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Toft CJ, Moreau MJJ, Perutka J, Mandapati S, Enyeart P, Sorenson AE, Ellington AD, Schaeffer PM. Delineation of the Ancestral Tus-Dependent Replication Fork Trap. Int J Mol Sci 2021; 22:ijms222413533. [PMID: 34948327 PMCID: PMC8707476 DOI: 10.3390/ijms222413533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 12/28/2022] Open
Abstract
In Escherichia coli, DNA replication termination is orchestrated by two clusters of Ter sites forming a DNA replication fork trap when bound by Tus proteins. The formation of a ‘locked’ Tus–Ter complex is essential for halting incoming DNA replication forks. However, the absence of replication fork arrest at some Ter sites raised questions about their significance. In this study, we examined the genome-wide distribution of Tus and found that only the six innermost Ter sites (TerA–E and G) were significantly bound by Tus. We also found that a single ectopic insertion of TerB in its non-permissive orientation could not be achieved, advocating against a need for ‘back-up’ Ter sites. Finally, examination of the genomes of a variety of Enterobacterales revealed a new replication fork trap architecture mostly found outside the Enterobacteriaceae family. Taken together, our data enabled the delineation of a narrow ancestral Tus-dependent DNA replication fork trap consisting of only two Ter sites.
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Affiliation(s)
- Casey J. Toft
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
- Centre of Tropical Bioinformatics and Molecular Biology, James Cook University, Douglas, QLD 4811, Australia
| | - Morgane J. J. Moreau
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
| | - Jiri Perutka
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Savitri Mandapati
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Peter Enyeart
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Alanna E. Sorenson
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
| | - Andrew D. Ellington
- Institute for Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; (J.P.); (S.M.); (P.E.); (A.D.E.)
| | - Patrick M. Schaeffer
- Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Douglas, QLD 4811, Australia; (C.J.T.); (M.J.J.M.); (A.E.S.)
- Centre of Tropical Bioinformatics and Molecular Biology, James Cook University, Douglas, QLD 4811, Australia
- Correspondence: ; Tel.: +61-(0)-7-4781-4448; Fax: +61-(0)-7-4781-6078
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Jameson KH, Rudolph CJ, Hawkins M. Termination of DNA replication at Tus-ter barriers results in under-replication of template DNA. J Biol Chem 2021; 297:101409. [PMID: 34780717 DOI: 10.1016/j.jbc.2021.101409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 02/05/2023] Open
Abstract
The complete and accurate duplication of genomic information is vital to maintain genome stability in all domains of life. In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the 'replication fork trap' region by multiple unidirectional fork barriers formed by the binding of Tus protein to genomic ter sites. Termination typically occurs away from Tus-ter complexes, but they become part of the fork fusion process when a delay to one replisome allows the second replisome to travel more than halfway around the chromosome. In this instance, replisome progression is blocked at the non-permissive interface of the Tus-ter complex, termination then occurs when a converging replisome meets the permissive interface. To investigate the consequences of replication fork fusion at Tus-ter complexes, we established a plasmid-based replication system where we could mimic the termination process at Tus-ter complexes in vitro. We developed a termination mapping assay to measure leading strand replication fork progression and demonstrate that the DNA template is under-replicated by 15-24 bases when replication forks fuse at Tus-ter complexes. This gap could not be closed by the addition of lagging strand processing enzymes or by the inclusion of several helicases that promote DNA replication. Our results indicate that accurate fork fusion at Tus-ter barriers requires further enzymatic processing, highlighting large gaps that still exist in our understanding of the final stages of chromosome duplication and the evolutionary advantage of having a replication fork trap.
