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Journal articles on the topic 'Rolling circle replication'

Author: Grafiati

Published: 4 June 2021

Last updated: 29 January 2023

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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

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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6

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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7

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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8

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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9

Rivera-Madrinan, Felipe, Katherine Di Iorio, and Paul G. Higgs. "Rolling Circles as a Means of Encoding Genes in the RNA World." Life 12, no. 9 (2022): 1373. http://dx.doi.org/10.3390/life12091373.

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The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice th

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10

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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11

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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12

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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13

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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14

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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15

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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16

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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17

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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18

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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19

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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20

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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21

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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22

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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23

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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24

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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25

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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26

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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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

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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29

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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30

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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31

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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32

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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33

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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34

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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35

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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36

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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37

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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38

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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39

Liu, Chen-Liwei, Xiang-Juan Kong, Jing Yuan, Ru-Qin Yu, and Xia Chu. "A dual-amplification fluorescent sensing platform for ultrasensitive assay of nuclease and ATP based on rolling circle replication and exonuclease III-aided recycling." RSC Advances 5, no. 92 (2015): 75055–61. http://dx.doi.org/10.1039/c5ra13301g.

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A ultrasensitive, easy operated and robust assay of S1 nuclease in real samples and ATP has been successfully achieved with the dual-amplification strategy based on rolling circle replication and Exo III-aided recycling.

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40

Lin, Chenxiang, Xing Wang, Yan Liu, Nadrian C. Seeman, and Hao Yan. "Rolling Circle Enzymatic Replication of a Complex Multi-Crossover DNA Nanostructure." Journal of the American Chemical Society 129, no. 46 (2007): 14475–81. http://dx.doi.org/10.1021/ja0760980.

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41

Chu, Sheng-Fen, Hung-Yu Shu, Ling-Chun Lin, Mao-Yen Chen, San-San Tsay, and Guang-Huey Lin. "Characterization of a rolling-circle replication plasmid from Thermus aquaticus NTU103." Plasmid 56, no. 1 (2006): 46–52. http://dx.doi.org/10.1016/j.plasmid.2006.01.005.

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42

Pristas, Peter, Jozef Ivan, and Peter Javorsky. "Structural instability of small rolling circle replication plasmids from Selenomonas ruminantium." Plasmid 64, no. 2 (2010): 74–78. http://dx.doi.org/10.1016/j.plasmid.2010.04.005.

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43

Fluit, A. C., P. D. Baas та H. S. Jansz. "Termination and reinitiation signals of bacteriophage φX174 rolling circle DNA replication". Virology 154, № 2 (1986): 357–68. http://dx.doi.org/10.1016/0042-6822(86)90461-7.

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44

Parker, Christopher, Xiao-lin Zhang, Dorian Henderson, Eric Becker, and Richard Meyer. "Conjugative DNA synthesis: R1162 and the question of rolling-circle replication." Plasmid 48, no. 3 (2002): 186–92. http://dx.doi.org/10.1016/s0147-619x(02)00105-1.

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45

Southerden, Lesley, Claudia Arbore, and Martin Webb. "PcrA Helicase and the Mechanism of Asymmetric Rolling Circle DNA Replication." Biophysical Journal 106, no. 2 (2014): 72a. http://dx.doi.org/10.1016/j.bpj.2013.11.475.

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46

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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47

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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48

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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49

Nakashima, Nobutaka, and Tomohiro Tamura. "Isolation and Characterization of a Rolling-Circle-Type Plasmid from Rhodococcus erythropolis and Application of the Plasmid to Multiple-Recombinant-Protein Expression." Applied and Environmental Microbiology 70, no. 9 (2004): 5557–68. http://dx.doi.org/10.1128/aem.70.9.5557-5568.2004.

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ABSTRACT We isolated, sequenced, and characterized the cryptic plasmid pRE8424 from Rhodococcus erythropolis DSM8424. Plasmid pRE8424 is a 5,987-bp circular plasmid; it carries six open reading frames and also contains cis-acting elements, specifically a single-stranded origin and a double-stranded origin, which are characteristic of rolling-circle-replication plasmids. Experiments with pRE8424 derivatives carrying a mutated single-stranded origin sequence showed that single-stranded DNA intermediates accumulated in the cells because of inefficient conversion from single-stranded DNA to double

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50

Ling, Feng, Akiko Hori, and Takehiko Shibata. "DNA Recombination-Initiation Plays a Role in the Extremely Biased Inheritance of Yeast [rho−] Mitochondrial DNA That Contains the Replication Origin ori5." Molecular and Cellular Biology 27, no. 3 (2006): 1133–45. http://dx.doi.org/10.1128/mcb.00770-06.

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ABSTRACT Hypersuppressiveness, as observed in Saccharomyces cerevisiae, is an extremely biased inheritance of a small mitochondrial DNA (mtDNA) fragment that contains a replication origin (HS [rho −] mtDNA). Our previous studies showed that concatemers (linear head-to-tail multimers) are obligatory intermediates for mtDNA partitioning and are primarily formed by rolling-circle replication mediated by Mhr1, a protein required for homologous mtDNA recombination. In this study, we found that Mhr1 is required for the hypersuppressiveness of HS [ori5] [rho −] mtDNA harboring ori5, one of the replic

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