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Journal articles on the topic 'Replication by rolling'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Ling, Feng, and Minoru Yoshida. "Rolling-Circle Replication in Mitochondrial DNA Inheritance: Scientific Evidence and Significance from Yeast to Human Cells." Genes 11, no. 5 (2020): 514. http://dx.doi.org/10.3390/genes11050514.

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Studies of mitochondrial (mt)DNA replication, which forms the basis of mitochondrial inheritance, have demonstrated that a rolling-circle replication mode exists in yeasts and human cells. In yeast, rolling-circle mtDNA replication mediated by homologous recombination is the predominant pathway for replication of wild-type mtDNA. In human cells, reactive oxygen species (ROS) induce rolling-circle replication to produce concatemers, linear tandem multimers linked by head-to-tail unit-sized mtDNA that promote restoration of homoplasmy from heteroplasmy. The event occurs ahead of mtDNA replicatio

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2

Khan, S. A. "Rolling-circle replication of bacterial plasmids." Microbiology and Molecular Biology Reviews 61, no. 4 (1997): 442–55. http://dx.doi.org/10.1128/mmbr.61.4.442-455.1997.

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Many bacterial plasmids replicate by a rolling-circle (RC) mechanism. Their replication properties have many similarities to as well as significant differences from those of single-stranded DNA (ssDNA) coliphages, which also replicate by an RC mechanism. Studies on a large number of RC plasmids have revealed that they fall into several families based on homology in their initiator proteins and leading-strand origins. The leading-strand origins contain distinct sequences that are required for binding and nicking by the Rep proteins. Leading-strand origins also contain domains that are required

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3

Khan, Saleem A. "Plasmid rolling-circle replication: recent developments." Molecular Microbiology 37, no. 3 (2002): 477–84. http://dx.doi.org/10.1046/j.1365-2958.2000.02001.x.

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4

Khan, S. A. "Rolling-circle replication of bacterial plasmids." Microbiology and molecular biology reviews : MMBR 61, no. 4 (1997): 442–55. http://dx.doi.org/10.1128/.61.4.442-455.1997.

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5

Fire, A., and S. Q. Xu. "Rolling replication of short DNA circles." Proceedings of the National Academy of Sciences 92, no. 10 (1995): 4641–45. http://dx.doi.org/10.1073/pnas.92.10.4641.

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6

Gregorova, Daniela, Jitka Matiasovicova, Alena Sebkova, Marcela Faldynova, and Ivan Rychlik. "Salmonella entericasubsp.entericaserovar Enteritidis harbours ColE1, ColE2, and rolling-circle-like replicating plasmids." Canadian Journal of Microbiology 50, no. 2 (2004): 107–12. http://dx.doi.org/10.1139/w03-113.

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Using DNA hybridization, at least three distinct groups of low molecular mass plasmids were identified in Salmonella enterica subsp. enterica serovar Enteritidis. After sequencing representative plasmids from each group, we concluded that they belonged to ColE1, ColE2, and rolling-circle-like replicating plasmids. Plasmid pK (4245 bp) is a representative of widely distributed ColE1 plasmids. Plasmid pP (4301 bp) is homologous to ColE2 plasmids and was present predominantly in single-stranded DNA form. The smallest plasmids pJ (2096 bp) and pB (1983 bp) were classified as rolling-circle-like re

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7

Wright, Laurel D., and Alan D. Grossman. "Autonomous Replication of the Conjugative Transposon Tn916." Journal of Bacteriology 198, no. 24 (2016): 3355–66. http://dx.doi.org/10.1128/jb.00639-16.

