scholarly journals Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs

2017 ◽  
Vol 45 (6) ◽  
pp. 1313-1321 ◽  
Author(s):  
Benjamin Gilman ◽  
Pilar Tijerina ◽  
Rick Russell
Keyword(s):  
Conformational Changes ◽  
Protein Complexes ◽  
Rna Helicase ◽  
Conformational Transitions ◽  
Messenger Rnas ◽  
Base Pairs ◽  
Dead Box ◽  
Evolutionarily Conserved ◽  
Partially Unfolded ◽  
Rna Protein Complexes

Structured RNAs and RNA–protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how their distinct mechanisms enable DEAD-box proteins to disrupt RNA base pairs on the surfaces of structured RNAs and RNPs, while some DEAH-box proteins are adept at disrupting base pairs in the interior of RNPs. Proteins from these families use these mechanisms to chaperone folding and promote rearrangements of structured RNAs and RNPs, including the spliceosome, and may use related mechanisms to maintain cellular messenger RNAs in unfolded or partially unfolded conformations.

scholarly journals DjCBC-1, a conserved DEAD box RNA helicase of the RCK/p54/Me31B family, is a component of RNA-protein complexes in planarian stem cells and neurons

2007 ◽  
Vol 236 (12) ◽  
pp. 3436-3450 ◽  
Author(s):  
Maki Yoshida-Kashikawa ◽  
Norito Shibata ◽  
Katsuaki Takechi ◽  
Kiyokazu Agata
Keyword(s):  
Stem Cells ◽  
Protein Complexes ◽  
Rna Helicase ◽  
Dead Box ◽  
Rna Protein Complexes

scholarly journals An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA

RNA ◽  
2011 ◽  
Vol 17 (4) ◽  
pp. 555-562 ◽  
Author(s):  
H. C. Moore ◽  
M. Johnston ◽  
S. M. Nicol ◽  
J.-C. Bourdon ◽  
A. M. Thompson ◽  
...  
Keyword(s):  
Rna Helicase ◽  
Novel Mirna ◽  
Dead Box ◽  
Helicase Gene ◽  
Evolutionarily Conserved ◽  
Alternatively Spliced

scholarly journals Dead or alive: DEAD-box ATPases as regulators of ribonucleoprotein complex condensation

2021 ◽  
Vol 402 (5) ◽  
pp. 653-661
Author(s):  
Karsten Weis
Keyword(s):  
Rna Processing ◽  
Atp Hydrolysis ◽  
Protein Complexes ◽  
Dependent Manner ◽  
Rna Helicases ◽  
Ribonucleoprotein Complexes ◽  
Dead Box ◽  
Rna Duplexes ◽  
Rna Protein Complexes

Abstract DEAD-box ATPase proteins are found in all clades of life and have been associated with a diverse array of RNA-processing reactions in eukaryotes, bacteria and archaea. Their highly conserved core enables them to bind RNA, often in an ATP-dependent manner. In the course of the ATP hydrolysis cycle, they undergo conformational rearrangements, which enable them to unwind short RNA duplexes or remodel RNA-protein complexes. Thus, they can function as RNA helicases or chaperones. However, when their conformation is locked, they can also clamp RNA and create ATP-dependent platforms for the formation of higher-order ribonucleoprotein complexes. Recently, it was shown that DEAD-box ATPases globally regulate the phase-separation behavior of RNA-protein complexes in vitro and control the dynamics of RNA-containing membraneless organelles in both pro- and eukaryotic cells. A role of these enzymes as regulators of RNA-protein condensates, or ‘condensases’, suggests a unifying view of how the biochemical activities of DEAD-box ATPases are used to keep cellular condensates dynamic and ‘alive’, and how they regulate the composition and fate of ribonucleoprotein complexes in different RNA processing steps.

Combinations of DEAD box proteins distinguish distinct types of RNA: Protein complexes in neurons

2009 ◽  
Vol 40 (4) ◽  
pp. 485-495 ◽  
Author(s):  
Linda C. Miller ◽  
Vanessa Blandford ◽  
Robyn McAdam ◽  
Maria R. Sanchez-Carbente ◽  
Frederique Badeaux ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Dead Box ◽  
Rna Protein Complexes

scholarly journals m6A mRNA Destiny: Chained to the rhYTHm by the YTH-Containing Proteins

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 49 ◽  
Author(s):  
Ditipriya Hazra ◽  
Clément Chapat ◽  
Marc Graille
Keyword(s):  
Protein Complexes ◽  
Messenger Rnas ◽  
Rna Modifications ◽  
Rna Regulation ◽  
Control Of Gene Expression ◽  
Cellular Processes ◽  
Highly Sensitive ◽  
Yth Domain ◽  
Rna Protein Complexes ◽  
Small Building

The control of gene expression is a multi-layered process occurring at the level of DNA, RNA, and proteins. With the emergence of highly sensitive techniques, new aspects of RNA regulation have been uncovered leading to the emerging field of epitranscriptomics dealing with RNA modifications. Among those post-transcriptional modifications, N6-methyladenosine (m6A) is the most prevalent in messenger RNAs (mRNAs). This mark can either prevent or stimulate the formation of RNA-protein complexes, thereby influencing mRNA-related mechanisms and cellular processes. This review focuses on proteins containing a YTH domain (for YT521-B Homology), a small building block, that selectively detects the m6A nucleotide embedded within a consensus motif. Thereby, it contributes to the recruitment of various effectors involved in the control of mRNA fates through adjacent regions present in the different YTH-containing proteins.

scholarly journals Dbp3p, a putative RNA helicase in Saccharomyces cerevisiae, is required for efficient pre-rRNA processing predominantly at site A3.

