Structure and RNA binding properties of Lsm1-7 and Lsm2-8 complexes

2020 ◽  
Author(s):  
SAMUEL BUTCHER
Keyword(s):  
Rna Binding ◽  
Binding Properties

scholarly journals Characterization and RNA-binding properties of a chloroplast S1-like ribosomal protein.

1992 ◽  
Vol 267 (27) ◽  
pp. 19075-19081
Author(s):  
B Franzetti ◽  
P Carol ◽  
R Mache
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Binding Properties

scholarly journals Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

2017 ◽  
Vol 73 (4) ◽  
pp. 294-315 ◽  
Author(s):  
Kimberly A. Stanek ◽  
Jennifer Patterson-West ◽  
Peter S. Randolph ◽  
Cameron Mura
Keyword(s):  
Rna Binding ◽  
Binding Pocket ◽  
Binding Mode ◽  
Evolutionary Conservation ◽  
Aquifex Aeolicus ◽  
Binding Properties ◽  
Bacterial Phyla ◽  
Mrna Targets ◽  
Small Regulatory Rnas ◽  
And Function

The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

scholarly journals RNA-binding properties of HCF152, an Arabidopsis PPR protein involved in the processing of chloroplast RNA

2003 ◽  
Vol 270 (20) ◽  
pp. 4070-4081 ◽  
Author(s):  
Takahiro Nakamura ◽  
Karin Meierhoff ◽  
Peter Westhoff ◽  
Gadi Schuster
Keyword(s):  
Rna Binding ◽  
Binding Properties ◽  
Ppr Protein ◽  
Chloroplast Rna

scholarly journals Nucleolin Controls Ribosome Biogenesis through Its RNA-Binding Properties

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 5056-5056 ◽  
Author(s):  
Julia Fremerey ◽  
Pavel Morozov ◽  
Cindy Meyer ◽  
Aitor Garzia ◽  
Marianna Teplova ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Binding Sites ◽  
Ribosome Biogenesis ◽  
Rna Binding ◽  
Binding Properties ◽  
Expression Levels ◽  
Rna Targets ◽  
Polymerase I

Abstract Introduction Nucleolin (NCL) is a multifunctional, proliferation-associated factor that is overexpressed in many cancers and has already been demonstrated to play a profound role in leukemogenesis (Abdelmohsen and Gorospe, 2012; Shen et al., 2014). This can be linked to an increased synthesis of ribosomal RNA (rRNA). Thus, in leukemic cells, high expression levels of NCL contribute to malignant transformation through the increase of rRNA synthesis, which is required to sustain high levels of protein synthesis. Physiologically, NCL is a highly abundant, nucleolar RNA-binding protein that is implicated in the regulation of polymerase I transcription, post-transcriptional gene regulation, and plays a central role in ribosome biogenesis (Srivastava and Pollard, 1999). To further elucidate the exact role of NCL, this study focused on the characterization of the RNA-binding properties and protein-interactions of NCL in the context of ribosome biogenesis. Methods In order to identify transcriptome-wide binding sites and the cellular RNA targets of NCL, PAR-CLIP (photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation) and RIP-Seq (RNA immunoprecipitation sequencing) analyses were carried out in HEK 293 cells. PAR-CLIP is characterized by the incorporation of 4-thiouridine into newly transcribed RNA that causes a T to C conversion in the corresponding cDNA of crosslinked RNA (Hafner et al., 2010). The RNA-binding properties and the interaction of NCL with its identified RNA targets were elucidated by electrophoretic mobility shift assays, isothermal titration calorimetry and size-exclusion chromatography. To further define the role of NCL in ribosome biogenesis and the effect on precursor rRNA levels, siRNA mediated knockdown of NCL was employed followed by RNA sequencing. Furthermore, to characterize the interaction network of NCL on a proteome-wide level, mass-spectrometry was performed. Results This study focuses on the characterization of the RNA-binding properties of NCL and provides the first PAR-CLIP data set of NCL and identifies small nucleolar RNAs (snoRNA) and precursor rRNA as main targets of NCL, both of which were further confirmed by RIP-Seq analysis. Binding sites of NCL were identified in the 5'ETS (external transcribed spacer), after the first cleavage site, in ITS1 and ITS2 (internal transcribed spacer) within the precursor rRNA, indicating that NCL might play a role in the early processing steps of ribosome biogenesis within the nucleolus. Biochemical and structural binding analyses reveal that NCL interacts along the complete precursor region and shows high binding affinity to G/C/U-rich repeat sequences, which is in agreement with the nucleotide composition of the primary rRNA transcript. Moreover, we propose that siRNA mediated knockdown of NCL inhibits polymerase I transcription, which is shown by decreased expression levels of the precursor rRNA transcript. On the proteome-wide level, mass-spectrometry analysis of NCL identified several interaction partners including block of proliferation 1 (BOP1), DEAD-box RNA helicase 18 (DDX18), and 5'-3' exoribonuclease 2 (XRN2) and numerous ribosomal proteins of the small and the large ribosomal subunits including RPS24, RPL11, RPL35A, and RPL36. Conclusion This study provides evidence that NCL is highly associated with the process of ribosome biogenesis on the proteome- and transcriptome-wide level. Therefore, NCL might serve as a promising biochemical target in the context of increased ribosome biogenesis in cancer. Disclosures No relevant conflicts of interest to declare.

