Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: insights from DNA complex structures.

Abstract:

:RecQ helicases are a widely conserved family of ATP-dependent motors with diverse roles in nearly every aspect of bacterial and eukaryotic genome maintenance. However, the physical mechanisms by which RecQ helicases recognize and process specific DNA replication and repair intermediates are largely unknown. Here, we solved crystal structures of the human RECQ1 helicase in complexes with tailed-duplex DNA and ssDNA. The structures map the interactions of the ssDNA tail and the branch point along the helicase and Zn-binding domains, which, together with reported structures of other helicases, define the catalytic stages of helicase action. We also identify a strand-separating pin, which (uniquely in RECQ1) is buttressed by the protein dimer interface. A duplex DNA-binding surface on the C-terminal domain is shown to play a role in DNA unwinding, strand annealing, and Holliday junction (HJ) branch migration. We have combined EM and analytical ultracentrifugation approaches to show that RECQ1 can form what appears to be a flat, homotetrameric complex and propose that RECQ1 tetramers are involved in HJ recognition. This tetrameric arrangement suggests a platform for coordinated activity at the advancing and receding duplexes of an HJ during branch migration.

authors

Pike AC,Gomathinayagam S,Swuec P,Berti M,Zhang Y,Schnecke C,Marino F,von Delft F,Renault L,Costa A,Gileadi O,Vindigni A

doi

10.1073/pnas.1417594112

subject

Has Abstract

pub_date

2015-04-07 00:00:00

pages

4286-91

issue

14

eissn

0027-8424

issn

1091-6490

pii

1417594112

journal_volume

112

pub_type

杂志文章
  • Positive regulatory role of strigolactone in plant responses to drought and salt stress.

    abstract::This report provides direct evidence that strigolactone (SL) positively regulates drought and high salinity responses in Arabidopsis. Both SL-deficient and SL-response [more axillary growth (max)] mutants exhibited hypersensitivity to drought and salt stress, which was associated with shoot- rather than root-related t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1322135111

    authors: Ha CV,Leyva-González MA,Osakabe Y,Tran UT,Nishiyama R,Watanabe Y,Tanaka M,Seki M,Yamaguchi S,Dong NV,Yamaguchi-Shinozaki K,Shinozaki K,Herrera-Estrella L,Tran LS

    更新日期:2014-01-14 00:00:00

  • Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states.

    abstract::Using brain transcriptomic profiles from 853 individual honey bees exhibiting 48 distinct behavioral phenotypes in naturalistic contexts, we report that behavior-specific neurogenomic states can be inferred from the coordinated action of transcription factors (TFs) and their predicted target genes. Unsupervised hierar...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1114093108

    authors: Chandrasekaran S,Ament SA,Eddy JA,Rodriguez-Zas SL,Schatz BR,Price ND,Robinson GE

    更新日期:2011-11-01 00:00:00

  • Crystal structure of human type II inosine monophosphate dehydrogenase: implications for ligand binding and drug design.

    abstract::Inosine monophosphate dehydrogenase (IMPDH) controls a key metabolic step in the regulation of cell growth and differentiation. This step is the NAD-dependent oxidation of inosine 5' monophosphate (IMP) to xanthosine 5' monophosphate, the rate-limiting step in the synthesis of the guanine nucleotides. Two isoforms of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.7.3531

    authors: Colby TD,Vanderveen K,Strickler MD,Markham GD,Goldstein BM

    更新日期:1999-03-30 00:00:00

  • Quantitative MS-based enzymology of caspases reveals distinct protein substrate specificities, hierarchies, and cellular roles.

    abstract::Proteases constitute the largest enzyme family, yet their biological roles are obscured by our rudimentary understanding of their cellular substrates. There are 12 human caspases that play crucial roles in inflammation and cell differentiation and drive the terminal stages of cell death. Recent N-terminomics technolog...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1524900113

    authors: Julien O,Zhuang M,Wiita AP,O'Donoghue AJ,Knudsen GM,Craik CS,Wells JA

    更新日期:2016-04-05 00:00:00

  • Dynamic updating of hippocampal object representations reflects new conceptual knowledge.

    abstract::Concepts organize the relationship among individual stimuli or events by highlighting shared features. Often, new goals require updating conceptual knowledge to reflect relationships based on different goal-relevant features. Here, our aim is to determine how hippocampal (HPC) object representations are organized and ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1614048113

    authors: Mack ML,Love BC,Preston AR

    更新日期:2016-11-15 00:00:00

  • Deletion mutants of Neurospora crassa mitochondrial DNA and their relationship to the "stop-start" growth phenotype.

