scholarly journals Precise Determination, Cross-Recognition, and Functional Analysis of the Double-Strand Origins of the Rolling-Circle Replication Plasmids in Haloarchaea

2008 ◽  
Vol 190 (16) ◽  
pp. 5710-5719 ◽  
Author(s):  
Ligang Zhou ◽  
Meixian Zhou ◽  
Chaomin Sun ◽  
Jing Han ◽  
Qiuhe Lu ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Functional Analysis ◽  
Mutation Analysis ◽  
Precise Determination ◽  
Hybrid Plasmid ◽  
Hairpin Structure ◽  
Rolling Circle Replication ◽  
Rolling Circle ◽  
Nick Site ◽  
Termination Process

ABSTRACT The precise nick site in the double-strand origin (DSO) of pZMX201, a 1,668-bp rolling-circle replication (RCR) plasmid from the haloarchaeon Natrinema sp. CX2021, was determined by electron microscopy and DSO mapping. In this plasmid, DSO nicking occurred between residues C404 and G405 within a heptanucleotide sequence (TCTC/GGC) located in the stem region of an imperfect hairpin structure. This nick site sequence was conserved among the haloarchaeal RCR plasmids, including pNB101, suggesting that the DSO nick site might be the same for all members of this plasmid family. Interestingly, the DSOs of pZMX201 and pNB101 were found to be cross-recognized in RCR initiation and termination in a hybrid plasmid system. Mutation analysis of the DSO from pZMX201 (DSOZ) in this hybrid plasmid system revealed that: (i) the nucleotides in the middle of the conserved TCTCGGC sequence play more-important roles in the initiation and termination process; (ii) the left half of the hairpin structure is required for initiation but not for termination; and (iii) a 36-bp sequence containing TCTCGGC and the downstream sequence is essential and sufficient for termination. In conclusion, these haloarchaeal plasmids, with novel features that are different from the characteristics of both single-stranded DNA phages and bacterial RCR plasmids, might serve as a good model for studying the evolution of RCR replicons.

scholarly journals Functional Analysis of Three Plasmids from Lactobacillus plantarum

2005 ◽  
Vol 71 (3) ◽  
pp. 1223-1230 ◽  
Author(s):  
Richard van Kranenburg ◽  
Natasa Golic ◽  
Roger Bongers ◽  
Rob J. Leer ◽  
Willem M. de Vos ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Bacillus Subtilis ◽  
Host Range ◽  
Lactobacillus Plantarum ◽  
Unknown Function ◽  
Conjugative Plasmid ◽  
Rolling Circle Replication ◽  
Cloning Vectors ◽  
Rolling Circle ◽  
Arsenite Resistance

ABSTRACT Lactobacillus plantarum WCFS1 harbors three plasmids, pWCFS101, pWCFS102, and pWCFS103, with sizes of 1,917, 2,365, and 36,069 bp, respectively. The two smaller plasmids are of unknown function and contain replication genes that are likely to function via the rolling-circle replication mechanism. The host range of the pWCFS101 replicon includes Lactobacillus species and Lactococcus lactis, while that of the pWCFS102 replicon also includes Carnobacterium maltaromaticum and Bacillus subtilis. The larger plasmid is predicted to replicate via the theta-type mechanism. The host range of its replicon seems restricted to L. plantarum. Cloning vectors were constructed based on the replicons of all three plasmids. Plasmid pWCFS103 was demonstrated to be a conjugative plasmid, as it could be transferred to L. plantarum NC8. It confers arsenate and arsenite resistance, which can be used as selective markers.

scholarly journals Two Widely Spaced Initiator Binding Sites Create an HMG1-Dependent Parvovirus Rolling-Hairpin Replication Origin

2000 ◽  
Vol 74 (3) ◽  
pp. 1332-1341 ◽  
Author(s):  
Susan F. Cotmore ◽  
Jesper Christensen ◽  
Peter Tattersall
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Initiation Site ◽  
Rolling Circle Replication ◽  
Specific Sequence ◽  
Rolling Circle ◽  
Nick Site ◽  
Origin Function ◽  
The Right

