The Experts below are selected from a list of 6855 Experts worldwide ranked by ideXlab platform
Brian R. Mcnaughton - One of the best experts on this subject based on the ideXlab platform.
-
An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription.
ACS chemical biology, 2016Co-Authors: David W. Crawford, Brett D. Blakeley, Po-han Chen, Chringma Sherpa, Stuart F. J. Le Grice, Ite A. Laird-offringa, Brian R. McnaughtonAbstract:Potent and selective Recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA Recognition Motif as a scaffold for tailoring new RNA hairpin Recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5′-untr...
-
an evolved RNA Recognition Motif that suppresses hiv 1 tat tar dependent transcription
ACS Chemical Biology, 2016Co-Authors: David W. Crawford, Brett D. Blakeley, Po-han Chen, Chringma Sherpa, Stuart Le F J Grice, Ite A Lairdoffringa, Brian R. McnaughtonAbstract:Potent and selective Recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA Recognition Motif as a scaffold for tailoring new RNA hairpin Recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5′-untr...
Birgitta M. Wöhrl - One of the best experts on this subject based on the ideXlab platform.
-
structural studies on the RNA Recognition Motif of nelf e a cellular negative transcription elongation factor involved in the regulation of hiv transcription
Biochemical Journal, 2006Co-Authors: Jampani Nageswara Rao, Liane Neumann, Sabine Wenzel, Kristian Schweimer, Paul Rösch, Birgitta M. WöhrlAbstract:The elongation of transcription of HIV RNA at the TAR (transactivation-response element) is highly regulated by positive and negative factors. The cellular negative transcription elongation factor NELF (negative elongation factor) was suggested to be involved in transcriptional regulation of HIV-1 (HIV type 1) by binding to the stem of the viral TAR RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. In the present study, we determined the solution structure of the RRM (RNA-Recognition Motif) of the RNA-binding subunit NELF E and studied its interaction with the viral TAR RNA. Our results show that the separately expressed recombinant NELF E RRM has alpha-helical and beta-strand elements adopting a betaalphabetabetaalphabeta fold and is able to bind to TAR RNA. Fluorescence equilibrium titrations with fluorescently labelled double- and single-stranded oligoribonucleotides representing the TAR RNA stem imply that NELF E RRM binds to the single-stranded TAR RNAs with K(d) values in the low-micromolar range.
-
Structural studies on the RNA-Recognition Motif of NELF E, a cellular negative transcription elongation factor involved in the regulation of HIV transcription
Biochemical Journal, 2006Co-Authors: Jampani Nageswara Rao, Liane Neumann, Sabine Wenzel, Kristian Schweimer, Paul Rösch, Birgitta M. WöhrlAbstract:The elongation of transcription of HIV RNA at the transactivation response element TAR is highly regulated by positive and negative factors. The cellular negative transcription elongation factor NELF was suggested to be involved in transcriptional regulation of human immunodeficiency virus type 1 (HIV-1) by binding to the stem of the viral TAR RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. Here we determined the solution structure of the RNA Recognition Motif (RRM) of the RNA binding subunit NELF E and studied its interaction with the viral TAR RNA. Our data show that the separately expressed recombinant NELF E RRM owns {alpha}-helical and {beta}-strand elements adopting a {beta}{alpha}{beta}{beta}{alpha}{beta} fold and is able to bind to TAR RNA. Fluorescence equilibrium titrations with fluorescently labeled double and single stranded oligoribonucleotides representing the TAR RNA stem imply that NELF E RRM binds to the single stranded TAR RNAs with K D}-values in the low {mu}M range.
Frederic H T Allain - One of the best experts on this subject based on the ideXlab platform.
-
a transient α helix in the n terminal RNA Recognition Motif of polypyrimidine tract binding protein senses RNA secondary structure
Nucleic Acids Research, 2020Co-Authors: Christophe Maris, Fred F Damberger, Sandrine Jayne, Irene Beusch, Georg Dorn, Sapna Ravindranathan, Frederic H T AllainAbstract:The polypyrimidine tract binding protein (PTB) is a multi-domain protein involved in alteRNAtive splicing, mRNA localization, stabilization, polyadenylation and translation initiation from inteRNAl ribosome entry sites (IRES). In this latter process, PTB promotes viral translation by interacting extensively with complex structured regions in the 5'-untranslated regions of viral RNAs at pyrimidine-rich targets located in single strand and hairpin regions. To better understand how PTB recognizes structured elements in RNA targets, we solved the solution structure of the N-terminal RNA Recognition Motif (RRM) in complex with an RNA hairpin embedding the loop sequence UCUUU, which is frequently found in IRESs of the picornovirus family. Surprisingly, a new three-turn α3 helix C-terminal to the RRM, folds upon binding the RNA hairpin. Although α3 does not mediate any contacts to the RNA, it acts as a sensor of RNA secondary structure, suggesting a role for RRM1 in detecting pyrimidine tracts in the context of structured RNA. Moreover, the degree of helix formation depends on the RNA loop sequence. Finally, we show that the α3 helix region, which is highly conserved in vertebrates, is crucial for PTB function in enhancing Encephalomyocarditis virus IRES activity.
