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Rastokina A, Cebrián J, Mozafari N, Mandel NH, Smith CI, Lopes M, Zain R, Mirkin S. Large-scale expansions of Friedreich's ataxia GAA•TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers. Nucleic Acids Res 2023; 51:8532-8549. [PMID: 37216608 PMCID: PMC10484681 DOI: 10.1093/nar/gkad441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/02/2023] [Accepted: 05/20/2023] [Indexed: 05/24/2023] Open
Abstract
Friedreich's ataxia (FRDA) is caused by expansions of GAA•TTC repeats in the first intron of the human FXN gene that occur during both intergenerational transmissions and in somatic cells. Here we describe an experimental system to analyze large-scale repeat expansions in cultured human cells. It employs a shuttle plasmid that can replicate from the SV40 origin in human cells or be stably maintained in S. cerevisiae utilizing ARS4-CEN6. It also contains a selectable cassette allowing us to detect repeat expansions that accumulated in human cells upon plasmid transformation into yeast. We indeed observed massive expansions of GAA•TTC repeats, making it the first genetically tractable experimental system to study large-scale repeat expansions in human cells. Further, GAA•TTC repeats stall replication fork progression, while the frequency of repeat expansions appears to depend on proteins implicated in replication fork stalling, reversal, and restart. Locked nucleic acid (LNA)-DNA mixmer oligonucleotides and peptide nucleic acid (PNA) oligomers, which interfere with triplex formation at GAA•TTC repeats in vitro, prevented the expansion of these repeats in human cells. We hypothesize, therefore, that triplex formation by GAA•TTC repeats stall replication fork progression, ultimately leading to repeat expansions during replication fork restart.
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Affiliation(s)
| | - Jorge Cebrián
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Negin Mozafari
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | | | - C I Edvard Smith
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Rula Zain
- Department of Laboratory Medicine, Translational Research Center Karolinska (TRACK), Karolinska Institutet, Karolinska University Hospital, SE-171 77 Stockholm, Sweden
- Center for Rare Diseases, Karolinska University Hospital, SE-17176 Stockholm, Sweden
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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2
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Castán A, Hernández P, Krimer DB, Schvartzman JB. The abundance of Fob1 modulates the efficiency of rRFBs to stall replication forks. Nucleic Acids Res 2017; 45:10089-10102. [PMID: 28973451 PMCID: PMC5622318 DOI: 10.1093/nar/gkx655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 07/17/2017] [Indexed: 11/24/2022] Open
Abstract
In eukaryotes, ribosomal genes (rDNA) are organized in tandem repeats localized in one or a few clusters. Each repeat encompasses a transcription unit and a non-transcribed spacer. Replication forks moving in the direction opposite to transcription are blocked at specific sites called replication fork barriers (rRFBs) in the non-transcribed spacer close to the 3′ end of the transcription unit. Here, we investigated and quantified the efficiency of rRFBs in Saccharomyces cerevisiae and to this end transfected budding yeast cells that express dissimilar quantities of Fob1 with circular minichromosomes containing different copies of the minimal 20-bp DNA segment that bind Fob1. To identify fork stalling we used high-resolution 2D agarose gel electrophoresis. The results obtained indicated that neighbor DNA sequences and the relative abundance of Fob1 modulate the efficiency of rRFBs to stall replication forks.
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Affiliation(s)
- Alicia Castán
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Pablo Hernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Dora B Krimer
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge B Schvartzman
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
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3
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Topoisomerase 2 is dispensable for the replication and segregation of small yeast artificial chromosomes (YACs). PLoS One 2014; 9:e104995. [PMID: 25115861 PMCID: PMC4130621 DOI: 10.1371/journal.pone.0104995] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
DNA topoisomerases are thought to play a critical role in transcription, replication and recombination as well as in the condensation and segregation of sister duplexes during cell division. Here, we used high-resolution two-dimensional agarose gel electrophoresis to study the replication intermediates and final products of small circular and linear minichromosomes of Saccharomyces cerevisiae in the presence and absence of DNA topoisomerase 2. The results obtained confirmed that whereas for circular minichromosomes, catenated sister duplexes accumulated in the absence of topoisomerase 2, linear YACs were able to replicate and segregate regardless of this topoisomerase. The patterns of replication intermediates for circular and linear YACs displayed significant differences suggesting that DNA supercoiling might play a key role in the modulation of replication fork progression. Altogether, this data supports the notion that for linear chromosomes the torsional tension generated by transcription and replication dissipates freely throughout the telomeres.
