The origin and diversification of mitochondria, Curr. Biol, vol.27, pp.1177-1192, 2017. ,
Mitochondria: in sickness and in health, Cell, vol.148, pp.1145-1159, 2012. ,
Mitochondrial ribosome assembly in health and disease, Cell Cycle, vol.14, pp.226-2250, 2015. ,
Male sterility and fertility restoration in crops, Annu. Rev. Plant. Biol, vol.65, pp.579-606, 2014. ,
Mitochondrion role in molecular basis of cytoplasmic male sterility, Mitochondrion, vol.19, pp.198-205, 2014. ,
Coordination of nuclear and mitochondrial genome expression during mitochondrial biogenesis in Arabidopsis, Plant Cell, vol.17, pp.1497-1512, 2005. ,
Mitochondrial protein synthesis: figuring the fundamentals, complexities and complications of mammalian mitochondrial translation, FEBS Lett, vol.588, pp.2496-2503, 2014. ,
RNA metabolism in plant mitochondria, Trends Plant Sci, vol.19, pp.380-389, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00999397
RNA processing in human mitochondria, Cell Cycle, vol.10, pp.2904-2916, 2011. ,
Pentatricopeptide repeat proteins in plants, Annu. Rev. Plant Biol, vol.65, pp.415-442, 2014. ,
The challenges of mitochondrial replacement, PLoS Genet, vol.10, p.1004315, 2014. ,
Pentatricopeptide repeat proteins, RNA Biol, vol.10, pp.1417-1418, 2013. ,
PPR336 is associated with polysomes in plant mitochondria, J. Mol. Biol, vol.375, pp.626-636, 2008. ,
An Arabidopsis dual-localized pentatricopeptide repeat protein interacts with nuclear proteins involved in gene expression regulation, Plant Cell, vol.23, pp.730-740, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00610460
The MTL1 pentatricopeptide repeat protein is required for both translation and splicing of the mitochondrial NADH dehydrogenase subunit 7 mRNA in Arabidopsis, Plant Physiol, vol.170, pp.354-366, 2016. ,
The process of mammalian mitochondrial protein synthesis, Cell Tissue Res, vol.367, pp.5-20, 2017. ,
Structure and function of the mitochondrial ribosome, Annu. Rev. Biochem, vol.85, pp.103-132, 2016. ,
The translational landscape of Arabidopsis mitochondria, Nucleic Acids Res, vol.46, pp.6218-6228, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02145349
A different genetic code in human mitochondria, Nature, vol.282, pp.189-194, 1979. ,
Search for characteristic structural features of mammalian mitochondrial tRNAs, RNA, vol.6, pp.1356-1379, 2000. ,
Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography, Nat. Commun, vol.6, p.6019, 2015. ,
Organization and regulation of mitochondrial protein synthesis, Annu. Rev. Biochem, vol.85, pp.77-101, 2016. ,
Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii Thalia Salinas-Gieg e, Nucleic Acids Res, vol.45, pp.12963-12973, 2017. ,
Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae, Eur. J. Biochem, vol.245, pp.449-456, 1997. ,
Mammalian mitochondrial ribosomal proteins. N-terminal amino acid sequencing, characterization, and identification of corresponding gene sequences, J. Biol. Chem, vol.273, pp.34828-34836, 1998. ,
A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins, J. Biol. Chem, vol.275, pp.32585-32591, 2000. ,
The large subunit of the mammalian mitochondrial ribosome: analysis of the complement of ribosomal proteins present, J. Biol. Chem, vol.276, pp.43958-43969, 2001. ,
Comparative analysis of bacterial-origin genes for plant mitochondrial ribosomal proteins, Mol. Biol. Evol, vol.23, pp.701-712, 2006. ,
The structure of the human mitochondrial ribosome, Science, vol.348, pp.95-98, 2015. ,
The complete structure of the 55S mammalian mitochondrial ribosome, Science, vol.348, pp.303-308, 2015. ,
The structure of the yeast mitochondrial ribosome, Science, vol.355, pp.528-531, 2017. ,
Human mitochondrial ribosomes can switch structural tRNAs -but when and why?, RNA Biol, vol.14, pp.1668-1671, 2017. ,
Structure of the large ribosomal subunit from human mitochondria, Science, vol.346, pp.718-722, 2014. ,
Higher-plant mitochondrial ribosomes contain a 5S ribosomal ribonucleic acid component, Biochem. J, vol.157, pp.275-277, 1976. ,
Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryotomography, EMBO Rep, vol.18, pp.1786-1800, 2017. ,
Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis, Plant Cell, vol.16, pp.2089-2103, 2004. ,
Nuclear fusion defective 1 encodes the Arabidopsis RPL21M protein and is required for karyogamy during female gametophyte development and fertilization, Plant Physiol, vol.141, pp.957-965, 2006. ,
Structure of the yeast mitochondrial large ribosomal subunit, Science, vol.343, pp.1485-1489, 2014. ,
Eukaryote-specific rRNA expansion segments function in ribosome biogenesis, RNA, vol.22, pp.1153-1162, 2016. ,
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY, EMBO J, vol.36, pp.475-486, 2017. ,
Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor, Nat. Plants, vol.4, pp.212-217, 2018. ,
Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes, Mol. Cell. Biol, vol.27, pp.6876-6888, 2007. ,
Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes, Mol. Cell, vol.42, pp.106-117, 2011. ,
Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes, Mol. Microbiol, vol.99, pp.1043-1058, 2016. ,
Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes, Science, vol.7735, p.422, 2018. ,
High-resolution structures of mitochondrial ribosomes and their functional implications, Curr. Opin. Struct. Biol, vol.49, pp.44-53, 2018. ,
A genome wide study in fission yeast reveals nine PPR proteins that regulate mitochondrial gene expression, Nucleic Acids Res, vol.39, pp.8029-8041, 2011. ,
The pentatricopeptide repeats present in Pet309 are necessary for translation but not for stability of the mitochondrial Cox1 mRNA in yeast, J. Biol. Chem, vol.283, pp.1472-1479, 2008. ,
LRPPRC is necessary for polyadenylation and coordination of translation of mitochondrial mRNAs, EMBO J, vol.31, pp.443-456, 2012. ,
Characterization of Raphanus sativus pentatricopeptide repeat proteins encoded by the fertility restorer locus for Ogura cytoplasmic male sterility, Plant Cell, vol.20, pp.3331-3345, 2008. ,
Yeast PPR proteins, watchdogs of mitochondrial gene expression, RNA Biol, vol.10, pp.1477-1494, 2013. ,
The structure and function of the eukaryotic ribosome, Cold Spring Harb. Perspect. Biol, vol.4, pp.11536-011536, 2012. ,
New insights into ribosome structure andfunction, Cold Spring Harb. Perspect. Biol, vol.7, p.32615, 2018. ,
Comparative analysis of sequences preceding protein-coding mitochondrial genes in flowering plants, Mol. Biol. Evol, vol.24, pp.1101-1112, 2007. ,
Floral dip: a simplified method for Agrobacteriummediated transformation of Arabidopsis thaliana, Plant J, vol.16, pp.735-743, 1998. ,
An effect size filter improves the reproducibility in spectral counting-based comparative proteomics, J. Proteom, vol.16, pp.55-65, 2013. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010. ,
Higher plant mitochondria encode an homologue of the nuclear-encoded 30-kDa subunit of bovine mitochondrial complex I, Eur. J. Biochem, vol.217, pp.831-838, 1993. ,
Monoclonal antibodies to the alternative oxidase of higher plant mitochondria, Plant Physiol, vol.89, pp.1311-1317, 1989. ,
l-Galactono-1,4-lactone dehydrogenase isrequired for the accumulation of plant respiratory complex I, J. Biol. Chem, vol.283, pp.32500-32505, 2008. ,
Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes, J. Biol. Chem, vol.285, pp.36138-36148, 2010. ,
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations, Nucleic Acids Res, vol.45, pp.1064-1074, 2017. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences, BMC Bioinformatics, vol.8, issue.2, 2007. ,
The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protoc, vol.10, p.845, 2015. ,
, 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index. Special Issue -Databases, vol.59, pp.1-7, 2018.
