1
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Yuan Z, Li H. Primase and polymerase α tango to make an RNA-DNA hybrid primer. FEBS J 2024; 291:1889-1891. [PMID: 38581152 PMCID: PMC11068480 DOI: 10.1111/febs.17129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024]
Abstract
Several recent cryo-electron microscopy (cryo-EM) studies about the eukaryotic primosome, including the human primosome described by Yin et al. in this issue, have uncovered the structural intricacies between the RNA primase and the DNA polymerase. These studies show that these two partners tango on DNA to synthesize a hybrid primer composed of ~ 10 nucleotide (nt) RNA and ~ 10-nt DNA. They reveal key intermediate steps involved in this process; from the self-inhibited apo state to the initiation of RNA primer synthesis, RNA primer handover to the polymerase, primer elongation by polymerase, and finally, primer termination and release. Remarkably, the polymerase domain orchestrates all major steps during primer synthesis.
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Affiliation(s)
- Zuanning Yuan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
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2
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Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
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3
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Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Human primosome requires replication protein A when copying DNA with inverted repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584335. [PMID: 38559116 PMCID: PMC10979909 DOI: 10.1101/2024.03.11.584335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polε). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA forming a G-quadruplex, RPA provides no assistance for primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Polα but not of Polε. The important factors for an efficient hairpin bypass by primosome are the high affinity of RPA to DNA based on four DNA-binding domains and the interaction of the winged-helix-turn-helix domain of RPA with Polα. Binding studies indicate that this interaction stabilizes the RPA/Polα complex on the primed template. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats.
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4
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Lim CJ. Telomere C-Strand Fill-In Machinery: New Insights into the Human CST-DNA Polymerase Alpha-Primase Structures and Functions. Subcell Biochem 2024; 104:73-100. [PMID: 38963484 DOI: 10.1007/978-3-031-58843-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Telomeres at the end of eukaryotic chromosomes are extended by a specialized set of enzymes and telomere-associated proteins, collectively termed here the telomere "replisome." The telomere replisome acts on a unique replicon at each chromosomal end of the telomeres, the 3' DNA overhang. This telomere replication process is distinct from the replisome mechanism deployed to duplicate the human genome. The G-rich overhang is first extended before the complementary C-strand is filled in. This overhang is extended by telomerase, a specialized ribonucleoprotein and reverse transcriptase. The overhang extension process is terminated when telomerase is displaced by CTC1-STN1-TEN1 (CST), a single-stranded DNA-binding protein complex. CST then recruits DNA polymerase α-primase to complete the telomere replication process by filling in the complementary C-strand. In this chapter, the recent structure-function insights into the human telomere C-strand fill-in machinery (DNA polymerase α-primase and CST) will be discussed.
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Affiliation(s)
- Ci Ji Lim
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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5
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and Distributive Synthesis Regulate RNA Priming and Handoff in Human DNA Polymerase α-Primase. J Mol Biol 2023; 435:168330. [PMID: 37884206 PMCID: PMC10872500 DOI: 10.1016/j.jmb.2023.168330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/22/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ∼30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ∼20 nucleotides of DNA. Here, we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the surprisingly low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Elwood A Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Brandt F Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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6
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He Q, Lim CJ. Models for human telomere C-strand fill-in by CST-Polα-primase. Trends Biochem Sci 2023; 48:860-872. [PMID: 37586999 PMCID: PMC10528720 DOI: 10.1016/j.tibs.2023.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Telomere maintenance is essential for the genome integrity of eukaryotes, and this function is underpinned by the two-step telomeric DNA synthesis process: telomere G-overhang extension by telomerase and complementary strand fill-in by DNA polymerase alpha-primase (polα-primase). Compared to the telomerase step, the telomere C-strand fill-in mechanism is less understood. Recent studies have provided new insights into how telomeric single-stranded DNA-binding protein CTC1-STN1-TEN1 (CST) and polα-primase coordinate to synthesize the telomeric C-strand for telomere overhang fill-in. Cryogenic electron microscopy (cryo-EM) structures of CST-polα-primase complexes have provided additional insights into how they assemble at telomeric templates and de novo synthesize the telomere C-strand. In this review, we discuss how these latest findings coalesce with existing understanding to develop a human telomere C-strand fill-in mechanism model.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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7
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Zabrady K, Li AWH, Doherty AJ. Mechanism of primer synthesis by Primase-Polymerases. Curr Opin Struct Biol 2023; 82:102652. [PMID: 37459807 DOI: 10.1016/j.sbi.2023.102652] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/15/2023] [Accepted: 06/19/2023] [Indexed: 09/16/2023]
Abstract
Members of the primase-polymerase (Prim-Pol) superfamily are found in all domains of life and play diverse roles in genome stability, including primer synthesis during DNA replication, lesion repair and damage tolerance. This review focuses primarily on Prim-Pol members capable of de novo primer synthesis that have experimentally derived structural models available. We discuss the mechanism of DNA primer synthesis initiation by Prim-Pol catalytic domains, based on recent structural and functional studies. We also describe a general model for primer initiation that also includes the ancillary domains/subunits, which stimulate the initiation of primer synthesis.