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4
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Olszewski P, Szambowska A, Barałska S, Narajczyk M, Węgrzyn G, Glinkowska M. A dual promoter system regulating λ DNA replication initiation. Nucleic Acids Res 2014; 42:4450-62. [PMID: 24500197 PMCID: PMC3985674 DOI: 10.1093/nar/gku103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Transcription and DNA replication are tightly regulated to ensure coordination of gene expression with growth conditions and faithful transmission of genetic material to progeny. A large body of evidence has accumulated, indicating that encounters between protein machineries carrying out DNA and RNA synthesis occur in vivo and may have important regulatory consequences. This feature may be exacerbated in the case of compact genomes, like the one of bacteriophage λ, used in our study. Transcription that starts at the rightward pR promoter and proceeds through the λ origin of replication and downstream of it was proven to stimulate the initiation of λ DNA replication. Here, we demonstrate that the activity of a convergently oriented pO promoter decreases the efficiency of transcription starting from pR. Our results show, however, that a lack of the functional pO promoter negatively influences λ phage and λ-derived plasmid replication. We present data, suggesting that this effect is evoked by the enhanced level of the pR-driven transcription, occurring in the presence of the defective pO, which may result in the impeded formation of the replication initiation complex. Our data suggest that the cross talk between the two promoters regulates λ DNA replication and coordinates transcription and replication processes.
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Affiliation(s)
- Paweł Olszewski
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland, Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdańsk, Poland and Laboratory of Electron Microscopy, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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5
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Schvartzman JB, Martínez-Robles ML, López V, Hernández P, Krimer DB. 2D gels and their third-dimension potential. Methods 2012; 57:170-8. [PMID: 22465282 DOI: 10.1016/j.ymeth.2012.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/03/2012] [Accepted: 03/10/2012] [Indexed: 11/19/2022] Open
Abstract
Two-dimensional (2D) agarose gel electrophoresis is one of the most powerful methods to analyze the mass and shape of replication intermediates. It is often use to map replication origins but it is also useful to characterize termination of replication, replication fork barriers and even replication fork reversal. Here, we present protocols, figures and movies with a thorough description of different modes of replication for linear DNA fragments and the corresponding patterns they generate in 2D gels.
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MESH Headings
- Autoradiography
- DNA Replication
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/isolation & purification
- Electrophoresis, Agar Gel/methods
- Electrophoresis, Gel, Two-Dimensional/methods
- Microscopy, Atomic Force
- Models, Molecular
- Nucleic Acid Conformation
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/isolation & purification
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Affiliation(s)
- Jorge B Schvartzman
- Department of Cell Proliferation and Development, Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.
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6
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Boubakri H, de Septenville AL, Viguera E, Michel B. The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo. EMBO J 2009; 29:145-57. [PMID: 19851282 PMCID: PMC2770101 DOI: 10.1038/emboj.2009.308] [Citation(s) in RCA: 188] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 09/23/2009] [Indexed: 11/22/2022] Open
Abstract
How living cells deal with head-on collisions of the replication and transcription complexes has been debated for a long time. Even in the widely studied model bacteria Escherichia coli, the enzymes that take care of such collisions are still unknown. We report here that in vivo, the DinG, Rep and UvrD helicases are essential for efficient replication across highly transcribed regions. We show that when rRNA operons (rrn) are inverted to face replication, the viability of the dinG mutant is affected and over-expression of RNase H rescues the growth defect, showing that DinG acts in vivo to remove R-loops. In addition, DinG, Rep and UvrD exert a common function, which requires the presence of two of these three helicases. After replication blockage by an inverted rrn, Rep in conjunction with DinG or UvrD removes RNA polymerase, a task that is fulfilled in its absence by the SOS-induced DinG and UvrD helicases. Finally, Rep and UvrD also act at inverted sequences other than rrn, and promote replication through highly transcribed regions in wild-type E. coli.