Scipion: a software framework toward integration, reproducibility and validation in 3D electron microscopy, J. Struct. Biol, vol.195, pp.93-99, 2016. ,
Xmipp 3.0: an improved software suite for image processing in electron microscopy, J. Struct. Biol, vol.184, pp.321-328, 2013. ,
CTFFIND4: fast and accurate defocus estimation from electron micrographs, J. Struct. Biol, vol.192, pp.216-221, 2015. ,
A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs, Bioinformatics, vol.29, pp.2460-2468, 2013. ,
RELION: implementation of a Bayesian approach to cryo-EM structure determination, J. Struct. Biol, vol.180, pp.519-530, 2012. ,
A new system for naming ribosomal proteins, Curr. Opin. Struct. Biol, vol.24, pp.165-169, 2014. ,
Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: Implication of potential sequencing errors caused by large-unit repeats, Proc. Natl Acad. Sci. USA, vol.98, pp.5099-5103, 2001. ,
Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts, Plant Cell, vol.14, pp.931-943, 2002. ,
High-resolution structure of the Escherichia coli ribosome, Nat. Struct. Mol. Biol, vol.22, pp.336-341, 2015. ,
, REFERENCES expression regulation. Plant Cell, vol.23, pp.730-770
MEF10 is required for RNA editing at nad2-842 in mitochondria of Arabidopsis thaliana and interacts with MORF8, Plant Mol Biol, vol.81, pp.337-346, 2013. ,
The enigma of ribonuclease P evolution, Trends Genet, vol.19, pp.561-569, 2003. ,
, , 2012.
, Ribonucleases P/MRP and the expanding ribonucleoprotein world, IUBMB Life, vol.64, pp.521-528
Relaxed transcription in Arabidopsis mitochondria is counterbalanced by RNA stability control mediated by polyadenylation and polynucleotide phosphorylase, Mol Cell Biol, vol.26, pp.2869-2876, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00092897
RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme, Cell, vol.135, pp.462-474, 2008. ,
Differential substrate recognition by isozymes of plant protein-only Ribonuclease P, RNA, vol.22, pp.782-792, 2016. ,
Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing, Proc Natl Acad Sci U S A, vol.109, pp.16149-16154, 2012. ,
Roles of RNase P and Its Subunits, Trends Genet, vol.33, pp.594-603, 2017. ,
GRSF1 regulates RNA processing in mitochondrial RNA granules, Cell Metab, vol.17, pp.399-410, 2013. ,
Protein structure prediction on the Web: a case study using the Phyre server, Nat. Protoc, vol.4, pp.363-371, 2009. ,
Arabidopsis thaliana mTERF proteins: evolution and functional classification, Front Plant Sci, vol.3, p.233, 2012. ,
Molecular recognition of pre-tRNA by Arabidopsis protein-only Ribonuclease P. RNA, 2017. ,
Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya, Mol Biol Evol, vol.32, pp.3186-3193, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01378700
Bases defining an ammonium and magnesium ion-dependent tertiary structure within the large subunit ribosomal RNA, J Mol Biol, vol.244, pp.572-585, 1994. ,
Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide, Nature, vol.382, pp.646-649, 1996. ,
Cleavage of model substrates by Arabidopsis thaliana PRORP1 reveals new insights into its substrate requirements, PLoS One, p.160246, 2016. ,
Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins, Biotechniques, vol.42, pp.725-730, 2007. ,
Gateway binary vectors with the bialaphos resistance gene, bar, as a selection marker for plant transformation, Biosci Biotechnol Biochem, vol.74, pp.1315-1319, 2010. ,
Two exoribonucleases act sequentially to process mature 3'-ends of atp9 mRNAs in Arabidopsis mitochondria, J Biol Chem, vol.279, pp.25440-25446, 2004. ,
PPR proteins shed a new light on RNase P biology, RNA Biol, vol.10, pp.1457-1468, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00875474
Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding, J. Biol. Chem, vol.292, pp.13904-13913, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01581835
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-179, 2010. ,
, tRNA biology in mitochondria. IJMS, vol.16, pp.4518-4532, 2015.
