The diverse roles of the eIF4A family: you are the company you keep

2014 ◽  
Vol 42 (1) ◽  
pp. 166-172 ◽  
Author(s):  
Wei-Ting Lu ◽  
Anna Wilczynska ◽  
Ewan Smith ◽  
Martin Bushell
Keyword(s):  
Atpase Activity ◽  
Rna Binding ◽  
Binding Capacity ◽  
Rna Helicase ◽  
Rna Metabolism ◽  
Present Review ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Dead Box ◽  
Partner Proteins

The eIF4A (eukaryotic initiation factor 4A) proteins belong to the extensive DEAD-box RNA helicase family, the members of which are involved in many aspects of RNA metabolism by virtue of their RNA-binding capacity and ATPase activity. Three eIF4A proteins have been characterized in vertebrates: eIF4A1 and eIF4A2 are cytoplasmic, whereas eIF4A3 is nuclear-localized. Although highly similar, they have been shown to possess rather diverse roles in the mRNA lifecycle. Their specific and diverse functions are often regulated and dictated by interacting partner proteins. The key differences between eIF4A family members are discussed in the present review.

Selective targeting of the DEAD-box RNA helicase eukaryotic initiation factor (eIF) 4A by natural products

2020 ◽  
Vol 37 (5) ◽  
pp. 609-616 ◽  
Author(s):  
Leo Shen ◽  
Jerry Pelletier
Keyword(s):  
Natural Products ◽  
Rna Binding ◽  
Rna Helicase ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Dead Box ◽  
Selective Targeting ◽  
Resident Time ◽  
The Dead

This highlight reviews natural products targeting of the eIF4A RNA helicase by interfering with RNA-binding or acting as interfacial inhibitors to increase RNA resident time.

scholarly journals The RNA Helicase eIF4A Is Required for Sapovirus Translation

2016 ◽  
Vol 90 (10) ◽  
pp. 5200-5204 ◽  
Author(s):  
Myra Hosmillo ◽  
Trevor R. Sweeney ◽  
Yasmin Chaudhry ◽  
Eoin Leen ◽  
Stephen Curry ◽  
...  
Keyword(s):  
Rna Structure ◽  
Untranslated Region ◽  
Rna Helicase ◽  
Dominant Negative ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Viral Translation ◽  
Porcine Sapovirus ◽  
Dead Box

The eukaryotic initiation factor 4A (eIF4A) is a DEAD box helicase that unwinds RNA structure in the 5′ untranslated region (UTR) of mRNAs. Here, we investigated the role of eIF4A in porcine sapovirus VPg-dependent translation. Using inhibitors and dominant-negative mutants, we found that eIF4A is required for viral translation and infectivity, suggesting that despite the presence of a very short 5′ UTR, eIF4A is required to unwind RNA structure in the sapovirus genome to facilitate virus translation.

The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis

1993 ◽  
Vol 13 (11) ◽  
pp. 6789-6798 ◽  
Author(s):  
A Pause ◽  
N Méthot ◽  
N Sonenberg
Keyword(s):  
Atpase Activity ◽  
Rna Binding ◽  
Atp Hydrolysis ◽  
Rna Helicase ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Cross Linking ◽  
Atp Binding ◽  
Eukaryotic Translation ◽  
The Dead

eIF-4A is a eukaryotic translation initiation factor that is required for mRNA binding to ribosomes. It exhibits single-stranded RNA-dependent ATPase activity, and in combination with a second initiation factor, eIF-4B, it exhibits duplex RNA helicase activity. eIF-4A is the prototype of a large family of proteins termed the DEAD box protein family, whose members share nine highly conserved amino acid regions. The functions of several of these conserved regions in eIF-4A have previously been assigned to ATP binding, ATPase, and helicase activities. To define the RNA-binding region of eIF-4A, a UV-induced cross-linking assay was used to analyze binding of mutant eIF-4A proteins to RNA. Mutants carrying mutations in the ATP-binding region (AXXXXGKT), ATPase region (DEAD), helicase region (SAT), and the most carboxy-terminal conserved region of the DEAD family, HRIGRXXR, were tested for RNA cross-linking. We show that mutations, either conservative or not, in any one of the three arginines in the HRIGRXXR sequence drastically reduced eIF-4A cross-linking to RNA. In addition, all the mutations in the HRIGRXXR region abrogate RNA helicase activity. Some but not all of these mutations affect ATP binding and ATPase activity. This is consistent with the hypothesis that the HRIGRXXR region is involved in the ATP hydrolysis reaction and would explain the coupling of ATPase and RNA-binding/helicase activities. Our results show that the HRIGRXXR region, which is QRXGRXXR or QXXGRXXR in the RNA and DNA helicases of the helicase superfamily II, is involved in ATP hydrolysis-dependent RNA interaction during unwinding. We also show that mutations in other regions of eIF-4A that abolish ATPase activity sharply decrease eIF-4A cross-linking to RNA. A model is proposed in which eIF-4A first binds ATP, resulting in a change in eIF-4A conformation which allows RNA binding that is dependent on the HRIGRXXR region. Binding of RNA induces ATP hydrolysis, leading to a more stable interaction with RNA. This process is then linked to unwinding of duplex RNA in the presence of eIF-4B.