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Affiliation(s)
- Hasna Boubakri
- CNRS, Centre de Génétique Moléculaire, FRE 3144, Gif-sur-Yvette, France
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7
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de la Loza MCD, Wellinger RE, Aguilera A. Stimulation of direct-repeat recombination by RNA polymerase III transcription. DNA Repair (Amst) 2009; 8:620-6. [PMID: 19168400 DOI: 10.1016/j.dnarep.2008.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 12/13/2008] [Accepted: 12/15/2008] [Indexed: 11/18/2022]
Abstract
Eukaryotic cells have to regulate the progression and integrity of DNA replication forks through concomitantly transcribed genes. A transcription-dependent increase of recombination within protein-coding and ribosomal genes of eukaryotic cells is well documented. Here we addressed whether tRNA transcription and tRNA-dependent transcription-associated replication pausing leads to genetic instability. Thus, we designed a plasmid based, LEU2 direct-repeat containing system for the analysis of factors that contribute to tRNA(SUP53)-dependent genetic instability. We show that tRNA(SUP53) transcription is recombinogenic and that recombination can be further stimulated by deletion of the 5' to 3' helicase Rrm3. Furthermore, tRNA(SUP53)-dependent recombination was markedly increased in the presence of 4-NQO in rrm3Delta cells only. The frequency of recombination events mediated by tRNA(SUP53) transcription does not correlate with the appearance and intensity of replication fork pausing sites. Our results provide evidence that the convergent encounter of replication and RNA polymerase III transcription machineries stimulates recombination, although to a lesser extent than RNA polymerase I or II transcription. However, there is no correlation between recombination and the specific replication fork pausing sites found at the tRNA (SUP53) gene. Our results indicate that tRNA-specific replication fork pausing sites are poorly recombinogenic.
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Affiliation(s)
- M C Díaz de la Loza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Universidad de Sevilla - CSIC, Avda. Américo Vespucio s/n, 41092 Sevilla, Spain
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8
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Narajczyk M, Barańska S, Szambowska A, Glinkowska M, Węgrzyn A, Węgrzyn G. Modulation of lambda plasmid and phage DNA replication by Escherichia coli SeqA protein. MICROBIOLOGY-SGM 2007; 153:1653-1663. [PMID: 17464080 DOI: 10.1099/mic.0.2006/005546-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
SeqA protein, a main negative regulator of the replication initiation of the Escherichia coli chromosome, also has several other functions which are still poorly understood. It was demonstrated previously that in seqA mutants the copy number of another replicon, the lambda plasmid, is decreased, and that the activity of the lambda p(R) promoter (whose function is required for stimulation of ori lambda) is lower than that in the wild-type host. Here, SeqA-mediated regulation of lambda phage and plasmid replicons was investigated in more detail. No significant influence of SeqA on ori lambda-dependent DNA replication in vitro was observed, indicating that a direct regulation of lambda DNA replication by this protein is unlikely. On the other hand, density-shift experiments, in which the fate of labelled lambda DNA was monitored after phage infection of host cells, strongly suggested the early appearance of sigma replication intermediates and preferential rolling-circle replication of phage DNA in seqA mutants. The directionality of lambda plasmid replication in such mutants was, however, only slightly affected. The stability of the heritable lambda replication complex was decreased in the seqA mutant relative to the wild-type host, but a stable fraction of the lambda O protein was easily detectable, indicating that such a heritable complex can function in the mutant. To investigate the influence of seqA gene function on heritable complex- and transcription-dependent lambda DNA replication, the efficiency of lambda plasmid replication in amino acid-starved relA seqA mutants was measured. Under these conditions, seqA dysfunction resulted in impairment of lambda plasmid replication. These results indicate that unlike oriC, SeqA modulates lambda DNA replication indirectly, most probably by influencing the stability of the lambda replication complex and the transcriptional activation of ori lambda.
