Selective degradation of reverse gyrase and DNA fragmentation induced by alkylating agent in the archaeon Sulfolobus solfataricus.

Abstract:

:Reverse gyrase is a peculiar DNA topoisomerase, specific of hyperthermophilic Archaea and Bacteria, which has the unique ability of introducing positive supercoiling into DNA molecules. Although the function of the enzyme has not been established directly, it has been suggested to be involved in DNA protection and repair. We show here that the enzyme is degraded after treatment of Sulfolobus solfataricus cells with the alkylating agent MMS. MMS-induced reverse gyrase degradation is highly specific, since (i) neither hydroxyurea (HU) nor puromycin have a similar effect, and (ii) topoisomerase VI and two chromatin components are not degraded. Reverse gyrase degradation does not depend on protein synthesis. Experiments in vitro show that direct exposure of cell extracts to MMS does not induce reverse gyrase degradation; instead, extracts from MMS-treated cells contain some factor(s) able to degrade the enzyme in extracts from control cells. In vitro, degradation is blocked by incubation with divalent metal chelators, suggesting that reverse gyrase is selectively degraded by a metal-dependent protease in MMS-treated cells. In addition, we find a striking concurrence of extensive genomic DNA degradation and reverse gyrase loss in MMS-treated cells. These results support the hypothesis that reverse gyrase plays an essential role in DNA thermoprotection and repair in hyperthermophilic organisms.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Valenti A,Napoli A,Ferrara MC,Nadal M,Rossi M,Ciaramella M

doi

10.1093/nar/gkl115

subject

Has Abstract

pub_date

2006-04-14 00:00:00

pages

2098-108

issue

7

eissn

0305-1048

issn

1362-4962

pii

34/7/2098

journal_volume

34

pub_type

杂志文章
  • YM500: a small RNA sequencing (smRNA-seq) database for microRNA research.

    abstract::MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1238

    authors: Cheng WC,Chung IF,Huang TS,Chang ST,Sun HJ,Tsai CF,Liang ML,Wong TT,Wang HW

    更新日期:2013-01-01 00:00:00

  • Markerless gene replacement in Escherichia coli stimulated by a double-strand break in the chromosome.

    abstract::A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.22.4409

    authors: Pósfai G,Kolisnychenko V,Bereczki Z,Blattner FR

    更新日期:1999-11-15 00:00:00

  • Promoter-enhancer looping at the PPARγ2 locus during adipogenic differentiation requires the Prmt5 methyltransferase.

    abstract::PPARγ2 is a critical lineage-determining transcription factor that is essential for adipogenic differentiation. Here we report characterization of the three-dimensional structure of the PPARγ2 locus after the onset of adipogenic differentiation and the mechanisms by which it forms. We identified a differentiation-depe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw129

    authors: LeBlanc SE,Wu Q,Lamba P,Sif S,Imbalzano AN

    更新日期:2016-06-20 00:00:00

  • Facile preparation of nuclease resistant 3' modified oligodeoxynucleotides.

    abstract::An efficient chemical procedure for the immobilization of carboxylate containing conjugate groups onto controlled pore glass (CPG) is described. The derivatized supports were used in the automated synthesis of an oligodeoxynucleotide (20-mer ODN) containing a 3' phosphodiester linked hexanol, aminohexyl, acridine, or ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.1.145

    authors: Gamper HB,Reed MW,Cox T,Virosco JS,Adams AD,Gall AA,Scholler JK,Meyer RB Jr

    更新日期:1993-01-11 00:00:00

  • Structural basis for single-stranded RNA recognition and cleavage by C3PO.

    abstract::Translin and translin-associated factor-x are highly conserved in eukaroytes; they can form heteromeric complexes (known as C3POs) and participate in various nucleic acid metabolism pathways. In humans and Drosophila, C3POs cleave the fragmented siRNA passenger strands and facilitate the activation of RNA-induced sile...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw776

    authors: Zhang J,Liu H,Yao Q,Yu X,Chen Y,Cui R,Wu B,Zheng L,Zuo J,Huang Z,Ma J,Gan J

    更新日期:2016-11-02 00:00:00

  • Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA.

    abstract::Aminoglycosides antibiotics negate dissociation and recycling of the bacterial ribosome's subunits by binding to Helix 69 (H69) of 23S rRNA. The differential binding of various aminoglycosides to the chemically synthesized terminal domains of the Escherichia coli and human H69 has been characterized using spectroscopy...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1253

    authors: Scheunemann AE,Graham WD,Vendeix FA,Agris PF

    更新日期:2010-05-01 00:00:00

  • Multiple RNA-RNA tertiary interactions are dispensable for formation of a functional U2/U6 RNA catalytic core in the spliceosome.

