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Płachetka M, Żyła-Uklejewicz D, Weigel C, Donczew R, Donczew M, Jakimowicz D, Zawilak-Pawlik A, Zakrzewska-Czerwinska J. Streptomycete origin of chromosomal replication with two putative unwinding elements. MICROBIOLOGY-SGM 2019; 165:1365-1375. [PMID: 31592764 DOI: 10.1099/mic.0.000859] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA replication is controlled mostly at the initiation step. In bacteria, replication of the chromosome starts at a single origin of replication called oriC. The initiator protein, DnaA, binds to specific sequences (DnaA boxes) within oriC and assembles into a filament that promotes DNA double helix opening within the DNA unwinding element (DUE). This process has been thoroughly examined in model bacteria, including Escherichia coli and Bacillus subtilis, but we have a relatively limited understanding of chromosomal replication initiation in other species. Here, we reveal new details of DNA replication initiation in Streptomyces, a group of Gram-positive soil bacteria that possesses a long linear (8-10 Mbps) and GC-rich chromosome with a centrally positioned oriC. We used comprehensive in silico, in vitro and in vivo analyses to better characterize the structure of Streptomyces oriC. We identified 14 DnaA-binding motifs and determined the consensus sequence of the DnaA box. Unexpectedly, our in silico analysis using the WebSIDD algorithm revealed the presence of two putative Streptomyces DUEs (DUE1 and DUE2) located very near one another toward the 5' end of the oriC region. In vitro P1 nuclease assay revealed that DNA unwinding occurs at both of the proposed sites, but using an in vivo replication initiation point mapping, we were able to confirm only one of them (DUE2). The previously observed transcriptional activity of the Streptomyces oriC region may help explain the current results. We speculate that transcription itself could modulate oriC activity in Streptomyces by determining whether DNA unwinding occurs at DUE1 or DUE2.
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Affiliation(s)
- Małgorzata Płachetka
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dorota Żyła-Uklejewicz
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Christoph Weigel
- Institute of Biotechnology, Faculty III, Technical University Berlin (TUB), Berlin, Germany
| | - Rafał Donczew
- Present address: Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
| | - Magdalena Donczew
- Present address: Center for Infectious Disease, Seattle, WA, USA.,Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Dagmara Jakimowicz
- Department of Molecular Microbiology, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław, Poland
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Urban JM, Foulk MS, Casella C, Gerbi SA. The hunt for origins of DNA replication in multicellular eukaryotes. F1000PRIME REPORTS 2015; 7:30. [PMID: 25926981 PMCID: PMC4371235 DOI: 10.12703/p7-30] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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Shen Z, Sathyan KM, Geng Y, Zheng R, Chakraborty A, Freeman B, Wang F, Prasanth KV, Prasanth SG. A WD-repeat protein stabilizes ORC binding to chromatin. Mol Cell 2010; 40:99-111. [PMID: 20932478 DOI: 10.1016/j.molcel.2010.09.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2010] [Revised: 05/28/2010] [Accepted: 08/27/2010] [Indexed: 01/31/2023]
Abstract
Origin recognition complex (ORC) plays critical roles in the initiation of DNA replication and cell-cycle progression. In metazoans, ORC associates with origin DNA during G1 and with heterochromatin in postreplicated cells. However, what regulates the binding of ORC to chromatin is not understood. We have identified a highly conserved, leucine-rich repeats and WD40 repeat domain-containing protein 1 (LRWD1) or ORC-associated (ORCA) in human cells that interacts with ORC and modulates chromatin association of ORC. ORCA colocalizes with ORC and shows similar cell-cycle dynamics. We demonstrate that ORCA efficiently recruits ORC to chromatin. Depletion of ORCA in human primary cells and embryonic stem cells results in loss of ORC association to chromatin, concomitant reduction of MCM binding, and a subsequent accumulation in G1 phase. Our results suggest ORCA-mediated association of ORC to chromatin is critical to initiate preRC assembly in G1 and chromatin organization in post-G1 cells.
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Affiliation(s)
- Zhen Shen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801, USA
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Abstract
Mechanisms regulating where and when eukaryotic DNA replication initiates remain a mystery. Recently, genome-scale methods have been brought to bear on this problem. The identification of replication origins and their associated proteins in yeasts is a well-integrated investigative tool, but corresponding data sets from multicellular organisms are scarce. By contrast, standardized protocols for evaluating replication timing have generated informative data sets for most eukaryotic systems. Here, I summarize the genome-scale methods that are most frequently used to analyse replication in eukaryotes, the kinds of questions each method can address and the technical hurdles that must be overcome to gain a complete understanding of the nature of eukaryotic replication origins.
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