Mechanistic and structural studies of protein-only RNase P compared to ribonucleoproteins reveal the two Faces of the same enzymatic activity, 2016. ,
Discovery of new RNA classes and global RNA-binding proteins, Curr. Opin. Microbiol, vol.39, pp.1-9, 2017. ,
Two NYN domain containing putative nucleases are involved in transcript maturation in Arabidopsis mitochondria, Plant J, vol.85, pp.278-288, 2016. ,
Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants, Proc Natl Acad Sci U S A, vol.109, pp.5104-5109, 2012. ,
Nuclear RNase P of Trypanosoma brucei: A Single Protein in Place of the Multicomponent RNAProtein Complex, Cell Rep, vol.2, pp.19-25, 2012. ,
PPR336 is associated with polysomes in plant mitochondria, J Mol Biol, vol.375, pp.626-636, 2008. ,
Analysis of the Cleavage Mechanism by Protein-Only RNase P Using Precursor tRNA Substrates with Modifications at the Cleavage Site, J. Mol. Biol, vol.428, pp.4917-4928, 2016. ,
A WW domain-containing yesassociated protein (YAP) is a novel transcriptional co-activator, EMBO J, vol.18, pp.2551-2562, 1999. ,
, Arabidopsis cells are ground by hand using a mortar and a pestle and a juice extractor is used for cauliflower
, In all cases the lysate was filtered and clarified by centrifugation at 1,500 g, 10 min at 4°C
, Supernatant was kept and centrifuged at 18,000 g, 15 min at 4°C. Organelle pellet was rebuffer: ? Flower: 300 mM sucrose, 15 mM tetrasodium-pyrophosphate decahydrate, 2 mM EDTA, 10 mM KH2PO4, 1% (w/v) PVP-40, 1% (w/v) BSA, 20 mM ascorbate, 5 mM cysteine
, ? Cells: 450 mM mannitol, 50 mM tetrasodium-pyrophosphate decahydrate, 0.5% (w/v) PVP-40, 0.5% (w/v) BSA, 20 mM ascorbate, 20 mM cysteine
300 mM mannitol, 30 mM tetrasodium-pyrophosphate decahydrate, 3 mM EDTA, 0.8% (w/v) PVP-25, 0.5% (w/v) BSA, 20 mM ascorbate, 5 mM cysteine, 2 mM ß mercaptoethanol ,
, ? Flower: 300 mM sucrose, 10 mM MOPS, 1 mM EGTA, vol.7
, ? Cells: 300 mM mannitol, 10 mM TES-KOH, pH, vol.7
300 mM mannitol, 10 mM phosphate buffer, 1 mM EDTA ,
, Gradient buffer: ? Flower: X% Percoll, 300 mM sucrose, 10 mM MOPS, pH 7.2 ? Cells: X% Percoll, 300 mM mannitol, 10 mM TES-KOH, vol.7
X% Percoll, 300 mM mannitol, 10 mM phosphate buffer, 1 mM EDTA, vol.7 ,
, Lysate was clarified by centrifugation at 30,000 g, 20 min at 4°C. The supernatant was loaded on a 50% sucrose cushion in monosome buffer (3 mL of cushion and 7-10 mL of supernatant) and centrifuged at 235,000 g, 3h, 4°C in an ultracentrifuge. The crude ribosomes pellet was resuspended in monosome buffer and loaded on a 10-30% sucrose gradient in the same buffer
, 100 mM KCl, 30 mM MgCl2, 1 mM DTT, 0.5 mg/ml heparin, 1.6% Triton X-100, 100 µg/ml chloramphenicol, ? Lysis buffer: 20 mM HEPES-KOH pH 7.6
20 mM HEPES-KOH pH 7.6, 100 mM KCl, 30 mM MgCl2, 1 mM DTT, p.50 ,
, /ml chloramphenicol
after selection of the excitation wavelength. The specific fluorescence ,
ribosome samples were analyzed by electron microscopy to assess the integrity and the purity of the samples. The samples were visualized with a CM120 100Kv (FEI) transmission electron microscope equipped with a CCD ORIUS 1000 Gatan Camera at the IGBMC ,
, INSERM Bordeaux)in the temperature-and humidity-controlled Vitrobot apparatus Mark IV (FEI, T = 4°C, humidity 100%, Blot Force 5, Blot waiting time 30 sec) and vitrified in liquid ethane pre-cooled by liquid nitrogen, p.300
TargetP was also used for target sequence prediction, 2007. ,
, Protein similarities were analyzed through MUSCLE Alignments, 2004.
, PPR domain predictions were performed with TPRpred, 2007.
2015) and molecular representations were prepared with the PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC or UCSF Chimera, Tridimensional structure predictions were built with Phyre2, 2004. ,
Expression data was obtained from the Genevestigator® platform, 2008. ,
To identify regions of similarity between biological sequences NCBI's BLAST was used. More specifically to find homologous proteins between organisms tblastn was used, 1997. ,
Structure at 2.8 Â resolution of F1-ATPase from bovine heart mitochondria, Nature, vol.370, pp.621-628, 1994. ,
The Revised Classification of Eukaryotes, J. Eukaryot. Microbiol, vol.59, pp.429-514, 2012. ,
The TOM core complex: the general protein import pore of the outer membrane of mitochondria, J. Cell Biol, vol.147, pp.959-968, 1999. ,
Ribosome Rescue and Translation Termination at Non-Standard Stop Codons by ICT1 in Mammalian Mitochondria, PLoS Genet, vol.10, p.1004616, 2014. ,
Licensed to Kill: Mitochondria, Chloroplasts, and Cell Death, Trends Plant Sci, vol.20, pp.754-766, 2015. ,
The function of genomes in bioenergetic organelles, Philos. Trans. R. Soc. B Biol. Sci, vol.358, pp.19-38, 2003. ,
A view of RNase P, Mol. Biosyst, vol.3, pp.604-607, 2007. ,
, , 1997.
a new generation of protein database search programs, Nucleic Acids Res, vol.25, pp.3389-3402 ,
Origins and Recombination of the Bacterial-Sized Multichromosomal Mitochondrial Genome of Cucumber, Plant Cell, vol.23, pp.2499-2513, 2011. ,
Structure of the yeast mitochondrial large ribosomal subunit, Science, vol.343, pp.1485-1489, 2014. ,
The structure of the human mitochondrial ribosome, Science, vol.348, pp.95-98, 2015. ,
The genome sequence of Rickettsia prowazekii and the origin ofmitochondria, Nature, vol.396, pp.133-140, 1998. ,
Mitochondrial RNA editing in trypanosomes: Small RNAs in control, Biochimie, vol.100, pp.125-131, 2014. ,
Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae, Nucleic Acids Res, vol.40, pp.6122-6134, 2012. ,
In Arabidopsis thaliana, 1% of the genome codes for a novel protein family unique to plants, Plant Mol. Biol, vol.42, pp.603-613, 2000. ,
,
A new system for naming ribosomal proteins, Curr. Opin. Struct. Biol, 2014. ,
The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants, Science, vol.332, pp.960-963, 2011. ,
Pentatricopeptide repeat proteins in plants, Annu. Rev. Plant Biol, vol.65, pp.415-442, 2014. ,
A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins, PLoS Genet, vol.8, pp.4-11, 2012. ,
The Structure of the Eukaryotic Ribosome at 3.0 A Resolution, Science, vol.334, pp.1524-1529, 2011. ,
, , 2012.