ABSTRACT Minute virus of mice (MVM) replicates via a linearized form of rolling-circle replication in which the viral nickase, NS1, initiates DNA synthesis by introducing a site-specific nick into either of two distinct origin sequences. In vitro nicking and replication assays with substrates that had deletions or mutations were used to explore the sequences and structural elements essential for activity of one of these origins, located in the right-end (5′) viral telomere. This structure contains 248 nucleotides, most-favorably arranged as a simple hairpin with six unpaired bases. However, a pair of opposing NS1 binding sites, located near its outboard end, create a 33-bp palindrome that could potentially assume an alternate cruciform configuration and hence directly bind HMG1, the essential cofactor for this origin. The palindromic nature of this sequence, and thus its ability to fold into a cruciform, was dispensable for origin function, as was the NS1 binding site occupying the inboard arm of the palindrome. In contrast, the NS1 site in the outboard arm was essential for initiation, even though positioned 120 bp from the nick site. The specific sequence of the nick site and an additional NS1 binding site which directly orients NS1 over the initiation site were also essential and delimited the inboard border of the minimal right-end origin. DNase I and hydroxyl radical footprints defined sequences protected by NS1 and suggest that HMG1 allows the NS1 molecules positioned at each end of the origin to interact, creating a distortion characteristic of a double helical loop.

Linear simian virus 40 DNA fragments exhibit a propensity for rolling-circle replication

1985 ◽  
Vol 5 (7) ◽  
pp. 1787-1790
Author(s):  
I Deichaite ◽  
Z Laver-Rudich ◽  
D Dorsett ◽  
E Winocour
Keyword(s):  
Electron Microscopy ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Dna Fragments ◽  
Rolling Circle Replication ◽  
Supercoiled Dna ◽  
Rolling Circle ◽  
Cos Cells ◽  
Dna Fragment ◽  
Replication Intermediates

A linear simian virus 40 origin-containing DNA fragment replicated in monkey COS cells, generating tandemly repeated (head-to-tail) structures. Electron microscopy revealed circle-and-tail configurations characteristic of rolling-circle replication intermediates. Circularization of the same DNA before transfection led to a theta type of replication which generated supercoiled DNA molecules.

scholarly journals Linear simian virus 40 DNA fragments exhibit a propensity for rolling-circle replication.

1985 ◽  
Vol 5 (7) ◽  
pp. 1787-1790 ◽  
Author(s):  
I Deichaite ◽  
Z Laver-Rudich ◽  
D Dorsett ◽  
E Winocour
Keyword(s):  
Electron Microscopy ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
Dna Fragments ◽  
Rolling Circle Replication ◽  
Supercoiled Dna ◽  
Rolling Circle ◽  
Cos Cells ◽  
Dna Fragment ◽  
Replication Intermediates

A linear simian virus 40 origin-containing DNA fragment replicated in monkey COS cells, generating tandemly repeated (head-to-tail) structures. Electron microscopy revealed circle-and-tail configurations characteristic of rolling-circle replication intermediates. Circularization of the same DNA before transfection led to a theta type of replication which generated supercoiled DNA molecules.

scholarly journals Targeted Allele Replacement Mutagenesis of Corynebacterium pseudotuberculosis

2011 ◽  
Vol 77 (10) ◽  
pp. 3532-3535 ◽  
Author(s):  
Caray A. Walker ◽  
Willie Donachie ◽  
David G. E. Smith ◽  
Michael C. Fontaine
Keyword(s):  
Corynebacterium Pseudotuberculosis ◽  
Sequence Length ◽  
Homologous Sequence ◽  
Proof Of Concept ◽  
Rolling Circle Replication ◽  
Content Type ◽  
Rolling Circle ◽  
Allele Replacement ◽  
Marker Free ◽  
The Relationship

ABSTRACTA two-step allele replacement mutagenesis procedure, using a conditionally replicating plasmid, was developed to allow the creation of targeted, marker-free mutations inCorynebacterium pseudotuberculosis. The relationship between homologous sequence length and recombination frequency was determined, and enhanced plasmid excision was observed due to the rolling-circle replication of the mutagenesis vector. Furthermore, an antibiotic enrichment procedure was applied to improve the recovery of mutants. Subsequently, as proof of concept, a marker-free,cp40-deficient mutant ofC. pseudotuberculosiswas constructed.

Homogeneous Detection of Single Rolling Circle Replication Products

2004 ◽  
Vol 76 (2) ◽  
pp. 495-498 ◽  
Author(s):  
Gerhard A. Blab ◽  
Thomas Schmidt ◽  
Mats Nilsson
Keyword(s):  
Rolling Circle Replication ◽  
Rolling Circle

scholarly journals Pf Filamentous Phage Requires UvrD for Replication in Pseudomonas aeruginosa

mSphere ◽  
2016 ◽  
Vol 1 (1) ◽  
Author(s):  
Eriel Martínez ◽  
Javier Campos-Gómez
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Dna Repair ◽  
Dna Helicase ◽  
Filamentous Phage ◽  
Rolling Circle Replication ◽  
Content Type ◽  
Rolling Circle ◽  
Initiator Protein ◽  
Biofilm Development ◽  
Filamentous Phages