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ABSTRACTIntegrative and conjugative elements (ICEs), also known as conjugative transposons, are self-transferable elements that are widely distributed among bacterial phyla and are important drivers of horizontal gene transfer. Many ICEs carry genes that confer antibiotic resistances to their host cells and are involved in the dissemination of these resistance genes. ICEs reside in host chromosomes but under certain conditions can excise to form a plasmid that is typically the substrate for transfer. A few ICEs are known to undergo autonomous replication following activation. However, it is no

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8

Flores, Ricardo, María-Eugenia Gas, Diego Molina-Serrano, et al. "Viroid Replication: Rolling-Circles, Enzymes and Ribozymes." Viruses 1, no. 2 (2009): 317–34. http://dx.doi.org/10.3390/v1020317.

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9

Espinosa, Manuel, Gloria del Solar, Fernando Rojo, and Juan C. Alonso. "Plasmid rolling circle replication and its control." FEMS Microbiology Letters 130, no. 2-3 (1995): 111–20. http://dx.doi.org/10.1111/j.1574-6968.1995.tb07707.x.

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10

Okamoto, Haruko, Taka-aki Watanabe, and Takashi Horiuchi. "Double rolling circle replication (DRCR) is recombinogenic." Genes to Cells 16, no. 5 (2011): 503–13. http://dx.doi.org/10.1111/j.1365-2443.2011.01507.x.

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11

Barran, L. R., N. Ritchot, and E. S. P. Bromfield. "Sinorhizobium meliloti Plasmid pRm1132f Replicates by a Rolling-Circle Mechanism." Journal of Bacteriology 183, no. 8 (2001): 2704–8. http://dx.doi.org/10.1128/jb.183.8.2704-2708.2001.

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ABSTRACT pRm1132f isolated from Sinorhizobium meliloti is a group III rolling-circle-replicating (RCR) plasmid. At least seven of eight open reading frames in the nucleotide sequence represented coding regions. The minimal replicon contained a rep gene and single- and double-stranded origins of replication. Detection of single-stranded plasmid DNA confirmed that pRm1132f replicated via an RCR mechanism.

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12

Anand, Syam P., Poulami Mitra, Asma Naqvi, and Saleem A. Khan. "Bacillus anthracis and Bacillus cereus PcrA Helicases Can Support DNA Unwinding and In Vitro Rolling-Circle Replication of Plasmid pT181 of Staphylococcus aureus." Journal of Bacteriology 186, no. 7 (2004): 2195–99. http://dx.doi.org/10.1128/jb.186.7.2195-2199.2004.

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ABSTRACT Replication of rolling-circle replicating (RCR) plasmids in gram-positive bacteria requires the unwinding of initiator protein-nicked plasmid DNA by the PcrA helicase. In this report, we demonstrate that heterologous PcrA helicases from Bacillus anthracis and Bacillus cereus are capable of unwinding Staphylococcus aureus plasmid pT181 from the initiator-generated nick and promoting in vitro replication of the plasmid. These helicases also physically interact with the RepC initiator protein of pT181. The ability of PcrA helicases to unwind noncognate RCR plasmids may contribute to the

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13

Blab, Gerhard A., Thomas Schmidt, and Mats Nilsson. "Homogeneous Detection of Single Rolling Circle Replication Products." Analytical Chemistry 76, no. 2 (2004): 495–98. http://dx.doi.org/10.1021/ac034987+.

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14

Carr, Stephen B., Lauren B. Mecia, Alice J. Stelfox, Christopher D. Thomas, and Simon E. V. Philipps. "Structural studies of rolling circle replication initiator proteins." Acta Crystallographica Section A Foundations of Crystallography 69, a1 (2013): s315. http://dx.doi.org/10.1107/s0108767313097274.

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15

Carr, Stephen B., Lauren B. Mecia, Alice J. Stelfox, Christopher D. Thomas, and Simon E. V. Phillips. "Structural studies of rolling-circle replication initiator proteins." Acta Crystallographica Section A Foundations of Crystallography 69, a1 (2013): s72. http://dx.doi.org/10.1107/s0108767313099388.