, RIP1, a member of an Arabidopsis protein family, interacts with the protein RARE1 and broadly affects RNA editing, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.1453-61
The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others), Biol. Direct, vol.7, p.23, 2012. ,
Genetic aspects of mitochondrial genome evolution, Mol. Phylogenet. Evol, vol.69, pp.328-338, 2013. ,
High-resolution structures of mitochondrial ribosomes and their functional implications, Curr. Opin. Struct. Biol, vol.49, pp.44-53, 2018. ,
Structure of the chloroplast ribosome with chl-RRF and hibernationpromoting factor, Nat. Plants, vol.4, pp.212-217, 2018. ,
Kinetics and Mechanism of Mammalian Mitochondrial Ribosome Assembly, Cell Rep, vol.22, pp.1935-1944, 2018. ,
Comparative Analysis of Bacterial-Origin Genes for Plant Mitochondrial Ribosomal Proteins, Mol. Biol. Evol, vol.23, pp.701-712, 2006. ,
Transfer RNA maturation in Chlamydomonas mitochondria, chloroplast and the nucleus by a single RNase P protein, Plant J, vol.87, pp.270-280, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01405505
Directed Alteration of Saccharomyces cerevisiae Mitochondrial DNA by Biolistic Transformation and Homologous Recombination, Methods in Molecular Biology, pp.153-166, 2007. ,
Two Interacting Proteins Are Necessary for the Editing of the NdhD-1 Site in Arabidopsis Plastids, Plant Cell, vol.24, pp.3684-3694, 2012. ,
The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein, Structure, vol.25, pp.1785-1794, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02177145
Ancient horizontal gene transfer, Nat. Rev. Genet, vol.4, pp.121-132, 2003. ,
Structure of the large ribosomal subunit from human mitochondria, Science, vol.346, pp.718-722, 2014. ,
Structures of the human mitochondrial ribosome in native states of assembly, Nat. Struct. Mol. Biol, vol.24, pp.866-869, 2017. ,
Group II intron splicing factors in plant mitochondria, Front. Plant Sci, vol.5, p.35, 2014. ,
Megacomplex organization of the oxidative phosphorylation system by structural analysis of respiratory supercomplexes from potato, Biochim. Biophys. Acta -Bioenerg, vol.1787, pp.60-67, 2009. ,
Mitochondrial genomes: anything goes, Trends Genet, vol.19, pp.709-716, 2003. ,
Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists, Genome Biol. Evol, vol.5, pp.418-438, 2013. ,
Leaderless mRNAs are circularized in Chlamydomonas reinhardtii mitochondria, Curr. Genet, vol.0, pp.1-13, 2018. ,
Arabidopsis encodes four tRNase Z enzymes, Plant Physiol, vol.150, pp.1494-1502, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00697567
Archaebacteria and Archezoa, Nature, vol.339, pp.100-101, 1989. ,
Analysis of the Legionella longbeachae Genome and Transcriptome Uncovers Unique Strategies to Cause Legionnaires' Disease, PLoS Genet, vol.6, p.1000851, 2010. ,
The generality of self-splicing RNA: Relationship to nuclear mRNA splicing, Cell, vol.44, pp.207-210, 1986. ,
Male Sterility and Fertility Restoration in Crops, Annu. Rev. Plant Biol, vol.65, pp.579-606, 2014. ,
Redefining the structural motifs that determine RNA binding and RNA editing by pentatricopeptide repeat proteins in land plants, Plant J, vol.85, pp.532-547, 2016. ,
Explosive invasion of plant mitochondria by a group I intron, Proc. Natl. Acad. Sci. U. S. A, vol.95, pp.14244-14249, 1998. ,
Identification of multiple transcriptional initiation sites on the yeast mitochondrial genome by in vitro capping with guanylyltransferase, J. Biol. Chem, vol.258, pp.14025-14033, 1983. ,
Human mitochondrial ribosomes can switch structural tRNAs -but when and why?, RNA Biol, vol.6286, pp.0-00, 2017. ,
Termination of protein synthesis in mammalian mitochondria, J. Biol. Chem, vol.286, pp.34479-34485, 2011. ,
Calcium Signaling, Cell, vol.131, pp.1047-1058, 2007. ,
Limitations to in vivo Import of Hydrophobic Proteins into Yeast Mitochondria. The Case of a Cytoplasmically Synthesized Apocytochrome b, Eur. J. Biochem, vol.228, pp.762-771, 1995. ,
Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana, Plant J, vol.16, pp.735-743, 1998. ,
Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles, RNA Biol, vol.10, pp.1557-1575, 2013. ,
An artificial PPR scaffold for programmable RNA recognition, Nat. Commun, vol.5, p.5729, 2014. ,
Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function, Proc. Natl. Acad. Sci. U. S. A, vol.107, pp.17252-17255, 2010. ,
Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity?, BioEssays, vol.27, pp.436-446, 2005. ,
Shape and attachment of the cristae mitochondriales in mouse hepatic cell mitochondria, J. Ultrastruct. Res, vol.16, pp.123-140, 1966. ,
On the origin of species by means of natural selection, or, the preservation of favoured races in the struggle for life, 1859. ,
Macromolecular organization of ATP synthase and complex I in whole mitochondria, Proc. Natl. Acad. Sci, vol.108, pp.14121-14126, 2011. ,
Preprotein translocase of the outer mitochondrial membrane: molecular dissection and assembly of the general import pore complex, Mol. Cell. Biol, vol.18, pp.6515-6524, 1998. ,
Bovine mitochondrial ribosomes possess a high affinity binding site for guanine nucleotides, J. Biol. Chem, vol.266, pp.9586-9590, 1991. ,
Activation of Yeast Mitochondrial Translation: Who Is in Charge?, Biochem, vol.83, pp.87-97, 2018. ,
The structure of the yeast mitochondrial ribosome, Science, vol.355, pp.528-531, 2017. ,
What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses, J. Cell Sci, vol.125, pp.1865-1875, 2012. ,
Evolution and Diversification of the Organellar Release Factor Family, Mol. Biol. Evol, vol.29, pp.3497-3512, 2012. ,
, , 1998.
