ND3 and ND4L subunits of mitochondrial complex I, both nucleus encoded in Chlamydomonas reinhardtii, are required for activity and assembly of the enzyme
[en] Made of more than 40 subunits, the rotenone-sensitive NADH:ubiquinone oxidoreductase (complex I) is the most intricate membrane-bound enzyme of the mitochondrial respiratory chain. In vascular plants, fungi, and animals, at least seven complex I subunits (ND1, -2, -3, -4, -4L, -5, and -6; ND is NADH dehydrogenase) are coded by mitochondrial genes. The role of these highly hydrophobic subunits in the enzyme activity and assembly is still poorly understood. In the unicellular green alga Chlamydomonas reinhardtii, the ND3 and ND4L subunits are encoded in the nuclear genome, and we show here that the corresponding genes, called NUO3 and NUO11, respectively, display features that facilitate their expression and allow the proper import of the corresponding proteins into mitochondria. In particular, both polypeptides show lower hydrophobicity compared to their mitochondrion-encoded counterparts. The expression of the NUO3 and NUO11 genes has been suppressed by RNA interference. We demonstrate that the absence of ND3 or ND4L polypeptides prevents the assembly of the 950-kDa whole complex I and suppresses the enzyme activity. The putative role of hydrophobic ND subunits is discussed in relation to the structure of the complex I enzyme. A model for the assembly pathway of the Chlamydomonas enzyme is proposed.
Disciplines :
Microbiology
Author, co-author :
Cardol, Pierre ; Université de Liège - ULiège > Département des sciences de la vie > Biochimie végétale
Lapaille, Marie ; Université de Liège - ULiège > Département des sciences de la vie > Génétique
Minet, P.
Franck, Fabrice ; Université de Liège - ULiège > Département des sciences de la vie > Biochimie végétale
Matagne, René-Fernand ; Université de Liège - ULiège > Services généraux (Faculté des sciences) > Relations académiques et scientifiques (Sciences)
Remacle, Claire ; Université de Liège - ULiège > Département des sciences de la vie > Génétique
Language :
English
Title :
ND3 and ND4L subunits of mitochondrial complex I, both nucleus encoded in Chlamydomonas reinhardtii, are required for activity and assembly of the enzyme
Publication date :
September 2006
Journal title :
Eukaryotic Cell
ISSN :
1535-9778
eISSN :
1535-9786
Publisher :
Amer Soc Microbiology, Washington, United States - Washington
Antonicka, H., I. Ogilvie, T. Taivassalo, R. P. Anitori, R. G. Haller, J. Vissing, N. G. Kennaway, and E. A. Shoubridge. 2003. Identification and characterization of a common set of complex I assembly intermediates in mitochondria from patients with complex I deficiency. J. Biol. Chem. 278:43081-43088.
Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
Brennicke, A., L. Grohmann, R. Hiesel, V. Knoop, and W. Schuster. 1993. The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett. 325:140-145.
Bullerwell, C. E., and M. W. Gray. 2004. Evolution of the mitochondrial genome: protist connections to animals, fungi and plants. Curr. Opin. Microbiol. 7:528-534.
Bykova, N. V., A. G. Rasmusson, A. U. Igamberdiev, P. Gardestrom, and I. M. Moller. 1999. Two separate transhydrogenase activities are present in plant mitochondria. Biochem. Biophys. Res. Commun. 265:106-111.
Cardol, P., R. F. Matagne, and C. Remacle. 2002. Impact of mutations affecting ND mitochondria-encoded subunits on the activity and assembly of complex I in Chlamydomonas. Implication for the structural organization of the enzyme. J. Mol. Biol. 319:1211-1221.
Cardol, P., F. Vanrobaeys, B. Devreese, J. Van Beeumen, R. F. Matagne, and C. Remacle. 2004. Higher plant-like subunit composition of the mitochondrial complex I from Chlamydomonas reinhardtii: 31 conserved components among eukaryotes. Biochim. Biophys. Acta 1658:212-224.
Cardol, P., D. Gonzälez-Halphen, A. Reyes-Prieto, D. Baurain, R. F. Matagne, and C. Remacle. 2005. The mitochondrial oxidative phosphorylation proteome of Chlamydomonas reinhardtii deduced from the Genome Sequencing Project. Plant Physiol. 137:447-459.
