scholarly journals The human RNA-binding protein RBFA promotes the maturation of the mitochondrial ribosome

2017 ◽  
Vol 474 (13) ◽  
pp. 2145-2158 ◽  
Author(s):  
Agata Rozanska ◽  
Ricarda Richter-Dennerlein ◽  
Joanna Rorbach ◽  
Fei Gao ◽  
Richard J. Lewis ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Rna ◽  
Mitochondrial Ribosomes ◽  
Mitochondrial Ribosome ◽  
Rrna Species

Accurate assembly and maturation of human mitochondrial ribosomes is essential for synthesis of the 13 polypeptides encoded by the mitochondrial genome. This process requires the correct integration of 80 proteins, 1 mt (mitochondrial)-tRNA and 2 mt-rRNA species, the latter being post-transcriptionally modified at many sites. Here, we report that human ribosome-binding factor A (RBFA) is a mitochondrial RNA-binding protein that exerts crucial roles in mitoribosome biogenesis. Unlike its bacterial orthologue, RBFA associates mainly with helices 44 and 45 of the 12S rRNA in the mitoribosomal small subunit to promote dimethylation of two highly conserved consecutive adenines. Characterization of RBFA-depleted cells indicates that this dimethylation is not a prerequisite for assembly of the small ribosomal subunit. However, the RBFA-facilitated modification is necessary for completing mt-rRNA maturation and regulating association of the small and large subunits to form a functional monosome implicating RBFA in the quality control of mitoribosome formation.

scholarly journals YBEY is an essential biogenesis factor for mitochondrial ribosomes

2019 ◽  
Author(s):  
Sabrina Summer ◽  
Anna Smirnova ◽  
Alessandro Gabriele ◽  
Ursula Toth ◽  
Fasemore Mandela ◽  
...  
Keyword(s):  
16S Rrna ◽  
Ribosome Biogenesis ◽  
Specific Interaction ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Translation ◽  
Mitochondrial Ribosomes ◽  
Mitochondrial Ribosome ◽  
Abnormal Mitochondria

ABSTRACTRibosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3’-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter recruits uS11m to the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation.

scholarly journals YBEY is an essential biogenesis factor for mitochondrial ribosomes

2020 ◽  
Vol 48 (17) ◽  
pp. 9762-9786 ◽  
Author(s):  
Sabrina Summer ◽  
Anna Smirnova ◽  
Alessandro Gabriele ◽  
Ursula Toth ◽  
Akinyemi Mandela Fasemore ◽  
...  
Keyword(s):  
16S Rrna ◽  
Ribosome Biogenesis ◽  
Specific Interaction ◽  
Ribosomal Subunit ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Translation ◽  
Mitochondrial Ribosomes ◽  
Mitochondrial Ribosome ◽  
Abnormal Mitochondria

Abstract Ribosome biogenesis requires numerous trans-acting factors, some of which are deeply conserved. In Bacteria, the endoribonuclease YbeY is believed to be involved in 16S rRNA 3′-end processing and its loss was associated with ribosomal abnormalities. In Eukarya, YBEY appears to generally localize to mitochondria (or chloroplasts). Here we show that the deletion of human YBEY results in a severe respiratory deficiency and morphologically abnormal mitochondria as an apparent consequence of impaired mitochondrial translation. Reduced stability of 12S rRNA and the deficiency of several proteins of the small ribosomal subunit in YBEY knockout cells pointed towards a defect in mitochondrial ribosome biogenesis. The specific interaction of mitoribosomal protein uS11m with YBEY suggests that the latter helps to properly incorporate uS11m into the nascent small subunit in its late assembly stage. This scenario shows similarities with final stages of cytosolic ribosome biogenesis, and may represent a late checkpoint before the mitoribosome engages in translation.

scholarly journals The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for proper mitochondrial function

2019 ◽  
Author(s):  
Hao Chen ◽  
Zhennan Shi ◽  
Jiaojiao Guo ◽  
Kao-jung Chang ◽  
Qianqian Chen ◽  
...  
Keyword(s):  
Mitochondrial Protein ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Rna ◽  
Protein Coding ◽  
Mitochondrial Ribosome ◽  
The Difference ◽  
And Function

ABSTRACTMitochondrial DNA (mtDNA) gene expression is coordinately regulated pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial ribosomal RNAs (mt-rRNAs) undergo a series of nucleotide modifications following release from polycistronic mitochondrial RNA (mtRNA) precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4 methylation (m4C) at position 839 of the 12S small subunit (SSU) mt-rRNA was identified decades ago, however, its biogenesis and function have not been elucidated in details. Here we demonstrate that human Methyltransferase Like 15 (METTL15) is responsible for 12S mt-rRNA methylation at C839 (m4C839) both in vivo and in vitro. We tracked the evolutionary history of RNA m4C methyltransferases and revealed the difference in substrates preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact on ribosome upon loss of m4C methylation in bacterial SSU rRNA, we found that depletion of METTL15 specifically causes severe defects in mitochondrial ribosome assembly, which leads to an impaired translation of mitochondrial protein-coding genes and a decreased mitochondrial respiration capacity. Our findings point to a co-evolution of methylatransferase specificities and modification patterns in rRNA with differential impact on prokaryotic ribosome versus eukaryotic mitochondrial ribosome.