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16

Maleszka, R., P. J. Skelly, and G. D. Clark-Walker. "Rolling circle replication of DNA in yeast mitochondria." EMBO Journal 10, no. 12 (1991): 3923–29. http://dx.doi.org/10.1002/j.1460-2075.1991.tb04962.x.

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17

Yasukawa, H. "Rolling-Circle Plasmid pKYM Re-initiates DNA Replication." DNA Research 4, no. 3 (1997): 193–97. http://dx.doi.org/10.1093/dnares/4.3.193.

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18

Sun, Wujin, Yue Lu, and Zhen Gu. "Rolling circle replication for engineering drug delivery carriers." Therapeutic Delivery 6, no. 7 (2015): 765–68. http://dx.doi.org/10.4155/tde.15.27.

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19

Koonin, Eugene V., and Tatyana V. Ilyina. "Computer-assisted dissection of rolling circle DNA replication." Biosystems 30, no. 1-3 (1993): 241–68. http://dx.doi.org/10.1016/0303-2647(93)90074-m.

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20

Phillips, Simon Edward Victor, Stephen B. Carr, Lauren B. Mecia, Alice J. Stelfox, and Christopher D. Thomas. "Structural Studies of Rolling Circle Replication Initiator Proteins." Biophysical Journal 104, no. 2 (2013): 73a—74a. http://dx.doi.org/10.1016/j.bpj.2012.11.444.

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21

Gu, Yun-qing, Tian-xing Fan, Jie-gang Mou, Wei-bo Yu, Gang Zhao, and Evan Wang. "Experiment Research on Hot-Rolling Processing of Nonsmooth Pit Surface." Applied Bionics and Biomechanics 2016 (2016): 1–10. http://dx.doi.org/10.1155/2016/4915974.

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In order to achieve the nonsmooth surface drag reduction structure on the inner polymer coating of oil and gas pipelines and improve the efficiency of pipeline transport, a structural model of the machining robot on the pipe inner coating is established. Based on machining robot, an experimental technique is applied to research embossing and coating problems of rolling-head, and then the molding process rules under different conditions of rolling temperatures speeds and depth are analyzed. Also, an orthogonal experiment analysis method is employed to analyze the different effects of hot-rollin

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22

Song, Sang Ik, and W. Allen Miller. "cis and trans Requirements for Rolling Circle Replication of a Satellite RNA." Journal of Virology 78, no. 6 (2004): 3072–82. http://dx.doi.org/10.1128/jvi.78.6.3072-3082.2004.

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ABSTRACT Satellite RNAs usurp the replication machinery of their helper viruses, even though they bear little or no sequence similarity to the helper virus RNA. In Cereal yellow dwarf polerovirus serotype RPV (CYDV-RPV), the 322-nucleotide satellite RNA (satRPV RNA) accumulates to high levels in the presence of the CYDV-RPV helper virus. Rolling circle replication generates multimeric satRPV RNAs that self-cleave via a double-hammerhead ribozyme structure. Alternative folding inhibits formation of a hammerhead in monomeric satRPV RNA. Here we determine helper virus requirements and the effects

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23

Meier, Anita Felicitas, Kurt Tobler, Remo Leisi, Anouk Lkharrazi, Carlos Ros, and Cornel Fraefel. "Herpes simplex virus co-infection facilitates rolling circle replication of the adeno-associated virus genome." PLOS Pathogens 17, no. 6 (2021): e1009638. http://dx.doi.org/10.1371/journal.ppat.1009638.

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Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin replication (RHR) mechanism initiated at the AAV 3’ inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. Using Southern analysis and nanopore sequencing as a novel, high-throughput approach to study viral genome replication we d

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24

Hughes, J. H. "Physical and chemical methods for enhancing rapid detection of viruses and other agents." Clinical Microbiology Reviews 6, no. 2 (1993): 150–75. http://dx.doi.org/10.1128/cmr.6.2.150.

