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1.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33526660

RESUMO

Human mitochondria contain their own genome, mitochondrial DNA, that is expressed in the mitochondrial matrix. This genome encodes 13 vital polypeptides that are components of the multisubunit complexes that couple oxidative phosphorylation (OXPHOS). The inner mitochondrial membrane that houses these complexes comprises the inner boundary membrane that runs parallel to the outer membrane, infoldings that form the cristae membranes, and the cristae junctions that separate the two. It is in these cristae membranes that the OXPHOS complexes have been shown to reside in various species. The majority of the OXPHOS subunits are nuclear-encoded and must therefore be imported from the cytosol through the outer membrane at contact sites with the inner boundary membrane. As the mitochondrially encoded components are also integral members of these complexes, where does protein synthesis occur? As transcription, mRNA processing, maturation, and at least part of the mitoribosome assembly process occur at the nucleoid and the spatially juxtaposed mitochondrial RNA granules, is protein synthesis also performed at the RNA granules close to these entities, or does it occur distal to these sites? We have adapted a click chemistry-based method coupled with stimulated emission depletion nanoscopy to address these questions. We report that, in human cells in culture, within the limits of our methodology, the majority of mitochondrial protein synthesis is detected at the cristae membranes and is spatially separated from the sites of RNA processing and maturation.


Assuntos
Compartimento Celular , Imageamento Tridimensional , Proteínas Mitocondriais/biossíntese , Biossíntese de Proteínas , Alcinos , Células Cultivadas , DNA Mitocondrial/genética , Glicina/análogos & derivados , Humanos , Cinética , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Ribossomos Mitocondriais/metabolismo , RNA Mitocondrial/metabolismo , Transdução de Sinais
2.
FEBS J ; 288(2): 437-451, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-32329962

RESUMO

In mammalian mitochondria, messenger RNA is processed and matured from large primary transcripts in structures known as RNA granules. The identity of the factors and process transferring the matured mRNA to the mitoribosome for translation is unclear. Nascent mature transcripts are believed to associate initially with the small mitoribosomal subunit prior to recruitment of the large subunit to form the translationally active monosome. When the small subunit fails to assemble, however, the stability of mt-mRNA is only marginally affected, and under these conditions, the LRPPRC/SLIRP RNA-binding complex has been implicated in maintaining mt-mRNA stability. Here, we exploit the activity of a bacterial ribotoxin, VapC20, to show that in the absence of the large mitoribosomal subunit, mt-mRNA species are selectively lost. Further, if the small subunit is also depleted, the mt-mRNA levels are recovered. As a consequence of these data, we suggest a natural pathway for loading processed mt-mRNA onto the mitoribosome.


Assuntos
Toxinas Bacterianas/genética , Mitocôndrias/genética , Ribossomos Mitocondriais/metabolismo , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA Ribossômico 16S/genética , Ribonucleases/genética , Toxinas Bacterianas/metabolismo , Sequência de Bases , Transporte Biológico , Engenharia Celular/métodos , Linhagem Celular , Células HEK293 , Humanos , Mitocôndrias/metabolismo , Mitocôndrias/ultraestrutura , ATPases Mitocondriais Próton-Translocadoras/genética , ATPases Mitocondriais Próton-Translocadoras/metabolismo , Ribossomos Mitocondriais/ultraestrutura , Mycobacterium tuberculosis/química , Mycobacterium tuberculosis/metabolismo , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neurospora crassa/química , Neurospora crassa/metabolismo , Conformação de Ácido Nucleico , Processamento Pós-Transcricional do RNA , Estabilidade de RNA , RNA Mensageiro/química , RNA Mensageiro/metabolismo , RNA Ribossômico 16S/química , RNA Ribossômico 16S/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Ribonucleases/metabolismo
3.
Methods Mol Biol ; 2192: 159-181, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33230773

RESUMO

Human mitochondria contain their own DNA (mtDNA) that encodes 13 proteins all of which are core subunits of oxidative phosphorylation (OXPHOS) complexes. To form functional complexes, these 13 components need to be correctly assembled with approximately 70 nuclear-encoded subunits that are imported following synthesis in the cytosol. How this complicated coordinated translation and assembly is choreographed is still not clear. Methods are being developed to determine whether all members of a particular complex are translated in close proximity, whether protein synthesis is clustered in submitochondrial factories, whether these align with incoming polypeptides, and if there is evidence for co-translational translation that is regulated and limited by the interaction of the incoming proteins with synthesis of their mtDNA-encoded partners. Two methods are described in this chapter to visualize the distribution of mitochondrial ribosomal RNAs in conjunction with newly synthesized mitochondrial proteins. The first combines RNA Fluorescent In Situ Hybridization (FISH) and super-resolution immunocytochemistry to pinpoint mitochondrial ribosomal RNA. The second localizes nascent translation within the mitochondrial network through non-canonical amino acid labeling, click chemistry and fluorescent microscopy.