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

RNA ◽  
2015 ◽  
Vol 21 (11) ◽  
pp. 1873-1884 ◽  
Author(s):  
Johannes Popow ◽  
Anne-Marie Alleaume ◽  
Tomaz Curk ◽  
Thomas Schwarzl ◽  
Sven Sauer ◽  
...  
Keyword(s):  
Rna Processing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mitochondrial Rna

scholarly journals Dynamics of Mitochondrial RNA-Binding Protein Complex in Trypanosoma brucei and Its Petite Mutant under Optimized Immobilization Conditions

2014 ◽  
Vol 13 (9) ◽  
pp. 1232-1240 ◽  
Author(s):  
Zhenqiu Huang ◽  
Sabine Kaltenbrunner ◽  
Eva Šimková ◽  
David Stanĕk ◽  
Julius Lukeš ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Binding ◽  
Fluorescent Protein ◽  
Binding Protein ◽  
Yellow Fluorescent Protein ◽  
Rna Binding Protein ◽  
Mitochondrial Rna ◽  
Content Type ◽  
Petite Mutant

ABSTRACT There are a variety of complex metabolic processes ongoing simultaneously in the single, large mitochondrion of Trypanosoma brucei . Understanding the organellar environment and dynamics of mitochondrial proteins requires quantitative measurement in vivo . In this study, we have validated a method for immobilizing both procyclic stage (PS) and bloodstream stage (BS) T. brucei brucei with a high level of cell viability over several hours and verified its suitability for undertaking fluorescence recovery after photobleaching (FRAP), with mitochondrion-targeted yellow fluorescent protein (YFP). Next, we used this method for comparative analysis of the translational diffusion of mitochondrial RNA-binding protein 1 (MRP1) in the BS and in T. b. evansi . The latter flagellate is like petite mutant Saccharomyces cerevisiae because it lacks organelle-encoded nucleic acids. FRAP measurement of YFP-tagged MRP1 in both cell lines illuminated from a new perspective how the absence or presence of RNA affects proteins involved in mitochondrial RNA metabolism. This work represents the first attempt to examine this process in live trypanosomes.

scholarly journals C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

2019 ◽  
Vol 47 (17) ◽  
pp. 9386-9399 ◽  
Author(s):  
Shreekara Gopalakrishna ◽  
Sarah F Pearce ◽  
Adam M Dinan ◽  
Florian A Schober ◽  
Miriam Cipullo ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Large Subunit ◽  
Regulation Of Gene Expression ◽  
Mitochondrial Protein ◽  
Rna Binding Protein ◽  
Mitochondrial Rna ◽  
Mitochondrial Translation

Abstract In all biological systems, RNAs are associated with RNA-binding proteins (RBPs), forming complexes that control gene regulatory mechanisms, from RNA synthesis to decay. In mammalian mitochondria, post-transcriptional regulation of gene expression is conducted by mitochondrial RBPs (mt-RBPs) at various stages of mt-RNA metabolism, including polycistronic transcript production, its processing into individual transcripts, mt-RNA modifications, stability, translation and degradation. To date, only a handful of mt-RBPs have been characterized. Here, we describe a putative human mitochondrial protein, C6orf203, that contains an S4-like domain—an evolutionarily conserved RNA-binding domain previously identified in proteins involved in translation. Our data show C6orf203 to bind highly structured RNA in vitro and associate with the mitoribosomal large subunit in HEK293T cells. Knockout of C6orf203 leads to a decrease in mitochondrial translation and consequent OXPHOS deficiency, without affecting mitochondrial RNA levels. Although mitoribosome stability is not affected in C6orf203-depleted cells, mitoribosome profiling analysis revealed a global disruption of the association of mt-mRNAs with the mitoribosome, suggesting that C6orf203 may be required for the proper maturation and functioning of the mitoribosome. We therefore propose C6orf203 to be a novel RNA-binding protein involved in mitochondrial translation, expanding the repertoire of factors engaged in this process.

scholarly journals The human mitochondrial 12S rRNA m4C methyltransferase METTL15 is required for mitochondrial function

2020 ◽  
Vol 295 (25) ◽  
pp. 8505-8513 ◽  
Author(s):  
Hao Chen ◽  
Zhennan Shi ◽  
Jiaojiao Guo ◽  
Kao-jung Chang ◽  
Qianqian Chen ◽  
...  
Keyword(s):  
Mitochondrial Function ◽  
Mitochondrial Protein ◽  
Nuclear Gene ◽  
Small Subunit ◽  
12S Rrna ◽  
Mitochondrial Rna ◽  
Small Subunit Rrna ◽  
Mitochondrial Ribosomes

