The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus

Senissar, Mériem; Saux, Agnès Le; Belgareh‐Touzé, Naïma; Adam, Céline; Banroques, Josette; Tanner, N. Kyle

doi:10.1093/nar/gku584

Cited by 47 publications

(113 citation statements)

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“…This suggests that protein-protein and protein-RNA associations dictate CrhR localization to the thylakoid membrane and polysome, respectively. RNA-and protein-protein-dependent association of RNA helicases has been observed in other systems (14,40,41). The ease with which CrhR was removed from the membrane fraction also indicates that protein-protein interactions and not direct membrane interactions are involved.…”

Section: Figmentioning

confidence: 75%

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

et al. 2016

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The cyanobacterium Synechocystis sp. strain PCC 6803 encodes a single DEAD box RNA helicase, CrhR, whose expression is tightly autoregulated in response to cold stress. Subcellular localization and proteomic analysis results indicate that CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with polysome and RNA degradosome components. Evidence is presented that either functional RNA helicase activity or a C-terminal localization signal was required for polysome but not thylakoid membrane localization. Polysome fractionation and runoff translation analysis results indicate that CrhR associates with actively translating polysomes. The data implicate a role for CrhR in translation or RNA degradation in the thylakoid region related to thylakoid biogenesis or stability, a role that is enhanced at low temperature. Furthermore, CrhR cosedimentation with polysome and RNA degradosome complexes links alteration of RNA secondary structure with a potential translation-RNA degradation complex in Synechocystis. IMPORTANCEThe interaction between mRNA translation and degradation is a major determinant controlling gene expression. Regulation of RNA function by alteration of secondary structure by RNA helicases performs crucial roles, not only in both of these processes but also in all aspects of RNA metabolism. Here, we provide evidence that the cyanobacterial RNA helicase CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with actively translating polysomes and RNA degradosome components. These findings link RNA helicase alteration of RNA secondary structure with translation and RNA degradation in prokaryotic systems and contribute to the data supporting the idea of the existence of a macromolecular machine catalyzing these reactions in prokaryotic systems, an association hitherto recognized only in archaea and eukarya. C ompartmentalization of metabolic processes is crucial for cells to avoid futile cycles. While this is efficiently achieved by lipid bilayers in eukaryotic cells, this solution does not generally apply in prokaryotes. Although prokaryotes have the ability to compartmentalize using invagination of the inner cell membrane, these compartments, for example, magnetosomes, tend to perform one specific function and are not widely used (1). Prokaryotes can also form proteinaceous microcompartments in which specific reactions occur, the primary cyanobacterial example being that of carboxysomes (2). Prokaryotes do not compartmentalize routine, everyday anabolic and catabolic processes such as transcription and translation or protein and RNA decay; however, there is a growing body of evidence indicating that prokaryotes spatially confine these cellular processes (3). A prime example is the localization of the RNA degradation complex, the degradosome, to the cytoplasmic membrane (CM) in Escherichia coli (4) and Bacillus subtilis (5).The E. coli degradosome consists of RNase E, polynucleotide phosphorylase (PNPase), enolase, and the DEAD box RNA he...

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Section: Figmentioning

confidence: 75%

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

et al. 2016

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“…Despite biochemical differences between DDX3X and Ded1p, DDX3X can at least partially complement a Ded1p defect in yeast (49). This observation suggests that the biological function of the helicase in yeast tolerates variation in biochemical parameters under the conditions examined in the complementation experiments.…”

Section: Discussionmentioning

confidence: 99%

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Sharma

Putnam

Jankowsky

2017

Journal of Molecular Biology

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DDX3X is a conserved DEAD-box RNA helicase involved in translation initiation and other processes of RNA metabolism. Mutations in human DDX3X and deregulation of its expression are linked to tumorigenesis and intellectual disability. The protein is also targeted by diverse viruses. Previous studies demonstrated helicase and NTPase activities for DDX3X, but important biochemical features of the enzyme remain unclear. Here, we systematically characterize enzymatic activities of human DDX3X and compare these to its closely related S. cerevisiae ortholog Ded1p. We show that DDX3X, like Ded1p, exclusively utilizes adenosine triphosphates to unwind helices, oligomerizes to function as efficient RNA helicase, and does not unwind DNA duplexes. The ATPase activity of DDX3X is markedly stimulated by RNA and weaker by DNA, although DNA binds to the enzyme. For RNA unwinding, DDX3X shows a greater preference than Ded1p for substrates with unpaired regions 3′ to the duplex over those with 5′ unpaired regions. DDX3X separates longer RNA duplexes faster than Ded1p and is less potent than Ded1p in facilitating strand annealing. Our results reveal that the biochemical activities of human DDX3X are typical for DEAD-box RNA helicases, but diverge quantitatively from its highly similar S. cerevisiae ortholog Ded1p.

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“…The binding site of DDX3 to CRM1 is a matter of debate. DDX3 has a classical N-terminal NES sequence that is conserved and required for CRM1 binding in the Saccharomyces cerevisiae homolog Ded1p48,49 and the Xenopus laevis homolog An3 31. However, Yedavalli et al observed binding between CRM1 and amino acids 260–517 of DDX3 4.…”

Section: Discussionmentioning

confidence: 99%

Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer

Voss¹,

Vesuna²,

Bol³

et al. 2017

OTT

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PurposeDEAD box protein 3 (DDX3) is an RNA helicase with oncogenic properties that shuttles between the cytoplasm and nucleus. The majority of DDX3 is found in the cytoplasm, but a subset of tumors has distinct nuclear DDX3 localization of yet unknown biological significance. This study aimed to evaluate the significance of and mechanisms behind nuclear DDX3 expression in colorectal and breast cancer.MethodsExpression of nuclear DDX3 and the nuclear exporter chromosome region maintenance 1 (CRM1) was evaluated by immunohistochemistry in 304 colorectal and 292 breast cancer patient samples. Correlations between the subcellular localization of DDX3 and CRM1 and the difference in overall survival between patients with and without nuclear DDX3 were studied. In addition, DDX3 mutants were created for in vitro evaluation of the mechanism behind nuclear retention of DDX3.ResultsDDX3 was present in the nucleus of 35% of colorectal and 48% of breast cancer patient samples and was particularly strong in the nucleolus. Nuclear DDX3 correlated with worse overall survival in both colorectal (hazard ratio [HR] 2.34, P<0.001) and breast cancer (HR 2.39, P=0.004) patients. Colorectal cancers with nuclear DDX3 expression more often had cytoplasmic expression of the nuclear exporter CRM1 (relative risk 1.67, P=0.04). In vitro analysis of DDX3 deletion mutants demonstrated that CRM1-mediated export was most dependent on the N-terminal nuclear export signal.ConclusionOverall, we conclude that nuclear DDX3 is partially CRM1-mediated and predicts worse survival in colorectal and breast cancer patients, putting it forward as a target for therapeutic intervention with DDX3 inhibitors under development in these cancer types.

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The DEAD-box helicase Ded1 from yeast is an mRNP cap-associated protein that shuttles between the cytoplasm and nucleus

Cited by 47 publications

References 100 publications

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Nuclear DDX3 expression predicts poor outcome in colorectal and breast cancer

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