45 results found
Noguchi Y, Yuan Z, Bai L, et al., 2017, Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model., Proc Natl Acad Sci U S A
During replication initiation, the core component of the helicase-the Mcm2-7 hexamer-is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide-oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2-Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion.
Riera A, Barbon M, Noguchi Y, et al., 2017, From structure to mechanism-understanding initiation of DNA replication, GENES & DEVELOPMENT, Vol: 31, Pages: 1073-1088, ISSN: 0890-9369
Yuan Z, Riera A, Bai L, et al., 2017, Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 24, Pages: 316-+, ISSN: 1545-9993
Riera A, Speck C, 2016, Licensing of replication origins, The Initiation of DNA Replication in Eukaryotes, Pages: 189-211, ISBN: 9783319246963
© 2016 Springer International Publishing Switzerland. All living organisms need to duplicate their genetic material prior to cell division in order to maintain genomic-stability. Cells have evolved sophisticated DNA replication mechanisms to ensure that this process is as faithful as possible. Eukaryotic i nitiation of DNA replication is a two-step process, where the replicative DNA helicase becomes loaded onto DNA to license DNA replication during late M-phase of the cell cycle prior to helicase-activation in S-phase. Importantly, helicase loading is entirely blocked in S-phase, which is a crucial regulatory mechanism that hinders re-replication of DNA and is crucial for genomic stability. Moreover, multiple copies of the replicative helicase become loaded at each origin to serve as backup-helicases in case a fork becomes terminally arrested. For these reasons it is imperative that helicase loading is as efficient as possible. MCM2-7 represent the core of the replicative helicase, which becomes loaded in an ATP-hydrolysis-dependent process as a double-hexamer onto double-stranded DNA. Current data suggest a model where ORC, Cdc6, and Cdt1 load in a stepwise process the MCM2-7 double-hexamer onto DNA. In this review we discuss the emerging mechanism of ATP-hydrolysis-driven helicase loading, the regulation of this process, and the structure and function of the MCM2-7 double-hexamer.
Speck C, 2016, Exceeding the limits-Cdc45 overexpression turns bad, CELL CYCLE, Vol: 15, Pages: 1809-1810, ISSN: 1538-4101
Speck C, Riera A, Yuan Z, et al., 2016, Key mechanism in the loading and activation of the replicative helicase MCM2-7, 41st FEBS Congress on Molecular and Systems Biology for a Better Life, Publisher: WILEY-BLACKWELL, Pages: 12-12, ISSN: 1742-464X
Sun J, Yuan Z, Stillman B, et al., 2016, Structure and function studies of replication initiation factors, The Initiation of DNA Replication in Eukaryotes, Pages: 427-441, ISBN: 9783319246963
© 2016 Springer International Publishing Switzerland. We have used negative stain EM and cryo-EM to visualize step by step the replication initiation events in S. cerevisiae, as the process is driven forward by the interplay of a dozen or so macromolecular initiation factors, leading to the establishment of pre-replication complexes (pre-RC) at each origin of DNA replication. This work took advantage of our ability to reconstitute the Mcm2-7 loading reaction with purified proteins. We determined the architecture of several previously known replication initiation complexes such as ORC, ORC-Cdc6 on DNA, and the Mcm2-7 double hexamer. We also captured by EM reaction intermediates such as the ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) and the ORC-Cdc6-Mcm2-7-Mcm2-7 (OCMM) that had evaded previous biochemical identification. In this chapter, we describe what we have learnt about the structure and interaction with origin DNA of the replication initiators. We further discuss what may be expected in the coming years as cryo-EM is becoming a near-atomic resolution structural tool, thanks to the recent advent of the direct electron detector.
Tognetti S, Speck C, 2016, Replicating repetitive DNA, NATURE CELL BIOLOGY, Vol: 18, Pages: 593-594, ISSN: 1465-7392
Chang F, Riera A, Evrin C, et al., 2015, Cdc6 ATPase activity disengages Cdc6 from the pre-replicative complex to promote DNA replication, ELIFE, Vol: 4, ISSN: 2050-084X
Herrera MC, Tognetti S, Riera A, et al., 2015, A reconstituted system reveals how activating and inhibitory interactions control DDK dependent assembly of the eukaryotic replicative helicase, NUCLEIC ACIDS RESEARCH, Vol: 43, Pages: 10238-10250, ISSN: 0305-1048
Riera A, Speck C, 2015, Opening the gate to DNA replication, CELL CYCLE, Vol: 14, Pages: 6-8, ISSN: 1538-4101
Tognetti S, Riera A, Speck C, 2015, Switch on the engine: how the eukaryotic replicative helicase MCM2-7 becomes activated, CHROMOSOMA, Vol: 124, Pages: 13-26, ISSN: 0009-5915
Evrin C, Fernandez-Cid A, Riera A, et al., 2014, The ORC/Cdc6/MCM2-7 complex facilitates MCM2-7 dimerization during prereplicative complex formation, NUCLEIC ACIDS RESEARCH, Vol: 42, Pages: 2257-2269, ISSN: 0305-1048
Riera A, Tognetti S, Speck C, 2014, Helicase loading: How to build a MCM2-7 double-hexamer, Seminars in Cell and Developmental Biology, Vol: 30, Pages: 104-109, ISSN: 1084-9521
A central step in eukaryotic initiation of DNA replication is the loading of the helicase at replication origins, misregulation of this reaction leads to DNA damage and genome instability. Here we discuss how the helicase becomes recruited to origins and loaded into a double-hexamer around double-stranded DNA. We specifically describe the individual steps in complex assembly and explain how this process is regulated to maintain genome stability. Structural analysis of the helicase loader and the helicase has provided key insights into the process of double-hexamer formation. A structural comparison of the bacterial and eukaryotic system suggests a mechanism of helicase loading. © 2014 Elsevier Ltd.