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Affiliation(s)
- Magdalena Narajczyk
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Sylwia Barańska
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Anna Szambowska
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Monika Glinkowska
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology (affiliated with University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 80-822 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
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9
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Wanrooij S, Goffart S, Pohjoismäki JL, Yasukawa T, Spelbrink JN. Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes. Nucleic Acids Res 2007; 35:3238-51. [PMID: 17452351 PMCID: PMC1904276 DOI: 10.1093/nar/gkm215] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mechanism of mitochondrial DNA replication is a subject of intense debate. One model proposes a strand-asynchronous replication in which both strands of the circular genome are replicated semi-independently while the other model proposes both a bidirectional coupled leading- and lagging-strand synthesis mode and a unidirectional mode in which the lagging-strand is initially laid-down as RNA by an unknown mechanism (RITOLS mode). Both the strand-asynchronous and RITOLS model have in common a delayed synthesis of the DNA-lagging strand. Mitochondrial DNA is replicated by a limited set of proteins including DNA polymerase gamma (POLG) and the helicase Twinkle. Here, we report the effects of expression of various catalytically deficient mutants of POLG1 and Twinkle in human cell culture. Both groups of mutants reduced mitochondrial DNA copy number by severe replication stalling. However, the analysis showed that while induction of POLG1 mutants still displayed delayed lagging-strand synthesis, Twinkle-induced stalling resulted in maturated, essentially fully double-stranded DNA intermediates. In the latter case, limited inhibition of POLG with dideoxycytidine restored the delay between leading- and lagging-strand synthesis. The observed cause-effect relationship suggests that Twinkle-induced stalling increases lagging-strand initiation events and/or maturation mimicking conventional strand-coupled replication.
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Affiliation(s)
- Sjoerd Wanrooij
- Institute of Medical Technology and Tampere University Hospital, Tampere, Finland and MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
| | - Steffi Goffart
- Institute of Medical Technology and Tampere University Hospital, Tampere, Finland and MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
| | - Jaakko L.O. Pohjoismäki
- Institute of Medical Technology and Tampere University Hospital, Tampere, Finland and MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
| | - Takehiro Yasukawa
- Institute of Medical Technology and Tampere University Hospital, Tampere, Finland and MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
| | - Johannes N. Spelbrink
- Institute of Medical Technology and Tampere University Hospital, Tampere, Finland and MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
- *To whom correspondence should be addressed: Tel: +358 3 35518598; Fax: +358 3 35517710;
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10
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Narajczyk M, Barańska S, Wegrzyn A, Wegrzyn G. Switch from theta to sigma replication of bacteriophage lambda DNA: factors involved in the process and a model for its regulation. Mol Genet Genomics 2007; 278:65-74. [PMID: 17377819 DOI: 10.1007/s00438-007-0228-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 02/26/2007] [Indexed: 10/23/2022]
Abstract
Bacteriophage lambda genome is one of the classical model replicons in studies on the regulation of DNA replication. Moreover, since genes coding for Shiga toxins are located in genomes of lambdoid phages, understanding of mechanisms controlling lambda DNA replication may be of bio-medical importance. During lytic development of bacteriophage lambda, its genome is replicated according to the theta (circle-to-circle) mode early after infection, and then it is switched to the sigma (rolling circle) mode. Two mechanisms of regulation of this switch were proposed recently and both suggested a crucial role for directionality of lambda DNA replication. Whereas one hypothesis assumed transient impairment of ClpP/ClpX-mediated proteolysis of the lambdaO initiator protein, another suggested a crucial role for transcriptional activation of the orilambda region and factors involved in the control of the p (R) promoter activity. Here we demonstrate that mutations in clpP and clpX genes had little influence on both directionality of lambda DNA replication and appearance of sigma replication intermediates. On the other hand, regulators affecting activity of the p (R) promoter (responsible for initiation of transcription, which activates orilambda) directly or indirectly influenced directionality of lambda DNA replication to various extents. Therefore, we conclude that regulation of the efficiency of transcriptional activation of orilambda, rather than transient impairment of the lambdaO proteolysis, is responsible for the control of the switch from theta to sigma replication, and propose a model for this control.