Assuntos
Química Click/métodos , Imuno-Histoquímica/métodos , Hibridização in Situ Fluorescente/métodos , Proteínas Mitocondriais/metabolismo , Ribossomos Mitocondriais/metabolismo , RNA Mitocondrial/metabolismo , RNA Ribossômico/metabolismo , Aminoácidos/química , Linhagem Celular Tumoral , DNA Mitocondrial/genética , Humanos , Microscopia de Fluorescência/métodos , Fosforilação Oxidativa , Biossíntese de Proteínas , Proteínas Ribossômicas/metabolismo
4.
J Cell Sci ; 133(1)2020 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-31896602

RESUMO

In the canonical process of translation, newly completed proteins escape from the ribosome following cleavage of the ester bond that anchors the polypeptide to the P-site tRNA, after which the ribosome can be recycled to initiate a new round of translation. Not all protein synthesis runs to completion as various factors can impede the progression of ribosomes. Rescuing of stalled ribosomes in mammalian mitochondria, however, does not share the same mechanisms that many bacteria use. The classic method for rescuing bacterial ribosomes is trans-translation. The key components of this system are absent from mammalian mitochondria; however, four members of a translation termination factor family are present, with some evidence of homology to members of a bacterial back-up rescue system. To date, there is no definitive demonstration of any other member of this family functioning in mitoribosome rescue. Here, we provide an overview of the processes and key players of canonical translation termination in both bacteria and mammalian mitochondria, followed by a perspective of the bacterial systems used to rescue stalled ribosomes. We highlight any similarities or differences with the mitochondrial translation release factors, and suggest potential roles for these proteins in ribosome rescue in mammalian mitochondria.


Assuntos
Bactérias/metabolismo , Ribossomos Mitocondriais/metabolismo , Animais
5.
Hum Mol Genet ; 27(10): 1743-1753, 2018 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-29518248

RESUMO

LonP1 is a mitochondrial matrix protease whose selective substrate specificity is essential for maintaining mitochondrial homeostasis. Recessively inherited, pathogenic defects in LonP1 have been previously reported to underlie cerebral, ocular, dental, auricular and skeletal anomalies (CODAS) syndrome, a complex multisystemic and developmental disorder. Intriguingly, although classical mitochondrial disease presentations are well-known to exhibit marked clinical heterogeneity, the skeletal and dental features associated with CODAS syndrome are pathognomonic. We have applied whole exome sequencing to a patient with congenital lactic acidosis, muscle weakness, profound deficiencies in mitochondrial oxidative phosphorylation associated with loss of mtDNA copy number and MRI abnormalities consistent with Leigh syndrome, identifying biallelic variants in the LONP1 (NM_004793.3) gene; c.1693T > C predicting p.(Tyr565His) and c.2197G > A predicting p.(Glu733Lys); no evidence of the classical skeletal or dental defects observed in CODAS syndrome patients were noted in our patient. In vitro experiments confirmed the p.(Tyr565His) LonP1 mutant alone could not bind or degrade a substrate, consistent with the predicted function of Tyr565, whilst a second missense [p.(Glu733Lys)] variant had minimal effect. Mixtures of p.(Tyr565His) mutant and wild-type LonP1 retained partial protease activity but this was severely depleted when the p.(Tyr565His) mutant was mixed with the p.(Glu733Lys) mutant, data consistent with the compound heterozygosity detected in our patient. In summary, we conclude that pathogenic LONP1 variants can lead to a classical mitochondrial disease presentations associated with severe biochemical defects in oxidative phosphorylation in clinically relevant tissues.