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Affiliation(s)
- Katie H Jameson
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge, UB8 3PH, UK
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
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Goodall DJ, Jameson KH, Hawkins M, Rudolph CJ. A Fork Trap in the Chromosomal Termination Area Is Highly Conserved across All Escherichia coli Phylogenetic Groups. Int J Mol Sci 2021; 22:ijms22157928. [PMID: 34360694 PMCID: PMC8347550 DOI: 10.3390/ijms22157928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/26/2022] Open
Abstract
Termination of DNA replication, the final stage of genome duplication, is surprisingly complex, and failures to bring DNA synthesis to an accurate conclusion can impact genome stability and cell viability. In Escherichia coli, termination takes place in a specialised termination area opposite the origin. A 'replication fork trap' is formed by unidirectional fork barriers via the binding of Tus protein to genomic ter sites. Such a fork trap system is found in some bacterial species, but it appears not to be a general feature of bacterial chromosomes. The biochemical properties of fork trap systems have been extensively characterised, but little is known about their precise physiological roles. In this study, we compare locations and distributions of ter terminator sites in E. coli genomes across all phylogenetic groups, including Shigella. Our analysis shows that all ter sites are highly conserved in E. coli, with slightly more variability in the Shigella genomes. Our sequence analysis of ter sites and Tus proteins shows that the fork trap is likely to be active in all strains investigated. In addition, our analysis shows that the dif chromosome dimer resolution site is consistently located between the innermost ter sites, even if rearrangements have changed the location of the innermost termination area. Our data further support the idea that the replication fork trap has an important physiological role that provides an evolutionary advantage.
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Affiliation(s)
- Daniel J. Goodall
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
| | - Katie H. Jameson
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (K.H.J.); (M.H.)
| | - Michelle Hawkins
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK; (K.H.J.); (M.H.)
| | - Christian J. Rudolph
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK;
- Correspondence:
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Wang Y, Zhang W, Yao Q. Copper-based biomaterials for bone and cartilage tissue engineering. J Orthop Translat 2021; 29:60-71. [PMID: 34094859 PMCID: PMC8164005 DOI: 10.1016/j.jot.2021.03.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 02/07/2023] Open
Abstract
Backgroud Tissue engineering using cells, scaffolds, and bioactive molecules can promote the repair and regeneration of injured tissues. Copper is an essential element for the human body that is involved in many physiological activities and in recent years, copper has been used increasingly in tissue engineering. Methods The current advances of copper-based biomaterial for bone and cartilage tissue engineering were searched on PubMed and Web of Science. Results Various forms of copper-based biomaterials, including pure copper, copper ions, copper nanoparticles, copper oxides, and copper alloy are introduced. The incorporation of copper into base materials provides unique properties, resulting in tuneable porosity, mechanical strength, degradation, and crosslinking of scaffolds. Copper also shows promising biological performance in cell migration, cell adhesion, osteogenesis, chondrogenesis, angiogenesis, and antibacterial activities. In vivo applications of copper for bone and cartilage tissue engineering are discussed. Conclusion This review focuses on copper’s physiochemical and biological effects, and its applications in bone and cartilage tissue engineering. The potential limitations and future perspectives are also discussed. Translational potential of this article This review introduces the recent advances in copper-based biomaterial for bone and cartilage tissue engineering. This revie could guide researchers to apply copper in biomaterials, improving the generation of bone and cartilages, decrease the possibility of infection and shorten the recovery time so as to decrease medical costs.
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Affiliation(s)
- Yufeng Wang
- Department of Orthopaedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.,School of Medicine, Southeast University, Nanjing, 210009, China
| | - Wei Zhang
- School of Medicine, Southeast University, Nanjing, 210009, China.,China Orthopedic Regenerative Medicine Group (CORMed), China
| | - Qingqiang Yao
- Department of Orthopaedic Surgery, Institute of Digital Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, China.,China Orthopedic Regenerative Medicine Group (CORMed), China
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Japaridze A, Gogou C, Kerssemakers JWJ, Nguyen HM, Dekker C. Direct observation of independently moving replisomes in Escherichia coli. Nat Commun 2020; 11:3109. [PMID: 32561741 PMCID: PMC7305307 DOI: 10.1038/s41467-020-16946-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/29/2020] [Indexed: 12/18/2022] Open
Abstract
The replication and transfer of genomic material from a cell to its progeny are vital processes in all living systems. Here we visualize the process of chromosome replication in widened E. coli cells. Monitoring the replication of single chromosomes yields clear examples of replication bubbles that reveal that the two replisomes move independently from the origin to the terminus of replication along each of the two arms of the circular chromosome, providing direct support for the so-called train-track model, and against a factory model for replisomes. The origin of replication duplicates near midcell, initially splitting to random directions and subsequently towards the poles. The probability of successful segregation of chromosomes significantly decreases with increasing cell width, indicating that chromosome confinement by the cell boundary is an important driver of DNA segregation. Our findings resolve long standing questions in bacterial chromosome organization.