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Affiliation(s)
- Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK. https://twitter.com/@KZabrady
| | - Arthur W H Li
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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8
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Boldinova EO, Baranovskiy AG, Gagarinskaya DI, Manukyan A, Makarova A, Tahirov T. The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis. Nucleic Acids Res 2023; 51:7541-7551. [PMID: 37326028 PMCID: PMC10415149 DOI: 10.1093/nar/gkad507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/28/2023] [Accepted: 05/31/2023] [Indexed: 06/17/2023] Open
Abstract
Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria. The zinc-binding motif (ZnFn) of the C-terminal domain (CTD) of PrimPol is required for DNA primase activity but the mechanism is not clear. In this work, we biochemically demonstrate that PrimPol initiates de novo DNA synthesis in cis-orientation, when the N-terminal catalytic domain (NTD) and the CTD of the same molecule cooperate for substrates binding and catalysis. The modeling studies revealed that PrimPol uses a similar mode of initiating NTP coordination as the human primase. The ZnFn motif residue Arg417 is required for binding the 5'-triphosphate group that stabilizes the PrimPol complex with a DNA template-primer. We found that the NTD alone is able to initiate DNA synthesis, and the CTD stimulates the primase activity of NTD. The regulatory role of the RPA-binding motif in the modulation of PrimPol binding to DNA is also demonstrated.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Diana I Gagarinskaya
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna A Manukyan
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Alena V Makarova
- Institute of Molecular Genetics, National Research Center "Kurchatov Institute", Kurchatov sq. 2, 123182 Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Vavilov 34/5, 119334 Moscow, Russia
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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9
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Cordoba JJ, Mullins EA, Salay LE, Eichman BF, Chazin WJ. Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551538. [PMID: 37577606 PMCID: PMC10418221 DOI: 10.1101/2023.08.01.551538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
DNA replication in eukaryotes relies on the synthesis of a ~30-nucleotide RNA/DNA primer strand through the dual action of the heterotetrameric polymerase α-primase (pol-prim) enzyme. Synthesis of the 7-10-nucleotide RNA primer is regulated by the C-terminal domain of the primase regulatory subunit (PRIM2C) and is followed by intramolecular handoff of the primer to pol α for extension by ~20 nucleotides of DNA. Here we provide evidence that RNA primer synthesis is governed by a combination of the high affinity and flexible linkage of the PRIM2C domain and the low affinity of the primase catalytic domain (PRIM1) for substrate. Using a combination of small angle X-ray scattering and electron microscopy, we found significant variability in the organization of PRIM2C and PRIM1 in the absence and presence of substrate, and that the population of structures with both PRIM2C and PRIM1 in a configuration aligned for synthesis is low. Crosslinking was used to visualize the orientation of PRIM2C and PRIM1 when engaged by substrate as observed by electron microscopy. Microscale thermophoresis was used to measure substrate affinities for a series of pol-prim constructs, which showed that the PRIM1 catalytic domain does not bind the template or emergent RNA-primed templates with appreciable affinity. Together, these findings support a model of RNA primer synthesis in which generation of the nascent RNA strand and handoff of the RNA-primed template from primase to polymerase α is mediated by the high degree of inter-domain flexibility of pol-prim, the ready dissociation of PRIM1 from its substrate, and the much higher affinity of the POLA1cat domain of polymerase α for full-length RNA-primed templates.
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Affiliation(s)
- John J. Cordoba
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Elwood A. Mullins
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Lauren E. Salay
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Brandt F. Eichman
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Walter J. Chazin
- Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
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10
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Bainbridge L, Zabrady K, Doherty A. Primase-polymerases: how to make a primer from scratch. Biosci Rep 2023; 43:BSR20221986. [PMID: 37358261 PMCID: PMC10345425 DOI: 10.1042/bsr20221986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 06/27/2023] Open
Abstract
To pass on genetic information to the next generation, cells must faithfully replicate their genomes to provide copies for each daughter cell. To synthesise these duplicates, cells employ specialised enzymes called DNA polymerases, which rapidly and accurately replicate nucleic acid polymers. However, most polymerases lack the ability to directly initiate DNA synthesis and required specialised replicases called primases to make short polynucleotide primers, from which they then extend. Replicative primases (eukaryotes and archaea) belong to a functionally diverse enzyme superfamily known as Primase-Polymerases (Prim-Pols), with orthologues present throughout all domains of life. Characterised by a conserved catalytic Prim-Pol domain, these enzymes have evolved various roles in DNA metabolism, including DNA replication, repair, and damage tolerance. Many of these biological roles are fundamentally underpinned by the ability of Prim-Pols to generate primers de novo. This review examines our current understanding of the catalytic mechanisms utilised by Prim-Pols to initiate primer synthesis.
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Affiliation(s)
- Lewis J. Bainbridge
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Katerina Zabrady
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
| | - Aidan J. Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, U.K
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11
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. Nat Commun 2023; 14:4396. [PMID: 37474605 PMCID: PMC10359460 DOI: 10.1038/s41467-023-40106-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/11/2023] [Indexed: 07/22/2023] Open
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome to couple DNA unwinding with RNA primer synthesis for DNA replication. How the primosome is assembled and how the primer length is defined are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates. We show that gp41 alone is an open spiral, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the ring closure and activates the helicase. Helicase activation exposes a cryptic hydrophobic surface to recruit the gp61 primase. The primase binds the helicase in a bipartite mode in which the N-terminal Zn-binding domain and the C-terminal RNA polymerase domain each contain a helicase-interacting motif that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Our study reveals the T4 primosome assembly process and sheds light on the RNA primer synthesis mechanism.
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Affiliation(s)
- Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michelle M Spiering
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | | | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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12
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Yuan Z, Georgescu R, Li H, O'Donnell ME. Molecular choreography of primer synthesis by the eukaryotic Pol α-primase. Nat Commun 2023; 14:3697. [PMID: 37344454 PMCID: PMC10284912 DOI: 10.1038/s41467-023-39441-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/14/2023] [Indexed: 06/23/2023] Open
Abstract
The eukaryotic polymerase α (Pol α) synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides. Pol α is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2. Pol1 and Pri1 contain the DNA polymerase and RNA primase activities, respectively. It has been unclear how Pol α hands over an RNA primer from Pri1 to Pol1 for DNA primer extension, and how the primer length is defined. Here we report the cryo-EM analysis of yeast Pol α in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states, revealing a series of very large movements. We reveal a critical point at which Pol1-core moves to take over the 3'-end of the RNA from Pri1. DNA extension is limited by a spiral motion of Pol1-core. Since both Pri1 and Pol1-core are flexibly attached to a stable platform, primer growth produces stress that limits the primer length.