Samel SA, Fernandez-Cid A, Sun J, et al., 2014, A unique DNA entry gate serves for regulated loading of the eukaryotic replicative helicase MCM2-7 onto DNA, GENES & DEVELOPMENT, Vol: 28, Pages: 1653-1666, ISSN: 0890-9369
Silva N, Ferrandiz N, Barroso C, et al., 2014, The Fidelity of Synaptonemal Complex Assembly Is Regulated by a Signaling Mechanism that Controls Early Meiotic Progression, DEVELOPMENTAL CELL, Vol: 31, Pages: 503-511, ISSN: 1534-5807
Stillman B, Speck C, Li H, 2014, Biochemical studies on replication of the genome in eukaryotes, Experimental Biology Meeting, Publisher: FEDERATION AMER SOC EXP BIOL, ISSN: 0892-6638
Sun J, Fernandez-Cid A, Riera A, et al., 2014, Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function, GENES & DEVELOPMENT, Vol: 28, Pages: 2291-2303, ISSN: 0890-9369
Evrin C, Fernandez-Cid A, Zech J, et al., 2013, In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization, NUCLEIC ACIDS RESEARCH, Vol: 41, Pages: 3162-3172, ISSN: 0305-1048
Fernandez-Cid A, Riera A, Tognetti S, et al., 2013, An ORC/Cdc6/MCM2-7 Complex Is Formed in a Multistep Reaction to Serve as a Platform for MCM Double-Hexamer Assembly, MOLECULAR CELL, Vol: 50, Pages: 577-588, ISSN: 1097-2765
Riera A, Fernandez-Cid A, Speck C, 2013, The ORC/Cdc6/MCM2-7 complex, a new power player for regulated helicase loading, CELL CYCLE, Vol: 12, Pages: 2155-2156, ISSN: 1538-4101
Riera A, Li H, Speck C, 2013, The MCM2-7 helicase trapped in complex with its DNA loader, CELL CYCLE, Vol: 12, Pages: 2917-2918, ISSN: 1538-4101
Sun J, Evrin C, Samel SA, et al., 2013, Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA, NATURE STRUCTURAL & MOLECULAR BIOLOGY, Vol: 20, Pages: 944-+, ISSN: 1545-9993
Sun J, Kawakami H, Zech J, et al., 2012, Cdc6-Induced Conformational Changes in ORC Bound to Origin DNA Revealed by Cryo-Electron Microscopy, STRUCTURE, Vol: 20, Pages: 534-544, ISSN: 0969-2126
Johansson E, Speck C, Chabes A, 2011, A top-down view on DNA replication and recombination from 9,000 feet above sea level., Genome Biol, Vol: 12
A report of the Keystone Symposium 'DNA Replication and Recombination' held in Keystone, USA, 27 February to 4 March 2011.
Evrin C, Clarke P, Zech J, et al., 2009, A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 106, Pages: 20240-20245, ISSN: 0027-8424
Chen Z, Speck C, Wendel P, et al., 2008, The architecture of the DNA replication origin recognition complex in Saccharomyces cerevisiae, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 105, Pages: 10326-10331, ISSN: 0027-8424
Majka J, Speck C, 2007, Analysis of protein-DNA interactions using surface plasmon resonance, ANALYTICS OF PROTEIN-DNA INTERACTIONS, Vol: 104, Pages: 13-36, ISSN: 0724-6145
Majka J, Speck C, 2007, Analysis of protein-DNA interactions using surface plasmon resonance., Adv Biochem Eng Biotechnol, Vol: 104, Pages: 13-36, ISSN: 0724-6145
Protein-DNA interactions are required for access and protection of the genetic information within the cell. Historically these interactions have been studied using genetic, biochemical, and structural methods resulting in qualitative or semiquantitative interaction data. In the future the focus will be on high quality quantitative data to model a huge number of interactions forming a specific network in system biology approaches. Toward this aim, BIAcore introduced in 1990 the first commercial machine that uses surface plasmon resonance (SPR) to study the real-time kinetics of biomolecular interactions. Since then systems have been developed to allow for robust analysis of a multitude of protein-DNA interactions. Here we provide a detailed guide for protein-DNA interaction analysis using the BIAcore, starting with a description of the SPR technology, giving recommendations on preliminary studies, and finishing with extensive information on quantitative and qualitative data analysis. One focus is on cooperative protein-DNA interactions, where proteins interact with each other to modulate their binding specificity or affinity. The BIAcore has been used for the last 14 years to study protein-DNA interactions; our literature review focuses on some high quality studies describing a wide range of experimental uses, covering simple 1 : 1 interactions, analysis of complicated multiprotein-DNA interaction systems, and analytical uses.
Speck C, Stillman B, 2007, Cdc6 ATPase activity regulates ORC center dot Cdc6 stability and the selection of specific DNA sequences as origins of DNA replication, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 282, Pages: 11705-11714, ISSN: 0021-9258
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