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Affiliation(s)
- Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Christos Gogou
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jacob W J Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Huyen My Nguyen
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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Midgley-Smith SL, Dimude JU, Taylor T, Forrester NM, Upton AL, Lloyd RG, Rudolph CJ. Chromosomal over-replication in Escherichia coli recG cells is triggered by replication fork fusion and amplified if replichore symmetry is disturbed. Nucleic Acids Res 2019; 46:7701-7715. [PMID: 29982635 PMCID: PMC6125675 DOI: 10.1093/nar/gky566] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/13/2018] [Indexed: 01/04/2023] Open
Abstract
Chromosome duplication initiates via the assembly of replication forks at defined origins. Forks proceed in opposite directions until they fuse with a converging fork. Recent work highlights that fork fusions are highly choreographed both in pro- and eukaryotic cells. The circular Escherichia coli chromosome is replicated from a single origin (oriC), and a single fork fusion takes place in a specialised termination area opposite oriC that establishes a fork trap mediated by Tus protein bound at ter sequences that allows forks to enter but not leave. Here we further define the molecular details of fork fusions and the role of RecG helicase in replication termination. Our data support the idea that fork fusions have the potential to trigger local re-replication of the already replicated DNA. In ΔrecG cells this potential is realised in a substantial fraction of cells and is dramatically elevated when one fork is trapped for some time before the converging fork arrives. They also support the idea that the termination area evolved to contain such over-replication and we propose that the stable arrest of replication forks at ter/Tus complexes is an important feature that limits the likelihood of problems arising as replication terminates.
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Affiliation(s)
- Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Toni Taylor
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Nicole M Forrester
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Amy L Upton
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
| | - Robert G Lloyd
- Medical School, Queen's Medical Centre, Nottingham University, Nottingham NG7 2UH, UK
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK
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Rescuing Replication from Barriers: Mechanistic Insights from Single-Molecule Studies. Mol Cell Biol 2019; 39:MCB.00576-18. [PMID: 30886122 DOI: 10.1128/mcb.00576-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
To prevent replication failure due to fork barriers, several mechanisms have evolved to restart arrested forks independent of the origin of replication. Our understanding of these mechanisms that underlie replication reactivation has been aided through unique dynamic perspectives offered by single-molecule techniques. These techniques, such as optical tweezers, magnetic tweezers, and fluorescence-based methods, allow researchers to monitor the unwinding of DNA by helicase, nucleotide incorporation during polymerase synthesis, and replication fork progression in real time. In addition, they offer the ability to distinguish DNA intermediates after obstacles to replication at high spatial and temporal resolutions, providing new insights into the replication reactivation mechanisms. These and other highlights of single-molecule techniques and remarkable studies on the recovery of the replication fork from barriers will be discussed in this review.