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Affiliation(s)
- Zuanning Yuan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana Georgescu
- DNA Replication Laboratory and Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, Rockefeller University, New York, NY, USA.
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13
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Yuan Z, Georgescu R, Li H, O'Donnell ME. Molecular choreography of primer synthesis by the eukaryotic Pol α-primase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539257. [PMID: 37205351 PMCID: PMC10187153 DOI: 10.1101/2023.05.03.539257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The eukaryotic polymerase α (Pol α) is a dual-function DNA polymerase/primase complex that synthesizes an RNA-DNA hybrid primer of 20-30 nucleotides for DNA replication. Pol α is composed of Pol1, Pol12, Primase 1 (Pri1), and Pri2, with Pol1 and Pri1 containing the DNA polymerase activity and RNA primase activity, respectively, whereas Pol12 and Pri2 serve a structural role. It has been unclear how Pol α hands over an RNA primer made by Pri1 to Pol1 for DNA primer extension, and how the primer length is defined, perhaps due to the difficulty in studying the highly mobile structure. Here we report a comprehensive cryo-EM analysis of the intact 4-subunit yeast Pol α in the apo, primer initiation, primer elongation, RNA primer hand-off from Pri1 to Pol1, and DNA extension states in a 3.5 Å - 5.6 Å resolution range. We found that Pol α is a three-lobed flexible structure. Pri2 functions as a flexible hinge that holds together the catalytic Pol1-core, and the noncatalytic Pol1 CTD that binds to Pol 12 to form a stable platform upon which the other components are organized. In the apo state, Pol1-core is sequestered on the Pol12-Pol1-CTD platform, and Pri1 is mobile perhaps in search of a template. Upon binding a ssDNA template, a large conformation change is induced that enables Pri1 to perform RNA synthesis, and positions Pol1-core to accept the future RNA primed site 50 Å upstream of where Pri1 binds. We reveal in detail the critical point at which Pol1-core takes over the 3'-end of the RNA from Pri1. DNA primer extension appears limited by the spiral motion of Pol1-core while Pri2-CTD stably holds onto the 5' end of the RNA primer. Since both Pri1 and Pol1-core are attached via two linkers to the platform, primer growth will produce stress within this "two-point" attachment that may limit the length of the RNA-DNA hybrid primer. Hence, this study reveals the large and dynamic series of movements that Pol α undergoes to synthesize a primer for DNA replication.
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14
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Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H. Structural basis of the T4 bacteriophage primosome assembly and primer synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539249. [PMID: 37205424 PMCID: PMC10187150 DOI: 10.1101/2023.05.03.539249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 Å. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.
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15
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Nasheuer HP, Onwubiko NO. Lagging Strand Initiation Processes in DNA Replication of Eukaryotes-Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes. Genes (Basel) 2023; 14:genes14051012. [PMID: 37239371 DOI: 10.3390/genes14051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In their influential reviews, Hanahan and Weinberg coined the term 'Hallmarks of Cancer' and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| | - Nichodemus O Onwubiko
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
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16
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He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH. Structures of human primosome elongation complexes. Nat Struct Mol Biol 2023; 30:579-583. [PMID: 37069376 PMCID: PMC10268227 DOI: 10.1038/s41594-023-00971-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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17
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Begemann A, Oneda B, Baumer A, Guldimann M, Tutschek B, Rauch A. A Xp22.11-p21.3 microdeletion in a three-generation family supports male lethality of POLA1 nullisomy resulting in reduced fertility of female carriers. Eur J Med Genet 2022; 65:104628. [PMID: 36182037 DOI: 10.1016/j.ejmg.2022.104628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 09/25/2022] [Indexed: 11/03/2022]
Abstract
POLA1 encodes a subunit of the DNA polymerase alpha, a key enzyme for the initiation of DNA synthesis. In males, hemizygous hypomorphic variants in POLA1 have been identified as the cause of X-linked pigmentary reticulate disorder (XLPDR) and a novel X-linked neurodevelopmental disorder termed Van Esch-O'Driscoll syndrome (VEODS), while female carriers have been reported to be healthy. Nullisomy for POLA1 was speculated to be lethal due to its crucial function, while the effect of loss of one allele in females remained unknown. Here, we report on a three-generation family harboring a deletion of POLA1 in females showing subfertility as the only phenotype. Our findings show that heterozygous deletions or truncating variants in females with skewed X inactivation do not cause VEODS and support the hypothesis of very early embryonic lethality in males with POLA1 nullisomy.