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Viral replication events can be enhanced by physical, chemical, or heat treatment of cells. The centrifugation of cells can stimulate them to proliferate, reduce their generation times, and activate gene expression. Human endothelial cells can be activated to release cyclo-oxygenase metabolites after rocking for 5 min, and mechanical stress can stimulate endothelial cells to proliferate. Centrifugation of virus-infected cultures can increase cytopathic effects (CPE), enhance the number of infected cells, increase viral yields, and reduce viral detection times and may increase viral isolation r

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25

Koonin, E. V., and T. V. Ilyina. "Geminivirus replication proteins are related to prokaryotic plasmid rolling circle DNA replication initiator proteins." Journal of General Virology 73, no. 10 (1992): 2763–66. http://dx.doi.org/10.1099/0022-1317-73-10-2763.

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26

Shavitt, O., and Z. Livneh. "Rolling-circle replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro." Journal of Bacteriology 171, no. 6 (1989): 3530–38. http://dx.doi.org/10.1128/jb.171.6.3530-3538.1989.

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27

Gros, M. F., H. te Riele, and S. D. Ehrlich. "Rolling circle replication of single-stranded DNA plasmid pC194." EMBO Journal 6, no. 12 (1987): 3863–69. http://dx.doi.org/10.1002/j.1460-2075.1987.tb02724.x.

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28

Baner, J., M. Nilsson, M. Mendel-Hartvig, and U. Landegren. "Signal amplification of padlock probes by rolling circle replication." Nucleic Acids Research 26, no. 22 (1998): 5073–78. http://dx.doi.org/10.1093/nar/26.22.5073.

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29

Leung, Siu Kai, and Joseph T. Y. Wong. "The replication of plastid minicircles involves rolling circle intermediates." Nucleic Acids Research 37, no. 6 (2009): 1991–2002. http://dx.doi.org/10.1093/nar/gkp063.

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30

Carr, Stephen B., Lauren B. Mecia, Alice J. Stelfox, Simon E. V. Phillips, and Christopher D. Thomas. "78 Structural studies of rolling circle replication initiator proteins." Journal of Biomolecular Structure and Dynamics 31, sup1 (2013): 50. http://dx.doi.org/10.1080/07391102.2013.786512.

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31

Pastrana, Cesar L., Carolina Carrasco, Parvez Akthar, Sanford H. Leuba, Saleem A. Khan, and Fernando Moreno-Herrero. "Towards Rolling-Circle Replication at the Single-Molecule Level." Biophysical Journal 112, no. 3 (2017): 372a. http://dx.doi.org/10.1016/j.bpj.2016.11.2019.

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32

Cheung, Andrew K. "Rolling-Circle Replication of an Animal Circovirus Genome in a Theta-Replicating Bacterial Plasmid in Escherichia coli." Journal of Virology 80, no. 17 (2006): 8686–94. http://dx.doi.org/10.1128/jvi.00655-06.

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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

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33

Sakatani, Yoshihiro, Ryo Mizuuchi, and Norikazu Ichihashi. "In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication." Protein Engineering, Design and Selection 32, no. 11 (2019): 481–87. http://dx.doi.org/10.1093/protein/gzaa011.

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Abstract Phi29 DNA polymerase is widely used for DNA amplification through rolling-circle replication or multiple displacement amplification. Here, we performed completely in vitro artificial evolution of phi29 DNA polymerase by combining the in vitro compartmentalization and the gene expression-coupled rolling-circle replication of a circular DNA encoding the polymerase. We conducted the experiments in six different conditions composed of three different levels of inhibitor concentrations with two different DNA labeling methods. One of the experiments was performed in our previous study and t

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34

Jain, Nimit, Lucas R. Blauch, Michal R. Szymanski, et al. "Transcription polymerase–catalyzed emergence of novel RNA replicons." Science 368, no. 6487 (2020): eaay0688. http://dx.doi.org/10.1126/science.aay0688.

