The post-transcriptional life of mammalian mitochondrial RNA

2012 ◽  
Vol 444 (3) ◽  
pp. 357-373 ◽  
Author(s):  
Joanna Rorbach ◽  
Michal Minczuk
Keyword(s):  
Messenger Rna ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Stability Control ◽  
Mitochondrial Rna ◽  
Mammalian Mitochondria ◽  
Mitochondrial Ribosome ◽  
Rna Maturation ◽  
Rna Polyadenylation

Mammalian mitochondria contain their own genome that encodes mRNAs for thirteen essential subunits of the complexes performing oxidative phosporylation as well as the RNA components (two rRNAs and 22 tRNAs) needed for their translation in mitochondria. All RNA species are produced from single polycistronic precursor RNAs, yet the relative concentrations of various RNAs differ significantly. This underscores the essential role of post-transcriptional mechanisms that control the maturation, stability and translation of mitochondrial RNAs. The present review provides a detailed summary on the role of RNA maturation in the regulation of mitochondrial gene expression, focusing mainly on messenger RNA polyadenylation and stability control. Furthermore, the role of mitochondrial ribosomal RNA stability, processing and modifications in the biogenesis of the mitochondrial ribosome is discussed.

The role of a conserved dodecamer sequence in yeast mitochondrial gene expression

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 757-760 ◽  
Author(s):  
Ronald A. Butow ◽  
Hong Zhu ◽  
Philip Perlman ◽  
Heather Conrad-Webb
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Rrna Gene ◽  
Mitochondrial Gene Expression ◽  
Reading Frame ◽  
Multicomponent Complex ◽  
Var1 Gene

All mRNAs on the yeast mitochondrial genome terminate at a conserved dodecamer sequence 5′-AAUAAUAUUCUU-3′. We have characterized two mutants with altered dodecamers. One contains a deletion of the dodecamer at the end of the var1 gene, and the other contains two adjacent transversions in the dodecamer at the end of the reading frame of fit1, a gene within the ω+ allele of the 21S rRNA gene. In each mutant, expression of the respective gene is blocked completely. A dominant nuclear suppressor, SUV3-1, was isolated that suppresses the var1 deletion but is without effect on the fit1 dodecamer mutations. Unexpectedly, however, we found that SUV3-1 blocks expression of the wild-type fit1 allele by blocking processing at its dodecamer. SUV3-1 has pleiotropic effects on mitochondrial gene expression, affecting RNA processing, RNA stability, and translation. Our results suggest that RNA metabolism and translation may be part of a multicomponent complex within mitochondria.Key words: mitochondria, yeast, mRNA, RNA processing, 3′ dodecamer.

scholarly journals UTP-Dependent and -Independent Pathways of mRNA Turnover in Trypanosoma brucei Mitochondria

2000 ◽  
Vol 20 (7) ◽  
pp. 2308-2316 ◽  
Author(s):  
Kevin T. Militello ◽  
Laurie K. Read
Keyword(s):  
Steady State ◽  
Trypanosoma Brucei ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Degradation Pathway ◽  
Mitochondrial Rna ◽  
In Organello ◽  
Steady State Levels ◽  
The Stability ◽  
Mrna Polyadenylation

ABSTRACT Although primary transcripts are polycistronic in the mitochondria of Trypanosoma brucei, steady-state levels of mature, monocistronic RNAs change throughout the parasitic life cycle. This indicates that steady-state RNA abundance is controlled by posttranscriptional mechanisms involving differential RNA stability. In this study, in organello pulse-chase labeling experiments were used to analyze the stability of different T. brucei mitochondrial RNA populations. In this system, total RNA and rRNA are stable for many hours. In contrast, mRNAs can be degraded by two biochemically distinct turnover pathways. The first pathway results in the rapid degradation of mRNA (half-life [t 1/2] of 11 to 18 min) and is dependent upon the presence of an mRNA poly(A) tail. Remarkably, this pathway also requires the addition of UTP and therefore is termed UTP dependent. The second pathway results in slow turnover of mitochondrial mRNA (t 1/2 of ∼3 h) and is not dependent upon the presence of an mRNA poly(A) tail or the addition of exogenous UTP. In summary, these results demonstrate the presence of a novel, UTP-dependent degradation pathway for T. bruceimitochondrial mRNAs and reveal an unprecedented role for both UTP and mRNA polyadenylation in T. brucei mitochondrial gene expression.

scholarly journals The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs

2021 ◽  
Vol 118 (15) ◽  
pp. e2009329118
Author(s):  
Hauke S. Hillen ◽  
Dmitriy A. Markov ◽  
Ireneusz D. Wojtas ◽  
Katharina B. Hofmann ◽  
Michael Lidschreiber ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Rna Stability ◽  
Mitochondrial Rna ◽  
Pentatricopeptide Repeat ◽  
Sequence Element ◽  
Posttranscriptional Gene Regulation ◽  
The Family ◽  
Ppr Proteins

Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5′ capping and 3′ polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3′-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3′-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.

scholarly journals NSUN2 introduces 5-methylcytosines in mammalian mitochondrial tRNAs

2019 ◽  
Author(s):  
Lindsey Van Haute ◽  
Song-Yi Lee ◽  
Beverly J. McCann ◽  
Christopher A. Powell ◽  
Dhiru Bansal ◽  
...  
Keyword(s):  
Oxidative Phosphorylation ◽  
Mitochondrial Gene ◽  
Proper Function ◽  
Mitochondrial Rna ◽  
Differentiated Cells ◽  
Pathogenic Variants ◽  
Cell Proliferation And Differentiation ◽  
Mammalian Mitochondria ◽  
Proliferation And Differentiation ◽  
The Matrix

AbstractMaintenance and expression of mitochondrial DNA is indispensable for proper function of the oxidative phosphorylation machinery. Post-transcriptional modification of mitochondrial RNA has emerged as one of the key regulatory steps of human mitochondrial gene expression. Mammalian NOP2/Sun RNA Methyltransferase Family Member 2 (NSUN2) has been characterised as an RNA methyltransferase that introduces 5-methylcytosine (m5C) in nuclear-encoded tRNAs, mRNAs, microRNA and noncoding RNAs. In these roles, NSUN2 has been associated with cell proliferation and differentiation. Pathogenic variants in NSUN2 have been linked with neurodevelopmental disorders. Here we employ spatially restricted proximity labelling and immunodetection to demonstrate that NSUN2 is imported into the matrix of mammalian mitochondria. Using three genetic models for NSUN2 inactivation – knockout mice, patient-derived fibroblasts and CRISPR/Cas9 knockout in human cells – we show that NSUN2 in necessary for the generation of m5C at positions 48, 49 and 50 of several mammalian mitochondrial tRNAs. Finally, we show that inactivation of NSUN2 does not have a profound effect on mitochondrial tRNA stability and oxidative phosphorylation in differentiated cells. We discuss the importance of the newly discovered function of NSUN2 in the context of human disease.

scholarly journals Relaxed Transcription in Arabidopsis Mitochondria Is Counterbalanced by RNA Stability Control Mediated by Polyadenylation and Polynucleotide Phosphorylase

2006 ◽  
Vol 26 (7) ◽  
pp. 2869-2876 ◽  
Author(s):  
Sarah Holec ◽  
Heike Lange ◽  
Kristina Kühn ◽  
Malek Alioua ◽  
Thomas Börner ◽  
...  
Keyword(s):  
Rna Stability ◽  
Rna Degradation ◽  
Stability Control ◽  
Open Reading Frames ◽  
Mitochondrial Rna ◽  
Polynucleotide Phosphorylase ◽  
Multiple Promoters ◽  
Rna Fragments ◽  
Opposite Strand ◽  
And Control

ABSTRACT Plant mitochondrial genomes are extraordinarily large and complex compared to their animal counterparts, due to the presence of large noncoding regions. Multiple promoters are common for plant mitochondrial genes, and transcription exhibits little or no modulation. Mature functional RNAs are produced through various posttranscriptional processes, and control of RNA stability has a major impact on RNA abundance. This control involves polyadenylation which targets RNA for degradation by polynucleotide phosphorylase (PNPase). Here, we have analyzed polyadenylated RNA fragments from Arabidopsis plants down-regulated for PNPase (PNP− plants). Because of their polyadenylated status and the accumulation of the corresponding RNA in PNP− versus wild-type plants, these sequences represent mitochondrial RNA degradation tags. Analysis of these tags revealed that PNPase is involved in degrading rRNA and tRNA maturation by-products but also RNA transcribed from regions that are in some cases highly expressed although lacking known functional genes. Some of these transcripts, such as RNA containing chimeric open reading frames created by recombination or antisense RNA transcribed on the opposite strand of a known gene, may present potential detrimental effects to mitochondrial function. Taken together, our data show that the relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and PNPase.

scholarly journals Distinct mechanisms of the human mitoribosome recycling and antibiotic resistance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ravi Kiran Koripella ◽  
Ayush Deep ◽  
Ekansh K. Agrawal ◽  
Pooja Keshavan ◽  
Nilesh K. Banavali ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Elongation Factor ◽  
Acid Resistance ◽  
Functional Specificity ◽  
Ribosomal Subunits ◽  
Sequence Of Events ◽  
Mitochondrial Ribosome ◽  
Distinct Sequence ◽  
Mitochondrial Elongation

AbstractRibosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Here we present cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) and the mitoribosomal large 39S subunit in complex with mitoribosome recycling factor (RRFmt) and a recycling-specific homolog of elongation factor G (EF-G2mt). These structures clarify an unusual role of a mitochondria-specific segment of RRFmt, identify the structural distinctions that confer functional specificity to EF-G2mt, and show that the deacylated tRNA remains with the dissociated 39S subunit, suggesting a distinct sequence of events in mitoribosome recycling. Furthermore, biochemical and structural analyses reveal that the molecular mechanism of antibiotic fusidic acid resistance for EF-G2mt is markedly different from that of mitochondrial elongation factor EF-G1mt, suggesting that the two human EF-Gmts have evolved diversely to negate the effect of a bacterial antibiotic.

scholarly journals TbDSS-1, an Essential Trypanosoma brucei Exoribonuclease Homolog That Has Pleiotropic Effects on Mitochondrial RNA Metabolism

2004 ◽  
Vol 3 (5) ◽  
pp. 1206-1216 ◽  
Author(s):  
Jonelle L. Penschow ◽  
Daniel A. Sleve ◽  
Christopher M. Ryan ◽  
Laurie K. Read
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Growth Defect ◽  
Mitochondrial Rna ◽  
Mitochondrial Ribosomes ◽  
Guide Rnas ◽  
Apocytochrome B ◽  
Biochemical Fractionation

ABSTRACT Mitochondrial gene expression in trypanosomes is controlled primarily at the levels of RNA processing and RNA stability. This regulation undoubtedly involves numerous ribonucleases. Here we characterize the Trypanosoma brucei homolog of the yeast DSS-1 mitochondrial exoribonuclease, which we term TbDSS-1. Biochemical fractionation indicates that TbDSS-1 is mitochondrially localized, as predicted by its N-terminal sequence. In contrast to its yeast homolog, TbDSS-1 does not appear to be associated with mitochondrial ribosomes. Targeted downregulation of TbDSS-1 by RNA interference in procyclic-form T. brucei results in a severe growth defect. In addition, TbDSS-1 depletion leads to a decrease in the levels of never edited cytochrome oxidase subunit I (COI) mRNA and both unedited and edited COIII mRNAs, indicating this enzyme functions in the control of mitochondrial RNA abundance. We also observe a considerable reduction in the level of edited apocytochrome b (CYb) mRNA and a corresponding increase in unedited CYb mRNA, suggesting that TbDSS-1 functions, either directly or indirectly, in the control of RNA editing. The abundance of both gCYb[560] and gA6[149] guide RNAs is reduced upon TbDSS-1 depletion, although the reduction in gCYb[560] is much more dramatic. The significant reduction in gCYb levels could potentially account for the observed decrease in CYb RNA editing. Western blot analyses of mitochondrial RNA editing and stability factors indicate that the perturbations of RNA levels observed in TbDSS-1 knock-downs do not result from secondary effects on other mitochondrial proteins. In all, these data demonstrate that TbDSS-1 is an essential protein that plays a role in mitochondrial RNA stability and RNA editing.

scholarly journals Structures of the human mitochondrial ribosome recycling complexes reveal distinct mechanisms of recycling and antibiotic resistance

2020 ◽  
Author(s):  
Ravi Kiran Koripella ◽  
Ayush Deep ◽  
Ekansh K. Agrawal ◽  
Pooja Keshavan ◽  
Nilesh K. Banavali ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Conformational Changes ◽  
Messenger Rna ◽  
Elongation Factor ◽  
Ribosome Recycling Factor ◽  
Ribosomal Subunits ◽  
Sequence Of Events ◽  
Mitochondrial Ribosome ◽  
Mitochondrial Elongation

AbstractRibosomes are recycled for a new round of translation initiation by dissociation of ribosomal subunits, messenger RNA and transfer RNA from their translational post-termination complex. Mitochondrial ribosome recycling factor (RRFmt) and a recycling-specific homolog of elongation factor G (EF-G2mt) are two proteins with mitochondria-specific additional sequences that catalyze the recycling step in human mitochondria. We have determined high-resolution cryo-EM structures of the human 55S mitochondrial ribosome (mitoribosome) in complex with RRFmt, and the mitoribosomal large 39S subunit in complex with both RRFmt and EF-G2mt. In addition, we have captured the structure of a short-lived intermediate state of the 55S•RRFmt•EF-G2mt complex. These structures clarify the role of a mitochondria-specific segment of RRFmt in mitoribosome recycling, identify the structural distinctions between the two isoforms of EF-Gmt that confer their functional specificity, capture recycling-specific conformational changes in the L7/L12 stalk-base region, and suggest a distinct mechanistic sequence of events in mitoribosome recycling. Furthermore, biochemical and structural assessments of the sensitivity of EF-G2mt to the antibiotic fusidic acid reveals that the molecular mechanism of antibiotic resistance for EF-G2mt is markedly different from that exhibited by mitochondrial elongation factor EF-G1mt, suggesting that these two homologous mitochondrial proteins have evolved diversely to negate the effect of a bacterial antibiotics.

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