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Affiliation(s)
- Anaïs Begemann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Beatrice Oneda
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Alessandra Baumer
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Marina Guldimann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Boris Tutschek
- Prenatal Zürich, Zurich, Switzerland; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland; University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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18
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He Q, Lin X, Chavez BL, Agrawal S, Lusk BL, Lim CJ. Structures of the human CST-Polα-primase complex bound to telomere templates. Nature 2022; 608:826-832. [PMID: 35830881 DOI: 10.1038/s41586-022-05040-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/29/2022] [Indexed: 01/26/2023]
Abstract
The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways1-4 such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα-primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα-primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα-primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα-primase into two separate domains and effectively arranges them in RNA-DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA-DNA primers by Polα-primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα-primase PIC and activation are also revealed in this study.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xiuhua Lin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Bianca L Chavez
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sourav Agrawal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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19
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Structure of Tetrahymena telomerase-bound CST with polymerase α-primase. Nature 2022; 608:813-818. [PMID: 35831498 PMCID: PMC9728385 DOI: 10.1038/s41586-022-04931-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/06/2022] [Indexed: 02/03/2023]
Abstract
Telomeres are the physical ends of linear chromosomes. They are composed of short repeating sequences (such as TTGGGG in the G-strand for Tetrahymena thermophila) of double-stranded DNA with a single-strand 3' overhang of the G-strand and, in humans, the six shelterin proteins: TPP1, POT1, TRF1, TRF2, RAP1 and TIN21,2. TPP1 and POT1 associate with the 3' overhang, with POT1 binding the G-strand3 and TPP1 (in complex with TIN24) recruiting telomerase via interaction with telomerase reverse transcriptase5 (TERT). The telomere DNA ends are replicated and maintained by telomerase6, for the G-strand, and subsequently DNA polymerase α-primase7,8 (PolαPrim), for the C-strand9. PolαPrim activity is stimulated by the heterotrimeric complex CTC1-STN1-TEN110-12 (CST), but the structural basis of the recruitment of PolαPrim and CST to telomere ends remains unknown. Here we report cryo-electron microscopy (cryo-EM) structures of Tetrahymena CST in the context of the telomerase holoenzyme, in both the absence and the presence of PolαPrim, and of PolαPrim alone. Tetrahymena Ctc1 binds telomerase subunit p50, a TPP1 orthologue, on a flexible Ctc1 binding motif revealed by cryo-EM and NMR spectroscopy. The PolαPrim polymerase subunit POLA1 binds Ctc1 and Stn1, and its interface with Ctc1 forms an entry port for G-strand DNA to the POLA1 active site. We thus provide a snapshot of four key components that are required for telomeric DNA synthesis in a single active complex-telomerase-core ribonucleoprotein, p50, CST and PolαPrim-that provides insights into the recruitment of CST and PolαPrim and the handoff between G-strand and C-strand synthesis.
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20
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Baranovskiy AG, Lisova AE, Morstadt LM, Babayeva ND, Tahirov TH. Insight into RNA-DNA primer length counting by human primosome. Nucleic Acids Res 2022; 50:6264-6270. [PMID: 35689638 PMCID: PMC9226528 DOI: 10.1093/nar/gkac492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58C) with the primer 5′-end, and (ii) flexible tethering of p58C and the DNA polymerase alpha catalytic core domain (p180core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
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21
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Salay LE, Blee AM, Raza MK, Gallagher KS, Chen H, Dorfeuille AJ, Barton JK, Chazin WJ. Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase. Biochemistry 2022; 61:1113-1123. [PMID: 35617695 DOI: 10.1021/acs.biochem.2c00100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA synthesis during replication begins with the generation of an ∼10-nucleotide primer by DNA primase. Primase contains a redox-active 4Fe-4S cluster in the C-terminal domain of the p58 subunit (p58C). The redox state of this 4Fe-4S cluster can be modulated via the transport of charge through the protein and the DNA substrate (redox switching); changes in the redox state of the cluster alter the ability of p58C to associate with its substrate. The efficiency of redox switching in p58C can be altered by mutating tyrosine residues that bridge the 4Fe-4S cluster and the nucleic acid binding site. Here, we report the effects of mutating bridging tyrosines to phenylalanines in yeast p58C. High-resolution crystal structures show that these mutations, even with six tyrosines simultaneously mutated, do not perturb the three-dimensional structure of the protein. In contrast, measurements of the electrochemical properties on DNA-modified electrodes of p58C containing multiple tyrosine to phenylalanine mutations reveal deficiencies in their ability to engage in DNA charge transport. Significantly, this loss of electrochemical activity correlates with decreased primase activity. While single-site mutants showed modest decreases in activity compared to that of the wild-type primase, the protein containing six mutations exhibited a 10-fold or greater decrease. Thus, many possible tyrosine-mediated pathways for charge transport in yeast p58C exist, but inhibiting these pathways together diminishes the ability of yeast primase to generate primers. These results support a model in which redox switching is essential for primase activity.
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Affiliation(s)
- Lauren E Salay
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Alexandra M Blee
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Md Kausar Raza
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kaitlyn S Gallagher
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Huiqing Chen
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Andrew J Dorfeuille
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States.,Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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22
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Baranovskiy AG, Babayeva ND, Lisova AE, Morstadt LM, Tahirov TH. Structural and functional insight into mismatch extension by human DNA polymerase α. Proc Natl Acad Sci U S A 2022; 119:e2111744119. [PMID: 35467978 PMCID: PMC9169922 DOI: 10.1073/pnas.2111744119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/08/2022] [Indexed: 12/11/2022] Open
Abstract
Human DNA polymerase α (Polα) does not possess proofreading ability and plays an important role in genome replication and mutagenesis. Polα extends the RNA primers generated by primase and provides a springboard for loading other replication factors. Here we provide the structural and functional analysis of the human Polα interaction with a mismatched template:primer. The structure of the human Polα catalytic domain in the complex with an incoming deoxycytidine triphosphate (dCTP) and the template:primer containing a T-C mismatch at the growing primer terminus was solved at a 2.9 Å resolution. It revealed the absence of significant distortions in the active site and in the conformation of the substrates, except the primer 3′-end. The T-C mismatch acquired a planar geometry where both nucleotides moved toward each other by 0.4 Å and 0.7 Å, respectively, and made one hydrogen bond. The binding studies conducted at a physiological salt concentration revealed that Polα has a low affinity to DNA and is not able to discriminate against a mispaired template:primer in the absence of deoxynucleotide triphosphate (dNTP). Strikingly, in the presence of cognate dNTP, Polα showed a more than 10-fold higher selectivity for a correct duplex versus a mismatched one. According to pre-steady-state kinetic studies, human Polα extends the T-C mismatch with a 249-fold lower efficiency due to reduction of the polymerization rate constant by 38-fold and reduced affinity to the incoming nucleotide by 6.6-fold. Thus, a mismatch at the postinsertion site affects all factors important for primer extension: affinity to both substrates and the rate of DNA polymerization.
