A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada.

Abstract:

:The transcriptional activity of many sequence-specific DNA binding proteins is directly regulated by posttranslational covalent modification. Although this form of regulation was first described nearly two decades ago, it remains poorly understood at a mechanistic level. The prototype for a transcription factor controlled by posttranslational modification is E. coli Ada protein, a chemosensor that both repairs methylation damage in DNA and coordinates the resistance response to genotoxic methylating agents. Ada repairs methyl phosphotriester lesions in DNA by transferring the aberrant methyl group to one of its own cysteine residues; this site-specific methylation enhances tremendously the DNA binding activity of the protein, thereby enabling it to activate a methylation-resistance regulon. Here, we report solution and X-ray structures of the Cys-methylated chemosensor domain of Ada bound to DNA. The structures reveal that both phosphotriester repair and methylation-dependent transcriptional activation function through a zinc- and methylation-dependent electrostatic switch.

journal_name

Mol Cell

journal_title

Molecular cell

authors

He C,Hus JC,Sun LJ,Zhou P,Norman DP,Dötsch V,Wei H,Gross JD,Lane WS,Wagner G,Verdine GL

doi

10.1016/j.molcel.2005.08.013

subject

Has Abstract

pub_date

2005-10-07 00:00:00

pages

117-29

issue

1

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(05)01555-8

journal_volume

20

pub_type

杂志文章
  • Unambiguous identification of miRNA:target site interactions by different types of ligation reactions.

    abstract::To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore i...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2014.03.049

    authors: Grosswendt S,Filipchyk A,Manzano M,Klironomos F,Schilling M,Herzog M,Gottwein E,Rajewsky N

    更新日期:2014-06-19 00:00:00

  • A transcriptional activator is part of an SCF ubiquitin ligase to control degradation of its cofactors.

    abstract::Multisubunit protein complexes pose a challenge to the coordinated regulation of individual components. We show how the yeast transactivating factor Met4 functions as a component of the SCF(Met30) ubiquitin ligase to synchronize its own activity with cofactor assembly. Cells maintain Met4 in a dormant state by a regul...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2010.11.018

    authors: Ouni I,Flick K,Kaiser P

    更新日期:2010-12-22 00:00:00

  • The Biogenesis, Functions, and Challenges of Circular RNAs.

    abstract::Covalently closed circular RNAs (circRNAs) are produced by precursor mRNA back-splicing of exons of thousands of genes in eukaryotes. circRNAs are generally expressed at low levels and often exhibit cell-type-specific and tissue-specific patterns. Recent studies have shown that their biogenesis requires spliceosomal m...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2018.06.034

    authors: Li X,Yang L,Chen LL

    更新日期:2018-08-02 00:00:00

  • Structural basis of microtubule plus end tracking by XMAP215, CLIP-170, and EB1.

    abstract::Microtubule plus end binding proteins (+TIPs) localize to the dynamic plus ends of microtubules, where they stimulate microtubule growth and recruit signaling molecules. Three main +TIP classes have been identified (XMAP215, EB1, and CLIP-170), but whether they act upon microtubule plus ends through a similar mechanis...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.07.023

    authors: Slep KC,Vale RD

    更新日期:2007-09-21 00:00:00

  • Destabilizing LSD1 by Jade-2 promotes neurogenesis: an antibraking system in neural development.

    abstract::Histone H3K4 demethylase LSD1 plays an important role in stem cell biology, especially in the maintenance of the silencing of differentiation genes. However, how the function of LSD1 is regulated and the differentiation genes are derepressed are not understood. Here, we report that elimination of LSD1 promotes embryon...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2014.06.006

    authors: Han X,Gui B,Xiong C,Zhao L,Liang J,Sun L,Yang X,Yu W,Si W,Yan R,Yi X,Zhang D,Li W,Li L,Yang J,Wang Y,Sun YE,Zhang D,Meng A,Shang Y

    更新日期:2014-08-07 00:00:00

  • The ER-Localized Transmembrane Protein TMEM39A/SUSR2 Regulates Autophagy by Controlling the Trafficking of the PtdIns(4)P Phosphatase SAC1.

    abstract::TMEM39A, encoding an ER-localized transmembrane protein, is a susceptibility locus for multiple autoimmune diseases. The molecular function of TMEM39A remains completely unknown. Here we demonstrated that TMEM39A, also called SUSR2, modulates autophagy activity by regulating the spatial distribution and levels of PtdI...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.10.035

    authors: Miao G,Zhang Y,Chen D,Zhang H

    更新日期:2020-02-06 00:00:00

  • A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing.