, The 80S rat liver ribosome at 25 å resolution by electron cryomicroscopy and angular reconstitution, Structure, vol.6, pp.389-399
Identity of a Prokaryotic Initiator tRNA, The Translational Apparatus, pp.23-33, 1993. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
Locating proteins in the cell using TargetP, SignalP and related tools, Nat. Protoc, vol.2, pp.953-971, 2007. ,
Archaea and the origin of eukaryotes, Nat. Rev. Microbiol, vol.15, pp.711-723, 2017. ,
New insights into the respiratory chain of plant mitochondria. Supercomplexes and a unique composition of complex II, Plant Physiol, vol.133, pp.274-286, 2003. ,
The Fragmented Mitochondrial Ribosomal RNAs of Plasmodium falciparum, PLoS One, vol.7, p.38320, 2012. ,
Respiratory metabolism: glycolysis, the TCA cycle and mitochondrial electron transport, Curr. Opin. Plant Biol, vol.7, pp.254-261, 2004. ,
Evolutionary aspects of "chloroplast-like" trnN and trnH expression in higher-plant mitochondria, Curr. Genet, vol.32, pp.358-360, 1997. ,
Modular recognition of nucleic acids by PUF, TALE and PPR proteins, Mol. Biosyst, vol.8, p.699, 2012. ,
Mapping of mitochondrial mRNA termini in Arabidopsis thaliana: t-elements contribute to 5' and 3' end formation, Nucleic Acids Res, vol.35, pp.3676-3692, 2007. ,
Functional and genomic analyses of alpha-solenoid proteins, PLoS One, vol.8, p.79894, 2013. ,
Low Complexity Regions behave as tRNA sponges to help co-translational folding of plasmodial proteins, FEBS Lett, vol.584, pp.448-454, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00526424
Polyadenylation accelerates the degradation of the mitochondrial mRNA associated with cytoplasmic male sterility in sunflower, EMBO J, vol.18, pp.3757-3766, 1999. ,
A single mammalian mitochondrial translation initiation factor functionally replaces two bacterial factors, Mol. Cell, vol.29, pp.180-190, 2008. ,
An ordered Arabidopsis thaliana mitochondrial cDNA library on high-density filters allows rapid systematic analysis of plant gene expression: a pilot study, Plant J, vol.15, pp.721-726, 1998. ,
Hydrogenosomes and mitosomes: conservation and evolution of functions, J. Eukaryot. Microbiol, vol.56, pp.221-231, 2009. ,
Disruptions in valine degradation affect seed development and germination in Arabidopsis, Plant J, vol.90, pp.1029-1039, 2017. ,
A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome, Plant Mol. Biol, vol.20, pp.1203-1207, 1992. ,
A single Arabidopsis organellar protein has RNase P activity, Nat. Struct. Mol. Biol, vol.17, pp.740-744, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00508570
Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography, EMBO Rep, 2017. ,
Mammalian mitochondrial ribosomal proteins. N-terminal amino acid sequencing, characterization, and identification of corresponding gene sequences, J. Biol. Chem, vol.273, pp.34828-34836, 1998. ,
Mitochondrial evolution, Cold Spring Harb. Perspect. Biol, vol.4, p.11403, 2012. ,
Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria, Proc. Natl. Acad. Sci. U. S. A, vol.112, pp.10133-10138, 2015. ,
Mitochondrial evolution, Science, vol.283, pp.1476-1481, 1999. ,
Structure and Function of the Mitochondrial Ribosome, Annu. Rev. Biochem, vol.85, 2016. ,
Architecture of the large subunit of the mammalian mitochondrial ribosome, Nature, vol.505, pp.515-519, 2013. ,
The complete structure of the 55S mammalian mitochondrial ribosome, Science, vol.348, pp.303-308, 2015. ,
, msmsTests: LC-MS/MS Differential Expression Tests, 2013.
The Many Shapes of Mitochondrial Membranes, Traffic, vol.2, pp.235-244, 2001. ,
The architecture of the mammalian respirasome, Nature, vol.537, pp.639-643, 2016. ,
Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation, Annu. Rev. Plant Biol, vol.68, pp.225-252, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01521803
RNA editing in wheat mitochondria results in the conservation of protein sequences, Nature, vol.341, pp.660-662, 1989. ,
Initiation of mRNA translation in prokaryotes, Biochemistry, vol.29, pp.5881-5889, 1990. ,
Mitochondrial Genome Evolution and the Emergence of PPR Proteins, Advances in Botanical Research, pp.253-313, 2012. ,
PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis, Genes Dev, vol.26, pp.1022-1027, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00701324
A genetic link between an mRNA-specific translational activator and the translation system in yeast mitochondria, Genetics, vol.125, pp.495-503, 1990. ,
Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology, Mol. Cell, vol.63, pp.445-456, 2016. ,
The pentatricopeptide repeat MTSF1 protein stabilizes the nad4 mRNA in Arabidopsis mitochondria, Nucleic Acids Res, vol.41, pp.6650-6663, 2013. ,
The MTL1 Pentatricopeptide Repeat Protein Is Required for Both Translation and Processing Enzyme, Cell, vol.135, pp.462-474, 2016. ,
SUBA4: the interactive data analysis centre for Arabidopsis subcellular protein locations, Nucleic Acids Res, vol.45, pp.1064-1074, 2017. ,
Mitochondrion role in molecular basis of cytoplasmic male sterility, 2014. ,
Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing, Proc. Natl. Acad. Sci, vol.109, pp.16149-16154, 2012. ,
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes, Adv. Bioinformatics, p.420747, 2008. ,
Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida, BMC Evol. Biol, vol.15, p.278, 2015. ,
A Small Multifunctional Pentatricopeptide Repeat Protein in the Chloroplast of Chlamydomonas reinhardtii, Mol. Plant, vol.8, pp.412-426, 2015. ,
Armless mitochondrial tRNAs in enoplea (nematoda), RNA Biol, vol.9, pp.1161-1166, 2012. ,
Small but large enough: structural properties of armless mitochondrial tRNAs from the nematode Romanomermis culicivorax, Nucleic Acids Res, vol.46, pp.9170-9180, 2018. ,
Malaria, Plasmodium falciparum and its apicoplast, Biochem. Soc. Trans, vol.38, pp.775-782, 2010. ,
A Eukaryote without a Mitochondrial Organelle, Curr. Biol, vol.26, pp.1274-1284, 2016. ,
TPRpred: a tool for prediction of TPR-, PPR-and SEL1-like repeats from protein sequences, BMC Bioinformatics, vol.8, issue.2, 2007. ,
Structural basis for RNA recognition by a dimeric PPR-protein complex, Nat. Struct. Mol. Biol, vol.20, pp.1377-1382, 2013. ,
The Phyre2 web portal for protein modeling, prediction and analysis, Nat. Protoc, vol.10, pp.845-858, 2015. ,
Structure of the human 80S ribosome, Nature, vol.520, pp.640-645, 2015. ,
Mitochondrial dual-coding genes in Trypanosoma brucei, PLoS Negl. Trop. Dis, vol.11, p.5989, 2017. ,
