The Human Mitochondrial DEAD-Box Protein DDX28 Resides in RNA Granules and Functions in Mitoribosome Assembly

Tu, Yuexing; Barrientos, Antoni

doi:10.1016/j.celrep.2015.01.033

Cited by 115 publications

(114 citation statements)

References 48 publications

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“…These results were confirmed in cultured human cells although biochemical studies localized most of the protein in mitochondria [127]. DDX28 interacts with the 16S rRNA and the mtLSU [127], most probably with a helix in domain V [128]. RNAi-mediated DDX28 silencing in HEK293T cells does not affect mitochondrial mRNA stability, 16S rRNA processing or modification.…”

Section: Rna Helicasessupporting

confidence: 72%

“…GFP-fused DDX28 was detected in punctate structures in COS1 cell mitochondria, about half of which co-localized with, or were adjacent to the mitochondrial nucleoids [126]. These results were confirmed in cultured human cells although biochemical studies localized most of the protein in mitochondria [127]. DDX28 interacts with the 16S rRNA and the mtLSU [127], most probably with a helix in domain V [128].…”

Section: Rna Helicasessupporting

confidence: 62%

“…RNAi-mediated DDX28 silencing in HEK293T cells does not affect mitochondrial mRNA stability, 16S rRNA processing or modification. However, it leads to reduced levels of 16S rRNA and mtLSU proteins, impaired mtLSU assembly and deeply attenuated mitochondrial protein synthesis [127]. Our findings have identified DDX28 essential for 16S rRNA stability, perhaps during the early stages of mitoribosome mtLSU biogenesis.…”

Section: Rna Helicasesmentioning

confidence: 87%

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Mitochondrial ribosome assembly in health and disease

et al. 2015

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The ribosome is a structurally and functionally conserved macromolecular machine universally responsible for catalyzing protein synthesis. Within eukaryotic cells, mitochondria contain their own ribosomes (mitoribosomes), which synthesize a handful of proteins, all essential for the biogenesis of the oxidative phosphorylation system. High-resolution cryo-EM structures of the yeast, porcine and human mitoribosomal subunits and of the entire human mitoribosome have uncovered a wealth of new information to illustrate their evolutionary divergence from their bacterial ancestors and their adaptation to synthesis of highly hydrophobic membrane proteins. With such structural data becoming available, one of the most important remaining questions is that of the mitoribosome assembly pathway and factors involved. The regulation of mitoribosome biogenesis is paramount to mitochondrial respiration, and thus to cell viability, growth and differentiation. Moreover, mutations affecting the rRNA and protein components produce severe human mitochondrial disorders. Despite its biological and biomedical significance, knowledge on mitoribosome biogenesis and its deviations from the much-studied bacterial ribosome assembly processes is scarce, especially the order of rRNA processing and assembly events and the regulatory factors required to achieve fully functional particles. This article focuses on summarizing the current available information on mitoribosome assembly pathway, factors that form the mitoribosome assembly machinery, and the effect of defective mitoribosome assembly on human health.

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Section: Rna Helicasessupporting

confidence: 72%

Section: Rna Helicasessupporting

confidence: 62%

Section: Rna Helicasesmentioning

confidence: 87%

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Mitochondrial ribosome assembly in health and disease

et al. 2015

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“…We show that three previously uncharacterized bona fide RNA granule proteins-two RNA helicases and one FASTKD family memberplay essential and apparently non-redundant roles in different aspects of mitochondrial ribosome assembly, and we identify the 16S rRNA as a target for two of them: DDX28 and FASTKD2. A role for DDX28 in mitoribosome assembly was also reported by Tu and Barrientos (2014) in this issue of Cell Reports. Our previous investigation of GRSF1, which binds to G-rich L-strand transcripts (Antonicka et al, 2013), showed that it is also required for ribosome assembly, as suppression of GRSF1 resulted in the accumulation of a mt-SSU subassembly and a decrease in mt-LSU content.…”