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Affiliation(s)
- Magdalena Narajczyk
- Department of Molecular Biology, University of Gdańsk, Kładki 24, 80-822, Gdańsk, Poland
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11
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Turgeon N, Frenette M, Moineau S. Characterization of a theta-replicating plasmid from Streptococcus thermophilus. Plasmid 2004; 51:24-36. [PMID: 14711526 DOI: 10.1016/j.plasmid.2003.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Plasmids of Streptococcus thermophilus were previously classified, based on DNA homology, into at least four groups (A-D). Here, we report the characterization of plasmids of group B and D. The sequence analysis of pSMQ173b (group D) indicates that this plasmid contains 4449 bp, five open reading frames (ORFs) and replicates via the rolling-circle mechanism of the pGI3 family. The plasmid pSMQ308 (group B) contains 8144 bp and six ORFs. Two ORFs likely encode a primase/helicase and an integrase. Northern blot experiments demonstrate that these two orfs are transcribed within the three strains containing plasmids of group B. Two-dimensional agarose gel electrophoresis shows that pSMQ308 replicates via a theta mechanism. To our knowledge, this is the first report of a plasmid replicating via a theta mode in S. thermophilus. Finally, a classification of 20 sequenced S. thermophilus plasmids into six groups based on their mode of replication is proposed.
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Affiliation(s)
- Nathalie Turgeon
- Département de biochimie et de microbiologie, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Canada G1K 7P4
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12
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Olavarrieta L, Martínez-Robles ML, Hernández P, Krimer DB, Schvartzman JB. Knotting dynamics during DNA replication. Mol Microbiol 2002; 46:699-707. [PMID: 12410827 DOI: 10.1046/j.1365-2958.2002.03217.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The topology of plasmid DNA changes continuously as replication progresses. But the dynamics of the process remains to be fully understood. Knotted bubbles form when topo IV knots the daughter duplexes behind the fork in response to their degree of intertwining. Here, we show that knotted bubbles can form during unimpaired DNA replication, but they become more evident in partially replicated intermediates containing a stalled fork. To learn more about the dynamics of knot formation as replication advances, we used two-dimensional agarose gel electrophoresis to identify knotted bubbles in partially replicated molecules in which the replication fork stalled at different stages of the process. The number and complexity of knotted bubbles rose as a function of bubble size, suggesting that knotting is affected by both precatenane density and bubble size.
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Affiliation(s)
- L Olavarrieta
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
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13
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Barańska S, Konopa G, Wegrzyn G. Directionality of lambda plasmid DNA replication carried out by the heritable replication complex. Nucleic Acids Res 2002; 30:1176-81. [PMID: 11861909 PMCID: PMC101236 DOI: 10.1093/nar/30.5.1176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
There are two 'pathways' of replication of lambda plasmids in Escherichia coli. One pathway requires the assembly of a new replication complex before replication and the second pathway is based on the activity of the replication complex inherited by one of two daughter plasmid copies after a preceding replication round. Such a phenomenon was postulated to occur also in other replicons, including Saccharomyces cerevisiae autonomously replicating sequences. Here we investigated directionality of lambda plasmid replication carried out by the heritable and newly assembled replication complexes. Using two-dimensional agarose gel electrophoresis and electron microscopy we demonstrated that in both normal growth conditions and during the relaxed response to amino acid starvation (when only replication carried out by the heritable complex is possible), bidirectionally and undirectionally replicating plasmid molecules occurred in host cells in roughly equal proportions. The results are compatible with the hypothesis that both complexes (heritable and newly assembled) are equivalent.