Identification and characterization of the genes for mitochondrial ribosomal proteins of Saccharomyces cerevisiae, Eur. J. Biochem, vol.245, pp.449-456, 1997. ,
A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins, J. Biol. Chem, vol.275, pp.32585-32591, 2000. ,
The Large Subunit of the Mammalian Mitochondrial Ribosome, J. Biol. Chem, vol.276, pp.43958-43969, 2001. ,
Import of mitochondrial carriers mediated by essential proteins of the intermembrane space, Science, vol.279, pp.369-373, 1998. ,
Eukaryotic initiator tRNA: Finely tuned and ready for action, FEBS Lett, vol.584, pp.396-404, 2010. ,
In vitro and in vivo studies on the mitochondrial import of CBS1, a translational activator of cytochrome b in yeast, Mol. Gen. Genet, vol.217, pp.162-167, 1989. ,
Pentatricopeptide motifs in the N-terminal extension domain of yeast mitochondrial RNA polymerase Rpo41p are not essential for its function, Biochem, vol.81, pp.1101-1110, 2016. ,
The Resolution Revolution, Science, vol.343, pp.1443-1444, 2014. ,
Phage-type RNA polymerase RPOTmp performs gene-specific transcription in mitochondria of Arabidopsis thaliana, Plant Cell, vol.21, pp.2762-2779, 2009. ,
Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM, Nature, vol.560, pp.263-267, 2018. ,
Mitochondrial translation initiation machinery: Conservation and diversification, Biochimie, vol.100, pp.132-140, 2014. ,
The function and synthesis of ribosomes, Nat. Rev. Mol. Cell Biol, vol.2, pp.514-520, 2001. ,
SLIRP Regulates the Rate of Mitochondrial Protein Synthesis and Protects LRPPRC from Degradation, PLOS Genet. | DOI, 2015. ,
Energetics and genetics across the prokaryote-eukaryote divide, Biol. Direct, vol.6, p.35, 2011. ,
Serial endosymbiosis or singular event at the origin of eukaryotes?, J. Theor. Biol, vol.434, pp.58-67, 2017. ,
The energetics of genome complexity, Nature, vol.467, pp.929-934, 2010. ,
An ancestral mitochondrial DNA resembling a eubacterial genome in miniature, Nature, vol.387, pp.493-497, 1997. ,
Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase, Nature, vol.481, pp.214-218, 2012. ,
Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya, Mol. Biol. Evol, vol.32, p.187, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01378700
Plant Mitochondria, 2011. ,
The transcription machineries of plant mitochondria and chloroplasts: Composition, function, and regulation, J. Plant Physiol, vol.168, pp.1345-1360, 2011. ,
Human pentatricopeptide proteins: only a few and what do they do?, RNA Biol, vol.10, pp.1433-1438, 2013. ,
The Essential Role of Mitochondria in the Biogenesis of Cellular Iron-Sulfur Proteins, Biol. Chem, vol.380, pp.1157-1166, 1999. ,
Human Mitochondrial Transcription Revisited, J. Biol. Chem, vol.285, pp.18129-18133, 2010. ,
Interaction of Mammalian Mitochondrial Ribosomes with the Inner Membrane, J. Biol. Chem, vol.275, pp.29400-29406, 2000. ,
Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis, Plant Cell, vol.16, pp.2089-2103, 2004. ,
Trans-splicing group II introns in plant mitochondria: the complete set of cis-arranged homologs in ferns, fern allies, and a hornwort, RNA, vol.4, pp.1599-1609, 1998. ,
An overview of pentatricopeptide repeat proteins and their applications, Biochimie, vol.113, pp.93-99, 2015. ,
The product of the nuclear gene PET309 is required for translation of mature mRNA and stability or production of intron-containing RNAs derived from the mitochondrial COX1 locus of Saccharomyces cerevisiae, EMBO J, vol.14, pp.4031-4043, 1995. ,
The mitochondrial genome of Arabidopsis is composed of both native and immigrant information, Trends Plant Sci, vol.4, pp.495-502, 1999. ,
Deep mitochondrial origin outside the sampled alphaproteobacteria, Nature, vol.557, pp.101-105, 2018. ,
On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells, Philos. Trans. R. Soc. B Biol. Sci, vol.358, pp.59-85, 2003. ,
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus, Proc. Natl. Acad. Sci, vol.99, pp.12246-12251, 2002. ,
The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells, Proc. Natl. Acad. Sci, vol.96, pp.8271-8276, 1999. ,
Origins, evolutionary history, and taxonomic distribution of alternative oxidase and plastoquinol terminal oxidase, Comp. Biochem. Physiol. Part D Genomics Proteomics, vol.1, pp.357-364, 2006. ,
One core, two shells: bacterial and eukaryotic ribosomes, Nat. Struct. Mol. Biol, vol.19, pp.560-567, 2012. ,
Cap-dependent and cap-independent translation in eukaryotic systems, Gene, vol.332, pp.1-11, 2004. ,
Molecular cloning and sequencing of cDNA for yeast porin, an outer mitochondrial membrane protein: a search for targeting signal in the primary structure, EMBO J, vol.4, pp.769-774, 1985. ,
TEFM (c17orf42) is necessary for transcription of human mtDNA, Nucleic Acids Res, vol.39, pp.4284-4299, 2011. ,
RNA-binding specificity landscapes of designer pentatricopeptide repeat proteins elucidate principles of PPR-RNA interactions, Nucleic Acids Res, vol.46, pp.2613-2623, 2018. ,
Coupling of Phosphorylation to Electron and Hydrogen Transfer by a ChemiOsmotic type of Mechanism, Nature, vol.191, pp.144-148, 1961. ,
Mitochondrial Dynamics and the ER: The Plant Perspective. Front, Cell Dev. Biol, vol.3, p.78, 2015. ,
Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria, Proc. Natl. Acad. Sci. U. S. A, vol.113, pp.8442-8447, 2016. ,
Structure-function insights into prokaryotic and eukaryotic translation initiation, Curr. Opin. Struct. Biol, vol.19, pp.300-309, 2009. ,
URL : https://hal.archives-ouvertes.fr/inserm-00420170
Highresolution structure of the Escherichia coli ribosome, Nat. Struct. Mol. Biol, vol.22, pp.336-341, 2015. ,
Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy, Curr. Genet, vol.44, pp.73-84, 2003. ,
Mitochondria: In sickness and in health, Cell, 2012. ,
A user's guide to the Arabidopsis T-DNA insertion mutant collections, Methods Mol. Biol, vol.1284, pp.323-342, 2015. ,
On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants, Mol. Biol. Evol, vol.25, pp.1120-1128, 2008. ,
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index, Plant Cell Physiol, vol.59, p.3, 2018. ,
The tRNA genes punctuate the reading of genetic information in human mitochondrial DNA, Cell, vol.22, pp.393-403, 1980. ,
tRNA punctuation model of RNA processing in human mitochondria, Nature, vol.290, pp.470-474, 1981. ,
Conserved domain structure of pentatricopeptide repeat proteins involved in chloroplast RNA editing, Proc. Natl. Acad. Sci, vol.104, pp.8178-8183, 2007. ,
