An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.

Abstract:

:Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to prevent premature ubiquitin chain removal and substrate escape. Here we reveal the ubiquitin-bound structure of Rpn11 from S. cerevisiae and the mechanisms for mechanochemical coupling of substrate degradation and deubiquitination. Ubiquitin binding induces a conformational switch of Rpn11's Insert-1 loop from an inactive closed state to an active β hairpin. This switch is rate-limiting for deubiquitination and strongly accelerated by mechanical substrate translocation into the AAA+ motor. Deubiquitination by Rpn11 and ubiquitin unfolding by the ATPases are in direct competition. The AAA+ motor-driven acceleration of Rpn11 is therefore important to ensure that poly-ubiquitin chains are removed only from committed substrates and fast enough to prevent their co-degradation.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Worden EJ,Dong KC,Martin A

doi

10.1016/j.molcel.2017.07.023

subject

Has Abstract

pub_date

2017-09-07 00:00:00

pages

799-811.e8

issue

5

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(17)30547-6

journal_volume

67

pub_type

杂志文章
  • Telomeres thrown for a loop.

    abstract::A remarkable paper from the de Lange lab (Wang et al., 2004) in a recent issue of Cell reveals that homologous recombination can result in the abrupt shortening of telomeres in a process that appears to involve reciprocal crossing over within the t-loop structure that protects chromosome ends. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2004.11.006

    authors: Haber JE

    更新日期:2004-11-19 00:00:00

  • Structure of the lnlB leucine-rich repeats, a domain that triggers host cell invasion by the bacterial pathogen L. monocytogenes.

    abstract::The L. monocytogenes protein lnlB activates phosphoinositide 3-kinase and induces phagocytosis in several mammalian cell types. The 1.86 A resolution X-ray crystal structure of the leucine-rich repeat domain of lnlB that is both necessary and sufficient to induce phagocytosis is presented here. The structure supports ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80234-8

    authors: Marino M,Braun L,Cossart P,Ghosh P

    更新日期:1999-12-01 00:00:00

  • RNase H and multiple RNA biogenesis factors cooperate to prevent RNA:DNA hybrids from generating genome instability.

    abstract::Genome instability, a hallmark of cancer progression, is thought to arise through DNA double strand breaks (DSBs). Studies in yeast and mammalian cells have shown that DSBs and instability can occur through RNA:DNA hybrids generated by defects in RNA elongation and splicing. We report that in yeast hybrids naturally f...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.10.017

    authors: Wahba L,Amon JD,Koshland D,Vuica-Ross M

    更新日期:2011-12-23 00:00:00

  • ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals.

    abstract::Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In t...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.04.009

    authors: Ishidate T,Ozturk AR,Durning DJ,Sharma R,Shen EZ,Chen H,Seth M,Shirayama M,Mello CC

    更新日期:2018-05-17 00:00:00

  • High-Throughput Approaches to Pinpoint Function within the Noncoding Genome.

    abstract::The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas nuclease system is a powerful tool for genome editing, and its simple programmability has enabled high-throughput genetic and epigenetic studies. These high-throughput approaches offer investigators a toolkit for functional interrogation of not...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2017.09.017

    authors: Montalbano A,Canver MC,Sanjana NE

    更新日期:2017-10-05 00:00:00

  • Phosphorylation of BRAF by AMPK impairs BRAF-KSR1 association and cell proliferation.

    abstract::BRAF is an oncogenic protein kinase that drives cell growth and proliferation through the MEK-ERK signaling pathway. BRAF inhibitors have demonstrated antitumor efficacy in melanoma therapy but have also been found to be associated with the development of cutaneous squamous cell carcinomas (cSCCs) in certain patients....

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2013.08.044

    authors: Shen CH,Yuan P,Perez-Lorenzo R,Zhang Y,Lee SX,Ou Y,Asara JM,Cantley LC,Zheng B

    更新日期:2013-10-24 00:00:00

  • Adjacent residues in the E1 initiator beta-hairpin define different roles of the beta-hairpin in Ori melting, helicase loading, and helicase activity.

    abstract::We have analyzed two residues in the helicase domain of the E1 initiator protein. These residues are part of a highly conserved structural motif, the beta-hairpin, which is present in the helicase domain of all papovavirus initiator proteins. These proteins are unique in their ability to transition from local template...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.02.009

    authors: Liu X,Schuck S,Stenlund A

    更新日期:2007-03-23 00:00:00

  • The Sjögren-Larsson syndrome gene encodes a hexadecenal dehydrogenase of the sphingosine 1-phosphate degradation pathway.