Carroll, J., I. M. Fearnley, R. J. Shannon, J. Hirst, and J. E. Walker. 2003. Analysis of the subunit composition of complex I from bovine heart mitochondria. Mol. Cell Proteomics 2:117-126.
Claros, M. G., J. Perea, Y. Shu, F. A. Samatey, J. L. Popot, and C. Jacq. 1995. Limitations to in vivo import of hydrophobic proteins into yeast mitochondria. The case of a cytoplasmically synthesized apocytochrome b. Eur. J. Biochem. 228:762-771.
Claros, M. G., and P. Vincens. 1996. Computational method to predict mitochondrially imported proteins and their targeting sequences. Eur. J. Biochem. 241:779-786.
Crimi, M., M. Sciacco, S. Galbiati, A. Bordoni, G. Malferrari, R. Del Bo, I. Biunno, N. Bresolin, and G. P. Comi. 2002. A collection of 33 novel human mtDNA homoplasmic variants. Hum. Mutat. 20:409.
Crimi, M., A. Papadimitriou, S. Galbiati, P. Palamidou, F. Fortunato, A. Bordoni, U. Papandreou, D. Papadimitriou, G. M. Hadjigeorgiou, E. Drogari, N. Bresolin, and G. P. Comi. 2004. A new mitochondrial DNA mutation in ND3 gene causing severe Leigh syndrome with early lethality. Pediatr. Res. 55:842-846.
Daley, D. O., R. Clifton, and J. Whelan. 2002. Intracellular gene transfer: reduced hydrophobicity facilitates gene transfer for subunit 2 of cytochrome c oxidase. Proc. Natl. Acad. Sci. USA 99:10510-10515.
Darrouzet, E., J. P. Issartel, J. Lunardi, and A. Dupuis. 1998. The 49-kDa subunit of NADH-ubiquinone oxidoreductase (complex I) is involved in the binding of piericidin and rotenone, two quinone-related inhibitors. FEBS Lett. 431:34-38.
Debuchy, R., S. Purton, and J. D. Rochaix. 1989. The argininosuccinate lyase gene of Chlamydomonas reinhardtii: an important tool for nuclear transformation and for correlating the genetic and molecular maps of the ARG7 locus. EMBO J. 8:2803-2809.
Di Bernardo, S., and T. Yagi. 2001. Direct interaction between a membrane domain subunit and a connector subunit in the H(+)-translocating NADH-quinone oxidoreductase. FEBS Lett. 508:385-388.
Djafarzadeh, R., S. Kerscher, K. Zwicker, M. Radermacher, M. Lindahl, H. Schagger, and U. Brandt. 2000. Biophysical and structural characterization of proton-translocating NADH-dehydrogenase (complex I) from the strictly aerobic yeast Yarrowia lipolytica. Biochim. Biophys. Acta 1459:230-238.
Duarte, M., H. Populo, A. Videira, T. Friedrich, and U. Schulte. 2002. Disruption of iron-sulphur cluster N2 from NADH: ubiquinone oxidoreductase by site-directed mutagenesis. Biochem. J. 364:833-839.
Duby, F., P. Cardol, R. F. Matagne, and C. Remacle. 2001. Structure of the telomeric ends of mt DNA, transcriptional analysis and complex I assembly in the dum24 mitochondrial mutant of Chlamydomonas reinhardtii. Mol. Genet. Genomics 266:109-114.
Dudkina, N. V., H. Eubel, W. Keegstra, E. J. Boekema, and H. P. Braun. 2005. Structure of a mitochondrial supercomplex formed by respiratory-chain complexes I and III. Proc. Natl. Acad. Sci. USA 102:3225-3229.
Elhafez, D., M. W. Murcha, R. Clifton, K. L. Soole, D. A. Day, and J. Whelan. 2006. Characterization of mitochondrial alternative NAD(P)H dehydrogenases in Arabidopsis: intraorganelle location and expression. Plant Cell. Physiol. 47:43-54.
Emanuelsson, O., H. Nielsen, S. Brunak, and G. von Heijne. 2000. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J. Mol. Biol. 300:1005-1016.