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Affiliation(s)
- Sylwia Barańska
- Department of Molecular Biology, University of Gdaásk, Kssadki 24, 80-822 Gdaásk, Poland
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14
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Olavarrieta L, Martínez-Robles ML, Sogo JM, Stasiak A, Hernández P, Krimer DB, Schvartzman JB. Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res 2002; 30:656-66. [PMID: 11809877 PMCID: PMC100290 DOI: 10.1093/nar/30.3.656] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the structure of partially replicated plasmids, we cloned the Escherichia coli polar replication terminator TerE in its active orientation at different locations in the ColE1 vector pBR18. The resulting plasmids, pBR18-TerE@StyI and pBR18-TerE@EcoRI, were analyzed by neutral/neutral two-dimensional agarose gel electrophoresis and electron microscopy. Replication forks stop at the Ter-TUS complex, leading to the accumulation of specific replication intermediates with a mass 1.26 times the mass of non-replicating plasmids for pBR18-TerE@StyI and 1.57 times for pBR18-TerE@EcoRI. The number of knotted bubbles detected after digestion with ScaI and the number and electrophoretic mobility of undigested partially replicated topoisomers reflect the changes in plasmid topology that occur in DNA molecules replicated to different extents. Exposure to increasing concentrations of chloroquine or ethidium bromide revealed that partially replicated topoisomers (CCCRIs) do not sustain positive supercoiling as efficiently as their non-replicating counterparts. It was suggested that this occurs because in partially replicated plasmids a positive DeltaLk is absorbed by regression of the replication fork. Indeed, we showed by electron microscopy that, at least in the presence of chloroquine, some of the CCCRIs of pBR18-Ter@StyI formed Holliday-like junction structures characteristic of reversed forks. However, not all the positive supercoiling was absorbed by fork reversal in the presence of high concentrations of ethidium bromide.
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Affiliation(s)
- L Olavarrieta
- Departamento de Biología Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain
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15
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Barańska S, Gabig M, Węgrzyn A, Konopa G, Herman-Antosiewicz A, Hernandez P, Schvartzman JB, Helinski DR, Węgrzyn G. Regulation of the switch from early to late bacteriophage lambda DNA replication. MICROBIOLOGY (READING, ENGLAND) 2001; 147:535-547. [PMID: 11238961 DOI: 10.1099/00221287-147-3-535] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There are two modes of bacteriophage lambda DNA replication following infection of its host, Escherichia coli. Early after infection, replication occurs according to the theta (theta or circle-to-circle) mode, and is later switched to the sigma (sigma or rolling-circle) mode. It is not known how this switch, occurring at a specific time in the infection cycle, is regulated. Here it is demonstrated that in wild-type cells the replication starting from orilambda proceeds both bidirectionally and unidirectionally, whereas in bacteria devoid of a functional DnaA protein, replication from orilambda is predominantly unidirectional. The regulation of directionality of replication from orilambda is mediated by positive control of lambda p(R) promoter activity by DnaA, since the mode of replication of an artificial lambda replicon bearing the p(tet) promoter instead of p(R) was found to be independent of DnaA function. These findings and results of density-shift experiments suggest that in dnaA mutants infected with lambda, phage DNA replication proceeds predominantly according to the unidirectional theta mechanism and is switched early after infection to the sigma mode. It is proposed that in wild-type E. coli cells infected with lambda, phage DNA replication proceeds according to a bidirectional theta mechanism early after infection due to efficient transcriptional activation of orilambda, stimulated by the host DnaA protein. After a few rounds of this type of replication, the resulting increased copy number of lambda genomic DNA may cause a depletion of free DnaA protein because of its interaction with the multiple DnaA-binding sites in lambda DNA. It is proposed that this may lead to inefficient transcriptional activation of orilambda resulting in unidirectional theta replication followed by sigma type replication.