    abstract::The active 3D conformation of the spliceosome's catalytic U2/U6 RNA core is stabilised by a network of secondary and tertiary RNA interactions, but also depends on spliceosomal proteins for its formation. To determine the contribution towards splicing of specific RNA secondary and tertiary interactions in the U2/U6 RN...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky966

    authors: Bao P,Boon KL,Will CL,Hartmuth K,Lührmann R

    更新日期:2018-12-14 00:00:00

  • Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

    abstract::The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1010

    authors: Schudoma C,May P,Nikiforova V,Walther D

    更新日期:2010-01-01 00:00:00

  • Tissue-specific translational regulation of alternative rabbit 15-lipoxygenase mRNAs differing in their 3'-untranslated regions.

    abstract::By screening a rabbit reticulocyte library, an alternative 15-LOX transcript of 3.6 kb (15-LOX mRNA2) was detected containing a 1019 nt longer 3'-untranslated region (UTR2) than the main 2.6 kb mRNA (15-LOX mRNA1). In anaemic animals, northern blotting showed that 15-LOX mRNA2 was predominantly expressed in non-erythr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.8.1828

    authors: Thiele BJ,Berger M,Huth A,Reimann I,Schwarz K,Thiele H

    更新日期:1999-04-15 00:00:00

  • Studies on the biological role of DNA methylation: III Role in excision of one-genome long single-stranded phi X 174 DNA.

    abstract::Accumulation of replicative intermediates of the bacteriophage phi X174 was observed in E. coli C infected cells when phage DNA methylation has been inhibited by nicotinamide or when cells were infected with a temperature-sensitive mutant in gene A. Analysis of the accumulating replicative intermediates by electron mi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.10.3483

    authors: Friedman J,Friedmann A,Razin A

    更新日期:1977-10-01 00:00:00

  • Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

    abstract::Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx616

    authors: Shaytan AK,Xiao H,Armeev GA,Wu C,Landsman D,Panchenko AR

    更新日期:2017-09-19 00:00:00

  • Selective disruption of the DNA polymerase III α-β complex by the umuD gene products.

    abstract::DNA polymerase III (DNA pol III) efficiently replicates the Escherichia coli genome, but it cannot bypass DNA damage. Instead, translesion synthesis (TLS) DNA polymerases are employed to replicate past damaged DNA; however, the exchange of replicative for TLS polymerases is not understood. The umuD gene products, whic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks229

    authors: Silva MC,Nevin P,Ronayne EA,Beuning PJ

    更新日期:2012-07-01 00:00:00

  • The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae.

    abstract::The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.23.5779

    authors: Rubtsov PM,Musakhanov MM,Zakharyev VM,Krayev AS,Skryabin KG,Bayev AA

    更新日期:1980-12-11 00:00:00

  • An in vitro RNA polymerase III system from S. cerevisiae: effects of deletions and point mutations upon SUP4 gene transcription.

    abstract::A soluble cell-free extract containing RNA polymerase III and factors essential for selective transcription of the yeast SUP4-o tRNATyr gene was prepared from Saccharomyces cerevisiae cells. An intragenic promoter for yeast RNA polymerase III was identified within the yeast tRNATyr coding sequence by testing several s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.24.8127

    authors: Koski RA,Allison DS,Worthington M,Hall BD

    更新日期:1982-12-20 00:00:00

  • A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements.

    abstract::Initiation of σ(54)-dependent transcription requires assistance to melt DNA at the promoter site but is impeded by numerous protein-protein and nucleo-protein interactions. To alleviate these inhibitory interactions, hexameric bacterial enhancer binding proteins (bEBP), a subset of the ATPases associated with various ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks661

    authors: Zhang N,Joly N,Buck M

    更新日期:2012-10-01 00:00:00

  • Open complex formation during transcription initiation at the Escherichia coli galP1 promoter: the role of the RNA polymerase alpha subunit at promoters lacking an UP-element.

    abstract::We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.9.2051

    authors: Burns HD,Ishihama A,Minchin SD

    更新日期:1999-05-01 00:00:00

  • In vitro chromatin assembly promoted by the Xenopus laevis S-150 cell-free extract is enhanced by treatment with RNase A.

    abstract::Cell-free extracts employed as chromatin assembly systems contain a myriad of proteins, polyanions and nucleic acids. The roles of ATP, MgCl2 and other cofactors in the catalysis of nucleosome formation by the Xenopus laevis oocyte S-150 have yet to be established unequivocally. In this study we examine the influence ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.4.889

    authors: Sekiguchi JM,Kmiec EB

    更新日期:1992-02-25 00:00:00

  • Single cell epigenetic visualization assay.

    abstract::Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based ep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkab009

    authors: Kint S,Van Criekinge W,Vandekerckhove L,De Vos WH,Bomsztyk K,Krause DS,Denisenko O

    更新日期:2021-01-28 00:00:00

  • In situ hybridization with fluoresceinated DNA.

    abstract::We have used fluorescein-11-dUTP in a nick-translation format to produce fluoresceinated human nucleic acid probes. After in situ hybridization of fluoresceinated DNAs to human metaphase chromosomes, the detection sensitivity was found to be 50-100 kb. The feasibility and the increase in detection sensitivity of micro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.12.3237

    authors: Wiegant J,Ried T,Nederlof PM,van der Ploeg M,Tanke HJ,Raap AK

    更新日期:1991-06-25 00:00:00

  • HIV-1 Tat directly binds to NFkappaB enhancer sequence: role in viral and cellular gene expression.