    abstract::"Stoppers" are a class of Neurospora crassa extranuclear mutants characterized by gross deficiencies of cytochromes b and aa3 and an unusual growth phenotype which involves irregular periods of growth andnongrowth. In the present work, mtDNAs from all four stopper mutants were found to contain deletions or insertions ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.10.6032

    authors: Bertrand H,Collins RA,Stohl LL,Goewert RR,Lambowitz AM

    更新日期:1980-10-01 00:00:00

  • Major histocompatibility complex class I genes of the coelacanth Latimeria chalumnae.

    abstract::The coelacanth fish Latimeria chalumnae is the sole surviving species of a phylogenetic lineage that was founded more than 400 million years ago and that has changed morphologically very little since that time. Little is known about the molecular evolution of this "living fossil," considered by some taxonomists to be ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.23.11065

    authors: Betz UA,Mayer WE,Klein J

    更新日期:1994-11-08 00:00:00

  • Retroviral sequences related to human T-lymphotropic virus type II in patients with chronic fatigue immune dysfunction syndrome.

    abstract::Chronic fatigue immune dysfunction syndrome (CFIDS) is a recently recognized illness characterized by debilitating fatigue as well as immunological and neurological abnormalities [Straus, S.E. (1988) J. Inf. Dis. 157, 405-412]. Once thought to be caused by Epstein-Barr virus, it is now thought to have a different but ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.7.2922

    authors: DeFreitas E,Hilliard B,Cheney PR,Bell DS,Kiggundu E,Sankey D,Wroblewska Z,Palladino M,Woodward JP,Koprowski H

    更新日期:1991-04-01 00:00:00

  • Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement.

    abstract::Coordinated changes in gene expression underlie the early patterning and cell-type specification of the central nervous system. However, much less is known about how such changes contribute to later stages of circuit assembly and refinement. In this study, we employ single-cell RNA sequencing to develop a detailed, wh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1717871115

    authors: Kalish BT,Cheadle L,Hrvatin S,Nagy MA,Rivera S,Crow M,Gillis J,Kirchner R,Greenberg ME

    更新日期:2018-01-30 00:00:00

  • Avian influenza A virus (H7N7) associated with human conjunctivitis and a fatal case of acute respiratory distress syndrome.

    abstract::Highly pathogenic avian influenza A viruses of subtypes H5 and H7 are the causative agents of fowl plague in poultry. Influenza A viruses of subtype H5N1 also caused severe respiratory disease in humans in Hong Kong in 1997 and 2003, including at least seven fatal cases, posing a serious human pandemic threat. Between...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0308352100

    authors: Fouchier RA,Schneeberger PM,Rozendaal FW,Broekman JM,Kemink SA,Munster V,Kuiken T,Rimmelzwaan GF,Schutten M,Van Doornum GJ,Koch G,Bosman A,Koopmans M,Osterhaus AD

    更新日期:2004-02-03 00:00:00

  • Crystal structure of yeast TATA-binding protein and model for interaction with DNA.

    abstract::The C-terminal 179-aa region of yeast (Saccharomyces cerevisiae) TATA-binding protein (TBP), phylogenetically conserved and sufficient for many functions, formed crystals diffracting to 1.7-A resolution. The structure of the protein, determined by molecular replacement with coordinates from Arabidopsis TBP and refined...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.17.8174

    authors: Chasman DI,Flaherty KM,Sharp PA,Kornberg RD

    更新日期:1993-09-01 00:00:00

  • Mechanisms for segregating T cell receptor and adhesion molecules during immunological synapse formation in Jurkat T cells.

    abstract::T cells interacting with antigen-presenting cells (APCs) form an "immunological synapse" (IS), a bull's-eye pattern composed of a central supramolecular activation cluster enriched with T cell receptors (TCRs) surrounded by a ring of adhesion molecules (a peripheral supramolecular activation cluster). The mechanism re...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0710258105

    authors: Kaizuka Y,Douglass AD,Varma R,Dustin ML,Vale RD

    更新日期:2007-12-18 00:00:00

  • Liquid drop of DNA libraries reveals total genome information.

    abstract::Conventional "bulk" PCR often yields inefficient and nonuniform amplification of complex templates in DNA libraries, introducing unwanted biases. Amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were e...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2017138117

    authors: Terekhov SS,Eliseev IE,Ovchinnikova LA,Kabilov MR,Prjibelski AD,Tupikin AE,Smirnov IV,Belogurov AA Jr,Severinov KV,Lomakin YA,Altman S,Gabibov AG