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Transcription polymerases can exhibit an unusual mode of regenerating certain RNA templates from RNA, yielding systems that can replicate and evolve with RNA as the information carrier. Two classes of pathogenic RNAs (hepatitis delta virus in animals and viroids in plants) are copied by host transcription polymerases. Using in vitro RNA replication by the transcription polymerase of T7 bacteriophage as an experimental model, we identify hundreds of new replicating RNAs, define three mechanistic hallmarks of replication (subterminal de novo initiation, RNA shape-shifting, and interrupted rollin

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35

Tinsley, Eowyn, and Saleem A. Khan. "A Bacillus anthracis-Based In Vitro System Supports Replication of Plasmid pXO2 as Well as Rolling-Circle-Replicating Plasmids." Applied and Environmental Microbiology 73, no. 15 (2007): 5005–10. http://dx.doi.org/10.1128/aem.00240-07.

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ABSTRACT Capsule-encoding virulence plasmid pXO2 of Bacillus anthracis is predicted to replicate by a unidirectional theta-type mechanism. To gain a better understanding of the mechanism of replication of pXO2 and other plasmids in B. anthracis and related organisms, we have developed a cell-free system based on B. anthracis that can faithfully replicate plasmid DNA in vitro. The newly developed system was shown to support the in vitro replication of plasmid pT181, which replicates by the rolling-circle mechanism. We also demonstrate that this system supports the replication of plasmid pXO2 of

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36

Bruand, Claude, and S. Dusko Ehrlich. "UvrD-dependent replication of rolling-circle plasmids in Escherichia coli." Molecular Microbiology 35, no. 1 (2000): 204–10. http://dx.doi.org/10.1046/j.1365-2958.2000.01700.x.

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37

Khan, Saleem A. "Plasmid rolling-circle replication: highlights of two decades of research." Plasmid 53, no. 2 (2005): 126–36. http://dx.doi.org/10.1016/j.plasmid.2004.12.008.

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38

Hasnain, Shahida, and Christopher M. Thomas. "Two Related Rolling Circle Replication Plasmids from Salt-Tolerant Bacteria." Plasmid 36, no. 3 (1996): 191–99. http://dx.doi.org/10.1006/plas.1996.0046.

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39

Cohen, S. "Evidence for rolling circle replication of tandem genes in Drosophila." Nucleic Acids Research 33, no. 14 (2005): 4519–26. http://dx.doi.org/10.1093/nar/gki764.

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40

Tanner, Nathan A., Joseph J. Loparo, Samir M. Hamdan, Slobodan Jergic, Nicholas E. Dixon, and Antoine M. van Oijen. "Real-time single-molecule observation of rolling-circle DNA replication." Nucleic Acids Research 37, no. 4 (2009): e27-e27. http://dx.doi.org/10.1093/nar/gkp006.

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41

Dasgupta, Santanu, Jan Zabielski, Magnus Simonsson, and Stanley Burnett. "Rolling-circle replication of a high-copy BPV-1 plasmid." Journal of Molecular Biology 228, no. 1 (1992): 1–6. http://dx.doi.org/10.1016/0022-2836(92)90485-3.

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42

Walker, Caray A., Willie Donachie, David G. E. Smith, and Michael C. Fontaine. "Targeted Allele Replacement Mutagenesis of Corynebacterium pseudotuberculosis." Applied and Environmental Microbiology 77, no. 10 (2011): 3532–35. http://dx.doi.org/10.1128/aem.01740-10.

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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. pseudotuber

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43

Deichaite, I., Z. Laver-Rudich, D. Dorsett, and E. Winocour. "Linear simian virus 40 DNA fragments exhibit a propensity for rolling-circle replication." Molecular and Cellular Biology 5, no. 7 (1985): 1787–90. http://dx.doi.org/10.1128/mcb.5.7.1787.

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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.

