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Tocilj A, On KF, Yuan Z, Sun J, Elkayam E, Li H, Stillman B, Joshua-Tor L. Structure of the active form of human origin recognition complex and its ATPase motor module. eLife 2017; 6. [PMID: 28112645 PMCID: PMC5291709 DOI: 10.7554/elife.20818] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/15/2017] [Indexed: 12/21/2022] Open
Abstract
Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations. DOI:http://dx.doi.org/10.7554/eLife.20818.001
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Affiliation(s)
- Ante Tocilj
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Kin Fan On
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Zuanning Yuan
- Biology Department, Brookhaven National Laboratory, New York, United States.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Jingchuan Sun
- Biology Department, Brookhaven National Laboratory, New York, United States
| | - Elad Elkayam
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Huilin Li
- Biology Department, Brookhaven National Laboratory, New York, United States.,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor, New York, United States.,Howard Hughes Medical Institute, Cold Spring Harbor, New York, United States.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
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Chiani F, Felice FD, Camilloni G. SIR2 modifies histone H4-K16 acetylation and affects superhelicity in the ARS region of plasmid chromatin in Saccharomyces cerevisiae. Nucleic Acids Res 2006; 34:5426-37. [PMID: 17012273 PMCID: PMC1636471 DOI: 10.1093/nar/gkl678] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The null mutation of the SIR2 gene in Saccharomyces cerevisiae has been associated with a series of different phenotypes including loss of transcriptional silencing, genome instability and replicative aging. Thus, the SIR2 gene product is an important constituent of the yeast cell. SIR2 orthologues and paralogues have been discovered in organisms ranging from bacteria to man, underscoring the pivotal role of this protein. Here we report that a plasmid introduced into sir2Delta cells accumulates more negative supercoils compared to the same plasmid introduced into wild-type (WT) cells. This effect appears to be directly related to SIR2 expression as shown by the reduction of negative supercoiling when SIR2 is overexpressed, and does not depend on the number or positioning of nucleosomes on plasmids. Our results indicate that this new phenotype is due to the lack of Sir2p histone deacetylase activity in the sir2Delta strain, because only the H4-K16 residue of the histone octamer undergoes an alteration of its acetylation state. A model proposing interference with the replication machinery is discussed.
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Affiliation(s)
| | | | - Giorgio Camilloni
- Istituto di Biologia e Patologia Molecolari, CNRRome, Italy
- To whom correspondence should be addressed. Tel: +390649912808; Fax: +390649912500;
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Miyake T, Loch CM, Li R. Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol Cell Biol 2002; 22:505-16. [PMID: 11756546 PMCID: PMC139751 DOI: 10.1128/mcb.22.2.505-516.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Autonomously replicating sequence-binding factor 1 (ABF1) is a multifunctional, site-specific DNA binding protein that is essential for cell viability in Saccharomyces cerevisiae. ABF1 plays a direct role in transcriptional activation, stimulation of DNA replication, and gene silencing at the mating-type loci. Here we demonstrate that all three activities of ABF1 are conferred by the C terminus of the protein (amino acids [aa] 604 to 731). Furthermore, a detailed mutational analysis has revealed two important clusters of amino acid residues in the C terminus (C-terminal sequence 1 [CS1], aa 624 to 628; and CS2, aa 639 to 662). While both regions play a pivotal role in supporting cell viability, they make distinct contributions to ABF1 functions in various nuclear processes. CS1 specifically participates in transcriptional silencing and/or repression in a context-dependent manner, whereas CS2 is universally required for all three functions of ABF1. When tethered to specific regions of the genome, a 30-aa fragment that contains CS2 alone is sufficient for activation of transcription and chromosomal replication. In addition, CS2 is responsible for ABF1-mediated chromatin remodeling. Based on these results, we suggest that ABF1 may function as a chromatin-reorganizing factor to increase accessibility of the local chromatin structure, which in turn facilitates the action of additional factors to establish either an active or repressed chromatin state.
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Affiliation(s)
- Tsuyoshi Miyake
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia 22908-0733, USA
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