Early steps of double-strand break repair in Bacillus subtilis.

Abstract:

:All organisms rely on integrated networks to repair DNA double-strand breaks (DSBs) in order to preserve the integrity of the genetic information, to re-establish replication, and to ensure proper chromosomal segregation. Genetic, cytological, biochemical and structural approaches have been used to analyze how Bacillus subtilis senses DNA damage and responds to DSBs. RecN, which is among the first responders to DNA DSBs, promotes the ordered recruitment of repair proteins to the site of a lesion. Cells have evolved different mechanisms for efficient end processing to create a 3'-tailed duplex DNA, the substrate for RecA binding, in the repair of one- and two-ended DSBs. Strand continuity is re-established via homologous recombination (HR), utilizing an intact homologous DNA molecule as a template. In the absence of transient diploidy or of HR, however, two-ended DSBs can be directly re-ligated via error-prone non-homologous end-joining. Here we review recent findings that shed light on the early stages of DSB repair in Firmicutes.

journal_name

DNA Repair (Amst)

journal_title

DNA repair

authors

Alonso JC,Cardenas PP,Sanchez H,Hejna J,Suzuki Y,Takeyasu K

doi

10.1016/j.dnarep.2012.12.005

subject

Has Abstract

pub_date

2013-03-01 00:00:00

pages

162-76

issue

3

eissn

1568-7864

issn

1568-7856

pii

S1568-7864(12)00308-4

journal_volume

12

pub_type

杂志文章,评审
  • Extracts of proliferating and non-proliferating human cells display different base excision pathways and repair fidelity.

    abstract::Base excision repair (BER) of damaged or inappropriate bases in DNA has been reported to take place by single nucleotide insertion or through incorporation of several nucleotides, termed short-patch and long-patch repair, respectively. We found that extracts from proliferating and non-proliferating cells both had capa...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2009.04.002

    authors: Akbari M,Peña-Diaz J,Andersen S,Liabakk NB,Otterlei M,Krokan HE

    更新日期:2009-07-04 00:00:00

  • Repair of radiation induced DNA double strand breaks by backup NHEJ is enhanced in G2.

    abstract::In higher eukaryotes DNA double strand breaks (DSBs) are repaired by homologous recombination (HRR) or non-homologous end joining (NHEJ). In addition to the DNA-PK dependent pathway of NHEJ (D-NHEJ), cells employ a backup pathway (B-NHEJ) utilizing Ligase III and PARP-1. The cell cycle dependence and coordination of t...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2007.11.008

    authors: Wu W,Wang M,Wu W,Singh SK,Mussfeldt T,Iliakis G

    更新日期:2008-02-01 00:00:00

  • Multiple pathways cooperate to facilitate DNA replication fork progression through alkylated DNA.

    abstract::Eukaryotic genomes are especially vulnerable to DNA damage during the S phase of the cell cycle, when chromosomes must be duplicated. The stability of DNA replication forks is critical to achieve faithful chromosome replication and is severely compromised when forks encounter DNA lesions. To maintain genome integrity,...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2008.06.014

    authors: Vázquez MV,Rojas V,Tercero JA

    更新日期:2008-10-01 00:00:00

  • The role of the DNA damage response in neuronal development, organization and maintenance.

    abstract::The DNA damage response is a key factor in the maintenance of genome stability. As such, it is a central axis in sustaining cellular homeostasis in a variety of contexts: development, growth, differentiation, and maintenance of the normal life cycle of the cell. It is now clear that diverse mechanisms encompassing cel...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2008.03.005

    authors: Barzilai A,Biton S,Shiloh Y

    更新日期:2008-07-01 00:00:00

  • APE1: A skilled nucleic acid surgeon.

    abstract::Before a deleterious DNA lesion can be replaced with its undamaged counterpart, the lesion must first be removed from the genome. This process of removing and replacing DNA lesions is accomplished by the careful coordination of several protein factors during DNA repair. One such factor is the multifunctional enzyme hu...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2018.08.012

    authors: Whitaker AM,Freudenthal BD

    更新日期:2018-11-01 00:00:00

  • Evaluation of the Escherichia coli HK82 and BS87 strains as tools for AlkB studies.