Assuntos
Proteases Dependentes de ATP/genética , Anormalidades Craniofaciais/genética , Anormalidades do Olho/genética , Transtornos do Crescimento/genética , Luxação Congênita de Quadril/genética , Doença de Leigh/genética , Doenças Mitocondriais/genética , Proteínas Mitocondriais/genética , Osteocondrodisplasias/genética , Anormalidades Dentárias/genética , Biópsia , Linhagem Celular , Anormalidades Craniofaciais/metabolismo , Anormalidades Craniofaciais/fisiopatologia , Exoma/genética , Anormalidades do Olho/metabolismo , Anormalidades do Olho/fisiopatologia , Transtornos do Crescimento/metabolismo , Transtornos do Crescimento/fisiopatologia , Luxação Congênita de Quadril/metabolismo , Luxação Congênita de Quadril/fisiopatologia , Humanos , Lactente , Doença de Leigh/metabolismo , Doença de Leigh/fisiopatologia , Masculino , Mitocôndrias/genética , Mitocôndrias/patologia , Doenças Mitocondriais/metabolismo , Doenças Mitocondriais/fisiopatologia , Músculo Esquelético/fisiopatologia , Mutação , Osteocondrodisplasias/metabolismo , Osteocondrodisplasias/fisiopatologia , Fosforilação Oxidativa , Anormalidades Dentárias/metabolismo , Anormalidades Dentárias/fisiopatologia , Sequenciamento do Exoma
6.
Biochem J ; 474(13): 2145-2158, 2017 06 13.
Artigo em Inglês | MEDLINE | ID: mdl-28512204

RESUMO

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.


Assuntos
Proteínas de Escherichia coli/metabolismo , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Ribossomos Mitocondriais/metabolismo , RNA Ribossômico/metabolismo , Proteínas de Ligação a RNA/metabolismo , Proteínas Ribossômicas/metabolismo , Sequência de Aminoácidos , Proteínas de Escherichia coli/genética , Células HEK293 , Humanos , Mitocôndrias/genética , Proteínas Mitocondriais/genética , RNA Ribossômico/genética , Proteínas de Ligação a RNA/genética , Proteínas Ribossômicas/genética , Homologia de Sequência de Aminoácidos
7.
Autophagy ; 13(1): 99-113, 2017 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-27791464

RESUMO

Macroautophagy/autophagy has profound implications for aging. However, the true features of autophagy in the progression of aging remain to be clarified. In the present study, we explored the status of autophagic flux during the development of cell senescence induced by oxidative stress. In this system, although autophagic structures increased, the degradation of SQSTM1/p62 protein, the yellow puncta of mRFP-GFP-LC3 fluorescence and the activity of lysosomal proteolytic enzymes all decreased in senescent cells, indicating impaired autophagic flux with lysosomal dysfunction. The influence of autophagy activity on senescence development was confirmed by both positive and negative autophagy modulators; and MTOR-dependent autophagy activators, rapamycin and PP242, efficiently suppressed cellular senescence through a mechanism relevant to restoring autophagic flux. By time-phased treatment of cells with the antioxidant N-acetylcysteine (NAC), the mitochondria uncoupler carbonyl cyanide m-chlorophenyl hydrazone (CCCP) and ambroxol, a reagent with the effect of enhancing lysosomal enzyme maturation, we found that mitochondrial dysfunction plays an initiating role, while lysosomal dysfunction is more directly responsible for autophagy impairment and senescence. Interestingly, the effect of rapamycin on autophagy flux is linked to its role in functional revitalization of both mitochondrial and lysosomal functions. Together, this study demonstrates that autophagy impairment is crucial for oxidative stress-induced cell senescence, thus restoring autophagy activity could be a promising way to retard senescence.


Assuntos
Autofagia , Senescência Celular/fisiologia , Lisossomos/metabolismo , Mitocôndrias/metabolismo , Estresse Oxidativo , Acetilcisteína/metabolismo , Trifosfato de Adenosina/química , Animais , Antioxidantes/química , Humanos , Peróxido de Hidrogênio/química , Camundongos , Microscopia Confocal , Células NIH 3T3 , Espécies Reativas de Oxigênio/metabolismo , Proteína Sequestossoma-1/metabolismo , Transdução de Sinais , Serina-Treonina Quinases TOR/metabolismo
8.
Nucleic Acids Res ; 44(14): 6868-82, 2016 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-27353330

