Novel circular DNA virus identified in Opuntia discolor (Cactaceae) that codes for proteins with similarity to those of geminiviruses

2021 ◽  
Vol 102 (11) ◽  
Author(s):  
Rafaela S. Fontenele ◽  
Matias Köhler ◽  
Lucas C. Majure ◽  
Jesús A. Avalos-Calleros ◽  
Gerardo R. Argüello-Astorga ◽  
...  
Keyword(s):  
South America ◽  
Rolling Circle Replication ◽  
Dna Virus ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Circular Dna ◽  
Rolling Circle ◽  
Rep Protein ◽  
Molecular Features ◽  
Viral Components

Viral metagenomic studies have enabled the discovery of many unknown viruses and revealed that viral communities are much more diverse and ubiquitous than previously thought. Some viruses have multiple genome components that are encapsidated either in separate virions (multipartite viruses) or in the same virion (segmented viruses). In this study, we identify what is possibly a novel bipartite plant-associated circular single-stranded DNA virus in a wild prickly pear cactus, Opuntia discolor, that is endemic to the Chaco ecoregion in South America. Two ~1.8 kb virus-like circular DNA components were recovered, one encoding a replication-associated protein (Rep) and the other a capsid protein (CP). Both of the inferred protein sequences of the Rep and CP are homologous to those encoded by members of the family Geminiviridae. These two putatively cognate components each have a nonanucleotide sequence within a likely hairpin structure that is homologous to the origins of rolling-circle replication (RCR), found in diverse circular single-stranded DNA viruses. In addition, the two components share similar putative replication-associated iterative sequences (iterons), which in circular single-stranded DNA viruses are important for Rep binding during the initiation of RCR. Such molecular features provide support for the possible bipartite nature of this virus, which we named utkilio virus (common name of the Opuntia discolor in South America) components A and B. In the infectivity assays conducted in Nicotiana benthamiana plants, only the A component of utkilio virus, which encodes the Rep protein, was found to move and replicate systemically in N. benthamiana. This was not true for component B, for which we did not detect replication, which may have been due to this being a defective molecule or because of the model plants (N. benthamiana) used for the infection assays. Future experiments need to be conducted with other plants, including O. discolor, to understand more about the biology of these viral components.

scholarly journals An improved experimental pipeline for preparing circular ssDNA viruses for next-generation sequencing

2020 ◽  
Author(s):  
Catherine D. Aimone ◽  
J. Steen Hoyer ◽  
Anna E. Dye ◽  
David O. Deppong ◽  
Siobain Duffy ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Rolling Circle Amplification ◽  
Next Generation ◽  
Viral Dna ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Short Read ◽  
Rolling Circle ◽  
Optimized Protocol ◽  
Generation Sequencing

AbstractWe present an optimized protocol for enhanced amplification and enrichment of viral DNA for Next Generation Sequencing of begomovirus genomes. The rapid ability of these viruses to evolve threatens many crops and underscores the importance of using next generation sequencing efficiently to detect and understand the diversity of these viruses. We combined enhanced rolling circle amplification (RCA) with EquiPhi29 polymerase and size selection to generate a cost-effective, short-read sequencing method. This optimized protocol produced short-read sequencing with at least 50% of the reads mapping to the viral reference genome. We provide other insights into common misconceptions about RCA and lessons we have learned from sequencing single-stranded DNA viruses. Our protocol can be used to examine viral DNA as it moves through the entire pathosystem from host to vector, providing valuable information for viral DNA population studies, and would likely work well with other CRESS DNA viruses.HighlightsProtocol for short-read, high throughput sequencing of single-stranded DNA viruses using random primersComparison of the sequencing of total DNA versus size-selected DNAComparison of phi29 and Equiphi29 DNA polymerases for rolling circle amplification of viral single-stranded DNA genomes

scholarly journals Genetic and Biochemical Characterization of the Streptococcus pneumoniae PcrA Helicase and Its Role in Plasmid Rolling Circle Replication

2006 ◽  
Vol 188 (21) ◽  
pp. 7416-7425 ◽  
Author(s):  
J. A. Ruiz-Masó ◽  
S. P. Anand ◽  
M. Espinosa ◽  
S. A. Khan ◽  
G. del Solar
Keyword(s):  
Streptococcus Pneumoniae ◽  
Biochemical Characterization ◽  
Essential Gene ◽  
Biochemical Properties ◽  
Dna Helicase ◽  
Rolling Circle Replication ◽  
Lower Efficiency ◽  
Rolling Circle ◽  
Rep Protein