scholarly journals G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits

2016 ◽  
Vol 212 (7) ◽  
Author(s):  
Nancy Kedersha ◽  
Marc D. Panas ◽  
Christopher A. Achorn ◽  
Shawn Lyons ◽  
Sarah Tisdale ◽  
...  
Keyword(s):  
Osmotic Stress ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Stress Granules ◽  
Stress Granule ◽  
Initiation Factor ◽  
Eukaryotic Initiation Factor ◽  
Ribosomal Subunits ◽  
Partner Proteins

Mammalian stress granules (SGs) contain stalled translation preinitiation complexes that are assembled into discrete granules by specific RNA-binding proteins such as G3BP. We now show that cells lacking both G3BP1 and G3BP2 cannot form SGs in response to eukaryotic initiation factor 2α phosphorylation or eIF4A inhibition, but are still SG-competent when challenged with severe heat or osmotic stress. Rescue experiments using G3BP1 mutants show that G3BP1-F33W, a mutant unable to bind G3BP partner proteins Caprin1 or USP10, rescues SG formation. Caprin1/USP10 binding to G3BP is mutually exclusive: Caprin binding promotes, but USP10 binding inhibits, SG formation. G3BP interacts with 40S ribosomal subunits through its RGG motif, which is also required for G3BP-mediated SG formation. We propose that G3BP mediates the condensation of SGs by shifting between two different states that are controlled by binding to Caprin1 or USP10.

scholarly journals The DEAD-box RNA helicase Ded1 has a role in the translational response to TORC1 inhibition

2019 ◽  
Vol 30 (17) ◽  
pp. 2171-2184 ◽  
Author(s):  
Peyman P. Aryanpur ◽  
David M. Renner ◽  
Emily Rodela ◽  
Telsa M. Mittelmeier ◽  
Aaron Byrd ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Rna Helicase ◽  
Initiation Factor ◽  
Untranslated Regions ◽  
Eukaryotic Initiation Factor ◽  
Functional Requirements ◽  
Dead Box ◽  
Eif4f Complex ◽  
Mrna Pool ◽  
Mutant Cells

Ded1 is a DEAD-box RNA helicase with essential roles in translation initiation. It binds to the eukaryotic initiation factor 4F (eIF4F) complex and promotes 48S preinitiation complex assembly and start-site scanning of 5′ untranslated regions of mRNAs. Most prior studies of Ded1 cellular function were conducted in steady-state conditions during nutrient-rich growth. In this work, however, we examine its role in the translational response during target of rapamycin (TOR)C1 inhibition and identify a novel function of Ded1 as a translation repressor. We show that C-terminal mutants of DED1 are defective in down-regulating translation following TORC1 inhibition using rapamycin. Furthermore, following TORC1 inhibition, eIF4G1 normally dissociates from translation complexes and is degraded, and this process is attenuated in mutant cells. Mapping of the functional requirements for Ded1 in this translational response indicates that Ded1 enzymatic activity and interaction with eIF4G1 are required, while homo-oligomerization may be dispensable. Our results are consistent with a model wherein Ded1 stalls translation and specifically removes eIF4G1 from translation preinitiation complexes, thus removing eIF4G1 from the translating mRNA pool and leading to the codegradation of both proteins. Shared features among DED1 orthologues suggest that this role is conserved and may be implicated in pathologies such as oncogenesis.

scholarly journals The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis.

