Catalytic Strand Separation by RECQ1 Is Required for RPA-Mediated Response to Replication Stress

Banerjee, Taraswi; Sommers, Joshua A.; Huang, Jing; Seidman, Michael M.; Brosh, Robert M.

doi:10.1016/j.cub.2015.09.026

Cited by 33 publications

(29 citation statements)

References 44 publications

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“…The recently determined X-ray crystal structure of PriA revealed a surface-exposed loop within the helicase core domain that was similar in sequence and position to the aromatic-rich loop (ARL) found in RecQ helicases (Figure 1) (16,23,34–36). This element is adjacent to motif II in both proteins.…”

Section: Resultsmentioning

confidence: 73%

“…In the RecQ subfamily of SF2 enzymes, the ARL interacts with ssDNA to structurally couple DNA-binding with ATP hydrolysis in bacteria enzymes; the same loop has been implicated in helicase function in the S. cerevisiae RecQ protein, Sgs1 and human RecQ proteins, RECQ1 and BLM (13,16,17,35,36). In the DEAD-box subfamily of RNA helicases, motif IIa (also referred to as ‘post-II’) forms a highly conserved RNA binding surface that appears to clash with dsRNA and may force strand separation (15,21,54).…”

Section: Discussionmentioning

confidence: 99%

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An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase

Windgassen¹,

Keck²

2016

Nucleic Acids Res

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Helicases couple ATP hydrolysis to nucleic acid binding and unwinding via molecular mechanisms that remain poorly defined for most enzyme subfamilies within the superfamily 2 (SF2) helicase group. A crystal structure of the PriA SF2 DNA helicase, which governs restart of prematurely terminated replication processes in bacteria, revealed the presence of an aromatic-rich loop (ARL) on the presumptive DNA-binding surface of the enzyme. The position and sequence of the ARL was similar to loops known to couple ATP hydrolysis with DNA binding in a subset of other SF2 enzymes, however, the roles of the ARL in PriA had not been investigated. Here, we show that changes within the ARL sequence uncouple PriA ATPase activity from DNA binding. In vitro protein-DNA crosslinking experiments define a residue- and nucleotide-specific interaction map for PriA, showing that the ARL binds replication fork junctions whereas other sites bind the leading or lagging strands. We propose that DNA binding to the ARL allosterically triggers ATP hydrolysis in PriA. Additional SF2 helicases with similarly positioned loops may also couple DNA binding to ATP hydrolysis using related mechanisms.

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Section: Resultsmentioning

confidence: 73%

Section: Discussionmentioning

confidence: 99%

An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase

Windgassen¹,

Keck²

2016

Nucleic Acids Res

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“…It is yet undetermined if RECQL1 contributes in some way to the repair of oxidative base damage, or it may serve a less direct role in DNA damage signaling or regulation of the response to oxidative stress. RECQL1 is implicated in the regulation of replication restart after cellular exposure to the topoisomerase inhibitor camptothecin [86], and was found to govern RPA’s availability to maintain normal replication dynamics and preserve genomic stability by suppressing the accumulation of DNA damage [87]. An analogous role of RECQL1 to govern RPA’s role in response to oxidative stress remains to be seen.…”

Section: Human Recq Helicases and Their Roles In Response To Nuclear mentioning

confidence: 99%

Mechanistic and biological considerations of oxidatively damaged DNA for helicase-dependent pathways of nucleic acid metabolism

Crouch

Brosh

2017

Free Radical Biology and Medicine

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Cells are under constant assault from reactive oxygen species that occur endogenously or arise from environmental agents. An important consequence of such stress is the generation of oxidatively damaged DNA, which is represented by a wide range of non-helix distorting and helix-distorting bulkier lesions that potentially affect a number of pathways including replication and transcription; consequently DNA damage tolerance and repair pathways are elicited to help cells cope with the lesions. The cellular consequences and metabolism of oxidatively damaged DNA can be quite complex with a number of DNA metabolic proteins and pathways involved. Many of the responses to oxidative stress involve a specialized class of enzymes known as helicases, the topic of this review. Helicases are molecular motors that convert the energy of nucleoside triphosphate hydrolysis to unwinding of structured polynucleic acids. Helicases by their very nature play fundamentally important roles in DNA metabolism and are implicated in processes that suppress chromosomal instability, genetic disease, cancer, and aging. We will discuss the roles of helicases in response to nuclear and mitochondrial oxidative stress and how this important class of enzymes help cells cope with oxidatively generated DNA damage through their functions in the replication stress response, DNA repair, and transcriptional regulation.

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“…Helicase domain is believed to mediate nucleotide-binding and translocation, but the accessory domains are expected to be equally significant in structure and functions of RECQ1. Substitution of two invariant aromatic loop residues, W227 and F231, located within the conserved aromatic-rich sequence between motifs II and III of helicase core of full-length RECQ1 with alanine resulted in abrogation of helicase and branch migration activities but retention of DNA binding, oligomerization, ATPase, and strand annealing [27]. A unique tyrosine residue (Y564), at the tip of the β-hairpin motif which forms a wing of the WH domain, controls the activity of RECQ1 to unwind a simple fork duplex without impacting single strand DNA-dependent ATPase activity [25].…”

Section: Introductionmentioning

confidence: 99%

Site-directed mutants of human RECQ1 reveal functional importance of the zinc binding domain

Sami

Gary

Fang

et al. 2016

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

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RecQ helicases are a highly conserved family of ATP-dependent DNA-unwinding enzymes with key roles in DNA replication and repair in all kingdoms of life. The RECQ1 gene encodes the most abundant RecQ homolog in humans. Mutations in RECQ1 significantly increase breast cancer susceptibility. We engineered full-length RECQ1 harboring point mutations in the zinc-binding motif (amino acids 419–480) within the conserved RecQ-specific-C-terminal (RQC) domain known to be critical for diverse biochemical and cellular functions of RecQ helicases. Wild-type RECQ1 contains a zinc ion. Substitution of three of the four conserved cysteine residues that coordinate zinc severely impaired the ATPase and DNA unwinding activities but retained DNA binding and single strand DNA annealing activities. Furthermore, alteration of these residues attenuated zinc binding and significantly changed the overall conformation of full-length RECQ1 protein. In contrast, substitution of cysteine residue at position 471 resulted in a wild-type like RECQ1 protein. Differential contribution of the conserved cysteine residues to the structure and functions of the RECQ1 protein is also inferred by homology modeling. Overall, our results indicate that the zinc binding motif in the RQC domain of RECQ1 is a key structural element that is essential for the structure-functions of RECQ1. Given the recent association of RECQ1 mutations with breast cancer, these observations will contribute to understanding the molecular basis of RECQ1 functions in cancer etiology.

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Catalytic Strand Separation by RECQ1 Is Required for RPA-Mediated Response to Replication Stress

Cited by 33 publications

References 44 publications

An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase

An aromatic-rich loop couples DNA binding and ATP hydrolysis in the PriA DNA helicase

Mechanistic and biological considerations of oxidatively damaged DNA for helicase-dependent pathways of nucleic acid metabolism

Site-directed mutants of human RECQ1 reveal functional importance of the zinc binding domain

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