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Affiliation(s)
- Andrey G. Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Nigar D. Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Alisa E. Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Lucia M. Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
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23
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Díaz-Talavera A, Montero-Conde C, Leandro-García LJ, Robledo M. PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. Biomolecules 2022; 12:248. [PMID: 35204749 PMCID: PMC8961649 DOI: 10.3390/biom12020248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer.
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Affiliation(s)
- Alberto Díaz-Talavera
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Cristina Montero-Conde
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Luis Javier Leandro-García
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; (C.M.-C.); (L.J.L.-G.); (M.R.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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24
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Onwubiko NO, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen helicase domain regions responsible for oligomerisation regulate Okazaki fragment synthesis initiation. FEBS Open Bio 2022; 12:649-663. [PMID: 35073603 PMCID: PMC8886539 DOI: 10.1002/2211-5463.13373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry School of Biological and Chemical Sciences Biomedical Sciences Building NUI Galway, New Castle Road, Galway, H91 W2TY Ireland
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D‐97080 Würzburg Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D‐97080 Würzburg Germany
| | - Heinz Peter Nasheuer
- Biochemistry School of Biological and Chemical Sciences Biomedical Sciences Building NUI Galway, New Castle Road, Galway, H91 W2TY Ireland
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25
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Starokadomskyy P, Escala Perez-Reyes A, Burstein E. Immune Dysfunction in Mendelian Disorders of POLA1 Deficiency. J Clin Immunol 2021; 41:285-293. [PMID: 33392852 DOI: 10.1007/s10875-020-00953-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
POLA1 encodes the catalytic unit of DNA polymerase α, which together with the Primase complex launches the DNA replication process. While complete deficiency of this essential gene is presumed to be lethal, at least two conditions due to partial POLA1 deficiency have been described. The first genetic syndrome to be mapped to POLA1 was X-linked reticulate pigmentary disorder (XLPDR, MIM #301220), a rare syndrome characterized by skin hyperpigmentation, sterile multiorgan inflammation, recurrent infections, and distinct facial features. XLPDR has been shown to be accompanied by profound activation of type I interferon signaling, but unlike other interferonopathies, it is not associated with autoantibodies or classical autoimmunity. Rather, it is accompanied by marked Natural Killer (NK) cell dysfunction, which may explain the recurrent infections seen in this syndrome. To date, all XLPDR cases are caused by the same recurrent intronic mutation, which results in gene missplicing. Several hypomorphic mutations in POLA1, distinct from the XLPDR intronic mutation, have been recently reported and these mutations associate with a separate condition, van Esch-O'Driscoll syndrome (VEODS, MIM #301030). This condition results in growth retardation, microcephaly, hypogonadism, and in some cases, overlapping immunological features to those seen in XLPDR. This review summarizes our current understanding of the clinical manifestations of POLA1 gene mutations with an emphasis on its immunological consequences, as well as recent advances in understanding of its pathophysiologic basis and potential therapeutic options.
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Affiliation(s)
- Petro Starokadomskyy
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA.
| | - Andrea Escala Perez-Reyes
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - Ezra Burstein
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA. .,Department of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines blvd, Dallas, TX, 75390-9151, USA.
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26
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Onwubiko NO, Borst A, Diaz SA, Passkowski K, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen interactions with ssDNA and replication protein A: a regulatory role of T antigen monomers in lagging strand DNA replication. Nucleic Acids Res 2020; 48:3657-3677. [PMID: 32128579 PMCID: PMC7144908 DOI: 10.1093/nar/gkaa138] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
DNA replication is a central process in all living organisms. Polyomavirus DNA replication serves as a model system for eukaryotic DNA replication and has considerably contributed to our understanding of basic replication mechanisms. However, the details of the involved processes are still unclear, in particular regarding lagging strand synthesis. To delineate the complex mechanism of coordination of various cellular proteins binding simultaneously or consecutively to DNA to initiate replication, we investigated single-stranded DNA (ssDNA) interactions by the SV40 large T antigen (Tag). Using single molecule imaging by atomic force microscopy (AFM) combined with biochemical and spectroscopic analyses we reveal independent activity of monomeric and oligomeric Tag in high affinity binding to ssDNA. Depending on ssDNA length, we obtain dissociation constants for Tag-ssDNA interactions (KD values of 10–30 nM) that are in the same order of magnitude as ssDNA binding by human replication protein A (RPA). Furthermore, we observe the formation of RPA-Tag-ssDNA complexes containing hexameric as well as monomeric Tag forms. Importantly, our data clearly show stimulation of primase function in lagging strand Okazaki fragment synthesis by monomeric Tag whereas hexameric Tag inhibits the reaction, redefining DNA replication initiation on the lagging strand.