RESUMO

LRPPRC is a protein that has attracted interest both for its role in post-transcriptional regulation of mitochondrial gene expression and more recently because numerous mutated variants have been characterized as causing severe infantile mitochondrial neurodegeneration. LRPPRC belongs to the pentatricopeptide repeat (PPR) protein family, originally defined by their RNA binding capacity, and forms a complex with SLIRP that harbours an RNA recognition motif (RRM) domain. We show here that LRPPRC displays a broad and strong RNA binding capacity in vitro in contrast to SLIRP that associates only weakly with RNA. The LRPPRC-SLIRP complex comprises a hetero-dimer via interactions by polar amino acids in the single RRM domain of SLIRP and three neighbouring PPR motifs in the second quarter of LRPPRC, which critically contribute to the LRPPRC-SLIRP binding interface to enhance its stability. Unexpectedly, specific amino acids at this interface are located within the PPRs of LRPPRC at positions predicted to interact with RNA and within the RNP1 motif of SLIRP's RRM domain. Our findings thus unexpectedly establish that despite the prediction that these residues in LRPPRC and SLIRP should bind RNA, they are instead used to facilitate protein-protein interactions, enabling the formation of a stable complex between these two proteins.


Assuntos
Proteínas de Neoplasias/metabolismo , Motivo de Reconhecimento de RNA , Proteínas de Ligação a RNA/metabolismo , Sequências Repetitivas de Aminoácidos , Sequência de Aminoácidos , Aminoácidos/genética , Sequência Conservada , Reagentes de Ligações Cruzadas/metabolismo , Células HEK293 , Humanos , Modelos Biológicos , Mutação/genética , Proteínas de Neoplasias/química , Ligação Proteica , Multimerização Proteica , Estabilidade Proteica , RNA/metabolismo , Proteínas de Ligação a RNA/química
9.
Brain ; 138(Pt 12): 3503-19, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26510951

RESUMO

Mitochondrial Complex IV [cytochrome c oxidase (COX)] deficiency is one of the most common respiratory chain defects in humans. The clinical phenotypes associated with COX deficiency include liver disease, cardiomyopathy and Leigh syndrome, a neurodegenerative disorder characterized by bilateral high signal lesions in the brainstem and basal ganglia. COX deficiency can result from mutations affecting many different mitochondrial proteins. The French-Canadian variant of COX-deficient Leigh syndrome is unique to the Saguenay-Lac-Saint-Jean region of Québec and is caused by a founder mutation in the LRPPRC gene. This encodes the leucine-rich pentatricopeptide repeat domain protein (LRPPRC), which is involved in post-transcriptional regulation of mitochondrial gene expression. Here, we present the clinical and molecular characterization of novel, recessive LRPPRC gene mutations, identified using whole exome and candidate gene sequencing. The 10 patients come from seven unrelated families of UK-Caucasian, UK-Pakistani, UK-Indian, Turkish and Iraqi origin. They resemble the French-Canadian Leigh syndrome patients in having intermittent severe lactic acidosis and early-onset neurodevelopmental problems with episodes of deterioration. In addition, many of our patients have had neonatal cardiomyopathy or congenital malformations, most commonly affecting the heart and the brain. All patients who were tested had isolated COX deficiency in skeletal muscle. Functional characterization of patients' fibroblasts and skeletal muscle homogenates showed decreased levels of mutant LRPPRC protein and impaired Complex IV enzyme activity, associated with abnormal COX assembly and reduced steady-state levels of numerous oxidative phosphorylation subunits. We also identified a Complex I assembly defect in skeletal muscle, indicating different roles for LRPPRC in post-transcriptional regulation of mitochondrial mRNAs between tissues. Patient fibroblasts showed decreased steady-state levels of mitochondrial mRNAs, although the length of poly(A) tails of mitochondrial transcripts were unaffected. Our study identifies LRPPRC as an important disease-causing gene in an early-onset, multisystem and neurological mitochondrial disease, which should be considered as a cause of COX deficiency even in patients originating outside of the French-Canadian population.


Assuntos
Deficiência de Citocromo-c Oxidase/genética , Doenças Mitocondriais/genética , Proteínas de Neoplasias/genética , Proteínas/genética , Canadá , Células Cultivadas , Pré-Escolar , Deficiência de Citocromo-c Oxidase/enzimologia , Complexo IV da Cadeia de Transporte de Elétrons/metabolismo , Feminino , Fibroblastos/metabolismo , Humanos , Lactente , Recém-Nascido , Proteínas de Repetições Ricas em Leucina , Masculino , Doenças Mitocondriais/enzimologia , Doenças Mitocondriais/metabolismo , Proteínas Mitocondriais/metabolismo , Músculo Esquelético/metabolismo , Mutação , Linhagem , Proteínas/metabolismo , RNA Mensageiro/metabolismo , RNA Mitocondrial
10.
Front Microbiol ; 5: 374, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25101074