1993 ◽  
Vol 13 (11) ◽  
pp. 6789-6798 ◽  
Author(s):  
A Pause ◽  
N Méthot ◽  
N Sonenberg
Keyword(s):  
Atpase Activity ◽  
Rna Binding ◽  
Atp Hydrolysis ◽  
Rna Helicase ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Cross Linking ◽  
Atp Binding ◽  
Eukaryotic Translation ◽  
The Dead

eIF-4A is a eukaryotic translation initiation factor that is required for mRNA binding to ribosomes. It exhibits single-stranded RNA-dependent ATPase activity, and in combination with a second initiation factor, eIF-4B, it exhibits duplex RNA helicase activity. eIF-4A is the prototype of a large family of proteins termed the DEAD box protein family, whose members share nine highly conserved amino acid regions. The functions of several of these conserved regions in eIF-4A have previously been assigned to ATP binding, ATPase, and helicase activities. To define the RNA-binding region of eIF-4A, a UV-induced cross-linking assay was used to analyze binding of mutant eIF-4A proteins to RNA. Mutants carrying mutations in the ATP-binding region (AXXXXGKT), ATPase region (DEAD), helicase region (SAT), and the most carboxy-terminal conserved region of the DEAD family, HRIGRXXR, were tested for RNA cross-linking. We show that mutations, either conservative or not, in any one of the three arginines in the HRIGRXXR sequence drastically reduced eIF-4A cross-linking to RNA. In addition, all the mutations in the HRIGRXXR region abrogate RNA helicase activity. Some but not all of these mutations affect ATP binding and ATPase activity. This is consistent with the hypothesis that the HRIGRXXR region is involved in the ATP hydrolysis reaction and would explain the coupling of ATPase and RNA-binding/helicase activities. Our results show that the HRIGRXXR region, which is QRXGRXXR or QXXGRXXR in the RNA and DNA helicases of the helicase superfamily II, is involved in ATP hydrolysis-dependent RNA interaction during unwinding. We also show that mutations in other regions of eIF-4A that abolish ATPase activity sharply decrease eIF-4A cross-linking to RNA. A model is proposed in which eIF-4A first binds ATP, resulting in a change in eIF-4A conformation which allows RNA binding that is dependent on the HRIGRXXR region. Binding of RNA induces ATP hydrolysis, leading to a more stable interaction with RNA. This process is then linked to unwinding of duplex RNA in the presence of eIF-4B.

scholarly journals Crystal structure of yeast initiation factor 4A, a DEAD-box RNA helicase

2000 ◽  
Vol 97 (24) ◽  
pp. 13080-13085 ◽  
Author(s):  
J. M. Caruthers ◽  
E. R. Johnson ◽  
D. B. McKay
Keyword(s):  
Crystal Structure ◽  
Rna Helicase ◽  
Initiation Factor ◽  
Dead Box

The multiple lives of DEAD-box RNA helicase DP103/DDX20/Gemin3

2018 ◽  
Vol 46 (2) ◽  
pp. 329-341 ◽  
Author(s):  
Frank Curmi ◽  
Ruben J. Cauchi
Keyword(s):  
Rna Binding ◽  
Muscular Atrophy ◽  
Essential Gene ◽  
Rna Helicase ◽  
Survival Motor Neuron ◽  
In Vivo Studies ◽  
Critical Function ◽  
Dead Box ◽  
Small Nuclear Ribonucleoprotein

Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro, it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function. This review article focuses on the known roles of Gemin3, first as a core member of the survival motor neuron (SMN) complex, in small nuclear ribonucleoprotein biogenesis. Although mechanistic details are lacking, a critical function for Gemin3 in this pathway is supported by numerous in vitro and in vivo studies. Gene expression activities of Gemin3 are next underscored, mainly messenger ribonucleoprotein trafficking, gene silencing via microRNA processing, and transcriptional regulation. The involvement of Gemin3 in abnormal cell signal transduction pathways involving p53 and NF-κB is also highlighted. Finally, the clinical implications of Gemin3 deregulation are discussed including links to spinal muscular atrophy, poliomyelitis, amyotrophic lateral sclerosis, and cancer. Impressive progress made over the past two decades since the discovery of Gemin3 bodes well for further work that refines the mechanism(s) underpinning its multiple activities.