ABSTRACT PcrA is a chromosomally encoded DNA helicase of gram-positive bacteria involved in replication of rolling circle replicating plasmids. Efficient interaction between PcrA and the plasmid-encoded replication initiator (Rep) protein is considered a requirement for the plasmid to replicate in a given host, and thus, the ability of a Rep protein to interact with heterologous PcrA helicases has been invoked as a determinant of plasmid promiscuity. We characterized transcription of the Streptococcus pneumoniae pcrA gene in its genetic context and studied the biochemical properties of its product, the PcrA Spn helicase. Transcription of the pneumococcal pcrA gene was directed by promoter Pa, consisting of an extended −10 box. Promoter Pa also accounted for expression of a second essential gene, radC, which was transcribed with much lower efficiency than pcrA, probably due to the presence of a terminator/attenuator sequence located between the two genes. PcrA Spn displayed single-stranded DNA-dependent ATPase activity. PcrA Spn showed 5′→3′ and 3′→5′ helicase activities and bound efficiently to partially duplex DNA containing a hairpin structure adjacent to a 6-nucleotide 5′ or 3′ single-stranded tail and one unpaired (flap) nucleotide in the complementary strand. PcrA Spn interacted specifically with RepC, the initiator of staphylococcal plasmid pT181. Although the pneumococcal helicase was able to initiate unwinding of the RepC-nicked pT181 DNA, it was much less processive in this activity than the cognate staphylococcal PcrA protein. Accordingly, PcrA Spn was inefficient in in vitro replication of pT181, and perhaps as a consequence, this plasmid could not be established in S. pneumoniae.

scholarly journals Rolling-Circle Replication of an Animal Circovirus Genome in a Theta-Replicating Bacterial Plasmid in Escherichia coli

2006 ◽  
Vol 80 (17) ◽  
pp. 8686-8694 ◽  
Author(s):  
Andrew K. Cheung
Keyword(s):  
Escherichia Coli ◽  
Dna Replication ◽  
Mammalian Cells ◽  
Unit Length ◽  
Release Mechanism ◽  
Rolling Circle Replication ◽  
Replication Process ◽  
Rolling Circle ◽  
Rep Protein ◽  
Bacterial Plasmid

ABSTRACT A bacterial plasmid containing 1.75 copies of double-stranded porcine circovirus (PCV) DNA in tandem (0.8 copy of PCV type 1 [PCV1], 0.95 copy of PCV2) with two origins of DNA replication (Ori) yielded three different DNA species when transformed into Escherichia coli: the input construct, a unit-length chimeric PCV1Rep/PCV2Cap genome with a composite Ori but lacking the plasmid vector, and a molecule consisting of the remaining 0.75 copy PCV1Cap/PCV2Rep genome with a different composite Ori together with the bacterial plasmid. Replication of the input construct was presumably via the theta replication mechanism utilizing the ColE1 Ori, while characteristics of the other two DNA species, including a requirement of two PCV Oris and the virus-encoded replication initiator Rep protein, suggest they were generated via the rolling-circle copy-release mechanism. Interestingly, the PCV-encoded Rep′ protein essential for PCV DNA replication in mammalian cells was not required in bacteria. The fact that the Rep′ protein function(s) can be compensated by the bacterial replication machinery to support the PCV DNA replication process echoes previous suggestions that circular single-stranded DNA animal circoviruses, plant geminiviruses, and nanoviruses may have evolved from prokaryotic episomal replicons.

scholarly journals New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics

PLoS ONE ◽  
2015 ◽  
Vol 10 (11) ◽  
pp. e0141952 ◽  
Author(s):  
Thomas Arn Hansen ◽  
Helena Fridholm ◽  
Tobias Guldberg Frøslev ◽  
Kristín Rós Kjartansdóttir ◽  
Eske Willerslev ◽  
...  
Keyword(s):  
Rattus Norvegicus ◽  
Dna Virus ◽  
Single Stranded Dna ◽  
Circular Dna ◽  
New Type

scholarly journals A Structural Perspective of Reps from CRESS-DNA Viruses and Their Bacterial Plasmid Homologues

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 37
Author(s):  
Elvira Tarasova ◽  
Reza Khayat
Keyword(s):  
Structural Information ◽  
Experimental Studies ◽  
Structural Data ◽  
Rolling Circle Replication ◽  
Dna Viruses ◽  
Rolling Circle ◽  
Structural Mechanism ◽  
Functional Sites ◽  
Bacterial Plasmid ◽  
Shed Light

Rolling circle replication (RCR) is ubiquitously used by cellular and viral systems for genome and plasmid replication. While the molecular mechanism of RCR has been described, the structural mechanism is desperately lacking. Circular-rep encoded single stranded DNA (CRESS-DNA) viruses employ a viral encoded replicase (Rep) to initiate RCR. The recently identified prokaryotic homologues of Reps may also be responsible for initiating RCR. Reps are composed of an endonuclease, oligomerization, and ATPase domain. Recent structural studies have provided structures for all these domains such that an overall mechanism of RCR initiation can begin to be synthesized. However, structures of Rep in complex with its various DNA substrates and/or ligands are lacking. Here we provide a 3D bioinformatic review of the current structural information available for Reps. We combine an excess of 1590 sequences with experimental and predicted structural data from 22 CRESS-DNA groups to identify similarities and differences between Reps that lead to potentially important functional sites. Experimental studies of these sites may shed light on how Reps execute their functions. Furthermore, we identify Rep-substrate or Rep-ligand structures that are urgently needed to better understand the structural mechanism of RCR.