-
Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination
Nature communications, 2017Co-Authors: Nana Diarra Dit Konté, Fred F Damberger, Miroslav Krepl, Nina Ripin, Olivier Duss, Jiří Šponer, Frederic H T AllainAbstract:The cyclooxygenase-2 is a pro-inflammatory and cancer marker, whose mRNA stability and translation is regulated by the CUG-binding protein 2 interacting with AU-rich sequences in the 3′ untranslated region. Here, we present the solution NMR structure of CUG-binding protein 2 RRM3 in complex with 5′-UUUAA-3′ originating from the COX-2 3′-UTR. We show that RRM3 uses the same binding surface and protein moieties to interact with AU- and UG-rich RNA Motifs, binding with low and high affinity, respectively. Using NMR spectroscopy, isothermal titration calorimetry and molecular dynamics simulations, we demonstrate that distinct sub-states characterized by different aromatic side-chain conformations at the RNA-binding surface allow for high- or low-affinity binding with functional implications. This study highlights a mechanism for RNA discrimination possibly common to multiple RRMs as several prominent members display a similar rearrangement of aromatic residues upon binding their targets. The RNA Recognition Motif (RRM) is the most ubiquitous RNA binding domain. Here the authors combined NMR and molecular dynamics simulations and show that the RRM RNA binding surface exists in different states and that a conformational switch of aromatic side-chains fine-tunes sequence specific binding affinities.
-
structural and mechanistic insights into poly uridine tract Recognition by the hnrnp c RNA Recognition Motif
Journal of the American Chemical Society, 2014Co-Authors: Zuzana Cienikova, Fred F Damberger, Jonathan Hall, Frederic H T Allain, Christophe MarisAbstract:HnRNP C is a ubiquitous RNA regulatory factor and the principal constituent of the nuclear hnRNP core particle. The protein contains one amino-terminal RNA Recognition Motif (RRM) known to bind uridine (U)-rich sequences. This work provides a molecular and mechanistic understanding of this interaction. We solved the solution structures of the RRM in complex with poly(U) oligomers of five and seven nucleotides. The five binding pockets of RRM recognize uridines with an unusual 5′-to-3′ gradient of base selectivity. The target Recognition is therefore strongly sensitive to base clustering, explaining the preference for contiguous uridine tracts. Using a novel approach integrating the structurally derived Recognition consensus of the RRM with a thermodynamic description of its multi-register binding, we modeled the saturation of cellular uridine tracts by this protein. The binding pattern is remarkably consistent with the experimentally observed transcriptome-wide cross-link distribution of the full-length h...
-
the RNA Recognition Motif a plastic RNA binding platform to regulate post transcriptional gene expression
FEBS Journal, 2005Co-Authors: Christophe Maris, Cyril Dominguez, Frederic H T AllainAbstract:The RNA Recognition Motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM–RNA or RRM–protein), we reviewed the structure–function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitMotif of the RRM–nucleic acid interface with its variations. Outside of the two conserved RNP Motifs that lie in the center of the RRM β-sheet, the two exteRNAl β-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific Recognition. Protein–RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.
-
The RNA Recognition Motif, a plastic RNA‐binding platform to regulate post‐transcriptional gene expression
The FEBS journal, 2005Co-Authors: Christophe Maris, Cyril Dominguez, Frederic H T AllainAbstract:The RNA Recognition Motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM–RNA or RRM–protein), we reviewed the structure–function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitMotif of the RRM–nucleic acid interface with its variations. Outside of the two conserved RNP Motifs that lie in the center of the RRM β-sheet, the two exteRNAl β-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific Recognition. Protein–RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.
Alberto C.c. Frasch - One of the best experts on this subject based on the ideXlab platform.