    abstract::Sphingosine 1-phosphate (S1P) functions not only as a bioactive lipid molecule, but also as an important intermediate of the sole sphingolipid-to-glycerolipid metabolic pathway. However, the precise reactions and the enzymes involved in this pathway remain unresolved. We report here that yeast HFD1 and the Sjögren-Lar...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.04.033

    authors: Nakahara K,Ohkuni A,Kitamura T,Abe K,Naganuma T,Ohno Y,Zoeller RA,Kihara A

    更新日期:2012-05-25 00:00:00

  • A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase.

    abstract::Plant pattern recognition receptors (PRRs) perceive microbial and endogenous molecular patterns to activate immune signaling. The cytoplasmic kinase BIK1 acts downstream of multiple PRRs as a rate-limiting component, whose phosphorylation and accumulation are central to immune signal propagation. Previous work identif...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2017.12.026

    authors: Wang J,Grubb LE,Wang J,Liang X,Li L,Gao C,Ma M,Feng F,Li M,Li L,Zhang X,Yu F,Xie Q,Chen S,Zipfel C,Monaghan J,Zhou JM

    更新日期:2018-02-01 00:00:00

  • Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

    abstract::Fidaxomicin is an antibacterial drug in clinical use for treatment of Clostridium difficile diarrhea. The active ingredient of fidaxomicin, lipiarmycin A3 (Lpm), functions by inhibiting bacterial RNA polymerase (RNAP). Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.02.026

    authors: Lin W,Das K,Degen D,Mazumder A,Duchi D,Wang D,Ebright YW,Ebright RY,Sineva E,Gigliotti M,Srivastava A,Mandal S,Jiang Y,Liu Y,Yin R,Zhang Z,Eng ET,Thomas D,Donadio S,Zhang H,Zhang C,Kapanidis AN,Ebright RH

    更新日期:2018-04-05 00:00:00

  • The BCL-2 family reunion.

    abstract::B cell CLL/lymphoma-2 (BCL-2) and its relatives comprise the BCL-2 family of proteins, which were originally characterized with respect to their roles in controlling outer mitochondrial membrane integrity and apoptosis. Current observations expand BCL-2 family function to include numerous cellular pathways. Here we wi...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2010.01.025

    authors: Chipuk JE,Moldoveanu T,Llambi F,Parsons MJ,Green DR

    更新日期:2010-02-12 00:00:00

  • FANCM and FAAP24 function in ATR-mediated checkpoint signaling independently of the Fanconi anemia core complex.

    abstract::The Fanconi anemia (FA) pathway is implicated in DNA repair and cancer predisposition. Central to this pathway is the FA core complex, which is targeted to chromatin by FANCM and FAAP24 following replication stress. Here we show that FANCM and FAAP24 interact with the checkpoint protein HCLK2 independently of the FA c...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2008.10.014

    authors: Collis SJ,Ciccia A,Deans AJ,Horejsí Z,Martin JS,Maslen SL,Skehel JM,Elledge SJ,West SC,Boulton SJ

    更新日期:2008-11-07 00:00:00

  • Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation.

    abstract::MYOD-directed fibroblast trans-differentiation into skeletal muscle provides a unique model to investigate how one transcription factor (TF) reconfigures the three-dimensional chromatin architecture to control gene expression, which is otherwise achieved by the combinatorial activities of multiple TFs. Integrative ana...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.07.036

    authors: Dall'Agnese A,Caputo L,Nicoletti C,di Iulio J,Schmitt A,Gatto S,Diao Y,Ye Z,Forcato M,Perera R,Bicciato S,Telenti A,Ren B,Puri PL

    更新日期:2019-11-07 00:00:00

  • Liquid Active Zones for Controlling the Phases of Synaptic Transmission.

    abstract::Wu et al. (2019) establish that the active zone proteins RIM and RIM-BP undergo liquid-liquid phase separation to tether Ca2+ channels. This important finding sets a new framework to study assembly and function of the presynaptic nerve terminal. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2019.02.020

    authors: Emperador-Melero J,Kaeser PS

    更新日期:2019-03-07 00:00:00

  • XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks.

