The Experts below are selected from a list of 714 Experts worldwide ranked by ideXlab platform

Elena Conti - One of the best experts on this subject based on the ideXlab platform.

  • structural analysis reveals the characteristic features of mtr4 a dexh helicase involved in nuclear rna processing and surveillance
    Proceedings of the National Academy of Sciences of the United States of America, 2010
    Co-Authors: John R Weir, Fabien Bonneau, Jendrik Hentschel, Elena Conti
    Abstract:

    Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) Complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in Complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a β-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA iMet , suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP Complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.

  • structural analysis reveals the characteristic features of mtr4 a dexh helicase involved in nuclear rna processing and surveillance
    Proceedings of the National Academy of Sciences of the United States of America, 2010
    Co-Authors: John R Weir, Fabien Bonneau, Jendrik Hentschel, Elena Conti
    Abstract:

    Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) Complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in Complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a beta-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA(iMet), suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP Complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.

Domenico Libri - One of the best experts on this subject based on the ideXlab platform.

  • transcription termination and nuclear degradation of cryptic unstable transcripts a role for the nrd1 nab3 pathway in genome surveillance
    Molecular Cell, 2006
    Co-Authors: Marilyne Thiebaut, Elena Kisselevaromanova, Mathieu Rougemaille, Jocelyne Boulay, Domenico Libri
    Abstract:

    Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP Complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

  • Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance.
    Molecular Cell, 2006
    Co-Authors: Marilyne Thiebaut, Mathieu Rougemaille, Jocelyne Boulay, Elena Kisseleva-romanova, Domenico Libri
    Abstract:

    Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP Complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

John R Weir - One of the best experts on this subject based on the ideXlab platform.

  • structural analysis reveals the characteristic features of mtr4 a dexh helicase involved in nuclear rna processing and surveillance
    Proceedings of the National Academy of Sciences of the United States of America, 2010
    Co-Authors: John R Weir, Fabien Bonneau, Jendrik Hentschel, Elena Conti
    Abstract:

    Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) Complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in Complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a β-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA iMet , suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP Complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.

  • structural analysis reveals the characteristic features of mtr4 a dexh helicase involved in nuclear rna processing and surveillance
    Proceedings of the National Academy of Sciences of the United States of America, 2010
    Co-Authors: John R Weir, Fabien Bonneau, Jendrik Hentschel, Elena Conti
    Abstract:

    Mtr4 is a conserved RNA helicase that functions together with the nuclear exosome. It participates in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA). It also interacts with the polyadenylating Trf4-Air2 heterodimer to form the so-called TRAMP (Trf4-Air2-Mtr4 Polyadenylation) Complex. TRAMP is involved in exosome-mediated degradation of aberrant RNAs in nuclear surveillance pathways. We report the 2.9-A resolution crystal structure of Saccharomyces cerevisiae Mtr4 in Complex with ADP and RNA. The structure shows a central ATPase core similar to that of other DExH helicases. Inserted in the DExH core is a region characteristic of Mtr4 orthologues that folds into an elongated stalk connected to a beta-barrel domain. This domain shows unexpected similarity to the KOW domain of L24, a ribosomal protein that binds 23S rRNA. We find that indeed the KOW domain of Mtr4 is able to bind in vitro transcribed tRNA(iMet), suggesting it might assist in presenting RNA substrates to the helicase core. The interaction of Mtr4 with Trf4-Air2 is mediated not by the stalk/KOW insertion but by the DExH core. We find that in the context of the TRAMP Complex, the DExH core functions independently in vitro as an RNA helicase and a protein-binding platform. Mtr4 has thus evolved specific structural and surface features to perform its multiple functions.

Marilyne Thiebaut - One of the best experts on this subject based on the ideXlab platform.

  • transcription termination and nuclear degradation of cryptic unstable transcripts a role for the nrd1 nab3 pathway in genome surveillance
    Molecular Cell, 2006
    Co-Authors: Marilyne Thiebaut, Elena Kisselevaromanova, Mathieu Rougemaille, Jocelyne Boulay, Domenico Libri
    Abstract:

    Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP Complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

  • Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance.
    Molecular Cell, 2006
    Co-Authors: Marilyne Thiebaut, Mathieu Rougemaille, Jocelyne Boulay, Elena Kisseleva-romanova, Domenico Libri
    Abstract:

    Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP Complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

Anderson, James T. - One of the best experts on this subject based on the ideXlab platform.

  • Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNA\u3csub\u3ei\u3c/sub\u3e \u3csup\u3eMet\u3c/sup\u3e Turnover in \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e and Mtr4p Enzymatic Activities \u3cem\u3eIn Vitro\u3c/em\u3e
    e-Publications@Marquette, 2016
    Co-Authors: Li Yan, Burclaff Joseph, Anderson, James T.
    Abstract:

    RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP Complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH and ratchet domain) coordinate with the helicase domains and what roles they are playing in regulating Mtr4p helicase activity are unknown. We created a library of Mtr4p structural domain mutants for the first time and screened for those defective in the turnover of TRAMP and exosome substrate, hypomodified tRNAiMet. We found these domains regulate Mtr4p enzymatic activities differently through characterizing the arch domain mutants K700N and P731S, WH mutant K904N, and ratchet domain mutant R1030G. Arch domain mutants greatly reduced Mtr4p RNA binding, which surprisingly did not lead to significant defects on either in vivo tRNAiMet turnover, or in vitro unwinding activities. WH mutant K904N and Ratchet domain mutant R1030G showed decreased tRNAiMet turnover in vivo, as well as reduced RNA binding, ATPase and unwinding activities of Mtr4p in vitro. Particularly, K904 was found to be very important for steady protein levels in vivo. Overall, we conclude that arch domain plays a role in RNA binding but is largely dispensable for Mtr4p enzymatic activities, however the structural domains in the helicase core significantly contribute to Mtr4p ATPase and unwinding activities

  • RNA Unwinding by the Trf4/Air2/Mtr4 Polyadenylation (TRAMP) Complex
    e-Publications@Marquette, 2012
    Co-Authors: Jia Huijue, Wang Xuying, Anderson, James T., Jankowsky Eckhard
    Abstract:

    Many RNA-processing events in the cell nucleus involve the Trf4/Air2/Mtr4 polyadenylation (TRAMP) Complex, which contains the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for processing by the nuclear exosome. In addition, TRAMP functions as an exosome cofactor during RNA degradation, and it has been speculated that this role involves disruption of RNA secondary structure. However, it is unknown whether TRAMP displays RNA unwinding activity. It is also not clear how unwinding would be coordinated with polyadenylation and the function of the RNA helicase Mtr4p in modulating poly(A) addition. Here, we show that TRAMP robustly unwinds RNA duplexes. The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation. Nonetheless, polyadenylation enables TRAMP to unwind RNA substrates that it otherwise cannot separate. Moreover, TRAMP displays optimal unwinding activity on substrates with a minimal Mtr4p binding site comprised of adenylates. Our results suggest a model for coordination between unwinding and polyadenylation activities by TRAMP that reveals remarkable synergy between helicase and poly(A) polymerase

  • The RNA Helicase Mtr4p Modulates Polyadenylation in the TRAMP Complex
    e-Publications@Marquette, 2011
    Co-Authors: Jia Huijue, Wang Xuying, Anderson, James T., Liu Fei, Guenther Ulf-peter, Srinivasan Sukanya, Jankowsky Eckhard
    Abstract:

    Many steps in nuclear RNA processing, surveillance, and degradation require TRAMP, a Complex containing the poly(A) polymerase Trf4p, the Zn-knuckle protein Air2p, and the RNA helicase Mtr4p. TRAMP polyadenylates RNAs designated for decay or trimming by the nuclear exosome. It has been unclear how polyadenylation by TRAMP differs from polyadenylation by conventional poly(A) polymerase, which produces poly(A) tails that stabilize RNAs. Using reconstituted S. cerevisiae TRAMP, we show that TRAMP inherently suppresses poly(A) addition after only 3–4 adenosines. This poly(A) tail length restriction is controlled by Mtr4p. The helicase detects the number of 3′-terminal adenosines and, over several adenylation steps, elicits precisely tuned adjustments of ATP affinities and rate constants for adenylation and TRAMP dissociation. Our data establish Mtr4p as a critical regulator of polyadenylation by TRAMP and reveal that an RNA helicase can control the activity of another enzyme in a highly Complex fashion and in response to features in RNA

  • Degradation of Hypomodified tRNA\u3csub\u3ei\u3c/sub\u3e\u3csup\u3eMet\u3c/sup\u3e in vivo Involves RNA-dependent ATPase Activity of the DExH Helicase Mtr4p
    e-Publications@Marquette, 2008
    Co-Authors: Wang Xuying, Jia Huijue, Jankowsky Eckhard, Anderson, James T.
    Abstract:

    Effective turnover of many incorrectly processed RNAs in yeast, including hypomodified tRNAi Met, requires the TRAMP Complex, which appends a short poly(A) tail to RNA designated for decay. The poly(A) tail stimulates degradation by the exosome. The TRAMP Complex contains the poly(A) polymerase Trf4p, the RNA-binding protein Air2p, and the DExH RNA helicase Mtr4p. The role of Mtr4p in RNA degradation processes involving the TRAMP Complex has been unclear. Here we show through a genetic analysis that MTR4 is required for degradation but not for polyadenylation of hypomodified tRNAi Met. A suppressor of the trm6-504 mutation in the tRNA m1A58 methyltransferase (Trm6p/Trm61p), which causes a reduced level of tRNAi Met, was mapped to MTR4. This mtr4-20 mutation changed a single amino acid in the conserved helicase motif VI of Mtr4p. The mutation stabilizes hypomodified tRNAi Met in vivo but has no effect on TRAMP Complex stability or polyadenylation activity in vivo or in vitro. We further show that purified recombinant Mtr4p displays RNA-dependent ATPase activity and unwinds RNA duplexes with a 3′-to-5′ polarity in an ATP-dependent fashion. Unwinding and RNA-stimulated ATPase activities are strongly reduced in the recombinant mutant Mtr4-20p, suggesting that these activities of Mtr4p are critical for degradation of polyadenylated hypomodified tRNAi Met