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Gritti I, Basso V, Rinchai D, Corigliano F, Pivetti S, Gaviraghi M, Rosano D, Mazza D, Barozzi S, Roncador M, Parmigiani G, Legube G, Parazzoli D, Cittaro D, Bedognetti D, Mondino A, Segalla S, Tonon G. Loss of ribonuclease DIS3 hampers genome integrity in myeloma by disrupting DNA:RNA hybrid metabolism. EMBO J 2022; 41:e108040. [PMID: 36215697 PMCID: PMC9670201 DOI: 10.15252/embj.2021108040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 07/25/2022] [Accepted: 09/23/2022] [Indexed: 01/13/2023] Open
Abstract
The ribonuclease DIS3 is one of the most frequently mutated genes in the hematological cancer multiple myeloma, yet the basis of its tumor suppressor function in this disease remains unclear. Herein, exploiting the TCGA dataset, we found that DIS3 plays a prominent role in the DNA damage response. DIS3 inactivation causes genomic instability by increasing mutational load, and a pervasive accumulation of DNA:RNA hybrids that induces genomic DNA double-strand breaks (DSBs). DNA:RNA hybrid accumulation also prevents binding of the homologous recombination (HR) machinery to double-strand breaks, hampering DSB repair. DIS3-inactivated cells become sensitive to PARP inhibitors, suggestive of a defect in homologous recombination repair. Accordingly, multiple myeloma patient cells mutated for DIS3 harbor an increased mutational burden and a pervasive overexpression of pro-inflammatory interferon, correlating with the accumulation of DNA:RNA hybrids. We propose DIS3 loss in myeloma to be a driving force for tumorigenesis via DNA:RNA hybrid-dependent enhanced genome instability and increased mutational rate. At the same time, DIS3 loss represents a liability that might be therapeutically exploited in patients whose cancer cells harbor DIS3 mutations.
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Affiliation(s)
- Ilaria Gritti
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Veronica Basso
- Division of Immunology, Transplantation and Infectious DiseaseIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | | | - Federica Corigliano
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Silvia Pivetti
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Marco Gaviraghi
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Dalia Rosano
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Davide Mazza
- Experimental Imaging CenterIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Sara Barozzi
- IFOM, The FIRC Institute of Molecular OncologyMilanoItaly
| | - Marco Roncador
- Department of Data SciencesDana Farber Cancer InstituteBostonMAUSA,Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Giovanni Parmigiani
- Department of Data SciencesDana Farber Cancer InstituteBostonMAUSA,Department of BiostatisticsHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Gaelle Legube
- MCD, Centre de Biologie Intégrative (CBI), CNRSUniversity of ToulouseToulouseFrance
| | | | - Davide Cittaro
- Center for Omics Sciences @OSR (COSR)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Davide Bedognetti
- Cancer Research DepartmentSidra MedicineDohaQatar,Dipartimento di Medicina Interna e Specialità MedicheUniversità degli Studi di GenovaGenoaItaly
| | - Anna Mondino
- Division of Immunology, Transplantation and Infectious DiseaseIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Simona Segalla
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly
| | - Giovanni Tonon
- Functional Genomics of Cancer Unit, Division of Experimental OncologyIstituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly,Center for Omics Sciences @OSR (COSR)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific InstituteMilanoItaly,Università Vita‐Salute San RaffaeleMilanItaly
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2
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Grossbach J, Gillet L, Clément‐Ziza M, Schmalohr CL, Schubert OT, Schütter M, Mawer JSP, Barnes CA, Bludau I, Weith M, Tessarz P, Graef M, Aebersold R, Beyer A. The impact of genomic variation on protein phosphorylation states and regulatory networks. Mol Syst Biol 2022; 18:e10712. [PMID: 35574625 PMCID: PMC9109056 DOI: 10.15252/msb.202110712] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high‐quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well‐defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
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Affiliation(s)
- Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Ludovic Gillet
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
| | - Mathieu Clément‐Ziza
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Lesaffre International Marcq‐en‐Barœul France
| | - Corinna L Schmalohr
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Olga T Schubert
- Department of Human Genetics University of California, Los Angeles Los Angeles CA USA
| | | | | | | | - Isabell Bludau
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany
| | - Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Martin Graef
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Max Planck Institute for Biology of Ageing Cologne Germany
| | - Ruedi Aebersold
- Department of Biology Institute of Molecular Systems Biology ETH Zurich Zurich Switzerland
- Faculty of Science University of Zurich Zurich Switzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne (CMMC) Medical Faculty, University of Cologne Cologne Germany
- Institute for Genetics Faculty of Mathematics and Natural Sciences University of Cologne Cologne Germany