scholarly journals Mechanism of DNA Interaction and Translocation by the Replicase of a Circular Rep-Encoding Single-Stranded DNA Virus

mBio ◽  
2021 ◽  
Author(s):  
Elvira Tarasova ◽  
Sonali Dhindwal ◽  
Matthew Popp ◽  
Sakeenah Hussain ◽  
Reza Khayat
Keyword(s):  
Dna Interaction ◽  
Dna Virus ◽  
Single Stranded Dna ◽  
Dna Viruses

CRESS-DNA viruses encompass a significant portion of the biosphere’s virome. However, little is known about the structure of Rep responsible for initiating the RCR of CRESS-DNA viruses.

scholarly journals Analysis of transcription of Porcine circovirus type 1

2002 ◽  
Vol 83 (11) ◽  
pp. 2743-2751 ◽  
Author(s):  
Annette Mankertz ◽  
Bernd Hillenbrand
Keyword(s):  
Infectious Clone ◽  
Porcine Circovirus Type ◽  
Open Reading Frames ◽  
Porcine Circovirus ◽  
Origin Of Replication ◽  
Rolling Circle Replication ◽  
Structural Protein ◽  
Rolling Circle ◽  
Rep Protein

Porcine circovirus type 1 (PCV1) contains two major open reading frames encoding the replication initiator proteins, Rep and Rep′, and the structural protein, Cap. The promoters of these two genes (P cap and P rep ) have been mapped. P cap is located within the rep open reading frame (nt 1328–1252). P rep has been mapped to the intergenic region immediately upstream of the rep gene (nt 640–796) and overlaps the origin of replication of PCV1. Although binding of both rep gene products to a fragment containing P rep and the overlapping origin of replication has been reported, only the full-length Rep protein repressed P rep , while the spliced isoform Rep′ did not. P rep repression is mediated by binding of the Rep protein to the two inner hexamers, H1 and H2, located in the origin of PCV1, whereas binding of Rep to hexamers H3 and H4 was not necessary. Use of Rep mutants indicated that the conserved rolling-circle replication domain II as well as the P loop are essential for repression of P rep . In contrast to P rep , transcription of P cap was not influenced by viral proteins. Additionally, the ratio of the rep and rep′ transcripts was analysed. Twelve hours after transfection of PK15 cells with an infectious clone of PCV1, similar amounts of both transcripts were detected, but later the amount of the two transcripts varied, indicating a balanced expression of the two rep transcripts.

scholarly journals Characterization of the Novel Fusobacterium nucleatum Plasmid pKH9 and Evidence of an Addiction System

2004 ◽  
Vol 70 (12) ◽  
pp. 6957-6962 ◽  
Author(s):  
Gilad Bachrach ◽  
Susan Kinder Haake ◽  
Alon Glick ◽  
Ronen Hazan ◽  
Ronit Naor ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Genetic Manipulation ◽  
Plasmid Stability ◽  
Protein A ◽  
Fusobacterium Nucleatum ◽  
Rolling Circle Replication ◽  
Rolling Circle ◽  
Rep Protein ◽  
Shuttle Plasmid ◽  
Plasmid Addiction System

ABSTRACT Fusobacterium nucleatum is an important oral anaerobic pathogen involved in periodontal and systemic infections. Studies of the molecular mechanisms involved in fusobacterial virulence and adhesion have been limited by lack of systems for efficient genetic manipulation. Plasmids were isolated from eight strains of F. nucleatum. The smallest plasmid, pKH9 (4,975 bp), was characterized and used to create new vectors for fusobacterial genetic manipulation. DNA sequence analysis of pKH9 revealed an open reading frame (ORF) encoding a putative autonomous rolling circle replication protein (Rep), an ORF predicted to encode a protein homologous to members of the FtsK/SpoIIIE cell division-DNA segregation protein family, and an operon encoding a putative toxin-antitoxin plasmid addiction system (txf-axf). Deletion analysis localized the pKH9 replication region in a 0.96-kbp fragment. The pKH9 rep gene is not present in this fragment, suggesting that pKH9 can replicate in fusobacteria independently of the Rep protein. A pKH9-based, compact Escherichia coli-F. nucleatum shuttle plasmid was constructed and found to be compatible with a previously described pFN1-based fusobacterial shuttle plasmid. Deletion of the pKH9 putative addiction system (txf-axf) reduced plasmid stability in fusobacteria, indicating its addiction properties and suggesting it to be the first plasmid addiction system described for fusobacteria. pKH9, its genetic elements, and its shuttle plasmid derivatives can serve as useful tools for investigating fusobacterial properties important in biofilm ecology and pathogenesis.

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