1997 ◽  
Vol 17 (3) ◽  
pp. 1354-1365 ◽  
Author(s):  
P L Weaver ◽  
C Sun ◽  
T H Chang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Slow Growth ◽  
Rna Helicase ◽  
Amino Terminus ◽  
Ribosomal Biogenesis ◽  
Rrna Processing ◽  
Ribosomal Subunits ◽  
Rnase Mrp ◽  
Dead Box ◽  
Evolutionarily Conserved

In Saccharomyces cerevisiae, ribosomal biogenesis takes place primarily in the nucleolus, in which a single 35S precursor rRNA (pre-rRNA) is first transcribed and sequentially processed into 25S, 5.8S, and 18S mature rRNAs, leading to the formation of the 40S and 60S ribosomal subunits. Although many components involved in this process have been identified, our understanding of this important cellular process remains limited. Here we report that one of the evolutionarily conserved DEAD-box protein genes in yeast, DBP3, is required for optimal ribosomal biogenesis. DBP3 encodes a putative RNA helicase, Dbp3p, of 523 amino acids in length, which bears a highly charged amino terminus consisting of 10 tandem lysine-lysine-X repeats ([KKX] repeats). Disruption of DBP3 is not lethal but yields a slow-growth phenotype. This genetic depletion of Dbp3p results in a deficiency of 60S ribosomal subunits and a delayed synthesis of the mature 25S rRNA, which is caused by a prominent kinetic delay in pre-rRNA processing at site A3 and to a lesser extent at sites A2 and A0. These data suggest that Dbp3p may directly or indirectly facilitate RNase MRP cleavage at site A3. The direct involvement of Dbp3p in ribosomal biogenesis is supported by the finding that Dbp3p is localized predominantly in the nucleolus. In addition, we show that the [KKX] repeats are dispensable for Dbp3p's function in ribosomal biogenesis but are required for its proper localization. The [KKX] repeats thus represent a novel signaling motif for nuclear localization and/or retention.

scholarly journals Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking

2018 ◽  
Author(s):  
Kalli Kappel ◽  
Rhiju Das
Keyword(s):  
Conformational Changes ◽  
Posttranscriptional Regulation ◽  
De Novo ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Low Resolution ◽  
Human Telomerase ◽  
Nucleotide Resolution ◽  
Rna Protein Complexes ◽  
Resolution Data

AbstractRNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe a Rosetta method called RNP-denovo to simultaneously fold and dock RNA to a protein surface. On a benchmark set of structurally diverse RNA-protein complexes that are not solvable with prior strategies, this fold-and-dock method consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges in which previous methods gave poor results: human telomerase, an RNA methyltransferase with a ribosomal RNA domain, and the spliceosome. When coupled with the same sparse FRET, cross-linking, and functional data used in previous work, RNP-denovo gave models with significantly improved accuracy. These results open a route to computationally modeling global folds of RNA-protein complexes from low-resolution data.

scholarly journals Alu RNA-protein complexes formed in vitro react with a novel lupus autoantibody.

1985 ◽  
Vol 260 (21) ◽  
pp. 11781-11786
Author(s):  
R Kole ◽  
L D Fresco ◽  
J D Keene ◽  
P L Cohen ◽  
R A Eisenberg ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Alu Rna ◽  
Rna Protein Complexes

scholarly journals Arabidopsis thaliana G3BP Ortholog Rescues Mammalian Stress Granule Phenotype across Kingdoms

2021 ◽  
Vol 22 (12) ◽  
pp. 6287
Author(s):  
Hendrik Reuper ◽  
Benjamin Götte ◽  
Lucy Williams ◽  
Timothy J. C. Tan ◽  
Gerald M. McInerney ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Fusion Proteins ◽  
Biological Function ◽  
Protein Complexes ◽  
Protein Family ◽  
Knock Out ◽  
Marker Proteins ◽  
Interaction Partners ◽  
Functional Analyses ◽  
Rna Protein Complexes

Stress granules (SGs) are dynamic RNA–protein complexes localized in the cytoplasm that rapidly form under stress conditions and disperse when normal conditions are restored. The formation of SGs depends on the Ras-GAP SH3 domain-binding protein (G3BP). Formations, interactions and functions of plant and human SGs are strikingly similar, suggesting a conserved mechanism. However, functional analyses of plant G3BPs are missing. Thus, members of the Arabidopsis thaliana G3BP (AtG3BP) protein family were investigated in a complementation assay in a human G3BP knock-out cell line. It was shown that two out of seven AtG3BPs were able to complement the function of their human homolog. GFP-AtG3BP fusion proteins co-localized with human SG marker proteins Caprin-1 and eIF4G1 and restored SG formation in G3BP double KO cells. Interaction between AtG3BP-1 and -7 and known human G3BP interaction partners such as Caprin-1 and USP10 was also demonstrated by co-immunoprecipitation. In addition, an RG/RGG domain exchange from Arabidopsis G3BP into the human G3BP background showed the ability for complementation. In summary, our results support a conserved mechanism of SG function over the kingdoms, which will help to further elucidate the biological function of the Arabidopsis G3BP protein family.

Sign in / Sign up

Export Citation Format

Share Document