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Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Angela Borst
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Suraya A Diaz
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Katharina Passkowski
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Heinz P Nasheuer
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
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27
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Yuan Z, Georgescu R, Santos RDLA, Zhang D, Bai L, Yao NY, Zhao G, O'Donnell ME, Li H. Ctf4 organizes sister replisomes and Pol α into a replication factory. eLife 2019; 8:47405. [PMID: 31589141 PMCID: PMC6800005 DOI: 10.7554/elife.47405] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022] Open
Abstract
The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol α-primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol α-primase into a replication factory. In the 2CMG–Ctf43–1Pol α-primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol α-primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
| | - Roxana Georgescu
- Howard Hughes Medical Institute, Chevy Chase, United States.,DNA Replication Laboratory, The Rockefeller University, New York, United States
| | | | - Daniel Zhang
- DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Lin Bai
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-EM Suite, Van Andel Institute, Grand Rapids, United States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Chevy Chase, United States.,DNA Replication Laboratory, The Rockefeller University, New York, United States
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, United States
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28
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Bergsch J, Allain FHT, Lipps G. Recent advances in understanding bacterial and archaeoeukaryotic primases. Curr Opin Struct Biol 2019; 59:159-167. [PMID: 31585372 DOI: 10.1016/j.sbi.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/05/2019] [Accepted: 08/26/2019] [Indexed: 11/16/2022]
Abstract
DNA replication in all forms of life relies upon the initiation of synthesis on a single strand template by formation of a short oligonucleotide primer, which is subsequently elongated by DNA polymerases. Two structurally distinct classes of enzymes have evolved to perform this function, namely the bacterial DnaG-type primases and the Archaeal and Eukaryotic primases (AEP). Structural and mechanistic insights have provided a clear understanding of the role of the different domains of these enzymes in the context of the replisome and recent work sheds light upon primase-substrate interactions. We herein review the emerging picture of the primase mechanism on the basis of the structural knowledge obtained to date and propose future directions of this essential aspect of DNA replication.
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Affiliation(s)
- Jan Bergsch
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland; Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland
| | - Frédéric H-T Allain
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Lipps
- Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland.
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29
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Holt ME, Salay LE, O’Brien E, Barton JK, Chazin WJ. Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs. PLoS One 2018; 13:e0209345. [PMID: 30562384 PMCID: PMC6298731 DOI: 10.1371/journal.pone.0209345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/14/2018] [Indexed: 01/15/2023] Open
Abstract
The regulatory subunit of human DNA primase has a C-terminal domain (p58C) that contains a [4Fe4S] cluster and binds DNA. Previous electrochemical analysis of a p58C construct revealed that its affinity for DNA is sensitive to the redox state of the [4Fe4S] cluster. Concerns about the validity of this conclusion have been raised, based in part on differences in X-ray crystal structures of the p58C272-464 construct used for that study and that of a N-terminally shifted p58C266-456 construct and consequently, an assumption that p58C272-464 has abnormal physical and functional properties. To address this controversy, a new p58C266-464 construct containing all residues was crystallized under the conditions previously used for crystallizing p58C272-464, and the solution structures of both constructs were assessed using circular dichroism and NMR spectroscopy. In the new crystal structure, p58C266-464 exhibits the same elements of secondary structure near the DNA binding site as observed in the crystal structure of p58C272-464. Moreover, in solution, circular dichroism and 15N,1H-heteronuclear single quantum coherence (HSQC) NMR spectra show there are no significant differences in the distribution of secondary structures or in the tertiary structure or the two constructs. To validate that the two constructs have the same functional properties, binding of a primed DNA template was measured using a fluorescence-based DNA binding assay, and the affinities for this substrate were the same (3.4 ± 0.5 μM and 2.7 ± 0.3 μM, respectively). The electrochemical properties of p58C266-464 were also measured and this p58C construct was able to engage in redox switching on DNA with the same efficiency as p58C272-464. Together, these results show that although p58C can be stabilized in different conformations in the crystalline state, in solution there is effectively no difference in the structure and functional properties of p58C constructs of different lengths.
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Affiliation(s)
- Marilyn E. Holt
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lauren E. Salay
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Walter J. Chazin
- Departments of Biochemistry and Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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30
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Lee JG, Park KR, An JY, Kang JY, Shen H, Wang J, Eom SH. Structural and biochemical insights into inhibition of human primase by citrate. Biochem Biophys Res Commun 2018; 507:383-388. [PMID: 30446220 DOI: 10.1016/j.bbrc.2018.11.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 10/27/2022]
Abstract
The eukaryotic primase/polymerase complex synthesizes approximately 107 primers, one per Okazaki fragment, during the replication of mammalian chromosomes, which contain 109 base pairs. Primase catalyzes the synthesis of a short RNA segment to a single-stranded DNA template. Primase is important in DNA replication because no known replicative DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA primer. The primase subcomplex is composed of a small catalytic subunit (p49), and a large accessory subunit (p58). Priming mechanisms remain poorly understood, although large numbers of structures of archaeal and eukaryotic p49 and/or p58 as well as structures of bacterial enzymes have been determined. In this study, we determined the structure of human p49 at 2.2 Å resolution with citrate in its inactive forms. Dibasic citrate was bound at the nucleotide triphosphate (NTP) β, γ-phosphate binding site through nine hydrogen bonds. We also measured the dissociation constant of citrate and NTPs. We further demonstrated that the p49 activity is regulated by pH and citrate, which was not previously recognized as a key regulator of DNA replication. We propose that the citrate inhibits the primase and regulates DNA replication at the replication fork.
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Affiliation(s)
- Jung-Gyu Lee
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea
| | - Kyoung Ryoung Park
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea
| | - Jun Yop An
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea
| | - Jung Youn Kang
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520-8114, USA.
| | - Soo Hyun Eom
- School of Life Sciences, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Steitz Center for Structural Biology, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea; Department of Chemistry, Gwangju Institute of Science & Technology, Gwangju, 61005, Republic of Korea.