    更新日期:2020-11-03 00:00:00

  • cDNA clone encoding Drosophila transcription factor TFIID.

    abstract::Proper initiation of transcription by RNA polymerase II requires the TATA-consensus-binding transcription factor TFIID. A cDNA clone encoding the Drosophila TFIID protein has been isolated and characterized. The deduced amino acid sequence reveals an open reading frame of 353 residues. The carboxyl-terminal 180 amino ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.23.9148

    authors: Muhich ML,Iida CT,Horikoshi M,Roeder RG,Parker CS

    更新日期:1990-12-01 00:00:00

  • Expression of chicken liver cell adhesion molecule fusion genes in transgenic mice.

    abstract::The tissue-specific expression of the chicken liver cell adhesion molecule (L-CAM) was studied by generating transgenic mice. The rat insulin II promoter was fused to a chicken L-CAM cDNA or to chicken genomic L-CAM sequences. Mice carrying the cDNA showed no expression of L-CAM. Mice carrying L-CAM genomic sequences ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.22.9042

    authors: Begemann M,Tan SS,Cunningham BA,Edelman GM

    更新日期:1990-11-01 00:00:00

  • The novel PII-interactor PirC identifies phosphoglycerate mutase as key control point of carbon storage metabolism in cyanobacteria.

    abstract::Nitrogen limitation imposes a major transition in the lifestyle of nondiazotrophic cyanobacteria that is controlled by a complex interplay of regulatory factors involving the pervasive signal processor PII Immediately upon nitrogen limitation, newly fixed carbon is redirected toward glycogen synthesis. How the metabol...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2019988118

    authors: Orthwein T,Scholl J,Spät P,Lucius S,Koch M,Macek B,Hagemann M,Forchhammer K

    更新日期:2021-02-09 00:00:00

  • SGTA antagonizes BAG6-mediated protein triage.

    abstract::The BAG6 complex was first identified as an upstream loading factor for tail-anchored membrane proteins entering the TRC40-dependent pathway for posttranslational delivery to the endoplasmic reticulum. Subsequently, BAG6 was shown to enhance the proteasomal degradation of mislocalized proteins by selectively promoting...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1209997109

    authors: Leznicki P,High S

    更新日期:2012-11-20 00:00:00

  • Transcriptional activating regions target a cyclin-dependent kinase.

    abstract::Several yeast activators are phosphorylated by SRB10, a cyclin-dependent kinase associated with the transcriptional machinery. Sites of phosphorylation are found outside the activating region in each case, and the modification has different physiological consequences in different cases. We show here that certain acidi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.232573899

    authors: Ansari AZ,Koh SS,Zaman Z,Bongards C,Lehming N,Young RA,Ptashne M

    更新日期:2002-11-12 00:00:00

  • The Escherichia coli RuvB branch migration protein forms double hexameric rings around DNA.

    abstract::The RuvB protein is induced in Escherichia coli as part of the SOS response to DNA damage. It is required for genetic recombination and the postreplication repair of DNA. In vitro, the RuvB protein promotes the branch migration of Holliday junctions and has a DNA helicase activity in reactions that require ATP hydroly...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.16.7618

    authors: Stasiak A,Tsaneva IR,West SC,Benson CJ,Yu X,Egelman EH

    更新日期:1994-08-02 00:00:00

  • Production of a tissue-like structure by contraction of collagen lattices by human fibroblasts of different proliferative potential in vitro.

    abstract::Fibroblasts can condense a hydrated collagen lattice to a tissue-like structure 1/28th the area of the starting gel in 24 hr. The rate of the process can be regulated by varying the protein content of the lattice, the cell number, or the concentration of an inhibitor such as Colcemid. Fibroblasts of high population do...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.3.1274

    authors: Bell E,Ivarsson B,Merrill C

    更新日期:1979-03-01 00:00:00

  • Ornitholimnology: Effects of grazing by the Andean flamingo (Phoenicoparrus andinus).

    abstract::Experimental exclusion of the Andean flamingo (Phoenicoparrus andinus) from shallow water areas of a salt lake in the Bolivian Andes caused large increases in the biomass of microorganisms inhabiting the surface sediments, especially a large diatom (Surirella wetzeli), amebas, ciliates, and nematodes. This is a conser...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.15.4766

    authors: Hurlbert SH,Chang CC

    更新日期:1983-08-01 00:00:00

  • Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming.

    abstract::Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1011564107

    authors: Tytell ED,Hsu CY,Williams TL,Cohen AH,Fauci LJ

    更新日期:2010-11-16 00:00:00

  • Periodic and chaotic host-parasite interactions in human malaria.