    abstract::Within a decade the family of AlkB dioxygenases has been extensively studied as a one-protein DNA/RNA repair system in Escherichia coli but also as a group of proteins of much wider functions in eukaryotes. Two strains, HK82 and BS87, are the most commonly used E. coli strains for the alkB gene mutations. The aim of t...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2015.12.010

    authors: Mielecki D,Sikora A,Wrzesiński M,Nieminuszczy J,Detman A,Żuchniewicz K,Gromadka R,Grzesiuk E

    更新日期:2016-03-01 00:00:00

  • SSB recruitment of Exonuclease I aborts template-switching in Escherichia coli.

    abstract::Misalignment of a nascent strand and the use of an alternative template during DNA replication, a process termed "template-switching", can give rise to frequent mutations and genetic rearrangements. Mutational hotspots are frequently found associated with imperfect inverted repeats ("quasipalindromes" or "QPs") in man...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2017.05.007

    authors: Laranjo LT,Gross SJ,Zeiger DM,Lovett ST

    更新日期:2017-09-01 00:00:00

  • Replication stalling and heteroduplex formation within CAG/CTG trinucleotide repeats by mismatch repair.

    abstract::Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized st...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2016.03.002

    authors: Viterbo D,Michoud G,Mosbach V,Dujon B,Richard GF

    更新日期:2016-06-01 00:00:00

  • The role of the SWI/SNF chromatin remodelling complex in the response to DNA double strand breaks.

    abstract::Mammalian cells possess multiple closely related SWI/SNF chromatin remodelling complexes. These complexes have been implicated in the cellular response to DNA double strand breaks (DSBs). Evidence suggests that SWI/SNF complexes contribute to successful repair via both the homologous recombination and non-homologous e...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2020.102919

    authors: Harrod A,Lane KA,Downs JA

    更新日期:2020-09-01 00:00:00

  • The splicing component ISY1 regulates APE1 in base excision repair.

    abstract::The integrity of cellular genome is continuously challenged by endogenous and exogenous DNA damaging agents. If DNA damage is not removed in a timely fashion the replisome may stall at DNA lesions, causing fork collapse and genetic instability. Base excision DNA repair (BER) is the most important pathway for the remov...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2019.102769

    authors: Jaiswal AS,Williamson EA,Srinivasan G,Kong K,Lomelino CL,McKenna R,Walter C,Sung P,Narayan S,Hromas R

    更新日期:2020-02-01 00:00:00

  • Measurement of DNA base and nucleotide excision repair activities in mammalian cells and tissues using the comet assay--a methodological overview.

    abstract::There is an increasing demand for phenotyping assays in the field of human functional genetics. DNA repair activity is representative of this functional approach, being seen as a valuable biomarker related to cancer risk. Repair activity is evaluated by incubating a cell extract with a DNA substrate containing lesions...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2013.07.011

    authors: Azqueta A,Langie SA,Slyskova J,Collins AR

    更新日期:2013-11-01 00:00:00

  • Mechanism of cell killing after ionizing radiation by a dominant negative DNA polymerase beta.

    abstract::Several types of DNA lesion are induced after ionizing irradiation (IR) of which double strand breaks (DSBs) are expected to be the most lethal, although single strand breaks (SSBs) and DNA base damages are quantitatively in the majority. Proteins of the base excision repair (BER) pathway repair these numerous lesions...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2008.11.008

    authors: Neijenhuis S,Verwijs-Janssen M,Kasten-Pisula U,Rumping G,Borgmann K,Dikomey E,Begg AC,Vens C

    更新日期:2009-03-01 00:00:00

  • Novel mutator mutants of E. coli nrdAB ribonucleotide reductase: insight into allosteric regulation and control of mutation rates.

    abstract::Ribonucleotide reductase (RNR) is the enzyme critically responsible for the production of the 5'-deoxynucleoside-triphosphates (dNTPs), the direct precursors for DNA synthesis. The dNTP levels are tightly controlled to permit high efficiency and fidelity of DNA synthesis. Much of this control occurs at the level of th...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2012.02.001

    authors: Ahluwalia D,Bienstock RJ,Schaaper RM

    更新日期:2012-05-01 00:00:00

  • Yeast genes involved in cadmium tolerance: Identification of DNA replication as a target of cadmium toxicity.

    abstract::Cadmium (Cd(2+)) is a ubiquitous environmental pollutant and human carcinogen. The molecular basis of its toxicity remains unclear. Here, to identify the landscape of genes and cell functions involved in cadmium resistance, we have screened the Saccharomyces cerevisiae deletion collection for mutants sensitive to cadm...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2008.04.005

    authors: Serero A,Lopes J,Nicolas A,Boiteux S

    更新日期:2008-08-02 00:00:00

  • AHNAK interacts with the DNA ligase IV-XRCC4 complex and stimulates DNA ligase IV-mediated double-stranded ligation.