RESUMO

Protein synthesis is central to life and maintaining a highly accurate and efficient mechanism is essential. What happens when a translating ribosome stalls on a messenger RNA? Many highly intricate processes have been documented in the cytosol of numerous species, but how does organellar protein synthesis resolve this stalling issue? Mammalian mitochondria synthesize just thirteen highly hydrophobic polypeptides. These proteins are all integral components of the machinery that couples oxidative phosphorylation. Consequently, it is essential that stalled mitochondrial ribosomes can be efficiently recycled. To date, there is no evidence to support any particular molecular mechanism to resolve this problem. However, here we discuss the observation that there are four predicted members of the mitochondrial translation release factor family and that only one member, mtRF1a, is necessary to terminate the translation of all thirteen open reading frames in the mitochondrion. Could the other members be involved in the process of recycling stalled mitochondrial ribosomes?

11.
Hum Mol Genet ; 23(23): 6345-55, 2014 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-25008111

RESUMO

The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of de novo mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. In vitro polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes.


Assuntos
Proteínas Mitocondriais/metabolismo , Polinucleotídeo Adenililtransferase/metabolismo , RNA Mensageiro/metabolismo , Fibroblastos/metabolismo , Expressão Gênica , Humanos , Proteínas Mitocondriais/genética , Mutação , Proteínas de Neoplasias/metabolismo , Fosforilação Oxidativa , Polinucleotídeo Adenililtransferase/genética , Cultura Primária de Células , Processamento Pós-Transcricional do RNA , RNA Mitocondrial , Proteínas de Ligação a RNA/metabolismo
12.
FEBS Lett ; 588(15): 2496-503, 2014 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-24911204

RESUMO

Mitochondrial protein synthesis is essential for all mammals, being responsible for providing key components of the oxidative phosphorylation complexes. Although only thirteen different polypeptides are made, the molecular details of this deceptively simple process remain incomplete. Central to this process is a non-canonical ribosome, the mitoribosome, which has evolved to address its unique mandate. In this review, we integrate the current understanding of the molecular aspects of mitochondrial translation with recent advances in structural biology. We identify numerous key questions that we will need to answer if we are to increase our knowledge of the molecular mechanisms underlying mitochondrial protein synthesis.


Assuntos
Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Biossíntese de Proteínas , Proteínas Ribossômicas/metabolismo , Animais , Humanos , Proteínas Mitocondriais/genética , RNA/genética , RNA/metabolismo , RNA Mitocondrial , Proteínas Ribossômicas/genética , Ribossomos/metabolismo
13.
Hum Mol Genet ; 23(4): 949-67, 2014 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-24092330

RESUMO

Mutations of mitochondrial DNA are linked to many human diseases. Despite the identification of a large number of variants in the mitochondrially encoded rRNA (mt-rRNA) genes, the evidence supporting their pathogenicity is, at best, circumstantial. Establishing the pathogenicity of these variations is of major diagnostic importance. Here, we aim to estimate the disruptive effect of mt-rRNA variations on the function of the mitochondrial ribosome. In the absence of direct biochemical methods to study the effect of mt-rRNA variations, we relied on the universal conservation of the rRNA fold to infer their disruptive potential. Our method, named heterologous inferential analysis or HIA, combines conservational information with functional and structural data obtained from heterologous ribosomal sources. Thus, HIA's predictive power is superior to the traditional reliance on simple conservation indexes. By using HIA, we have been able to evaluate the disruptive potential for a subset of uncharacterized 12S mt-rRNA variations. Our analysis revealed the existence of variations in the rRNA component of the human mitoribosome with different degrees of disruptive power. In cases where sufficient information regarding the genetic and pathological manifestation of the mitochondrial phenotype is available, HIA data can be used to predict the pathogenicity of mt-rRNA mutations. In other cases, HIA analysis will allow the prioritization of variants for additional investigation. Eventually, HIA-inspired analysis of potentially pathogenic mt-rRNA variations, in the context of a scoring system specifically designed for these variants, could lead to a powerful diagnostic tool.