ABSTRACT Biofilm development is a key component of the ability of Pseudomonas aeruginosa to evade host immune defenses and resist multiple drugs. Induction of the filamentous phage Pf, which usually is lysogenized in clinical and environmental isolates of P. aeruginosa, plays an important role in biofilm assembly, maturation, and dispersal. Despite the clinical relevance of Pf, the molecular biology of this phage is largely unknown. In this study, we found that rolling circle replication of Pf depends on UvrD, a DNA helicase normally involved in DNA repair. We also identified the initiator protein of Pf and found that it shares structural similarity with that of Vibrio cholerae phages CTXφ and VGJφ, which also use UvrD for replication. Our results reveal that, in addition to DNA repair, UvrD plays an essential role in rolling circle replication of filamentous phages among diverse bacteria genera, adding a new, previously unrecognized function of this accessory helicase. Pf is a lysogenic filamentous phage that promotes biofilm development in Pseudomonas aeruginosa. Pf replicates by a rolling circle replication system which depends on a phage-encoded initiator protein and host factors usually involved in chromosome replication. Rep, an accessory replicative DNA helicase, is crucial for replication of filamentous phages in Escherichia coli. In contrast, here we show that, instead of depending on Rep, Pf replication depends on UvrD, an accessory helicase implicated in DNA repair. In this study, we also identified the initiator protein of Pf and found that it shares similarities with that of Vibrio phages CTXφ and VGJφ, which also depend on UvrD for replication. A structural comparative analysis of the initiator proteins of most known filamentous phages described thus far suggested that UvrD, known as a nonreplicative helicase, is involved in rolling circle replication of filamentous phages in diverse bacteria genera. This report consolidates knowledge on the new role of UvrD in filamentous phage replication, a function previously thought to be exclusive of Rep helicase. IMPORTANCE Biofilm development is a key component of the ability of Pseudomonas aeruginosa to evade host immune defenses and resist multiple drugs. Induction of the filamentous phage Pf, which usually is lysogenized in clinical and environmental isolates of P. aeruginosa, plays an important role in biofilm assembly, maturation, and dispersal. Despite the clinical relevance of Pf, the molecular biology of this phage is largely unknown. In this study, we found that rolling circle replication of Pf depends on UvrD, a DNA helicase normally involved in DNA repair. We also identified the initiator protein of Pf and found that it shares structural similarity with that of Vibrio cholerae phages CTXφ and VGJφ, which also use UvrD for replication. Our results reveal that, in addition to DNA repair, UvrD plays an essential role in rolling circle replication of filamentous phages among diverse bacteria genera, adding a new, previously unrecognized function of this accessory helicase.

scholarly journals Subcellular Localization and Rolling Circle Replication of Peach Latent Mosaic Viroid: Hallmarks of Group A Viroids

1999 ◽  
Vol 73 (8) ◽  
pp. 6353-6360 ◽  
Author(s):  
F. Bussière ◽  
J. Lehoux ◽  
D. A. Thompson ◽  
L. J. Skrzeczkowski ◽  
J.-P. Perreault
Keyword(s):  
Subcellular Localization ◽  
Cellular Level ◽  
Symmetric Mode ◽  
Rolling Circle Replication ◽  
Dot Blot ◽  
Rolling Circle ◽  
Group A ◽  
Group B ◽  
Contrast Group ◽  
Replication Intermediates

ABSTRACT We characterized the peach latent mosaic viroid (PLMVd) replication intermediates that accumulate in infected peach leaves and determined the tissue and subcellular localization of the RNA species. Using in situ hybridization, we showed that PLMVd strands of both plus and minus polarities concentrate in the cells forming the palisade parenchyma. At the cellular level, PLMVd was found to accumulate predominantly in chloroplasts. Northern blot analyses demonstrated that PLMVd replicates via a symmetric mode involving the accumulation of both circular and linear monomeric strands of both polarities. No multimeric conformer was detected, indicating that both strands self-cleave efficiently via their hammerhead sequences. Dot blot hybridizations revealed that PLMVd strands of both polarities accumulate equally but that the relative concentrations vary by more than 50-fold between peach cultivars. Taken together these results establish two hallmarks for the classification of viroids. Group A viroids (e.g., PLMVd), which possess hammerhead structures, replicate in the chloroplasts via the symmetric mode. By contrast, group B viroids, which share a conserved central region, replicate in the nucleus via an asymmetric mechanism. This is an important difference between self-cleaving and non-self-cleaving viroids, and the implications for the evolutionary origin and replication are discussed.

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