Mitochondrial DNA gene expression is coordinately regulated both pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial rRNAs (mt-rRNAs) undergo a series of nucleotide modifications after release from polycistronic mitochondrial RNA precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N4-methylation (m4C) at position 839 (m4C839) of the 12S small subunit mt-rRNA was identified decades ago; however, its biogenesis and function have not been elucidated in detail. Here, using several approaches, including immunofluorescence, RNA immunoprecipitation and methylation assays, and bisulfite mapping, we demonstrate that human methyltransferase-like 15 (METTL15), encoded by a nuclear gene, is responsible for 12S mt-rRNA methylation at m4C839 both in vivo and in vitro. We tracked the evolutionary history of RNA m4C methyltransferases and identified a difference in substrate preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact of a loss of m4C methylation in bacterial small subunit rRNA on the ribosome, we found that METTL15 depletion results in impaired translation of mitochondrial protein-coding mRNAs and decreases mitochondrial respiration capacity. Our findings reveal that human METTL15 is required for mitochondrial function, delineate the evolution of methyltransferase substrate specificities and modification patterns in rRNA, and highlight a differential impact of m4C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.

scholarly journals RBP38, a Novel RNA-Binding Protein from Trypanosomatid Mitochondria, Modulates RNA Stability

2003 ◽  
Vol 2 (3) ◽  
pp. 560-568 ◽  
Author(s):  
Sandro Sbicego ◽  
Juan D. Alfonzo ◽  
Antonio M. Estévez ◽  
Mary Anne T. Rubio ◽  
Xuedong Kang ◽  
...  
Keyword(s):  
Rna Binding ◽  
Dissociation Constants ◽  
Binding Protein ◽  
Rna Stability ◽  
Rna Binding Protein ◽  
Homologous Gene ◽  
Mitochondrial Rna ◽  
Isolation And Characterization ◽  
Labeled Rna ◽  
The Stability

ABSTRACT We describe here the isolation and characterization of a novel RNA-binding protein, RBP38, from Leishmania tarentolae mitochondria. This protein does not contain any known RNA-binding motifs and is highly conserved among the trypanosomatids, but no homologues were found in other organisms. Recombinant LtRBP38 binds single and double-stranded (ds) RNA substrates with dissociation constants in the 100 nM range, as determined by fluorescence polarization analysis. Downregulation of expression of the homologous gene, TbRBP38, in procyclic Trypanosoma brucei by using conditional dsRNA interference resulted in 80% reduction of steady-state levels of RNAs transcribed from both maxicircle and minicircle DNA. In organello pulse-chase labeling experiments were used to determine the stability of RNAs in mitochondria that were depleted of TbRBP38. The half-life of metabolically labeled RNA decreased from ∼160 to ∼60 min after depletion. In contrast, there was no change in transcriptional activity. These observations suggest a role of RBP38 in stabilizing mitochondrial RNA.

Loss of Mitochondrial RNA Binding Protein PTCD1 Leads to Cardiomyopathy

2018 ◽  
Vol 27 ◽  
pp. S49
Author(s):  
L. Hughes ◽  
K. Perks ◽  
G. Rossetti ◽  
J. Ermer ◽  
H. Viola ◽  
...  
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Mitochondrial Rna

scholarly journals LRP130, a Pentatricopeptide Motif Protein with a Noncanonical RNA-Binding Domain, Is Bound In Vivo to Mitochondrial and Nuclear RNAs

2003 ◽  
Vol 23 (14) ◽  
pp. 4972-4982 ◽  
Author(s):  
Stavroula Mili ◽  
Serafín Piñol-Roma
Keyword(s):  
Rna Binding ◽  
Binding Protein ◽  
Mitochondrial Gene ◽  
Rna Binding Protein ◽  
Mitochondrial Rna ◽  
Potential Candidate ◽  
Pentatricopeptide Repeat ◽  
Oxidase Deficiency

ABSTRACT LRP130 (also known as LRPPRC) is an RNA-binding protein that is a constituent of postsplicing nuclear RNP complexes associated with mature mRNA. It belongs to a growing family of pentatricopeptide repeat (PPR) motif-containing proteins, several of which have been implicated in organellar RNA metabolism. We show here that only a fraction of LRP130 proteins are in nuclei and are directly bound in vivo to at least some of the same RNA molecules as the nucleocytoplasmic shuttle protein hnRNP A1. The majority of LRP130 proteins are located within mitochondria, where they are directly bound to polyadenylated RNAs in vivo. In vitro, LRP130 binds preferentially to polypyrimidines. This RNA-binding activity maps to a domain in its C-terminal region that does not contain any previously described RNA-binding motifs and that contains only 2 of the 11 predicted PPR motifs. Therefore, LRP130 is a novel type of RNA-binding protein that associates with both nuclear and mitochondrial mRNAs and as such is a potential candidate for coordinating nuclear and mitochondrial gene expression. These findings provide the first identification of a mammalian protein directly bound to mitochondrial RNA in vivo and provide a possible molecular explanation for the recently described association of mutations in LRP130 with cytochrome c oxidase deficiency in humans.

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