Assuntos
RNA Ribossômico/genética , RNA/genética , Simulação por Computador , Sequência Conservada , Análise Mutacional de DNA , Estudos de Associação Genética , Humanos , Modelos Moleculares , Mutação , Neoplasias/genética , Conformação de Ácido Nucleico , RNA/química , RNA Mitocondrial , RNA Ribossômico/química
14.
PLoS One ; 8(5): e64670, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23741365

RESUMO

The Escherichia coli oligoribonuclease, ORN, has a 3' to 5' exonuclease activity specific for small oligomers that is essential for cell viability. The human homologue, REXO2, has hitherto been incompletely characterized, with only its in vitro ability to degrade small single-stranded RNA and DNA fragments documented. Here we show that the human enzyme has clear dual cellular localization being present both in cytosolic and mitochondrial fractions. Interestingly, the mitochondrial form localizes to both the intermembrane space and the matrix. Depletion of REXO2 by RNA interference causes a strong morphological phenotype in human cells, which show a disorganized network of punctate and granular mitochondria. Lack of REXO2 protein also causes a substantial decrease of mitochondrial nucleic acid content and impaired de novo mitochondrial protein synthesis. Our data constitute the first in vivo evidence for an oligoribonuclease activity in human mitochondria.


Assuntos
Proteínas 14-3-3/genética , Biomarcadores Tumorais/genética , Exorribonucleases/genética , Mitocôndrias/enzimologia , Membranas Mitocondriais/enzimologia , Proteínas Mitocondriais/genética , Proteínas 14-3-3/antagonistas & inibidores , Proteínas 14-3-3/metabolismo , Biomarcadores Tumorais/antagonistas & inibidores , Biomarcadores Tumorais/metabolismo , Escherichia coli/enzimologia , Escherichia coli/genética , Exorribonucleases/antagonistas & inibidores , Exorribonucleases/metabolismo , Células HeLa , Humanos , Mitocôndrias/genética , Mitocôndrias/ultraestrutura , Membranas Mitocondriais/ultraestrutura , Proteínas Mitocondriais/antagonistas & inibidores , Proteínas Mitocondriais/metabolismo , Ácidos Nucleicos/química , Biossíntese de Proteínas , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo
15.
RNA Biol ; 10(9): 1433-8, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23635806

RESUMO

Pentatricopeptide repeat (PPR) proteins constitute a large family of RNA-binding proteins that contain a canonical 35 residue repeat motif. Originally identified in Arabidopsis thaliana, family members are found in protists, fungi, and metazoan but are by far most abundant in plant organelles. Seven examples have been identified in human mitochondria and roles have been tentatively ascribed to each. In this review, we briefly outline each of these PPR proteins and discuss the role each is believed to play in facilitating mitochondrial gene expression.


Assuntos
Mitocôndrias/genética , Proteínas de Ligação a RNA/metabolismo , Sequência de Aminoácidos , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Sequência Conservada , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Humanos , Mitocôndrias/metabolismo , Proteínas Mitocondriais/genética , Proteínas Mitocondriais/metabolismo , Proteínas de Neoplasias/química , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Processamento Pós-Transcricional do RNA , Proteínas de Ligação a RNA/genética , Ribonuclease P/genética , Ribonuclease P/metabolismo , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo
16.
Int J Oncol ; 40(3): 851-9, 2012 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-22108807

RESUMO

MDM2 is a 90 kDa nucleo-phosphoprotein that binds p53 and other proteins contributing to its oncogenic properties. Its structure includes an amino proximal p53 binding site, a central acidic domain and a carboxy region which incorporates Zinc and Ring Finger domains suggestive of nucleic acid binding or transcription factor function. It has previously been reported that a bacculovirus expressed MDM2 protein binds RNA in a sequence-specific manner through the Ring Finger domain, however, its ability to bind DNA has yet to be examined. We report here that a bacterially expressed human MDM2 protein binds both DNA as well as the previously defined RNA consensus sequence. DNA binding appears selective and involves the carboxy-terminal domain of the molecule. RNA binding is inhibited by an MDM2 specific antibody, which recognises an epitope within the carboxy region of the protein. Selection cloning and sequence analysis of MDM2 DNA binding sequences, unlike RNA binding sequences, revealed no obvious DNA binding consensus sequence, but preferential binding to oligopurine:pyrimidine-rich stretches. Our results suggest that the observed preferential DNA binding may occur through the Zinc Finger or in a charge-charge interaction through the Ring Finger, thereby implying potentially different mechanisms for DNA and RNA MDM2 binding.