-
An RNA Recognition Motif Mediates the Nucleocytoplasmic Transport of a Trypanosome RNA-binding Protein
The Journal of biological chemistry, 2009Co-Authors: Alejandro Cassola, Alberto C.c. FraschAbstract:RNA-binding proteins (RBPs) and RNA metabolism are considered to be important for modulating gene expression in trypanosomes, because these protozoan parasites mainly rely on post-transcriptional mechanisms to regulate protein levels. Previously, we have identified TcUBP1, a single RNA Recognition Motif (RRM)-type RBP from Trypanosoma cruzi. TcUBP1 is a cytoplasmic protein with roles in stabilization/degradation of mRNAs and in the protection of transcripts through their recruitment into cytoplasmic granules. We now show that TcUBP1, and the closely related protein TcUBP2, can be found in small amounts in the nucleus under normal conditions, and are able to accumulate in the nucleus under arsenite stress. The kinetics of nuclear accumulation, and export to the cytoplasm, are consistent with the shuttling of TcUBP1 between the nucleus and the cytoplasm. The sequence required for TcUBP1 nuclear accumulation was narrowed to the RRM, and point mutations affecting RNA binding abolished nuclear import. This RRM was also shown to be efficiently exported from the nucleus in unstressed parasites, a property that relied on the binding to RNA. TcUBP1 nuclear accumulation was dependent on active transcription, and colocalized with transcripts in the nucleus, suggesting nuclear binding of the mRNA. We propose that TcUBP1 could be linking the mRNA metabolism at both sides of the nuclear pore complex, using the RRM as a nuclear localization signal, and being exported as a cargo on mRNA.
-
RNA Recognition Motif type RNA binding proteins in trypanosoma cruzi form a family involved in the interaction with specific transcripts in vivo
Journal of Biological Chemistry, 2003Co-Authors: Javier G De Gaudenzi, Ivan Dorso, Alberto C.c. FraschAbstract:Trypanosomes, protozoan parasites from the order Kinetoplastida, have to deal with environmental changes during the interaction with their hosts. Trypanosoma cruzi, the causative agent of Chagas' disease, uses post-transcriptional mechanisms to regulate gene expression. However, few RNA-binding proteins involved in mRNA turnover control have been identified to date. In this work, an RNA Recognition Motif (RRM)-type RNA-binding protein family named T. cruzi RNA-binding protein (TcRBP) and composed of at least six members was identified. The genomic organization of four members revealed a head to tail arrangement within a region of 15 kilobase pairs. TcRBP members have a common RRM and different auxiliary domains with a high content of glycine, glutamine, and histidine residues within their N- and C-terminal regions. TcRBPs differ in their expression patterns as well as in their homoribopolymer binding interaction in vitro, although they preferentially recognize poly(U) and poly(G) RNAs. An interesting observation was the relaxed RNA-binding interactions with several trypanosome transcripts in vitro. In contrast, co-immunoprecipitation experiments of TcRBP-containing ribonucleoprotein complexes formed in vivo revealed a highly restricted binding interaction with specific RNAs. Several TcRBP-containing complexes are stage-specific and, in some cases, bear the poly(A)-binding protein TcPABP1. Altogether, these results suggest that TcRBPs might be modulated in vivo, to favor or preclude the interaction with specific transcripts in a developmentally regulated manner.
David W. Crawford - One of the best experts on this subject based on the ideXlab platform.
-
An Evolved RNA Recognition Motif That Suppresses HIV-1 Tat/TAR-Dependent Transcription.
ACS chemical biology, 2016Co-Authors: David W. Crawford, Brett D. Blakeley, Po-han Chen, Chringma Sherpa, Stuart F. J. Le Grice, Ite A. Laird-offringa, Brian R. McnaughtonAbstract:Potent and selective Recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA Recognition Motif as a scaffold for tailoring new RNA hairpin Recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5′-untr...
-
an evolved RNA Recognition Motif that suppresses hiv 1 tat tar dependent transcription
ACS Chemical Biology, 2016Co-Authors: David W. Crawford, Brett D. Blakeley, Po-han Chen, Chringma Sherpa, Stuart Le F J Grice, Ite A Lairdoffringa, Brian R. McnaughtonAbstract:Potent and selective Recognition and modulation of disease-relevant RNAs remain a daunting challenge. We previously examined the utility of the U1A N-terminal RNA Recognition Motif as a scaffold for tailoring new RNA hairpin Recognition and showed that as few as one or two mutations can result in moderate affinity (low μM dissociation constant) for the human immunodeficiency virus (HIV) trans-activation response element (TAR) RNA, an RNA hairpin controlling transcription of the human immunodeficiency virus (HIV) genome. Here, we use yeast display and saturation mutagenesis of established RNA-binding regions in U1A to identify new synthetic proteins that potently and selectively bind TAR RNA. Our best candidate has truly altered, not simply broadened, RNA-binding selectivity; it binds TAR with subnanomolar affinity (apparent dissociation constant of ∼0.5 nM) but does not appreciably bind the original U1A RNA target (U1hpII). It specifically recognizes the TAR RNA hairpin in the context of the HIV-1 5′-untr...
