Replicative intermediates of maize streak virus found during leaf development

Erdmann, Julia B.; Shepherd, Dionne N.; Martin, Darren P.; Varsani, Arvind; Rybicki, Edward P.; Jeske, Holger

doi:10.1099/vir.0.017574-0

Cited by 28 publications

(20 citation statements)

References 18 publications

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“…It should be possible to test this model using two-dimensional gel electrophoresis to look for the spe- cific branched replication intermediates predicted to occur near the termini during replication. This technique has been used successfully to monitor the replication of viruses utilizing RCR, such as maize streak virus (11). Evolutionary considerations.…”

Section: Discussionmentioning

confidence: 99%

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication

Oke

Kerou

Liu

et al. 2011

J Virol

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The Rudiviridae are a family of rod-shaped archaeal viruses with covalently closed, linear double-stranded DNA (dsDNA) genomes. Their replication mechanisms remain obscure, although parallels have been drawn to the Poxviridae and other large cytoplasmic eukaryotic viruses. Here we report that a protein encoded in the 34-kbp genome of the rudivirus SIRV1 is a member of the replication initiator (Rep) superfamily of proteins, which initiate rolling-circle replication (RCR) of diverse viruses and plasmids. We show that SIRV Rep nicks the viral hairpin terminus, forming a covalent adduct between an active-site tyrosine and the 5 end of the DNA, releasing a 3 DNA end as a primer for DNA synthesis. The enzyme can also catalyze the joining reaction that is necessary to reseal the DNA hairpin and terminate replication. The dimeric structure points to a simple mechanism through which two closely positioned active sites, each with a single tyrosine residue, work in tandem to catalyze DNA nicking and joining. We propose a novel mechanism for rudivirus DNA replication, incorporating the first known example of a Rep protein that is not linked to RCR. The implications for Rep protein function and viral replication are discussed.Archaeal viruses display tremendous diversity of both morphology and genome content. Seven viral families from the Crenarchaeota have been described, all with linear or circular double-stranded DNA (dsDNA) genomes but with few genes in common (28). The Rudiviridae are a family of nonenveloped rod-shaped viruses infecting thermophilic crenarchaea (27). Members include SIRV1 and SIRV2 (24), ARV1 (36), and SRV1 (37), all of which have covalently closed linear dsDNA genomes of 30 to 40 kb encoding up to 50 open reading frames (ORFs). The genome arrangement, including the presence of inverted terminal repeats (ITRs), is reminiscent of those of the large cytoplasmic DNA viruses, such as the Poxviridae (3, 10). Replication of the poxvirus genome, which occurs in cytoplasmic DNA replication factories (29), results in the generation of head-to-head concatemers that are resolved by a Holliday junction-resolving enzyme (7, 12). The Rudiviridae also generate head-to-head intermediates, ruling out a rolling-circle mechanism of replication (24), and encode a resolving enzyme that is assumed to be required for the deconcatamerization of the replicated rudiviral genome (2). A replication model for rudiviruses has been postulated based on the observed similarities with the Poxviridae. This involves replication initiation by an unidentified nicking enzyme at a site that is 11 nucleotides (nt) from the covalently closed terminus, yielding a 3Ј-hydroxyl suitable for priming DNA synthesis (3).Small circular DNA viruses such as phiX174 and M13 in bacteria, geminiviruses in plants, and circoviruses in animals replicate by rolling-circle replication (RCR). RCR requires a replication initiator (Rep) protein, which nicks the circular DNA, forming a 5Ј DNA adduct and releasing a free 3Ј end to act as a primer for DNA synthesis. ...

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Section: Discussionmentioning

confidence: 99%

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication

Oke

Kerou

Liu

et al. 2011

J Virol

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“…It thus remains to be determined which experimental factor enhances the putative methylation of cccDNA. As observed previously (17), ocDNA levels remained constant during the course of infection and could be used as internal controls to estimate equal loading of the sample pairs. Although the reason for the constant amount of the ocDNA portion is unknown, this observation was confirmed by four independent sets of experiments ( Fig.…”

Section: Resultsmentioning

confidence: 77%

“…Viral DNAs, either digested with the enzyme or treated similarly without enzyme (Fig. 5, Eϩ and EϪ lanes), were resolved in one-dimensional chloroquine-containing agarose gels for optimal resolution of their different conformations, as shown previously (17,56). Under these conditions, the most prominent and reproducible effects were the reduction of multimeric DNA (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…All investigations with respect to sequence-specific DNA methylation have been based on the PCR technique and were thus not able to discriminate between the multitude of geminivirus DNA forms described (3,17,40,41,59). In particular, we were interested in determining whether there are differences in methylation between heterogeneous linear dsDNA and the circular dsDNA conformers.…”

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confidence: 99%

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Conformation-Selective Methylation of Geminivirus DNA

