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.

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.

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.

scholarly journals PRH75, a new nucleus-localized member of the DEAD-box protein family from higher plants.

1997 ◽  
Vol 17 (4) ◽  
pp. 2257-2265 ◽  
Author(s):  
Z J Lorković ◽  
R G Herrmann ◽  
R Oelmüller
Keyword(s):  
Amino Acids ◽  
Rna Binding ◽  
Protein Family ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Rna Helicases ◽  
Nuclear Targeting ◽  
Dead Box ◽  
Cell Extracts ◽  
The Dead

The putative RNA helicases of the DEAD-box protein family are involved in pre-mRNA splicing, rRNA maturation, ribosome assembly, and translation. Members of this protein family have been identified in organisms from Escherichia coli to humans, but except for the translation initiation factor 4A, there have been no reports on the characterization of other DEAD-box proteins from plants. Here we report on a novel member of the DEAD-box protein family, the plant RNA helicase 75 (PRH75). PRH75 is localized in the nucleus and contains two domains for RNA binding. One is located at the C terminus and is similar to RGG RNA-binding domains of nucleus-localized RNA-binding proteins. The other one is located between amino acids 308 and 622, a region containing the conserved motif VI characteristic of DEAD-box proteins and known as the RNA-binding site of eIF-4A. The N-terminal 81 amino acids are sufficient for nuclear targeting of the protein. Northern and Western blot analyses show that PRH75 is mainly expressed in young and rapidly developing tissues. The purified recombinant PRH75 has a weak ATPase activity which is barely stimulated by RNA ligands. The fractionation of spinach whole-cell extracts by glycerol gradient centrifugation and gel filtration on a Superdex 200 column shows that the protein exists in a complex of about 500 kDa. Possible biological functions of PRH75 as well as structure-function relationships in the context of its modular primary structure are discussed.

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 The DEAD-box RNA helicase Ded1 from yeast is associated with the signal recognition particle (SRP), and its enzymatic activity is regulated by SRP21

2020 ◽  
Author(s):  
Hilal Yeter-Alat ◽  
Naïma Belgareh-Touzé ◽  
Emmeline Huvelle ◽  
Molka Mokdadi ◽  
Josette Banroques ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Rna Binding ◽  
Signal Recognition Particle ◽  
Rna Helicase ◽  
Signal Recognition ◽  
Dead Box ◽  
Enzymatic Regulation ◽  
The Dead

ABSTRACTThe DEAD-box RNA helicase Ded1 is an essential yeast protein involved in translation initiation. It belongs to the DDX3 subfamily of proteins implicated in developmental and cell-cycle regulation. In vitro, the purified Ded1 protein is an ATP-dependent RNA binding protein and an RNA-dependent ATPase, but it lacks RNA substrate specificity and enzymatic regulation. Here we demonstrate by yeast genetics, in situ localization and in vitro biochemical approaches that Ded1 is associated with, and regulated by, the signal recognition particle (SRP), which is a universally conserved ribonucleoprotein complex required for the co-translational translocation of polypeptides into the endoplasmic reticulum lumen and membrane. Ded1 is physically associated with SRP components in vivo and in vitro. Ded1 is genetically linked with SRP proteins. Finally, the enzymatic activity of Ded1 is inhibited by SRP21 with SCR1 RNA. We propose a model where Ded1 actively participates in the translocation of proteins during translation. Our results open a new comprehension of the cellular role of Ded1 during translation.

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 Association of the Cold Shock DEAD-Box RNA Helicase RhlE to the RNA Degradosome in Caulobacter crescentus

2017 ◽  
Vol 199 (13) ◽  
Author(s):  
Angel A. Aguirre ◽  
Alexandre M. Vicente ◽  
Steven W. Hardwick ◽  
Daniela M. Alvelos ◽  
Ricardo R. Mazzon ◽  
...  
Keyword(s):  
Low Temperature ◽  
Caulobacter Crescentus ◽  
Immunoblot Analysis ◽  
Rna Helicase ◽  
Rnase E ◽  
Rna Helicases ◽  
Content Type ◽  
Dead Box ◽  
Rna Degradosome ◽  
The Dead

ABSTRACT In diverse bacterial lineages, multienzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic Gram-negative bacterium Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below those optimum for growth. Phenotype analyses of rhlE, rhlB, and rhlE rhlB mutant strains show that RhlE is important for cell fitness at low temperature and its role may not be substituted by RhlB. Transcriptional and translational fusions of rhlE to the lacZ reporter gene and immunoblot analysis of an epitope-tagged RhlE indicate that its expression is induced upon temperature decrease, mainly through posttranscriptional regulation. RNase E pulldown assays show that other proteins, including the transcription termination factor Rho, a second DEAD-box RNA helicase, and ribosomal protein S1, also associate with the degradosome at low temperature. The results suggest that the RNA degradosome assembly can be remodeled with environmental change to alter its repertoire of helicases and other accessory proteins. IMPORTANCE DEAD-box RNA helicases are often present in the RNA degradosome complex, helping unwind secondary structures to facilitate degradation. Caulobacter crescentus is an interesting organism to investigate degradosome remodeling with change in temperature, because it thrives in freshwater bodies and withstands low temperature. In this study, we show that at low temperature, the cold-induced DEAD-box RNA helicase RhlE is recruited to the RNA degradosome, along with other helicases and the Rho protein. RhlE is essential for bacterial fitness at low temperature, and its function may not be complemented by RhlB, although RhlE is able to complement for rhlB loss. These results suggest that RhlE has a specific role in the degradosome at low temperature, potentially improving adaptation to this condition.

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