Assuntos
Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Proteínas Oncogênicas/metabolismo , Proteínas Proto-Oncogênicas c-mdm2/metabolismo , Proteínas de Ligação a RNA/metabolismo , RNA/metabolismo , Sítios de Ligação , Sequência Consenso , DNA/genética , Proteínas de Ligação a DNA/genética , Histidina/metabolismo , Humanos , Proteínas Ligantes de Maltose/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Proteínas Oncogênicas/genética , Ligação Proteica , Proteínas Proto-Oncogênicas c-mdm2/genética , RNA/genética , Proteínas de Ligação a RNA/genética , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Análise de Sequência/métodos , Análise de Sequência de DNA/métodos , Dedos de Zinco/genética
17.
Brain ; 134(Pt 1): 183-95, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21169334

RESUMO

Mutations in several mitochondrial DNA and nuclear genes involved in mitochondrial protein synthesis have recently been reported in combined respiratory chain deficiency, indicating a generalized defect in mitochondrial translation. However, the number of patients with pathogenic mutations is small, implying that nuclear defects of mitochondrial translation are either underdiagnosed or intrauterine lethal. No comprehensive studies have been reported on large cohorts of patients with combined respiratory chain deficiency addressing the role of nuclear genes affecting mitochondrial protein synthesis to date. We investigated a cohort of 52 patients with combined respiratory chain deficiency without causative mitochondrial DNA mutations, rearrangements or depletion, to determine whether a defect in mitochondrial translation defines the pathomechanism of their clinical disease. We followed a combined approach of sequencing known nuclear genes involved in mitochondrial protein synthesis (EFG1, EFTu, EFTs, MRPS16, TRMU), as well as performing in vitro functional studies in 22 patient cell lines. The majority of our patients were children (<15 years), with an early onset of symptoms <1 year of age (65%). The most frequent clinical presentation was mitochondrial encephalomyopathy (63%); however, a number of patients showed cardiomyopathy (33%), isolated myopathy (15%) or hepatopathy (13%). Genomic sequencing revealed compound heterozygous mutations in the mitochondrial transfer ribonucleic acid modifying factor (TRMU) in a single patient only, presenting with early onset, reversible liver disease. No pathogenic mutation was detected in any of the remaining 51 patients in the other genes analysed. In vivo labelling of mitochondrial polypeptides in 22 patient cell lines showed overall (three patients) or selective (four patients) defects of mitochondrial translation. Immunoblotting for mitochondrial proteins revealed decreased steady state levels of proteins in some patients, but normal or increased levels in others, indicating a possible compensatory mechanism. In summary, candidate gene sequencing in this group of patients has a very low detection rate (1/52), although in vivo labelling of mitochondrial translation in 22 patient cell lines indicate that a nuclear defect affecting mitochondrial protein synthesis is responsible for about one-third of combined respiratory chain deficiencies (7/22). In the remaining patients, the impaired respiratory chain activity is most likely the consequence of several different events downstream of mitochondrial translation. Clinical classification of patients with biochemical analysis, genetic testing and, more importantly, in vivo labelling and immunoblotting of mitochondrial proteins show incoherent results, but a systematic review of these data in more patients may reveal underlying mechanisms, and facilitate the identification of novel factors involved in combined respiratory chain deficiency.


Assuntos
Núcleo Celular/genética , Mitocôndrias/genética , Doenças Mitocondriais/genética , Músculo Esquelético/patologia , Biossíntese de Proteínas , Adolescente , Adulto , Western Blotting , Linhagem Celular , Núcleo Celular/metabolismo , Criança , Pré-Escolar , DNA Mitocondrial/genética , DNA Mitocondrial/metabolismo , Transporte de Elétrons/genética , Feminino , Genótipo , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Mitocôndrias/metabolismo , Doenças Mitocondriais/metabolismo , Doenças Mitocondriais/patologia , Músculo Esquelético/metabolismo , Mutação
18.
Biochem Soc Trans ; 38(6): 1523-6, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21118119

RESUMO

Mitochondria are ubiquitous and essential organelles for all nucleated cells of higher eukaryotes. They contain their own genome [mtDNA (mitochondrial DNA)], and this autosomally replicating extranuclear DNA encodes a complement of genes whose products are required to couple oxidative phosphorylation. Sequencing of this human mtDNA more than 20 years ago revealed unusual features that included a modified codon usage. Specific deviations from the standard genetic code include recoding of the conventional UGA stop to tryptophan, and, strikingly, the apparent recoding of two arginine triplets (AGA and AGG) to termination signals. This latter reassignment was made because of the absence of cognate mtDNA-encoded tRNAs, and a lack of tRNAs imported from the cytosol. Each of these codons only occurs once and, in both cases, at the very end of an open reading frame. The presence of both AGA and AGG is rarely found in other mammals, and the molecular mechanism that has driven the change from encoding arginine to dictating a translational stop has posed a challenging conundrum. Mitochondria from the majority of other organisms studied use only UAA and UAG, leaving the intriguing question of why human organelles appear to have added the complication of a further two stop codons, AGA and AGG, or have they? In the present review, we report recent data to show that mammalian mitochondria can utilize a -1 frameshift such that only the standard UAA and UAG stop codons are required to terminate the synthesis of all 13 polypeptides.