    abstract::Using genome-wide approaches, we have elucidated the regulatory circuitry governed by the XBP1 transcription factor, a key effector of the mammalian unfolded protein response (UPR), in skeletal muscle and secretory cells. We identified a core group of genes involved in constitutive maintenance of ER function in all ce...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.06.011

    authors: Acosta-Alvear D,Zhou Y,Blais A,Tsikitis M,Lents NH,Arias C,Lennon CJ,Kluger Y,Dynlacht BD

    更新日期:2007-07-06 00:00:00

  • RRM Transcription Factors Interact with NLRs and Regulate Broad-Spectrum Blast Resistance in Rice.

    abstract::Nucleotide-binding site leucine-rich repeat (NLR) receptors perceive pathogen effectors and trigger plant immunity. However, the mechanisms underlying NLR-triggered defense responses remain obscure. The recently discovered Pigm locus in rice encodes a cluster of NLRs, including PigmR, which confers broad-spectrum resi...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.03.013

    authors: Zhai K,Deng Y,Liang D,Tang J,Liu J,Yan B,Yin X,Lin H,Chen F,Yang D,Xie Z,Liu JY,Li Q,Zhang L,He Z

    更新日期:2019-06-06 00:00:00

  • Autophagic Degradation of the 26S Proteasome Is Mediated by the Dual ATG8/Ubiquitin Receptor RPN10 in Arabidopsis.

    abstract::Autophagic turnover of intracellular constituents is critical for cellular housekeeping, nutrient recycling, and various aspects of growth and development in eukaryotes. Here we show that autophagy impacts the other major degradative route involving the ubiquitin-proteasome system by eliminating 26S proteasomes, a pro...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.04.023

    authors: Marshall RS,Li F,Gemperline DC,Book AJ,Vierstra RD

    更新日期:2015-06-18 00:00:00

  • The Promise of Proteomics for the Study of ADP-Ribosylation.

    abstract::ADP-ribosylation is a post-translational modification where single units (mono-ADP-ribosylation) or polymeric chains (poly-ADP-ribosylation) of ADP-ribose are conjugated to proteins by ADP-ribosyltransferases. This post-translational modification and the ADP-ribosyltransferases (also known as PARPs) responsible for it...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.06.012

    authors: Daniels CM,Ong SE,Leung AK

    更新日期:2015-06-18 00:00:00

  • Long noncoding RNAs add another layer to pre-mRNA splicing regulation.

    abstract::In this issue of Molecular Cell, Tripathi and coworkers (Tripathi et al., 2010) decode some of the functions of a long noncoding RNA MALAT1. They provide evidence that MALAT1 regulates alternative splicing by controlling the activity of the SR protein family of splicing factors. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2010.09.003

    authors: Ankö ML,Neugebauer KM

    更新日期:2010-09-24 00:00:00

  • A major conformational change in p97 AAA ATPase upon ATP binding.

    abstract::AAA ATPases play central roles in cellular activities. The ATPase p97, a prototype of this superfamily, participates in organelle membrane fusion. Cryoelectron microscopy and single-particle analysis revealed that a major conformational change of p97 during the ATPase cycle occurred upon nucleotide binding and not dur...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00144-1

    authors: Rouiller I,Butel VM,Latterich M,Milligan RA,Wilson-Kubalek EM

    更新日期:2000-12-01 00:00:00

  • A global profile of germline gene expression in C. elegans.

    abstract::We used DNA microarrays to profile gene expression patterns in the C. elegans germline and identified 1416 germline-enriched transcripts that define three groups. The sperm-enriched group contains an unusually large number of protein kinases and phosphatases. The oocyte-enriched group includes potentially new componen...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00059-9

    authors: Reinke V,Smith HE,Nance J,Wang J,Van Doren C,Begley R,Jones SJ,Davis EB,Scherer S,Ward S,Kim SK

    更新日期:2000-09-01 00:00:00

  • Coupling of transcription with alternative splicing: RNA pol II promoters modulate SF2/ASF and 9G8 effects on an exonic splicing enhancer.

    abstract::Alternative mRNA splicing of the fibronectin EDI exon is controlled by a purine-rich exonic splicing enhancer (ESE), postulated as a binding site for SR proteins. By using a transient expression alternative splicing assay combined with promoter swapping, we have demonstrated that the promoter can also control EDI spli...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80372-x

    authors: Cramer P,Cáceres JF,Cazalla D,Kadener S,Muro AF,Baralle FE,Kornblihtt AR