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3
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Wang C, Liu Y, DeMario SM, Mandric I, Gonzalez-Figueroa C, Chanfreau GF. Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress. Cell Rep 2021; 31:107754. [PMID: 32521279 PMCID: PMC7587046 DOI: 10.1016/j.celrep.2020.107754] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 11/21/2019] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The nuclear RNA exosome is essential for RNA processing and degradation. Here, we show that the exosome nuclear-specific subunit Rrp6p promotes cell survival during heat stress through the cell wall integrity (CWI) pathway, independently of its catalytic activity or association with the core exosome. Rrp6p exhibits negative genetic interactions with the Slt2/Mpk1p or Paf1p elongation factors required for expression of CWI genes during stress. Overexpression of Rrp6p or of its catalytically inactive or exosome-independent mutants can partially rescue the growth defect of the mpk1Δ mutant and stimulates expression of the Mpk1 p target gene FKS2. The rrp6Δ and mpk1Δ mutants show similarities in deficient expression of CWI genes during heat shock, and overexpression of the CWI gene HSP150 can rescue the stress-induced lethality of the mpk1Δrp6Δ mutant. These results demonstrate that Rrp6p moonlights independently from the exosome to ensure proper expression of CWI genes and to promote cell survival during stress. Wang et al. show that Rrp6 functions with the Slt2/Mpk1 and Paf1 elongation factors for the proper expression of CWI genes during heat stress. The role of Rrp6p in promoting heat-stress-induced gene expression does not require Rrp6 catalytic activity or interaction with the nuclear RNA exosome.
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Affiliation(s)
- Charles Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yanru Liu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Samuel M DeMario
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Igor Mandric
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos Gonzalez-Figueroa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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4
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Whalen C, Tuohy C, Tallo T, Kaufman JW, Moore C, Kuehner JN. RNA Polymerase II Transcription Attenuation at the Yeast DNA Repair Gene, DEF1, Involves Sen1-Dependent and Polyadenylation Site-Dependent Termination. G3 (Bethesda) 2018; 8:2043-58. [PMID: 29686108 DOI: 10.1534/g3.118.200072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Termination of RNA Polymerase II (Pol II) activity serves a vital cellular role by separating ubiquitous transcription units and influencing RNA fate and function. In the yeast Saccharomyces cerevisiae, Pol II termination is carried out by cleavage and polyadenylation factor (CPF-CF) and Nrd1-Nab3-Sen1 (NNS) complexes, which operate primarily at mRNA and non-coding RNA genes, respectively. Premature Pol II termination (attenuation) contributes to gene regulation, but there is limited knowledge of its prevalence and biological significance. In particular, it is unclear how much crosstalk occurs between CPF-CF and NNS complexes and how Pol II attenuation is modulated during stress adaptation. In this study, we have identified an attenuator in the DEF1 DNA repair gene, which includes a portion of the 5′-untranslated region (UTR) and upstream open reading frame (ORF). Using a plasmid-based reporter gene system, we conducted a genetic screen of 14 termination mutants and their ability to confer Pol II read-through defects. The DEF1 attenuator behaved as a hybrid terminator, relying heavily on CPF-CF and Sen1 but without Nrd1 and Nab3 involvement. Our genetic selection identified 22 cis-acting point mutations that clustered into four regions, including a polyadenylation site efficiency element that genetically interacts with its cognate binding-protein Hrp1. Outside of the reporter gene context, a DEF1 attenuator mutant increased mRNA and protein expression, exacerbating the toxicity of a constitutively active Def1 protein. Overall, our data support a biologically significant role for transcription attenuation in regulating DEF1 expression, which can be modulated during the DNA damage response.
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5
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Patrick EM, Srinivasan S, Jankowsky E, Comstock MJ. The RNA helicase Mtr4p is a duplex-sensing translocase. Nat Chem Biol 2016; 13:99-104. [PMID: 27870836 DOI: 10.1038/nchembio.2234] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 09/29/2016] [Indexed: 12/30/2022]
Abstract
The conserved Saccharomyces cerevisiae Ski2-like RNA helicase Mtr4p plays essential roles in eukaryotic nuclear RNA processing. RNA helicase activity of Mtr4p is critical for biological functions of the enzyme, but the molecular basis for RNA unwinding is not understood. Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3'-to-5' translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. We further show that RNA unwinding by Mtr4p requires interaction with upstream RNA duplex. Inclusion of Mtr4p within the TRAMP complex increases the rate constant for unwinding initiation but does not change the characteristics of Mtr4p's helicase mechanism. Our data indicate that Mtr4p utilizes a previously unknown unwinding mode that combines aspects of canonical translocating helicases and non-canonical duplex-sensing helicases, thereby restricting directional translocation to duplex regions.