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31
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Baranovskiy AG, Duong VN, Babayeva ND, Zhang Y, Pavlov YI, Anderson KS, Tahirov TH. Activity and fidelity of human DNA polymerase α depend on primer structure. J Biol Chem 2018; 293:6824-6843. [PMID: 29555682 DOI: 10.1074/jbc.ra117.001074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/09/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerase α (Polα) plays an important role in genome replication. In a complex with primase, Polα synthesizes chimeric RNA-DNA primers necessary for replication of both chromosomal DNA strands. During RNA primer extension with deoxyribonucleotides, Polα needs to use double-stranded helical substrates having different structures. Here, we provide a detailed structure-function analysis of human Polα's interaction with dNTPs and DNA templates primed with RNA, chimeric RNA-DNA, or DNA. We report the crystal structures of two ternary complexes of the Polα catalytic domain containing dCTP, a DNA template, and either a DNA or an RNA primer. Unexpectedly, in the ternary complex with a DNA:DNA duplex and dCTP, the "fingers" subdomain of Polα is in the open conformation. Polα induces conformational changes in the DNA and hybrid duplexes to produce the universal double helix form. Pre-steady-state kinetic studies indicated for both duplex types that chemical catalysis rather than product release is the rate-limiting step. Moreover, human Polα extended DNA primers with higher efficiency but lower processivity than it did with RNA and chimeric primers. Polα has a substantial propensity to make errors during DNA synthesis, and we observed that its fidelity depends on the type of sugar at the primer 3'-end. A detailed structural comparison of Polα with other replicative DNA polymerases disclosed common features and some differences, which may reflect the specialization of each polymerase in genome replication.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Vincent N Duong
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Yinbo Zhang
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and.,the Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, and Genetics and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 and
| | - Karen S Anderson
- the Departments of Pharmacology and Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, and
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32
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Lue NF. Evolving Linear Chromosomes and Telomeres: A C-Strand-Centric View. Trends Biochem Sci 2018; 43:314-326. [PMID: 29550242 DOI: 10.1016/j.tibs.2018.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 02/08/2023]
Abstract
Recent studies have resulted in deeper understanding of a variety of telomere maintenance mechanisms as well as plausible models of telomere evolution. Often overlooked in the discussion of telomere regulation and evolution is the synthesis of the DNA strand that bears the 5'-end (i.e., the C-strand). Herein, I describe a scenario for telomere evolution that more explicitly accounts for the evolution of the C-strand synthesis machinery. In this model, CTC1-STN1-TEN1 (CST), the G-strand-binding complex that regulates primase-Pol α-mediated C-strand synthesis, emerges as a pivotal player and evolutionary link. Itself arising from RPA, CST not only coordinates telomere synthesis, but also gives rise to the POT1-TPP1 complex, which became part of shelterin and regulates telomerase in G-strand elongation.
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Affiliation(s)
- Neal F Lue
- Department of Microbiology and Immunology, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA.
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33
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Baranovskiy AG, Siebler HM, Pavlov YI, Tahirov TH. Iron-Sulfur Clusters in DNA Polymerases and Primases of Eukaryotes. Methods Enzymol 2017; 599:1-20. [PMID: 29746236 PMCID: PMC5947875 DOI: 10.1016/bs.mie.2017.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Research during the past decade witnessed the discovery of [4Fe-4S] clusters in several members of the eukaryotic DNA replication machinery. The presence of clusters was confirmed by UV-visible absorption, electron paramagnetic resonance spectroscopy, and metal analysis for primase and the B-family DNA polymerases δ and ζ. The crystal structure of primase revealed that the [4Fe-4S] cluster is buried inside the protein and fulfills a structural role. Although [4Fe-4S] clusters are firmly established in the C-terminal domains of catalytic subunits of DNA polymerases δ and ζ, no structures are currently available and their precise roles have not been ascertained. The [4Fe-4S] clusters in the polymerases and primase play a structural role ensuring proper protein folding and stability. In DNA polymerases δ and ζ, they can potentially play regulatory role by sensing hurdles during DNA replication and assisting with DNA polymerase switches by oscillation between oxidized-reduced states.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States
| | | | - Youri I Pavlov
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, United States.
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34
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Ganduri S, Lue NF. STN1-POLA2 interaction provides a basis for primase-pol α stimulation by human STN1. Nucleic Acids Res 2017; 45:9455-9466. [PMID: 28934486 PMCID: PMC5766158 DOI: 10.1093/nar/gkx621] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/06/2017] [Indexed: 01/12/2023] Open
Abstract
The CST (CTC1–STN1–TEN1) complex mediates critical functions in maintaining telomere DNA and overcoming genome-wide replication stress. A conserved biochemical function of the CST complex is its primase-Pol α (PP) stimulatory activity. In this report, we demonstrate the ability of purified human STN1 alone to promote PP activity in vitro. We show that this regulation is mediated primarily by the N-terminal OB fold of STN1, but does not require the DNA-binding activity of this domain. Rather, we observed a strong correlation between the PP-stimulatory activity of STN1 variants and their abilities to bind POLA2. Remarkably, the main binding target of STN1 in POLA2 is the latter's central OB fold domain. In the substrate-free structure of PP, this domain is positioned so as to block nucleic acid entry to the Pol α active site. Thus the STN1–POLA2 interaction may promote the necessary conformational change for nucleic acid delivery to Pol α and subsequent DNA synthesis. A disease-causing mutation in human STN1 engenders a selective defect in POLA2-binding and PP stimulation, indicating that these activities are critical for the in vivo function of STN1. Our findings have implications for the molecular mechanisms of PP, STN1 and STN1-related molecular pathology.