    abstract::AHNAK is a high molecular weight protein that is under-expressed in several radiosensitive neuroblastoma cell lines. Using immunoaffinity purification or purified proteins, we show that AHNAK interacts specifically with the DNA ligase IV-XRCC4 complex, a complex that functions in DNA non-homologous end-joining. Furthe...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2003.11.001

    authors: Stiff T,Shtivelman E,Jeggo P,Kysela B

    更新日期:2004-03-04 00:00:00

  • Paradoxical roles of cyclin D1 in DNA stability.

    abstract::Maintenance of DNA integrity is vital for all of the living organisms. Consequence of DNA damaging ranges from, introducing harmless synonymous mutations, to causing disease-associated mutations, genome instability, and cell death. A cell cycle protein cyclin D1 is an established cancer-driving protein. However, contr...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2016.04.011

    authors: Jirawatnotai S,Sittithumcharee G

    更新日期:2016-06-01 00:00:00

  • Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research.

    abstract::Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for ...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2014.03.009

    authors: Nagel ZD,Chaim IA,Samson LD

    更新日期:2014-07-01 00:00:00

  • The mechanism of human tyrosyl-DNA phosphodiesterase 1 in the cleavage of AP site and its synthetic analogs.

    abstract::The mechanism of hydrolysis of the apurinic/apyrimidinic (AP) site and its synthetic analogs by using tyrosyl-DNA phosphodiesterase 1 (Tdp1) was analyzed. Tdp1 catalyzes the cleavage of AP site and the synthetic analog of the AP site, 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran (THF), in DNA by hydrolysis of the phosph...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2013.09.008

    authors: Lebedeva NA,Rechkunova NI,Ishchenko AA,Saparbaev M,Lavrik OI

    更新日期:2013-12-01 00:00:00

  • Nucleotide excision repair in chronic neurodegenerative diseases.

    abstract::Impaired DNA repair involving the nucleotide excision repair (NER)/transcription-coupled repair (TCR) pathway cause human pathologies associated with severe neurological symptoms. These clinical observations suggest that defective NER/TCR might also play a critical role in chronic neurodegenerative disorders (ND), suc...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2013.04.009

    authors: Sepe S,Payan-Gomez C,Milanese C,Hoeijmakers JH,Mastroberardino PG

    更新日期:2013-08-01 00:00:00

  • High levels of oxidatively generated DNA damage 8,5'-cyclo-2'-deoxyadenosine accumulate in the brain tissues of xeroderma pigmentosum group A gene-knockout mice.

    abstract::Xeroderma pigmentosum (XP) is a genetic disorder associated with defects in nucleotide excision repair, a pathway that eliminates a wide variety of helix-distorting DNA lesions, including ultraviolet-induced pyrimidine dimers. In addition to skin diseases in sun-exposed areas, approximately 25% of XP patients develop ...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2019.04.004

    authors: Mori T,Nakane H,Iwamoto T,Krokidis MG,Chatgilialoglu C,Tanaka K,Kaidoh T,Hasegawa M,Sugiura S

    更新日期:2019-08-01 00:00:00

  • Novel role of tyrosine in catalysis by human AP endonuclease 1.

    abstract::Apurinic/apyrimidinic endonuclease (AP endo, HAP1) recognizes abasic sites in ds DNA and makes a single nick in the backbone 5' to the abasic site. In this report we examine the roles of three conserved tyrosine residues in close proximity to the active site. We show that Tyr(128) and Tyr(269), which interact upstream...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2004.06.009

    authors: Mundle ST,Fattal MH,Melo LF,Coriolan JD,O'Regan NE,Strauss PR

    更新日期:2004-11-02 00:00:00

  • MutSα deficiency increases tolerance to DNA damage in yeast lacking postreplication repair.

    abstract::By combining mutations in DNA repair genes, important and unexpected interactions between different repair pathways can be discovered. In this study, we identified a novel link between mismatch repair (MMR) genes and postreplication repair (PRR) in Saccharomyces cerevisiae. Strains lacking Rad5 (HLTF in mammals), a pr...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2020.102870

    authors: Berg IL,Persson JO,Åström SU

    更新日期:2020-01-01 00:00:00

  • Stopped in its tracks: the RNA polymerase molecular motor as a robust sensor of DNA damage.