    abstract::Epigenetic silencing of transposons by Piwi-interacting RNAs (piRNAs) constitutes an RNA-based genome defense mechanism. Piwi endonuclease action amplifies the piRNA pool by generating new piRNAs from target transcripts by a poorly understood mechanism. Here, we identified mouse Fkbp6 as a factor in this biogenesis pa...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.07.019

    authors: Xiol J,Cora E,Koglgruber R,Chuma S,Subramanian S,Hosokawa M,Reuter M,Yang Z,Berninger P,Palencia A,Benes V,Penninger J,Sachidanandam R,Pillai RS

    更新日期:2012-09-28 00:00:00

  • Regulated Proteolysis of MutSγ Controls Meiotic Crossing Over.

    abstract::Crossover recombination is essential for accurate chromosome segregation during meiosis. The MutSγ complex, Msh4-Msh5, facilitates crossing over by binding and stabilizing nascent recombination intermediates. We show that these activities are governed by regulated proteolysis. MutSγ is initially inactive for crossing ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.02.001

    authors: He W,Rao HBDP,Tang S,Bhagwat N,Kulkarni DS,Ma Y,Chang MAW,Hall C,Bragg JW,Manasca HS,Baker C,Verhees GF,Ranjha L,Chen X,Hollingsworth NM,Cejka P,Hunter N

    更新日期:2020-04-02 00:00:00

  • Blast from the Past: Reassessing Forgotten Translation Inhibitors, Antibiotic Selectivity, and Resistance Mechanisms to Aid Drug Development.

    abstract::Protein synthesis is a major target within the bacterial cell for antibiotics. Investigations into ribosome-targeting antibiotics have provided much needed functional and structural insight into their mechanism of action. However, the increasing prevalence of multi-drug-resistant bacteria has limited the utility of ou...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2015.10.019

    authors: Arenz S,Wilson DN

    更新日期:2016-01-07 00:00:00

  • Facultative heterochromatin: is there a distinctive molecular signature?

    abstract::The Latin word "facultas" literally means "opportunity." Facultative heterochromatin (fHC) then designates genomic regions in the nucleus of a eukaryotic cell that have the opportunity to adopt open or compact conformations within temporal and spatial contexts. This review focuses on the molecular and functional aspec...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2007.09.011

    authors: Trojer P,Reinberg D

    更新日期:2007-10-12 00:00:00

  • Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats.

    abstract::Heterochromatin formation is generally thought to result in transcriptional repression of target loci. However, RNAi-mediated heterochromatin assembly requires RNA polymerase II (Pol II) transcription. The mechanism facilitating Pol II accessibility to heterochromatin is unknown. We show that the fission yeast Epe1, a...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.05.010

    authors: Zofall M,Grewal SI

    更新日期:2006-06-09 00:00:00

  • EM visualization of transcription by RNA polymerase II: downstream termination requires a poly(A) signal but not transcript cleavage.

    abstract::We have used EM visualization of active genes on plasmid vectors in Xenopus oocyte nuclei to investigate the relationship between poly(A) signals and RNA polymerase II transcription termination. Although a functional poly(A) signal is required for efficient termination, cotranscriptional RNA cleavage at the poly(A) si...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80465-7

    authors: Osheim YN,Proudfoot NJ,Beyer AL

    更新日期:1999-03-01 00:00:00

  • Caspase-2-mediated cleavage of Mdm2 creates a p53-induced positive feedback loop.

    abstract::Caspase-2 is an evolutionarily conserved caspase, yet its biological function and cleavage targets are poorly understood. Caspase-2 is activated by the p53 target gene product PIDD (also known as LRDD) in a complex called the Caspase-2-PIDDosome. We show that PIDD expression promotes growth arrest and chemotherapy res...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.06.012

    authors: Oliver TG,Meylan E,Chang GP,Xue W,Burke JR,Humpton TJ,Hubbard D,Bhutkar A,Jacks T

    更新日期:2011-07-08 00:00:00

  • The little elongation complex functions at initiation and elongation phases of snRNA gene transcription.

    abstract::The small nuclear RNA (snRNA) genes have been widely used as a model system for understanding transcriptional regulation due to the unique aspects of their promoter structure, selectivity for either RNA polymerase (Pol) II or III, and because of their unique mechanism of termination that is tightly linked with the pro...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2013.07.003

    authors: Hu D,Smith ER,Garruss AS,Mohaghegh N,Varberg JM,Lin C,Jackson J,Gao X,Saraf A,Florens L,Washburn MP,Eissenberg JC,Shilatifard A

    更新日期:2013-08-22 00:00:00

  • Lysyl Oxidase 3 Is a Dual-Specificity Enzyme Involved in STAT3 Deacetylation and Deacetylimination Modulation.