Paprotka

Deuschle

Metzler

et al. 2011

J Virol

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Geminiviruses with small circular single-stranded DNA genomes replicate in plant cell nuclei by using various double-stranded DNA (dsDNA) intermediates: distinct open circular and covalently closed circular as well as heterogeneous linear DNA. Their DNA may be methylated partially at cytosine residues, as detected previously by bisulfite sequencing and subsequent PCR. In order to determine the methylation patterns of the circular molecules, the DNAs of tomato yellow leaf curl Sardinia virus (TYLCSV) and Abutilon mosaic virus were investigated utilizing bisulfite treatment followed by rolling circle amplification. Shotgun sequencing of the products yielded a randomly distributed 50% rate of C maintenance after the bisulfite reaction for both viruses. However, controls with unmethylated single-stranded bacteriophage DNA resulted in the same level of C maintenance. Only one short DNA stretch within the C2/C3 promoter of TYLCSV showed hyperprotection of C, with the protection rate exceeding the threshold of the mean value plus 1 standard deviation. Similarly, the use of methylation-sensitive restriction enzymes suggested that geminiviruses escape silencing by methylation very efficiently, by either a rolling circle or recombination-dependent replication mode. In contrast, attempts to detect methylated bases positively by using methylcytosine-specific antibodies detected methylated DNA only in heterogeneous linear dsDNA, and methylation-dependent restriction enzymes revealed that the viral heterogeneous linear dsDNA was methylated preferentially.Methylation of DNA is commonly investigated using methylation-sensitive restriction enzymes and bisulfite sequencing, which converts unmethylated cytosines into uracil. The products are usually amplified by PCR and sequenced after bacterial cloning (14, 23). The critical steps in various protocols are the complete conversion of unmethylated cytosines to uracil (26, 78) and the design of appropriate primers for the converted DNA (reviewed in references 58 and 85). Several bioinformatic tools have been developed to analyze the results (9, 46-48, 66, 71), including recent improvements for the analysis of plant DNA cytosine methylation (27,35).Eukaryotes methylate cytosine at C 5 by methyltransferases, which differ between plants, fungi, and mammals (reviewed in reference 25). In mammals, symmetric CpG sites are usually preferred, whereas nearly every cytosine residue in plant DNA can be methylated (reviewed in reference 5). As a result, only 2 to 8% of mammalian DNA is methylated, compared to up to 50% of DNA in higher plants (reviewed in reference 84). The methylation status is highly dynamic. In plants, demethylation is mediated by DNA glycosylases and strand cleavage (84), a mechanism which would inactivate single-stranded DNA (ssDNA). In addition to C-methylation, N 6 -adenine methylation is well known for bacteria but rarely described for plants (19,74).The circular ssDNA-containing geminiviruses (reviewed in reference 37) are important plant pathogens causing severe damag...

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“…Whereas the MP and Cp are involved in virus movement and encapsidation [25], Rep is an crucial initiator of virus replication, and RepA plays regulatory role of host and viral gene transcription [15,16]. Masterviruses family adopts host DNA replication and double-stranded DNA break repair proteins in their genome replication via rolling-circle mechanism [2] and recombination-dependent mechanism [8].…”

Section: Introductionmentioning

confidence: 99%

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

2015

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This study aims to identifying and characterizing some molecular properties of geminiviruses co-infection in squash field crop cultivated in Egypt. Squash crops observed to be heavily infected with several insect vectors, also severe chlorosis and stunting was observed. Electron microscopic analysis has revealed geminate capsid particles which indicate the infection of Geminiviruses, especially SqLCV which represent an economic problem to squash filed crop in Egypt. We have investigated possible mixed infections with different plant viruses associated with chlorotic stunt diseases and or other genus groups of geminiviruses. The main objective of this study is to investigate the recombination events, possible recombinants and variants among these genera in the same family differing in vector transmission. This is the first report of the molecular characterization, phylogenetic analysis and putative recombination events of the full length genome of the Chickpea Chlorotic Dwarf Mastrevirus in Egypt. And the first report of co-infection with another begomovirus infecting squash plants. A full length clone of both viruses were isolated and characterized at the molecular level. The complete nucleotide sequence of DNA-A was determined (2,572 bp) and submitted to the genbank under accession no. KF692356. The isolate from Egypt has about 97.8 % homology with the Chickpea chlorotic dwarf virus (CpCDV) isolate from Syria DNA-A isolate FR687959, a 83.2 % homology with the Sudan isolate AM933134 and a 82.7 % homology with Pakistan isolate FR687960. To best of our knowledge this is the first report of complete genome of CpCDV that infect squash plants in Egypt and worldwide.

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Replicative intermediates of maize streak virus found during leaf development

Cited by 28 publications

References 18 publications

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication

A Dimeric Rep Protein Initiates Replication of a Linear Archaeal Virus Genome: Implications for the Rep Mechanism and Viral Replication

Conformation-Selective Methylation of Geminivirus DNA

First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash

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