scholarly journals Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq

2011 ◽  
Vol 40 (4) ◽  
pp. 1856-1867 ◽  
Author(s):  
Tatsuhiko Someya ◽  
Seiki Baba ◽  
Mai Fujimoto ◽  
Gota Kawai ◽  
Takashi Kumasaka ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Bacillus Subtilis ◽  
Rna Binding ◽  
Rna Aptamer ◽  
Binding Properties ◽  
Insight Into

Ribosomal Protein S15 from Thermus Thermophilus. Cloning, Sequencing, Overexpression of the Gene and RNA-Binding Properties of the Protein

1997 ◽  
Vol 246 (2) ◽  
pp. 291-300 ◽  
Author(s):  
Alexander Serganov ◽  
Alexey Rak ◽  
Maria Garber ◽  
Joseph Reinbolt ◽  
Bernard Ehresmann ◽  
...  
Keyword(s):  
Ribosomal Protein ◽  
Rna Binding ◽  
Thermus Thermophilus ◽  
Binding Properties ◽  
Ribosomal Protein S15

Detection and in vitro studies of Cucurbita maxima phloem serpin-1 RNA-binding properties

Biochimie ◽  
2020 ◽  
Vol 170 ◽  
pp. 118-127 ◽  
Author(s):  
Eugeny A. Tolstyko ◽  
Alexander A. Lezzhov ◽  
Anna V. Pankratenko ◽  
Marina V. Serebryakova ◽  
Andrey G. Solovyev ◽  
...  
Keyword(s):  
Rna Binding ◽  
In Vitro Studies ◽  
Cucurbita Maxima ◽  
Binding Properties

scholarly journals Unravelling the RNA-Binding Properties of SAFB Proteins in Breast Cancer Cells

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Elaine Hong ◽  
Andrew Best ◽  
Hannah Gautrey ◽  
Jas Chin ◽  
Anshuli Razdan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Open Reading Frames ◽  
Rna Recognition Motif ◽  
Binding Properties ◽  
Intergenic Regions ◽  
Mcf 7

Scaffold attachment factor B1 (SAFB1) and SAFB2 proteins are oestrogen (ER) corepressors that bind to and modulate ER activity through chromatin remodelling or interaction with the basal transcription machinery. SAFB proteins also have an internal RNA-recognition motif but little is known about the RNA-binding properties of SAFB1 or SAFB2. We utilised crosslinking and immunoprecipitation (iCLIP) coupled with high-throughput sequencing to enable a transcriptome-wide mapping of SAFB1 protein-RNA interactions in breast cancer MCF-7 cells. Analysis of crosslinking frequency mapped to transcript regions revealed that SAFB1 binds to coding and noncoding RNAs (ncRNAs). The highest proportion of SAFB1 crosslink sites mapped to ncRNAs, followed by intergenic regions, open reading frames (ORFs), introns, and 3′ or 5′ untranslated regions (UTR). Furthermore, we reveal that SAFB1 binds directly to RNA and its binding is particularly enriched at purine-rich sequences not dissimilar to the RNA-binding motifs for SR proteins. Using RNAi, we also show, for the first time, that single depletion of either SAFB1 or SAFB2 leads to an increase in expression of the other SAFB protein in both MCF-7 and MDA-MD231 breast cancer cells.

scholarly journals Solution Structure of the Carbon Storage Regulator Protein CsrA from Escherichia coli

2005 ◽  
Vol 187 (10) ◽  
pp. 3496-3501 ◽  
Author(s):  
Pablo Gutiérrez ◽  
Yan Li ◽  
Michael J. Osborne ◽  
Ekaterina Pomerantseva ◽  
Qian Liu ◽  
...  
Keyword(s):  
Carbon Storage ◽  
Solution Structure ◽  
Rna Binding ◽  
Binding Motif ◽  
Binding Properties ◽  
Nmr Titration ◽  
C Terminus ◽  
Regulator Protein ◽  
Carbon Storage Regulator ◽  
Α Helix

ABSTRACT The carbon storage regulator A (CsrA) is a protein responsible for the repression of a variety of stationary-phase genes in bacteria. In this work, we describe the nuclear magnetic resonance (NMR)-based structure of the CsrA dimer and its RNA-binding properties. CsrA is a dimer of two identical subunits, each composed of five strands, a small α-helix and a flexible C terminus. NMR titration experiments suggest that the β1-β2 and β3-β4 loops and the C-terminal helix are important elements in RNA binding. Even though the β3-β4 loop contains a highly conserved RNA-binding motif, GxxG, typical of KH domains, our structure excludes CsrA from being a member of this protein family, as previously suggested. A mechanism for the recognition of mRNAs downregulated by CsrA is proposed.

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