    abstract::In mammalian cells, histone deacetylase (HDAC) and Sirtuin (SIRT) are two families responsible for removing acetyl groups from acetylated proteins. Here, we describe protein deacetylation coupled with deacetylimination as a function of lysyl oxidase (LOX) family members. LOX-like 3 (Loxl3) associates with Stat3 in the...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2016.12.002

    authors: Ma L,Huang C,Wang XJ,Xin DE,Wang LS,Zou QC,Zhang YS,Tan MD,Wang YM,Zhao TC,Chatterjee D,Altura RA,Wang C,Xu YS,Yang JH,Fan YS,Han BH,Si J,Zhang X,Cheng J,Chang Z,Chin YE

    更新日期:2017-01-19 00:00:00

  • Replicational Dilution of H3K27me3 in Mammalian Cells and the Role of Poised Promoters.

    abstract::Polycomb repressive complex 2 (PRC2) places H3K27me3 at developmental genes and is causally implicated in keeping bivalent genes silent. It is unclear if that silence requires minimum H3K27me3 levels and how the mark transmits faithfully across mammalian somatic cell generations. Mouse intestinal cells lacking EZH2 me...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.01.017

    authors: Jadhav U,Manieri E,Nalapareddy K,Madha S,Chakrabarti S,Wucherpfennig K,Barefoot M,Shivdasani RA

    更新日期:2020-04-02 00:00:00

  • Reversible SUMOylation of TBL1-TBLR1 regulates β-catenin-mediated Wnt signaling.

    abstract::Dysregulation of Wnt signaling has been implicated in tumorigenesis. The role of Transducin β-like proteins TBL1-TBLR1 in the promotion of Wnt/β-catenin-mediated oncogenesis has recently been emphasized; however, the molecular basis of activation of Wnt signaling by the corepressor TBL1-TBLR1 is incompletely understoo...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.05.027

    authors: Choi HK,Choi KC,Yoo JY,Song M,Ko SJ,Kim CH,Ahn JH,Chun KH,Yook JI,Yoon HG

    更新日期:2011-07-22 00:00:00

  • The kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with the yeast RasGAP neurofibromin homologs Ira1 and Ira2.

    abstract::The G protein-coupled receptor Gpr1 and associated Galpha subunit Gpa2 govern dimorphic transitions in response to extracellular nutrients by signaling coordinately with Ras to activate adenylyl cyclase in the yeast Saccharomyces cerevisiae. Gpa2 forms a protein complex with the kelch Gbeta mimic subunits Gpb1/2, and ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.05.011

    authors: Harashima T,Anderson S,Yates JR 3rd,Heitman J

    更新日期:2006-06-23 00:00:00

  • Diabetes mutations delineate an atypical POU domain in HNF-1alpha.

    abstract::Mutations in Hnf-1alpha are the most common Mendelian cause of diabetes mellitus. To elucidate the molecular function of a mutational hotspot, we cocrystallized human HNF-1alpha 83-279 with a high-affinity promoter and solved the structure of the complex. Two identical protein molecules are bound to the promoter. Each...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(02)00704-9

    authors: Chi YI,Frantz JD,Oh BC,Hansen L,Dhe-Paganon S,Shoelson SE

    更新日期:2002-11-01 00:00:00

  • Y14 and hUpf3b form an NMD-activating complex.

    abstract::Messenger RNAs with premature translation termination codons (PTCs) are degraded by nonsense-mediated mRNA decay (NMD). In mammals, PTCs are discriminated from physiological stop codons by a process thought to involve the splicing-dependent deposition of an exon junction complex (EJC), EJC-mediated recruitment of Upf3...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00142-4

    authors: Gehring NH,Neu-Yilik G,Schell T,Hentze MW,Kulozik AE

    更新日期:2003-04-01 00:00:00

  • Control of Glucocorticoid Receptor Levels by PTEN Establishes a Failsafe Mechanism for Tumor Suppression.

    abstract::The PTEN tumor suppressor controls cell death and survival by regulating functions of various molecular targets. While the role of PTEN lipid-phosphatase activity on PtdIns(3,4,5)P3 and inhibition of PI3K pathway is well characterized, the biological relevance of PTEN protein-phosphatase activity remains undefined. He...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.09.027

    authors: Yip HYK,Chee A,Ang CS,Shin SY,Ooms LM,Mohammadi Z,Phillips WA,Daly RJ,Cole TJ,Bronson RT,Nguyen LK,Tiganis T,Hobbs RM,McLean CA,Mitchell CA,Papa A

    更新日期:2020-10-15 00:00:00

  • Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway.

    abstract::mRNAs form ribonucleoprotein complexes (mRNPs) by association with proteins that are crucial for mRNA metabolism. While the mRNP proteome has been well characterized, little is known about mRNP organization. Using a single-molecule approach, we show that mRNA conformation changes depending on its cellular localization...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.10.010

    authors: Adivarahan S,Livingston N,Nicholson B,Rahman S,Wu B,Rissland OS,Zenklusen D