    abstract::HIV-1 Tat protein reprograms cellular gene expression of infected as well as uninfected cells apart from its primary function of transactivating HIV-1 long terminal repeat (LTR) promoter by binding to a nascent RNA stem-loop structure known as the transactivator response region (TAR). Tat also induces chromatin remode...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh289

    authors: Dandekar DH,Ganesh KN,Mitra D

    更新日期:2004-02-23 00:00:00

  • Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells.

    abstract::A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in the following order: (5') H2B25,35-H455,65-H375,85,95/H488-H2B105,11 5-H2A118-H3135,145/H2A145 (3') (the subscripts giv...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.10.3439

    authors: Bavykin SG,Usachenko SI,Lishanskaya AI,Shick VV,Belyavsky AV,Undritsov IM,Strokov AA,Zalenskaya IA,Mirzabekov AD

    更新日期:1985-05-24 00:00:00

  • Direct interaction between Rsc6 and Rsc8/Swh3,two proteins that are conserved in SWI/SNF-related complexes.

    abstract::The RSC complex of Saccharomyces cerevisiae is closely related to the SWI/SNF complex. Both complexes are involved in remodeling chromatin structure and they share conserved components. The RSC proteins Sth1, Rsc8/Swh3, Sfh1 and Rsc6 are homologs of the SWI/SNF proteins Swi2/Snf2, Swi3, Snf5 and Swp73 respectively. To...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.16.3739

    authors: Treich I,Ho L,Carlson M

    更新日期:1998-08-15 00:00:00

  • Interplay between positive and negative activities that influence the role of Bicoid in transcription.

    abstract::The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is un...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki691

    authors: Fu D,Ma J

    更新日期:2005-07-19 00:00:00

  • 'Solo' large terminal repeats (LTR) of an endogenous retrovirus-like gene family (VL30) in the mouse genome.

    abstract::VL30 genetic elements constitute a murine multicopy gene family that is retrovirus-like, despite the lack of sequence homology with any known retrovirus. Over one hundred copies of VL30 units are dispersed throughout the mouse genome. We report here that the mouse genome also contains 'solo' VL30 long terminal repeats...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.5.2273

    authors: Rotman G,Itin A,Keshet E

    更新日期:1984-03-12 00:00:00

  • Global miRNA expression analysis identifies novel key regulators of plasma cell differentiation and malignant plasma cell.

    abstract::MicroRNAs (miRNAs) are small noncoding RNAs that attenuate expression of their mRNA targets. Here, we developed a new method and an R package, to easily infer candidate miRNA-mRNA target interactions that could be functional during a given biological process. Using this method, we described, for the first time, a comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx327

    authors: Kassambara A,Jourdan M,Bruyer A,Robert N,Pantesco V,Elemento O,Klein B,Moreaux J

    更新日期:2017-06-02 00:00:00

  • Cloning of multiple copies of immunoglobulin variable kappa genes in cosmid vectors.

    abstract::The possibility of cloning large segments of DNA in cosmid vectors offers distinct advantages, in particular for the study of multigene families. Large size fragments of mouse embryo DNA were successfully cloned in the cosmid pHC 79. Twelve recombinants hybridizing specifically to an immunoglobulin kappa chain variabl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.12.2777

    authors: Cattaneo R,Gorski J,Mach B

    更新日期:1981-06-25 00:00:00

  • High frequency vector-mediated transformation and gene replacement in Tetrahymena.

    abstract::Recently, we developed a mass DNA-mediated transformation technique for the ciliated protozoan Tetrahymena thermophila that introduces transforming DNA by electroporation into conjugating cells. Other studies demonstrated that a neomycin resistance gene flanked by Tetrahymena H4-I gene regulatory sequences transformed...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.24.5391

    authors: Gaertig J,Gu L,Hai B,Gorovsky MA

    更新日期:1994-12-11 00:00:00

  • Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution.

    abstract::The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational prope...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.11.4399

    authors: Cheng DM,Dhingra MM,Sarma RH

    更新日期:1978-11-01 00:00:00

  • Restriction endonuclease isoschizomers ItaI, BsoFI and Fsp4HI are characterised by differences in their sensitivities to CpG methylation.

    abstract::BsoFI , ItaI and Fsp4HI are isoshizomers of Fnu4HI (5'-GC NGC-3'). Both Fnu4HI and BsoFI have previously been shown to be inhibited by cytosine-specific methylation within the recognition sequence. Fnu4HI is inhibited if either the internal cytosine at position 2 or the external cytosine at position 5 of the restricti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.16.3196

    authors: Ramsahoye BH,Burnett AK,Taylor C

    更新日期:1997-08-15 00:00:00

  • Molecular structure of (m5 dC-dG)3: the role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA.

    abstract::The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.23.7879

    authors: Fujii S,Wang AH,van der Marel G,van Boom JH,Rich A

    更新日期:1982-12-11 00:00:00