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Affiliation(s)
- Swapna Ganduri
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medical College, New York, NY 10065, USA
| | - Neal F Lue
- Department of Microbiology & Immunology, W. R. Hearst Microbiology Research Center, Weill Cornell Medical College, New York, NY 10065, USA.,Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10065, USA
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35
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Baranovskiy AG, Babayeva ND, Zhang Y, Blanco L, Pavlov YI, Tahirov TH. Comment on "The [4Fe4S] cluster of human DNA primase functions as a redox switch using DNA charge transport". Science 2017; 357:357/6348/eaan2396. [PMID: 28729484 DOI: 10.1126/science.aan2396] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/13/2017] [Indexed: 12/27/2022]
Abstract
O'Brien et al (Research Article, 24 February 2017, eaag1789) proposed a novel mechanism of primase function based on redox activity of the iron-sulfur cluster buried inside the C-terminal domain of the large primase subunit (p58C). Serious problems in the experimental design and data interpretation raise concerns about the validity of the conclusions.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yinbo Zhang
- Department of Immunology, University of Washington, Seattle WA 98195, USA
| | - Luis Blanco
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid 28049, Spain
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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36
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Holt ME, Salay LE, Chazin WJ. A Polymerase With Potential: The Fe-S Cluster in Human DNA Primase. Methods Enzymol 2017; 595:361-390. [PMID: 28882207 DOI: 10.1016/bs.mie.2017.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Replication of DNA in eukaryotes is primarily executed by the combined action of processive DNA polymerases δ and ɛ. These enzymes cannot initiate synthesis of new DNA without the presence of a primer on the template ssDNA. The primers on both the leading and lagging strands are generated by DNA polymerase α-primase (pol-prim). DNA primase is a DNA-dependent RNA polymerase that synthesizes the first ~10 nucleotides and then transfers the substrate to polymerase α to complete primer synthesis. The mechanisms governing the coordination and handoff between primase and polymerase α are largely unknown. Isolated DNA primase contains a [4Fe-4S]2+ cluster that has been shown to serve as a redox switch modulating DNA binding affinity. This discovery suggests a mechanism for modulating the priming activity of primase and handoff to polymerase α. In this chapter, we briefly discuss the current state of knowledge of primase structure and function, including the role of its iron-sulfur cluster. This is followed by providing the methods for expressing, purifying, and biophysically/structurally characterizing primase and its iron-sulfur cluster-containing domain, p58C.
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Affiliation(s)
- Marilyn E Holt
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Lauren E Salay
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Walter J Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.
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37
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Baranovskiy AG, Gu J, Babayeva ND, Kurinov I, Pavlov YI, Tahirov TH. Crystal structure of the human Polϵ B-subunit in complex with the C-terminal domain of the catalytic subunit. J Biol Chem 2017; 292:15717-15730. [PMID: 28747437 DOI: 10.1074/jbc.m117.792705] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/21/2017] [Indexed: 12/13/2022] Open
Abstract
The eukaryotic B-family DNA polymerases include four members: Polα, Polδ, Polϵ, and Polζ, which share common architectural features, such as the exonuclease/polymerase and C-terminal domains (CTDs) of catalytic subunits bound to indispensable B-subunits, which serve as scaffolds that mediate interactions with other components of the replication machinery. Crystal structures for the B-subunits of Polα and Polδ/Polζ have been reported: the former within the primosome and separately with CTD and the latter with the N-terminal domain of the C-subunit. Here we present the crystal structure of the human Polϵ B-subunit (p59) in complex with CTD of the catalytic subunit (p261C). The structure revealed a well defined electron density for p261C and the phosphodiesterase and oligonucleotide/oligosaccharide-binding domains of p59. However, electron density was missing for the p59 N-terminal domain and for the linker connecting it to the phosphodiesterase domain. Similar to Polα, p261C of Polϵ contains a three-helix bundle in the middle and zinc-binding modules on each side. Intersubunit interactions involving 11 hydrogen bonds and numerous hydrophobic contacts account for stable complex formation with a buried surface area of 3094 Å2 Comparative structural analysis of p59-p261C with the corresponding Polα complex revealed significant differences between the B-subunits and CTDs, as well as their interaction interfaces. The B-subunit of Polδ/Polζ also substantially differs from B-subunits of either Polα or Polϵ. This work provides a structural basis to explain biochemical and genetic data on the importance of B-subunit integrity in replisome function in vivo.
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Affiliation(s)
- Andrey G Baranovskiy
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Jianyou Gu
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Nigar D Babayeva
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
| | - Igor Kurinov
- the Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Advanced Photon Source, Argonne, Illinois 60439
| | - Youri I Pavlov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and.,the Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, and Genetics and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198 and
| | - Tahir H Tahirov
- From the Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center and
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38
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Boldinova EO, Wanrooij PH, Shilkin ES, Wanrooij S, Makarova AV. DNA Damage Tolerance by Eukaryotic DNA Polymerase and Primase PrimPol. Int J Mol Sci 2017; 18:E1584. [PMID: 28754021 PMCID: PMC5536071 DOI: 10.3390/ijms18071584] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/14/2017] [Accepted: 07/16/2017] [Indexed: 12/31/2022] Open
Abstract
PrimPol is a human deoxyribonucleic acid (DNA) polymerase that also possesses primase activity and is involved in DNA damage tolerance, the prevention of genome instability and mitochondrial DNA maintenance. In this review, we focus on recent advances in biochemical and crystallographic studies of PrimPol, as well as in identification of new protein-protein interaction partners. Furthermore, we discuss the possible functions of PrimPol in both the nucleus and the mitochondria.
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Affiliation(s)
- Elizaveta O Boldinova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
| | - Evgeniy S Shilkin
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
| | - Alena V Makarova
- Institute of Molecular Genetics of Russian Academy of Sciences, Kurchatov sq. 2, 123182 Moscow, Russia.
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