Pentatricopeptide Repeat Proteins with the DYW Motif Have Distinct Molecular Functions in RNA Editing and RNA Cleavage in Arabidopsis Chloroplasts, PLANT CELL ONLINE, vol.21, pp.146-156, 2009. ,
Mitochondria-targeting sequence, a multi-role sorting sequence recognized at all steps of protein import into mitochondria, J. Biochem, vol.123, pp.1010-1016, 1998. ,
Co-translational membrane insertion of mitochondrially encoded proteins, Biochim. Biophys. Acta -Mol. Cell Res, vol.1803, pp.767-775, 2010. ,
Mba1, a membrane-associated ribosome receptor in mitochondria, EMBO J, vol.25, pp.1603-1610, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00132809
Organization and Regulation of Mitochondrial Protein Synthesis, Annu. Rev. Biochem, vol.85, 2016. ,
A small particulate component of the cytoplasm, J. Cell Biol, vol.1, pp.59-68, 1955. ,
Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances, Trends Biochem. Sci, vol.42, pp.625-639, 2017. ,
AtmtPNPase is required for multiple aspects of the 18S rRNA metabolism in Arabidopsis thaliana mitochondria, Nucleic Acids Res, vol.32, pp.5174-5182, 2004. ,
3D Gel Map of Arabidopsis Complex I. Front, Plant Sci, vol.4, p.153, 2013. ,
UCSF Chimera?A visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004. ,
Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography, Nat. Commun, vol.6, p.6019, 2015. ,
PPR proteins shed a new light on RNase P biology, RNA Biol, vol.10, pp.1457-1468, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00875474
Biophysical analysis of Arabidopsis protein-only RNase P alone and in complex with tRNA provides a refined model of tRNA binding, J. Biol. Chem, vol.292, pp.13904-13913, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01581835
Engulfed by speculation, Nature, vol.447, pp.913-913, 2007. ,
NUCLEAR FUSION DEFECTIVE1 Encodes the Arabidopsis RPL21M Protein and Is Required for Karyogamy during Female Gametophyte Development and Fertilization, Plant Physiol, vol.141, pp.957-965, 2006. ,
PET111, a Saccharomyces cerevisiae nuclear gene required for translation of the mitochondrial mRNA encoding cytochrome c oxidase subunit II, Genetics, vol.115, pp.637-647, 1987. ,
Mechanism of RNA stabilization and translational activation by a pentatricopeptide repeat protein, Proc. Natl. Acad. Sci. U. S. A, vol.108, pp.415-420, 2011. ,
Pentatricopeptide repeat proteins in Trypanosoma brucei function in mitochondrial ribosomes, Mol. Cell. Biol, vol.27, pp.6876-6888, 2007. ,
Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes, Science, 2018. ,
A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome, EMBO J, vol.29, pp.1116-1125, 2010. ,
Structure of human mitochondrial RNA polymerase, Nature, vol.478, pp.269-273, 2011. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-140, 2010. ,
Engaging the ribosome: universal IFs of translation, Trends Biochem. Sci, vol.26, pp.705-709, 2001. ,
LRPPRC is necessary for polyadenylation and coordination of translation of mitochondrial mRNAs, EMBO J, vol.31, pp.443-456, 2012. ,
On the origin of mitosing cells, J. Theor. Biol, vol.14, pp.225-231, 1967. ,
tRNA Biology in Mitochondria, Int. J. Mol. Sci, vol.16, pp.4518-4559, 2015. ,
Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii, Nucleic Acids Res, pp.1-11, 2017. ,
Recent advances in tRNA mitochondrial import, Trends Biochem. Sci, vol.33, pp.320-329, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00309524
A hypothesis on the identification of the editing enzyme in plant organelles, FEBS Lett, vol.581, pp.4132-4138, 2007. ,
Perspectives on: SGP symposium on mitochondrial physiology and medicine: the renaissance of mitochondrial pH, J. Gen. Physiol, vol.139, pp.415-423, 2012. ,
The prokaryote-eukaryote dichotomy: meanings and mythology. Microbiol, Mol. Biol. Rev, vol.69, pp.292-305, 2005. ,
The evolution of posttranscriptional regulation, Wiley Interdiscip. Rev. RNA, vol.9, p.1485, 2018. ,
Mechanistic and Structural Studies of Protein-Only RNase P Compared to Ribonucleoproteins Reveal the Two Faces of the Same Enzymatic Activity, Biomol, vol.6, p.30, 2016. ,
Über die Entwicklung der Chlorophyllkörner und Farbkörper, 1883. ,
Pentatricopeptide repeat proteins: a socket set for organelle gene expression, Trends Plant Sci, vol.13, pp.663-670, 2008. ,
Release factors differing in specificity for terminator codons, Proc. Natl. Acad. Sci. U. S. A, vol.61, pp.768-774, 1968. ,
Coupling the mitochondrial transcription machinery to human disease, Trends Genet, vol.20, pp.513-519, 2004. ,
Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins, Cell, vol.115, pp.97-108, 2003. ,
Structure of a mitochondrial ribosome with minimal RNA, Proc. Natl. Acad. Sci. U. S. A, vol.106, pp.9637-9642, 2009. ,
Structural basis for specific single-stranded RNA recognition by designer pentatricopeptide repeat proteins, Nat. Commun, vol.7, p.11285, 2016. ,
In Vitro RNA-Binding Assay for Studying Trans-Factors for RNA Editing in Chloroplasts, Methods in Molecular Biology, pp.199-208, 2011. ,
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites, Proc. Natl. Acad. Sci. U. S. A, vol.71, pp.1342-1346, 1974. ,
Systematic Chromosomal Deletion of Bacterial Ribosomal Protein Genes, J. Mol. Biol, vol.413, pp.751-761, 2011. ,
LRPPRC-mediated folding of the mitochondrial transcriptome, Nat. Commun, vol.8, p.1532, 2017. ,
Mitochondrial ribosome assembly in health and disease, Cell Cycle, vol.14, pp.2226-2250, 2015. ,
Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22, Nature, vol.384, pp.582-585, 1996. ,
Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates, PLoS Biol, vol.10, p.1001241, 2012. ,
Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes, Plant Cell, vol.30, pp.525-527, 2018. ,
Cytonuclear integration and co-evolution, Nat. Rev. Genet, vol.19, pp.635-648, 2018. ,
Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes, Genome Biol. Evol, vol.7, pp.1235-1251, 2015. ,
The PPR motif -a TPR-related motif prevalent in plant organellar proteins, Trends Biochem. Sci, vol.25, pp.46-47, 2000. ,
Evolution of linear mitochondrial DNA in three known lineages of Polytomella, Curr. Genet, vol.56, pp.427-438, 2010. ,
, , 2007.
, Reconstructing the evolution of the mitochondrial ribosomal proteome, Nucleic Acids Res, vol.35, pp.4686-4703
A Heme-Sensing Mechanism in the Translational Regulation of Mitochondrial Cytochrome c Oxidase Biogenesis, Cell Metab, vol.16, pp.801-813, 2012. ,
, , p.144, 2016.