Assuntos
DNA Mitocondrial/metabolismo , Mitocôndrias/genética , Mitocôndrias/metabolismo , Terminação Traducional da Cadeia Peptídica , Biossíntese de Proteínas , Ribossomos/metabolismo , Códon , DNA Mitocondrial/genética , Código Genético , Humanos , Ribossomos/genética
19.
RNA Biol ; 7(3): 282-6, 2010.
Artigo em Inglês | MEDLINE | ID: mdl-20458175

RESUMO

Until recently, human mitochondria were regarded as unusual as they appeared to employ four stop codons to terminate translation. In addition to the UAA/UAG of the universal genetic code, two arginine triplets (AGA/AGG) had been re-assigned as termination signals. This posed the conundrum of what factor was responsible for recognizing these triplets to promote translation termination? Recent data indicates that in fact no protein is required to recognize AGA/AGG. Indeed, it is the absence of any cognate factor, tRNA or polypeptide that is important. On encountering either of these 'hungry' codons at the end of an open reading frame, instead of requiring a novel or modified release factor, human mitoribosomes employ -1 frameshifting to reposition a standard UAG codon in the A-site, indicating that only the universal UAA and UAG are used as stop codons. This renders a single mitochondrial release factor, mtRF1a, previously shown to be capable of terminating 11 of the 13 open reading frames encoded by the mitochondrial genome, to be sufficient to release all nascent human mitochondrial gene products from the mitoribosome.


Assuntos
Proteínas Mitocondriais/metabolismo , Terminação Traducional da Cadeia Peptídica/fisiologia , Sequência de Aminoácidos , Códon de Terminação/metabolismo , Formação de Conceito , Humanos , Proteínas Mitocondriais/genética , Modelos Biológicos , Dados de Sequência Molecular , Terminação Traducional da Cadeia Peptídica/genética , Fatores de Terminação de Peptídeos/metabolismo , Fatores de Terminação de Peptídeos/fisiologia , Biossíntese de Proteínas/genética , Pensamento
20.
EMBO J ; 29(6): 1116-25, 2010 Mar 17.
Artigo em Inglês | MEDLINE | ID: mdl-20186120

RESUMO

Bioinformatic analysis classifies the human protein encoded by immature colon carcinoma transcript-1 (ICT1) as one of a family of four putative mitochondrial translation release factors. However, this has not been supported by any experimental evidence. As only a single member of this family, mtRF1a, is required to terminate the synthesis of all 13 mitochondrially encoded polypeptides, the true physiological function of ICT1 was unclear. Here, we report that ICT1 is an essential mitochondrial protein, but unlike the other family members that are matrix-soluble, ICT1 has become an integral component of the human mitoribosome. Release-factor assays show that although ICT1 has retained its ribosome-dependent PTH activity, this is codon-independent; consistent with its loss of both domains that promote codon recognition in class-I release factors. Mutation of the GGQ domain common to ribosome-dependent PTHs causes a loss of activity in vitro and, crucially, a loss of cell viability, in vivo. We suggest that ICT1 may be essential for hydrolysis of prematurely terminated peptidyl-tRNA moieties in stalled mitoribosomes.


Assuntos
Hidrolases de Éster Carboxílico/metabolismo , Mitocôndrias/metabolismo , Proteínas/metabolismo , Ribossomos/metabolismo , Sequência de Aminoácidos , Hidrolases de Éster Carboxílico/química , Hidrolases de Éster Carboxílico/genética , Células HeLa , Humanos , Hidrólise , Proteínas Mitocondriais/genética , Proteínas Mitocondriais/metabolismo , Dados de Sequência Molecular , Fatores de Terminação de Peptídeos/genética , Fatores de Terminação de Peptídeos/metabolismo , Conformação Proteica , Proteínas/química , Proteínas/genética , Proteínas Ribossômicas
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