Section: Discussionmentioning

confidence: 59%

Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis

Antonická¹,

Shoubridge²

2015

Cell Reports

259

282

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Cytoplasmic RNA granules play a central role in mRNA metabolism, but the importance of mitochondrial RNA granules remains relatively unexplored. We characterized their proteome and found that they contain a large toolbox of proteins dedicated to RNA metabolism. Investigation of four uncharacterized putative RNA-binding proteins-two RNA helicases, DHX30 and DDX28, and two proteins of the Fas-activated serine-threonine kinase (FASTKD) family, FASTKD2 and FASTKD5-demonstrated that both helicases and FASTKD2 are required for mitochondrial ribosome biogenesis. RNA-sequencing (RNA-seq) analysis showed that DDX28 and FASTKD2 bound the 16S rRNA. FASTKD5 is required for maturing precursor mRNAs that are not flanked by tRNAs and that therefore cannot be processed by the canonical mRNA maturation pathway. Silencing FASTKD5 rendered mature COX I mRNA almost undetectable, which severely reduced the synthesis of COX I, resulting in a complex IV assembly defect. These data demonstrate that mitochondrial RNA granules are centers for posttranscriptional RNA processing and the biogenesis of mitochondrial ribosomes.

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“…Thus, selective depletion of RNR2 may occur due to its aberrant processing or due to ribosome misassembly. Indeed, recent studies suggest that failure to assemble RNR2 with mitochondrial ribosomal proteins leads to its selective depletion, which has been proposed to be mediated by the mitochondrial degradosome (Antonicka and Shoubridge 2015;Tu and Barrientos 2015). The levels of isoleucyl tRNA (TRNI), one of the heavystrand-encoded tRNAs highly enriched in FASTKD2-GFP libraries, are unaffected by depletion of FASTKD2 by RNAi and CRISPR/Cas9-mediated mutagenesis (Fig.…”

Section: Depletion Of Fastkd2 Affects the Levels Of Several Of Its Tamentioning

confidence: 99%

FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

Popow

Alleaume

Curk

et al. 2015

RNA

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Mitochondrial RNA processing is an essential step for the synthesis of the components of the electron transport chain in all eukaryotic organisms, yet several aspects of mitochondrial RNA biogenesis and regulation are not sufficiently understood. RNA interactome capture identified several disease-relevant RNA-binding proteins (RBPs) with noncanonical RNAbinding architectures, including all six members of the FASTK (FAS-activated serine/threonine kinase) family of proteins. A mutation within one of these newly assigned FASTK RBPs, FASTKD2, causes a rare form of Mendelian mitochondrial encephalomyopathy. To investigate whether RNA binding of FASTKD2 contributes to the disease phenotype, we identified the RNA targets of FASTKD2 by iCLIP. FASTKD2 interacts with a defined set of mitochondrial transcripts including 16S ribosomal RNA (RNR2) and NADH dehydrogenase subunit 6 (ND6) messenger RNA. CRISPR-mediated deletion of FASTKD2 leads to aberrant processing and expression of RNR2 and ND6 mRNA that encodes a subunit of the respiratory complex I. Metabolic phenotyping of FASTKD2-deficient cells reveals impaired cellular respiration with reduced activities of all respiratory complexes. This work identifies key aspects of the molecular network of a previously uncharacterized, disease-relevant RNAbinding protein, FASTKD2, by a combination of genomic, molecular, and metabolic analyses.

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The Human Mitochondrial DEAD-Box Protein DDX28 Resides in RNA Granules and Functions in Mitoribosome Assembly

Cited by 115 publications

References 48 publications

Mitochondrial ribosome assembly in health and disease

Mitochondrial ribosome assembly in health and disease

Mitochondrial RNA Granules Are Centers for Posttranscriptional RNA Processing and Ribosome Biogenesis

FASTKD2 is an RNA-binding protein required for mitochondrial RNA processing and translation

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