    更新日期:2018-11-15 00:00:00

  • H2AX prevents DNA breaks from progressing to chromosome breaks and translocations.

    abstract::Histone H2AX promotes DNA double-strand break (DSB) repair and immunoglobulin heavy chain (IgH) class switch recombination (CSR) in B-lymphocytes. CSR requires activation-induced cytidine deaminase (AID) and involves joining of DSB intermediates by end joining. We find that AID-dependent IgH locus chromosome breaks oc...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.01.005

    authors: Franco S,Gostissa M,Zha S,Lombard DB,Murphy MM,Zarrin AA,Yan C,Tepsuporn S,Morales JC,Adams MM,Lou Z,Bassing CH,Manis JP,Chen J,Carpenter PB,Alt FW

    更新日期:2006-01-20 00:00:00

  • MicroRNAs cross the line: the battle for mRNA stability enters the coding sequence.

    abstract::A study in this issue of Molecular Cell (Elcheva et al., 2009) shows the inherent instability of the betaTrCP1 mRNA to be caused by microRNA-183 targeting the coding sequence; interestingly, this action is directly opposed by the RNA-binding protein CRD-BP. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2009.07.006

    authors: Nielsen AF,Gloggnitzer J,Martinez J

    更新日期:2009-07-31 00:00:00

  • Methylation of Histone H3K79 by Dot1L Requires Multiple Contacts with the Ubiquitinated Nucleosome.

    abstract::Cryo-EM structures of Dot1L in complex with a ubiquitinated nucleosome provide the long-sought-after molecular mechanism of Dot1L-mediated methylation of lysine 79 in histone H3 and explain crosstalk with histone H2B ubiquitination. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2019.05.013

    authors: Zhang Y,Kutateladze TG

    更新日期:2019-06-06 00:00:00

  • Linking differential chromatin loops to transcriptional decisions.

    abstract::GATA-1 and GATA-2 control proliferation and differentiation of hematopoietic progenitor cells via transcriptional regulation. In this issue of Molecular Cell, Jing et al. (2008) demonstrate that GATA factor exchange on the Kit locus directs a transcriptional switch by reconfiguring chromatin loops. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2008.01.008

    authors: Apostolou E,Thanos D

    更新日期:2008-02-01 00:00:00

  • A structurally unique E2-binding domain activates ubiquitination by the ERAD E2, Ubc7p, through multiple mechanisms.

    abstract::Cue1p is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates Ubc7p via unknown mechanisms. We have now determined the crystal str...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2013.04.004

    authors: Metzger MB,Liang YH,Das R,Mariano J,Li S,Li J,Kostova Z,Byrd RA,Ji X,Weissman AM

    更新日期:2013-05-23 00:00:00

  • Crystal structure of the PP2A phosphatase activator: implications for its PP2A-specific PPIase activity.

    abstract::PTPA, an essential and specific activator of protein phosphatase 2A (PP2A), functions as a peptidyl prolyl isomerase (PPIase). We present here the crystal structures of human PTPA and of the two yeast orthologs (Ypa1 and Ypa2), revealing an all alpha-helical protein fold that is radically different from other PPIases....

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.07.008

    authors: Leulliot N,Vicentini G,Jordens J,Quevillon-Cheruel S,Schiltz M,Barford D,van Tilbeurgh H,Goris J

    更新日期:2006-08-04 00:00:00

  • SLX4IP Antagonizes Promiscuous BLM Activity during ALT Maintenance.

    abstract::Cancer cells acquire unlimited proliferative capacity by either re-expressing telomerase or inducing alternative lengthening of telomeres (ALT), which relies on telomere recombination. Here, we show that ALT recombination requires coordinate regulation of the SMX and BTR complexes to ensure the appropriate balance of ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.07.010

    authors: Panier S,Maric M,Hewitt G,Mason-Osann E,Gali H,Dai A,Labadorf A,Guervilly JH,Ruis P,Segura-Bayona S,Belan O,Marzec P,Gaillard PL,Flynn RL,Boulton SJ

    更新日期:2019-10-03 00:00:00

  • A Calreticulin Tail: C-terminal Mutants of Calreticulin Allow Cancer Cells to Evade Phagocytosis.

    abstract::In the current issue of Molecular Cell, Liu et al. (2020) show that the secretion of cancer-linked forms of mutant calreticulin allow cancer cells to escape protective immune responses induced by chemotherapeutic and immunotherapeutic drugs, thereby promoting tumor growth. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2020.01.024

    authors: Kaur A,Raghavan M

    更新日期:2020-02-20 00:00:00