP) sequence is highly homologous to that of Indian cassava mosaic virus (90%). Two mutations that truncated the CP after amino acids 65 or 172 did not affect systemic movement and symptom development in either N. benthamiana or tomato. However, the symptoms caused by mutant viruses were different from those in plants infected with unmodified viruses, and plants infected with the mutants had markedly reduced amounts of single-stranded viral DNA. Comparison of sequences and other biological features of ToLCV-India with other geminiviruses showed that ToLCV-India is a distinct virus and is related to the WTGs from the Old World. It is similar to African cassava mosaic virus in its requirement for B component and dispensability of coat protein for symptom development, unlike other geminiviruses that infect tomato in the Old World. It is proposed that ToLCV-India evolved more recently as compared to other geminiviruses that infect tomato in the Old World.

Inheritance of resistance to stem rust in six wheat lines having adult plant resistance

Inheritance of resistance to race 15B-1 of stem rust (Puccinia graminis Pers. f. sp. tritici Eriks, and Henn.) was studied in six lines of wheat (Triticum aestivum L.) having adult plant resistance. The six lines were crossed to a susceptible line and the progenies were advanced to the F5 generation by the single seed descent method. From 91 to 135 F5-derived F7 lines from each cross were tested with race 15B-1 in field nurseries and selected lines were tested in a multirace nursery. The number of genes controlling resistance was estimated by grouping the F7 lines into those as resistant as the resistant parent and other lines, and testing against the ratios expected with various numbers of genes. In 1982, for all six crosses, the segregations fit best to either three- or four-gene ratios. The mean rust severities for the F7 lines in each cross were concentrated at the susceptible end of the distribution. Apparently the genes for resistance had small effects that were multiplicative rather than additive. Under lighter epiphytotics in 1983 and 1984, additional F7 lines were classified as resistant as the resistant parents. The F7 lines were generally more resistant to the multirace mixture than to race 15B-1. The resistant parents probably carried genes for specific seedling resistance to some of the races but in some cases may have carried additional genes for adult plant resistance.Key words: stem rust, Puccinia graminis tritici, wheat, Triticum aestivum, adult plant resistance.

Inheritance of resistance to stem rust in 'Bonza', 'Chris', 'FKN-II-50-17', 'MRFY', 'Thatcher', 'Marquillo', and 'Hope' wheats

Resistance to stem rust (Puccinia graminis Pers. f. sp. tritici Eriks, and Henn.), particularly adult plant resisitance to race 15B-1, was studied in seven wheat (Triticum aestivum L.) cultivars or lines: 'Bonza', 'Chris', 'FKN-II-50-17', 'MRFY', 'Thatcher', 'Marquillo', and 'Hope'. Each of the seven was crossed with a susceptible parent and either F4- or F5-derived lines developed by single seed descent. All of the lines were tested with race 15B-1 in field nurseries. Lines derived from parents carrying seedling resistance to race 15B-1 were also tested as seedlings in the greenhouse with race 15B-1, and in some cases races 56, 29, and C65. The data indicated that 'Bonza' carries Sr6, probably Sr5, an unidentified gene giving resistance to race 56, two unidentified genes for resistance to race C65, and two minor genes that combine to produce intermediate adult plant resistance. 'Chris' carries Sr5, Sr7a, Sr8a, and Sr12. In addition, it may have three minor genes for adult plant resistance. 'FKN-II-50-17' carries Sr6 and may have four minor genes that combine to produce moderate adult plant resistance. 'MRFY', which is seedling susceptible to race 15B-1, carries Sr9b, possibly Sr5, plus an unidentified gene for resistance to C65. In addition, it appears to have one major gene for adult plant resistance plus two or more minor genes. 'Thatcher', 'Marquillo', and 'Hope' had only limited resistance to race 15B-1 in the field and no genetic analysis of their crosses was possible. The four parents that had good resistance to race 15B-1 in the field, 'Bonza', 'Chris', 'FKN-II-50-17', and 'MRFY', all carry minor genes for adult plant resistance that had little effect individually but produced moderate resistance when combined. The genes Sr5 and Sr9b, which have no effect on resistance to 15B-1 is seedlings, were found to significantly increase resistance in adult plants in the field.Key words: stem rust, Puccinia graminis tritici, wheat, Triticum aestivum, adult plant rust resistance.