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Affiliation(s)
- Eric M Patrick
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
| | - Sukanya Srinivasan
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western University, Cleveland, Ohio, USA
| | - Eckhard Jankowsky
- Center for RNA Molecular Biology and Department of Biochemistry, Case Western University, Cleveland, Ohio, USA
| | - Matthew J Comstock
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan, USA
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6
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Del-moral-stevenel MÁ, Villalobos-osnaya A, López-casamichana M, Quintas-granados LI, López-camarillo C, Sánchez JMF, Zarate-guerra S, Alvarez-sánchez ME. Transcriptional profile of processing machinery of 3′ end of mRNA in Trichomonas vaginalis. Genes Genomics 2015; 37:399-408. [DOI: 10.1007/s13258-015-0268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Taylor LL, Jackson RN, Rexhepaj M, King AK, Lott LK, van Hoof A, Johnson SJ. The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding. Nucleic Acids Res 2014; 42:13861-72. [PMID: 25414331 PMCID: PMC4267639 DOI: 10.1093/nar/gku1208] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3′-5′ turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The ‘ratchet helix’ is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.
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Affiliation(s)
- Lacy L Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Megi Rexhepaj
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Alejandra Klauer King
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Lindsey K Lott
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Sean J Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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8
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Schuch B, Feigenbutz M, Makino DL, Falk S, Basquin C, Mitchell P, Conti E. The exosome-binding factors Rrp6 and Rrp47 form a composite surface for recruiting the Mtr4 helicase. EMBO J 2014; 33:2829-46. [PMID: 25319414 DOI: 10.15252/embj.201488757] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The exosome is a conserved multi-subunit ribonuclease complex that functions in 3' end processing, turnover and surveillance of nuclear and cytoplasmic RNAs. In the yeast nucleus, the 10-subunit core complex of the exosome (Exo-10) physically and functionally interacts with the Rrp6 exoribonuclease and its associated cofactor Rrp47, the helicase Mtr4 and Mpp6. Here, we show that binding of Mtr4 to Exo-10 in vitro is dependent upon both Rrp6 and Rrp47, whereas Mpp6 binds directly and independently of other cofactors. Crystallographic analyses reveal that the N-terminal domains of Rrp6 and Rrp47 form a highly intertwined structural unit. Rrp6 and Rrp47 synergize to create a composite and conserved surface groove that binds the N-terminus of Mtr4. Mutation of conserved residues within Rrp6 and Mtr4 at the structural interface disrupts their interaction and inhibits growth of strains expressing a C-terminal GFP fusion of Mtr4. These studies provide detailed structural insight into the interaction between the Rrp6-Rrp47 complex and Mtr4, revealing an important link between Mtr4 and the core exosome.
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Affiliation(s)
- Benjamin Schuch
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Monika Feigenbutz
- Molecular Biology and Biotechnology Department, The University of Sheffield, Sheffield, UK
| | - Debora L Makino
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Falk
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Claire Basquin
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Phil Mitchell
- Molecular Biology and Biotechnology Department, The University of Sheffield, Sheffield, UK
| | - Elena Conti
- Structural Cell Biology Department, Max Planck Institute of Biochemistry, Martinsried, Germany
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9
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Abstract
Ski2-like RNA helicases are large multidomain proteins involved in a variety of RNA processing and degradation events. Recent structures of Mtr4, Ski2 and Brr2 provide our first view of these intricate helicases. Here we review these structures, which reveal a conserved ring-like architecture that extends beyond the canonical RecA domains to include a winged helix and ratchet domain. Comparison of apo- and RNA-bound Mtr4 structures suggests a role for the winged helix domain as a molecular hub that coordinates RNA interacting events throughout the helicase. Unique accessory domains provide expanded diversity and functionality to each Ski2-like family member. A common theme is the integration of Ski2-like RNA helicases into larger protein assemblies. We describe the central role of Mtr4 and Ski2 in formation of complexes that activate RNA decay by the eukaryotic exosome. The current structures provide clues into what promises to be a fascinating view of these dynamic assemblies.
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Affiliation(s)
- Sean J Johnson
- Department of Chemistry & Biochemistry, Utah State University, Logan, UT, USA.
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