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8
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Postberg J, Jönsson F, Weil PP, Bulic A, Juranek SA, Lipps HJ. 27nt-RNAs guide histone variant deposition via 'RNA-induced DNA replication interference' and thus transmit parental genome partitioning in Stylonychia. Epigenetics Chromatin 2018; 11:31. [PMID: 29895326 PMCID: PMC5996456 DOI: 10.1186/s13072-018-0201-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During sexual reproduction in the unicellular ciliate Stylonychia somatic macronuclei differentiate from germline micronuclei. Thereby, programmed sequence reduction takes place, leading to the elimination of > 95% of germline sequences, which priorly adopt heterochromatin structure via H3K27me3. Simultaneously, 27nt-ncRNAs become synthesized from parental transcripts and are bound by the Argonaute protein PIWI1. RESULTS These 27nt-ncRNAs cover sequences destined to the developing macronucleus and are thought to protect them from degradation. We provide evidence and propose that RNA/DNA base-pairing guides PIWI1/27nt-RNA complexes to complementary macronucleus-destined DNA target sequences, hence transiently causing locally stalled replication during polytene chromosome formation. This spatiotemporal delay enables the selective deposition of temporarily available histone H3.4K27me3 nucleosomes at all other sequences being continuously replicated, thus dictating their prospective heterochromatin structure before becoming developmentally eliminated. Concomitantly, 27nt-RNA-covered sites remain protected. CONCLUSIONS We introduce the concept of 'RNA-induced DNA replication interference' and explain how the parental functional genome partition could become transmitted to the progeny.
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Affiliation(s)
- Jan Postberg
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448 Witten, Germany
- HELIOS University Hospital Wuppertal, Centre for Clinical and Translational Research (CCTR), HELIOS Medical Centre Wuppertal, Witten/Herdecke University, Heusnerstr. 40, 42283 Wuppertal, Germany
| | - Franziska Jönsson
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Patrick Philipp Weil
- Clinical Molecular Genetics and Epigenetics, Centre for Biomedical Education and Research (ZBAF), Faculty of Health, Witten/Herdecke University, Alfred-Herrhausen-Str. 50, 58448 Witten, Germany
- HELIOS University Hospital Wuppertal, Centre for Clinical and Translational Research (CCTR), HELIOS Medical Centre Wuppertal, Witten/Herdecke University, Heusnerstr. 40, 42283 Wuppertal, Germany
| | - Aneta Bulic
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
| | - Stefan Andreas Juranek
- iPSC CRISPR Facility, European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, Groningen, The Netherlands
| | - Hans-Joachim Lipps
- Institute of Cell Biology, Centre for Biomedical Education and Research (ZBAF), Witten/Herdecke University, Witten, Germany
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Dimude JU, Midgley-Smith SL, Stein M, Rudolph CJ. Replication Termination: Containing Fork Fusion-Mediated Pathologies in Escherichia coli. Genes (Basel) 2016; 7:genes7080040. [PMID: 27463728 PMCID: PMC4999828 DOI: 10.3390/genes7080040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/12/2016] [Accepted: 07/19/2016] [Indexed: 01/18/2023] Open
Abstract
Duplication of bacterial chromosomes is initiated via the assembly of two replication forks at a single defined origin. Forks proceed bi-directionally until they fuse in a specialised termination area opposite the origin. This area is flanked by polar replication fork pause sites that allow forks to enter but not to leave. The precise function of this replication fork trap has remained enigmatic, as no obvious phenotypes have been associated with its inactivation. However, the fork trap becomes a serious problem to cells if the second fork is stalled at an impediment, as replication cannot be completed, suggesting that a significant evolutionary advantage for maintaining this chromosomal arrangement must exist. Recently, we demonstrated that head-on fusion of replication forks can trigger over-replication of the chromosome. This over-replication is normally prevented by a number of proteins including RecG helicase and 3’ exonucleases. However, even in the absence of these proteins it can be safely contained within the replication fork trap, highlighting that multiple systems might be involved in coordinating replication fork fusions. Here, we discuss whether considering the problems associated with head-on replication fork fusion events helps us to better understand the important role of the replication fork trap in cellular metabolism.
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Affiliation(s)
- Juachi U Dimude
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Sarah L Midgley-Smith
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Monja Stein
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
| | - Christian J Rudolph
- Division of Biosciences, College of Health and Life Sciences, Brunel University London, Uxbridge UB8 3PH, UK.
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