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44

Deichaite, I., Z. Laver-Rudich, D. Dorsett, and E. Winocour. "Linear simian virus 40 DNA fragments exhibit a propensity for rolling-circle replication." Molecular and Cellular Biology 5, no. 7 (1985): 1787–90. http://dx.doi.org/10.1128/mcb.5.7.1787-1790.1985.

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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.

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45

Yasukawa, H., E. Ozaki, K. Nakahama, and Y. Masamune. "HU protein binding to the replication origin of the rolling-circle plasmid pKYM enhances DNA replication." Molecular and General Genetics MGG 254, no. 5 (1997): 548–54. http://dx.doi.org/10.1007/s004380050450.

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46

Mani, Nagraj, Alexander Yuzhakov, Olga Yuzhakov, et al. "Nonstructural Protein 5A (NS5A) and Human Replication Protein A Increase the Processivity of Hepatitis C Virus NS5B Polymerase ActivityIn Vitro." Journal of Virology 89, no. 1 (2014): 165–80. http://dx.doi.org/10.1128/jvi.01677-14.

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ABSTRACTThe precise role(s) and topological organization of different factors in the hepatitis C virus (HCV) RNA replication complex are not well understood. In order to elucidate the role of viral and host proteins in HCV replication, we have developed a novelin vitroreplication system that utilizes a rolling-circle RNA template. Under close-to-physiological salt conditions, HCV NS5BΔ21, an RNA-dependent RNA polymerase, has poor affinity for the RNA template. Human replication protein A (RPA) and HCV NS5A recruit NS5BΔ21 to the template. Subsequently, NS3 is recruited to the replication compl

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47

Backert, S., P. Dörfel, R. Lurz, and T. Börner. "Rolling-circle replication of mitochondrial DNA in the higher plant Chenopodium album (L.)." Molecular and Cellular Biology 16, no. 11 (1996): 6285–94. http://dx.doi.org/10.1128/mcb.16.11.6285.

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The mitochondrial genomes of higher plants are larger and more complex than those of all other groups of organisms. We have studied the in vivo replication of chromosomal and plasmid mitochondrial DNAs prepared from a suspension culture and whole plants of the dicotyledonous higher plant Chenopodium album (L.). Electron microscopic studies revealed sigma-shaped, linear, and open circular molecules (subgenomic circles) of variable size as well as a minicircular plasmid of 1.3 kb (mp1). The distribution of single-stranded mitochondrial DNA in the sigma structures and the detection of entirely si

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48

Galli, D. M., and D. J. Leblanc. "Transcriptional analysis of rolling circle replicating plasmid pVT736-1: evidence for replication control by antisense RNA." Journal of bacteriology 177, no. 15 (1995): 4474–80. http://dx.doi.org/10.1128/jb.177.15.4474-4480.1995.

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49

Lee, So Yeon, Kyoung-Ran Kim, Duhee Bang, Se Won Bae, Hak Joong Kim, and Dae-Ro Ahn. "Biophysical and chemical handles to control the size of DNA nanoparticles produced by rolling circle amplification." Biomaterials Science 4, no. 9 (2016): 1314–17. http://dx.doi.org/10.1039/c6bm00296j.

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50

Ward, Donald E., Ingrid M. Revet, Renu Nandakumar, et al. "Characterization of Plasmid pRT1 from Pyrococcus sp. Strain JT1." Journal of Bacteriology 184, no. 9 (2002): 2561–66. http://dx.doi.org/10.1128/jb.184.9.2561-2566.2002.

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ABSTRACT We discovered a 3,373-bp plasmid (pRT1) in the hyperthermophilic archaeon Pyrococcus sp. strain JT1. Two major open reading frames were identified, and analysis of the sequence revealed some resemblance to motifs typically found in plasmids that replicate via a rolling-circle mechanism. The presence of single-stranded DNA replication intermediates of pRT1 was detected, confirming this mode of replication.

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