    abstract::DNA repair is often a complex, multi-component, multi-step process; this makes detailed kinetic analysis of the different steps of repair a challenging task using standard biochemical methods. At the same time, single-molecule methods are well-suited for extracting kinetic information despite time-averaging due to dif...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2014.02.018

    authors: Howan K,Monnet J,Fan J,Strick TR

    更新日期:2014-08-01 00:00:00

  • Proteasome inhibition suppresses DNA-dependent protein kinase activation caused by camptothecin.

    abstract::The ubiquitin-proteasome pathway plays an important role in DNA damage signaling and repair by facilitating the recruitment and activation of DNA repair factors and signaling proteins at sites of damaged chromatin. Proteasome activity is generally not thought to be required for activation of apical signaling kinases i...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2009.10.008

    authors: Sakasai R,Teraoka H,Tibbetts RS

    更新日期:2010-01-02 00:00:00

  • Lung cancer risk and variation in MGMT activity and sequence.

    abstract::O(6)-Alkylguanine-DNA alkyltransferase (MGMT) repairs DNA adducts that result from alkylation at the O(6) position of guanine. These lesions are mutagenic and toxic and can be produced by a variety of agents including the tobacco-specific nitrosamines, carcinogens present in cigarette smoke. Here, we review some of ou...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2007.03.022

    authors: Povey AC,Margison GP,Santibáñez-Koref MF

    更新日期:2007-08-01 00:00:00

  • A proposal: Evolution of PCNA's role as a marker of newly replicated DNA.

    abstract::Processivity clamps that hold DNA polymerases to DNA for processivity were the first proteins known to encircle the DNA duplex. At the time, polymerase processivity was thought to be the only function of ring shaped processivity clamps. But studies from many laboratories have identified numerous proteins that bind and...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2015.01.015

    authors: Georgescu R,Langston L,O'Donnell M

    更新日期:2015-05-01 00:00:00

  • Enhanced gene amplification in human cells knocked down for DNA-PKcs.

    abstract::Gene amplification, a key mechanism for oncogene activation and drug resistance in tumour cells, involves the generation and joining of DNA double-strand breaks. Amplified DNA can be carried either on intra-chromosomal arrays or on extra-chromosomal elements (double minutes). We previously showed that, in rodent cells...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2008.08.015

    authors: Salzano A,Kochiashvili N,Nergadze SG,Khoriauli L,Smirnova A,Ruiz-Herrera A,Mondello C,Giulotto E

    更新日期:2009-01-01 00:00:00

  • Characterization in vitro and in vivo of the DNA helicase encoded by Deinococcus radiodurans locus DR1572.

    abstract::Deinococcus radiodurans survives extremely high doses of ionizing and ultraviolet radiation and treatment with various DNA-damaging chemicals. As an effort to identify and characterize proteins that function in DNA repair in this organism, we have studied the protein encoded by locus DR1572. This gene is predicted to ...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2008.12.011

    authors: Cao Z,Julin DA

    更新日期:2009-05-01 00:00:00

  • Is RecG a general guardian of the bacterial genome?

    abstract::The RecG protein of Escherichia coli is a double-stranded DNA translocase that unwinds a variety of branched DNAs in vitro, including Holliday junctions, replication forks, D-loops and R-loops. Coupled with the reported pleiotropy of recG mutations, this broad range of potential targets has made it hard to pin down wh...

    journal_title:DNA repair

    pub_type: 杂志文章,评审

    doi:10.1016/j.dnarep.2009.12.014

    authors: Rudolph CJ,Upton AL,Briggs GS,Lloyd RG

    更新日期:2010-03-02 00:00:00

  • Disruption of SUMO-targeted ubiquitin ligases Slx5-Slx8/RNF4 alters RecQ-like helicase Sgs1/BLM localization in yeast and human cells.

    abstract::RecQ-like helicases are a highly conserved protein family that functions during DNA repair and, when mutated in humans, is associated with cancer and/or premature aging syndromes. The budding yeast RecQ-like helicase Sgs1 has important functions in double-strand break (DSB) repair of exogenously induced breaks, as wel...

    journal_title:DNA repair

    pub_type: 杂志文章

    doi:10.1016/j.dnarep.2014.12.004

    authors: Böhm S,Mihalevic MJ,Casal MA,Bernstein KA

    更新日期:2015-02-01 00:00:00