    更新日期:1999-08-01 00:00:00

  • Negative regulation of the mammalian UV response by Myc through association with Miz-1.

    abstract::The Myc oncoprotein represses initiator-dependent transcription through the POZ domain transcription factor Miz-1. We now show that transactivation by Miz-1 is negatively regulated by association with topoisomerase II binding protein (TopBP1); UV irradiation downregulates expression of TopBP1 and releases Miz-1. Miz-1...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(02)00633-0

    authors: Herold S,Wanzel M,Beuger V,Frohme C,Beul D,Hillukkala T,Syvaoja J,Saluz HP,Haenel F,Eilers M

    更新日期:2002-09-01 00:00:00

  • The Haystack Is Full of Needles: Technology Rescues Sugars!

    abstract::The recent paper by Stadlmann et al. (2017) provides a novel algorithm for glycoproteomics in which complex glycopeptides can be identified in complex mixtures to aid in characterizing both the site of glycosylation and the glycan structure. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2017.11.024

    authors: Cummings RD

    更新日期:2017-12-07 00:00:00

  • Suv39h-dependent H3K9me3 marks intact retrotransposons and silences LINE elements in mouse embryonic stem cells.

    abstract::Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP sequencing in mouse embryonic stem cells (ESCs). Refined bioinformat...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2014.05.029

    authors: Bulut-Karslioglu A,De La Rosa-Velázquez IA,Ramirez F,Barenboim M,Onishi-Seebacher M,Arand J,Galán C,Winter GE,Engist B,Gerle B,O'Sullivan RJ,Martens JH,Walter J,Manke T,Lachner M,Jenuwein T

    更新日期:2014-07-17 00:00:00

  • Syndecan-4 regulates subcellular localization of mTOR Complex2 and Akt activation in a PKCalpha-dependent manner in endothelial cells.

    abstract::Mammalian target of rapamycin (mTOR) activity is regulated by assembly of two functionally distinct complexes, mTORC1 and mTORC2. In syndecan-4 (S4) null endothelial cells, mTORC2 activity is reduced, resulting in decreased Akt activation, while mTORC1 activity is increased. Levels of rictor, mLST8, and mSin-1 are unc...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2008.09.010

    authors: Partovian C,Ju R,Zhuang ZW,Martin KA,Simons M

    更新日期:2008-10-10 00:00:00

  • A viral mechanism for remodeling chromatin structure in G0 cells.

    abstract::Small DNA viruses force quiescent cells to reenter the cell cycle in order to replicate their DNA. We report here that the adenovirus E1A protein creates an S phase environment in quiescent cells by overcoming the nucleosomal repression of E2F-targeted genes. These genes are surrounded by Lys-9-methylated H3 histones,...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00225-9

    authors: Ghosh MK,Harter ML

    更新日期:2003-07-01 00:00:00

  • Odilorhabdins, Antibacterial Agents that Cause Miscoding by Binding at a New Ribosomal Site.

    abstract::Growing resistance of pathogenic bacteria and shortage of antibiotic discovery platforms challenge the use of antibiotics in the clinic. This threat calls for exploration of unconventional sources of antibiotics and identification of inhibitors able to eradicate resistant bacteria. Here we describe a different class o...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.03.001

    authors: Pantel L,Florin T,Dobosz-Bartoszek M,Racine E,Sarciaux M,Serri M,Houard J,Campagne JM,de Figueiredo RM,Midrier C,Gaudriault S,Givaudan A,Lanois A,Forst S,Aumelas A,Cotteaux-Lautard C,Bolla JM,Vingsbo Lundberg C,Huseby

    更新日期:2018-04-05 00:00:00

  • Phosphatidic Acid Signals via the Hippo Pathway.

    abstract::In this issue of Molecular Cell, Han et al. (2018) show that phosphatidic acid inhibits the action of the LATS kinases, key mediators of Hippo pathway signaling, which leads to an increase in the nuclear activity of the transcriptional regulator YAP. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2018.10.004

    authors: Stampouloglou E,Varelas X

    更新日期:2018-10-18 00:00:00

  • A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions.

    abstract::Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.10.037

    authors: Cheung R,Insigne KD,Yao D,Burghard CP,Wang J,Hsiao YE,Jones EM,Goodman DB,Xiao X,Kosuri S

    更新日期:2019-01-03 00:00:00