scholarly journals The temperature-regulated DEAD-box RNA helicase CrhR interactome: Autoregulation and photosynthesis-related transcripts

2021 ◽  
Author(s):  
Anzhela Migur ◽  
Florian Heyl ◽  
Janina Fuss ◽  
Afshan Srikumar ◽  
Bruno Huettel ◽  
...  
Keyword(s):  
Stress Responses ◽  
Rna Binding ◽  
Regulation Of Gene Expression ◽  
Physiological Role ◽  
Photosynthetic Electron Transport ◽  
Gene Families ◽  
Rna Helicase ◽  
Rna Helicases ◽  
Diverse Range ◽  
Dead Box

RNA helicases play crucial functions in RNA biology. In plants, RNA helicases are encoded by large gene families, performing roles in abiotic stress responses, development, the post-transcriptional regulation of gene expression as well as house-keeping functions. Several of these RNA helicases are targeted to the organelles, mitochondria and chloroplasts. Cyanobacteria are the direct evolutionary ancestors of plant chloroplasts. The cyanobacterium Synechocystis 6803 encodes a single DEAD-box RNA helicase, CrhR, that is induced by a range of abiotic stresses, including low temperature. Though the ΔcrhR mutant exhibits a severe cold-sensitive phenotype, the physiological function(s) performed by CrhR have not been described. To identify transcripts interacting with CrhR, we performed RNA co-immunoprecipitation with extracts from a Synechocystis crhR deletion mutant expressing the FLAG-tagged native CrhR or a K57A mutated version with an anticipated enhanced RNA binding. The composition of the interactome was strikingly biased towards photosynthesis-associated and redox-controlled transcripts. A transcript highly enriched in all experiments was the crhR mRNA, suggesting an auto-regulatory molecular mechanism. The identified interactome explains the described physiological role of CrhR in response to the redox poise of the photosynthetic electron transport chain and characterizes CrhR as an enzyme with a diverse range of transcripts as molecular targets.

scholarly journals Structural insights into RNA recognition by the Chikungunya virus nsP2 helicase

2019 ◽  
Vol 116 (19) ◽  
pp. 9558-9567 ◽  
Author(s):  
Yee-Song Law ◽  
Age Utt ◽  
Yaw Bia Tan ◽  
Jie Zheng ◽  
Sainan Wang ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Chikungunya Virus ◽  
Rna Binding ◽  
Nonstructural Protein ◽  
Rna Helicase ◽  
Viral Rna ◽  
Helicase Domain ◽  
Stacking Interactions ◽  
Adaptive Mutations ◽  
Rna Backbone

Chikungunya virus (CHIKV) is transmitted to humans through mosquitoes and causes Chikungunya fever. Nonstructural protein 2 (nsP2) exhibits the protease and RNA helicase activities that are required for viral RNA replication and transcription. Unlike for the C-terminal protease, the structure of the N-terminal RNA helicase (nsP2h) has not been determined. Here, we report the crystal structure of the nsP2h bound to the conserved 3′-end 14 nucleotides of the CHIKV genome and the nonhydrolyzable transition-state nucleotide analog ADP-AlF4. Overall, the structural analysis revealed that nsP2h adopts a uniquely folded N-terminal domain followed by a superfamily 1 RNA helicase fold. The conserved helicase motifs establish polar contacts with the RNA backbone. There are three hydrophobic residues (Y161, F164, and F287) which form stacking interactions with RNA bases and thereby bend the RNA backbone. An F287A substitution that disrupted these stacking interactions increased the basal ATPase activity but decreased the RNA binding affinity. Furthermore, the F287A substitution reduced viral infectivity by attenuating subgenomic RNA synthesis. Replication of the mutant virus was restored by pseudoreversion (A287V) or adaptive mutations in the RecA2 helicase domain (T358S or V410I). Y161A and/or F164A substitutions, which were designed to disrupt the interactions with the RNA molecule, did not affect the ATPase activity but completely abolished the replication and transcription of viral RNA and the infectivity of CHIKV. Our study sheds light on the roles of the RNA helicase region in viral replication and provides insights that might be applicable to alphaviruses and other RNA viruses in general.

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