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Affiliation(s)
- Sylwia Barańska
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
| | - Magdalena Gabig
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
| | - Alicja Węgrzyn
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
| | - Grażyna Konopa
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
| | - Anna Herman-Antosiewicz
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
| | - Pablo Hernandez
- Departamento de Biologı́a Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain3
| | - Jorge B Schvartzman
- Departamento de Biologı́a Celular y del Desarrollo, Centro de Investigaciones Biológicas (CSIC), Velázquez 144, 28006 Madrid, Spain3
| | - Donald R Helinski
- Center for Molecular Genetics and Department of Biology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA4
| | - Grzegorz Węgrzyn
- Marine Biology Center, Polish Academy of Sciences, Św. Wojciecha 5, 81-347 Gdynia, Poland5
- Department of Molecular Biology, University of Gdańsk1 and Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences2, Kładki 24, 80-822 Gdańsk, Poland
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Santamaría D, Viguera E, Martínez-Robles ML, Hyrien O, Hernández P, Krimer DB, Schvartzman JB. Bi-directional replication and random termination. Nucleic Acids Res 2000; 28:2099-107. [PMID: 10773078 PMCID: PMC105368 DOI: 10.1093/nar/28.10.2099] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two-dimensional (2D) agarose gel electrophoresis was used to study termination of DNA replication in a shuttle vector, YRp7', when it replicated in Escherichia coli, Saccharomyces cerevisiae and Xenopus egg extracts. In E. coli, the 2D gel patterns obtained were consistent with uni-directional replication initiated at a specific site, the ColE1 origin. In consequence, termination also occurred precisely at the ColE1 origin. In Xenopus egg extracts, the particular shape of the bubble arc as well as the triangular smear detected to the left of the simple-Y pattern indicated random initiation and termination. In S.cerevisiae, initiation occurred at the ARS1 origin and replication proceeded in a bi-directional manner. However, termination did not always occur at a specific site 180 degrees across from the origin, but almost all along the south hemisphere of the plasmid. Inversion, deletion or replacement of DNA sequences located throughout this hemisphere did not eliminate random termination. Analysis of the replication intermediates of another yeast plasmid bearing a different origin, ARS305, also exhibited random termination. We propose that the random termination events observed in S.cerevisiae could be due to an asynchronous departure of both forks from the bi-directional origin in addition to differences in the rate of fork progression. These observations could be extended to all bi-directional origins.
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Affiliation(s)
- D Santamaría
- Departamento de Biología Celular y del Desarrollo, CIB (CSIC), Velázquez 144, 28006 Madrid, Spain
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Muller M, Lucchini R, Sogo JM. Replication of yeast rDNA initiates downstream of transcriptionally active genes. Mol Cell 2000; 5:767-77. [PMID: 10882113 DOI: 10.1016/s1097-2765(00)80317-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the yeast S. cerevisiae, ARS (autonomously replicating sequence) elements located in the intergenic spacers of the rRNA gene locus are infrequently activated as origins of replication. We analyzed the rARS activation with a combination of neutral/neutral (N/N) two-dimensional (2D) gel electrophoresis and either the intercalating drug psoralen, which in vivo specifically marks the transcribing gene copies, or the selective accessibility of restriction sites in transcriptionally active genes. We found that initiation of replication starts at those rARSs placed immediately downstream of transcribing rRNA genes. This correlation between transcription and replication is consistent with the presence of nucleosome-free enhancers at each transcriptionally active gene copy and suggests that the transcription factor Abf1p is involved in replication initiation at the ARS in the rDNA gene locus.
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Affiliation(s)
- M Muller
- Institute of Cell Biology, ETH Hönggerberg, Zürich, Switzerland
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Santamaría D, de la Cueva G, Martínez-Robles ML, Krimer DB, Hernández P, Schvartzman JB. DnaB helicase is unable to dissociate RNA-DNA hybrids. Its implication in the polar pausing of replication forks at ColE1 origins. J Biol Chem 1998; 273:33386-96. [PMID: 9837915 DOI: 10.1074/jbc.273.50.33386] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A series of plasmids were constructed containing two unidirectional ColE1 replication origins in either the same or opposite orientations and their replication mode was investigated using two-dimensional agarose gel electrophoresis. The results obtained showed that, in these plasmids, initiation of DNA replication occurred at only one of the two potential origins per replication round regardless of origins orientation. In those plasmids with inversely oriented origins, the silent origin act as a polar pausing site for the replication fork initiated at the other origin. The distance between origins (up to 5.8 kilobase pairs) affected neither the interference between them to initiate replication nor the pausing function of the silent origin. A deletion analysis indicated that the presence of a transcription promoter upstream of the origin was the only essential requirement for it to initiate replication as well as to account for its polar pausing function. Finally, in vitro helicase assays showed that Escherichia coli DnaB is able to melt DNA-DNA homoduplexes but is very inefficient to unwind RNA-DNA hybrids. Altogether, these observations strongly suggest that replication forks pause at silent ColE1 origins due to the inability of DnaB helicase, which leads the replication fork in vivo, to unwind RNA-DNA hybrids.
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Affiliation(s)
- D Santamaría
- Departamento de Biología Celular y del Desarrollo, CIB (Consejo Superior de Investigaciones Científicas), Velázquez 144, 28006 Madrid, Spain
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