Mitochondrial Respiratory Chain Complexes, pp.167-227, 2018. ,
The bc:caa3 supercomplexes from the Gram positive bacterium Bacillus subtilis respiratory chain: A megacomplex organization?, Arch. Biochem. Biophys, vol.537, pp.153-160, 2013. ,
Suppressor analyses of temperature-sensitive cbp1 strains of Saccharomyces cerevisiae: the product of the nuclear gene SOC1 affects mitochondrial cytochrome b mRNA post-transcriptionally, Genetics, vol.138, pp.565-575, 1994. ,
The role of mitochondria in cellular iron-sulfur protein biogenesis: mechanisms, connected processes, and diseases, Cold Spring Harb. Perspect. Biol, vol.5, p.11312, 2013. ,
Molecular Architecture of the Rotary Motor in ATP Synthase, Science, vol.286, pp.1700-1705, 1999. ,
Two NYN domain containing putative nucleases are involved in transcript maturation in Arabidopsis mitochondria, Plant J, vol.85, pp.278-288, 2016. ,
RNA Processing Factor 7 and Polynucleotide Phosphorylase Are Necessary for Processing and Stability of nad2 mRNA in Arabidopsis Mitochondria, RNA Biol, vol.11, pp.968-976, 2014. ,
The Unexpected Diversity of Plant Organelle RNA Editosomes, Trends Plant Sci, vol.21, pp.962-973, 2016. ,
Ribosome binding to the Oxa1 complex facilitates co-translational protein insertion in mitochondria, EMBO J, vol.22, pp.6448-6457, 2003. ,
The mitochondrial genome: structure, transcription, translation and replication, Biochim. Biophys. Acta -Bioenerg, vol.1410, pp.103-123, 1999. ,
The process of RNA editing in plant mitochondria, Mitochondrion, vol.8, pp.35-46, 2008. ,
Hungry codons promote frameshifting in human mitochondrial ribosomes, Science, vol.327, p.301, 2010. ,
Identification of a novel human nuclear-encoded mitochondrial poly(A) polymerase, Nucleic Acids Res, vol.32, pp.6001-6014, 2004. ,
Whole mitochondrial genome sequence of an Indian Plasmodium falciparum field isolate, Korean J. Parasitol, vol.52, pp.99-103, 2014. ,
The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides, Nat. Genet, vol.15, pp.57-61, 1997. ,
PPR336 is Associated with Polysomes in Plant Mitochondria, J. Mol. Biol, vol.375, pp.626-636, 2008. ,
MAM (mitochondria-associated membranes) in mammalian cells: Lipids and beyond, Biochim. Biophys. Acta -Mol. Cell Biol. Lipids, vol.1841, pp.595-609, 2014. ,
Alternative Oxidase: A Mitochondrial Respiratory Pathway to Maintain Metabolic and Signaling Homeostasis during Abiotic and Biotic Stress in Plants, Int. J. Mol. Sci, vol.14, pp.6805-6847, 2013. ,
Three-dimensional structure of the yeast ribosome, Nucleic Acids Res, vol.26, pp.655-661, 1998. ,
The Role of Mitochondria in Apoptosis, Annu. Rev. Genet, vol.43, p.95, 2009. ,
Chloroplast RNA-Binding Protein RBD1 Promotes Chilling Tolerance through 23S rRNA Processing in Arabidopsis, PLOS Genet, vol.12, p.1006027, 2016. ,
Structural and Functional Insights into Human Re-initiation Complexes, Mol. Cell, vol.67, pp.447-456, 2017. ,
Biological evidence for the world's smallest tRNAs, Biochimie, vol.100, pp.151-158, 2014. ,
Population structure of mitochondrial genomes in Saccharomyces cerevisiae, BMC Genomics, vol.16, p.451, 2015. ,
Elucidation of the RNA Recognition Code for Pentatricopeptide Repeat Proteins Involved in Organelle RNA Editing in Plants, PLoS One, vol.8, p.57286, 2013. ,
Roles of bound quinone in the single subunit NADH-quinone oxidoreductase (Ndi1) from Saccharomyces cerevisiae, J. Biol. Chem, vol.282, pp.6012-6020, 2007. ,
, , 2013.
, Structural basis for the modular recognition of single-stranded RNA by PPR proteins, Nature, vol.504, pp.168-171
Large facilities and the evolving ribosome, the cellular machine for genetic-code translation, J. R. Soc. Interface, vol.6, pp.575-585, 2009. ,
Structural basis for messenger RNA movement on the ribosome, Nature, vol.444, pp.391-394, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00188236
Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, vol.541, pp.353-358, 2017. ,
Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane, Cell Metab, vol.27, pp.645-656, 2018. ,
The Saccharomyces cerevisiae ATP22 Gene Codes for the Mitochondrial ATPase Subunit 6-Specific Translation Factor, Genetics, vol.175, pp.55-63, 2006. ,
Nuclear Control of the Messenger RNA Expression for Mitochondrial ATPase Subunit 9 in a New Yeast Mutant, J. Mol. Biol, vol.229, pp.909-916, 1993. ,
On the Origin of Eukaryotes, Science, vol.325, pp.666-668, 2009. ,
, Résumé en français
, Résultats Au cours de ma thèse, j'ai tout d'abord établi un protocole efficace de purification de mitochondries d'Arabidopsis thaliana à partir de cultures cellulaires
De plus un suivie de la purification a été réalisé à l'aide d'anticorps permettant soit la détection d'une protéine ribosomale cytosolique soit d'une protéine ribosomale mitochondriale. Pour me permettre d'analyser de façon efficace la composition du ribosome mitochondrial d'Arabidopsis, j'ai créé une lignée de plante complémentée exprimant avec une version étiquetée d'une de mes protéines candidates, -Esplanade), mais également directement sur microscope électronique à transmission en collaboration avec Yaser Hashem (IBMC, Strasbourg puis INSERM Bordeaux), 2008. ,
, utilisé cette lignée pour purifier des mitochondries et réaliser des co-immuno-précipitation de rPPR1HA. La co-immuno-précipitation a permis de confirmer que rPPR1 était un composant du mitoribosome d'Arabidopsis, associé à la petite sous-unité
, En croisant les données de protéomiques obtenues par purification biochimique classique avec mes données de co-immuno-précipitation, j'ai pu obtenir une liste complète des composants protéiques du mitoribosome d'Arabidopsis. Cela m'a permis d'établir que le mitoribosome est constitué de 81 protéines différentes, dont 19 sont spécifiques des plantes. Parmi ces protéines, 10 font partie de la famille des protéines PPR. En séparant biochimiquement petite et grande sousunités du ribosome
, L'analyse par cryo-électron microscopie des mitoribosomes d'Arabidopsis a permis de