    abstract::It has been recognized since ancient times that malaria fever is highly periodic but the mechanism has been poorly understood. Malaria fever is related to the parasite growth cycle in erythrocytes. After a fixed period of replication, a mature parasite (schizont) causes the infected erythrocyte to rupture, releasing p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.12.5111

    authors: Kwiatkowski D,Nowak M

    更新日期:1991-06-15 00:00:00

  • Organ boundary1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs.

    abstract::We identify a gene, organ boundary1 (OBO1), by its unique pattern of enhancer- driven GFP expression at the boundaries between the apical meristems and lateral organs in Arabidopsis embryos, seedlings, and mature plants. OBO1 also is expressed at the root apical meristem and in distinct cell files surrounding this are...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1018542108

    authors: Cho E,Zambryski PC

    更新日期:2011-02-01 00:00:00

  • VHL loss in renal cell carcinoma leads to up-regulation of CUB domain-containing protein 1 to stimulate PKC{delta}-driven migration.

    abstract::A common genetic mutation found in clear cell renal cell carcinoma (CC-RCC) is the loss of the von Hippel-Lindau (VHL) gene, which results in stabilization of hypoxia-inducible factors (HIFs), and contributes to cancer progression and metastasis. CUB-domain-containing protein 1 (CDCP1) was shown to promote metastasis ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1011777108

    authors: Razorenova OV,Finger EC,Colavitti R,Chernikova SB,Boiko AD,Chan CK,Krieg A,Bedogni B,LaGory E,Weissman IL,Broome-Powell M,Giaccia AJ

    更新日期:2011-02-01 00:00:00

  • Molecular mass, biochemical composition, and physicochemical behavior of the infectious form of the scrapie precursor protein monomer.

    abstract::A highly purified fraction obtained from scrapie (263-K strain)-infected hamsters' brains by an alternative procedure without proteinase K treatment contained a protease-resistant form of the scrapie precursor protein (PrPSc) and infectivity of 9.9 +/- 0.7 log LD50/ml. Polyclonal antibodies produced against hamster sc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.16.6373

    authors: Safar J,Wang W,Padgett MP,Ceroni M,Piccardo P,Zopf D,Gajdusek DC,Gibbs CJ Jr

    更新日期:1990-08-01 00:00:00

  • Ribonucleic acid synthesis of vesicular stomatitis virus, II. An RNA polymerase in the virion.

    abstract::The virions of vesicular stomatitis virus contain an enzyme that catalyzes the incorporation of ribonucleotides into RNA. The product of the reaction is mainly RNA complementary in base sequence to that of vesicular stomatitis virus RNA. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.66.2.572

    authors: Baltimore D,Huang AS,Stampfer M

    更新日期:1970-06-01 00:00:00

  • Nerve growth factor stimulates protein tyrosine phosphorylation in PC-12 pheochromocytoma cells.

    abstract::The cellular actions of nerve growth factor (NGF) and epidermal growth factor (EGF) may be mediated by changes in protein phosphorylation. The tyrosine phosphorylation of two predominant proteins of molecular mass 40 and 42 kDa is seen in PC-12 cells treated with NGF or EGF, correlating with activation of a previously...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.7.2653

    authors: Miyasaka T,Sternberg DW,Miyasaka J,Sherline P,Saltiel AR

    更新日期:1991-04-01 00:00:00

  • Functional association between Wwox tumor suppressor protein and p73, a p53 homolog.

    abstract::The WWOX gene is a recently cloned tumor suppressor gene that spans the FRA16D fragile region. Wwox protein contains two WW domains that are generally known to mediate protein-protein interaction. Here we show that Wwox physically interacts via its first WW domain with the p53 homolog, p73. The tyrosine kinase, Src, p...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0400805101

    authors: Aqeilan RI,Pekarsky Y,Herrero JJ,Palamarchuk A,Letofsky J,Druck T,Trapasso F,Han SY,Melino G,Huebner K,Croce CM

    更新日期:2004-03-30 00:00:00

  • Loss of O-GlcNAc glycosylation in forebrain excitatory neurons induces neurodegeneration.

    abstract::O-GlcNAc glycosylation (or O-GlcNAcylation) is a dynamic, inducible posttranslational modification found on proteins associated with neurodegenerative diseases such as α-synuclein, amyloid precursor protein, and tau. Deletion of the O-GlcNAc transferase (ogt) gene responsible for the modification causes early postnata...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1606899113

    authors: Wang AC,Jensen EH,Rexach JE,Vinters HV,Hsieh-Wilson LC

    更新日期:2016-12-27 00:00:00