Fearnley, I. M., and J. E. Walker. 1992. Conservation of sequences of subunits of mitochondrial complex I and their relationships with other proteins. Biochim. Biophys. Acta 1140:105-134.
Fuhrmann, M., A. Stahlberg, E. Govorunova, S. Rank, and P. Hegemann. 2001. The abundant retinal protein of the Chlamydomonas eye is not the photoreceptor for photoaxis and photophobic responses. J. Cell Sci. 114:3857-3863.
Funes, S., E. Davidson, M. G. Claros, R. van Lis, X. Perez-Martinez, M. Vazquez-Acevedo, M. P. King, and D. González-Halphen. 2002. The typically mitochondrial DNA-encoded ATP6 subunit of the F1F0-ATPase is encoded by a nuclear gene in Chlamydomonas reinhardtii. J. Biol. Chem. 277:6051-6058.
Galanis, M., R. J. Devenish, and P. Nagley. 1991. Duplication of leader sequence for protein targeting to mitochondria leads to increased import efficiency. FEBS Lett. 282:425-430.
Glaser, E., S. Sjoling, M. Tanudji, and J. Whelan. 1998. Mitochondrial protein import in plants. Signals, sorting, targeting, processing and regulation. Plant Mol. Biol. 38:331-338.
González-Halphen, D., S. Funes, X. Perez-Martinez, A. Reyes-Prieto, M. G. Claros, E. Davidson, and M. P. King. 2004. Genetic correction of mitochondrial diseases: using the natural migration of mitochondrial genes to the nucleus in chlorophyte algae as a model system. Ann. N. Y. Acad. Sci. 1019:232-239.
German, D. S., and R. P. Levine. 1965. Cytochrome f and plastocyanin: their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 54:1665-1669.
Gray, M. W., G. Burger, and B. F. Lang. 1999. Mitochondrial evolution. Science 283:1476-1481.
Grigorieff, N. 1998. Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 277:1033-1046.
Grossman, A. R., E. E. Harris, C. Hauser, P. A. Lefebvre, D. Martinez, D. Rokhsar, J. Shrager, C. D. Silflow, D. Stern, O. Vallon, and Z. Zhang. 2003. Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot. Cell 2:1137-1150.
Gutierres, S., M. Sabar, C. Lelandais, P. Chetrit, P. Diolez, H. Degand, M. Boutry, F. Vedel, Y. de Kouchkovsky, and R. De Paepe. 1997. Lack of mitochondrial and nuclear-encoded subunits of complex I and alteration of the respiratory chain in Nicotiana sylvestris mitochondrial deletion mutants. Proc. Natl. Acad. Sci. USA 94:3436-3441.
Harris, E. H. 1989. The Chlamydomonas sourcebook. Academic Press, San Diego, Calif.
Heazlewood, J. L., K. A. Howell, and A. H. Millar. 2003. Mitochondrial complex I from Arabidopsis and rice: orthologs of mammalian and fungal components coupled with plant-specific subunits. Biochim. Biophys. Acta 1604:159-169.
Hinchliffe, P., and L. A. Sazanov. 2005. Organization of iron-sulfur clusters in respiratory complex I. Science 309:771-774.
Hirst, J., J. Carroll, I. M. Fearnley, R. J. Shannon, and J. E. Walker. 2003. The nuclear encoded subunits of complex I from bovine heart mitochondria. Biochim. Biophys. Acta 1604:135-150.
Holt, P. J., D. J. Morgan, and L. A. Sazanov. 2003. The location of NuoL and NuoM subunits in the membrane domain of the Escherichia coli complex I: implications for the mechanism of proton pumping. J. Bio. Chem. 278:43114-43120.
Kao, M. C., S. Di Bernardo, M. Perego, E. Nakamaru-Ogiso, A. Matsuno-Yagi, and T. Yagi. 2004. Functional roles of four conserved charged residues in the membrane domain subunit NuoA of the proton-translocating NADH-quinone oxidoreductase from Escherichia coli. J. Biol. Chem. 279:32360-32366.
Kao, M. C., A. Matsuno-Yagi, and T. Yagi. 2004. Subunit proximity in the H+-translocating NADH-quinone oxidoreductase probed by zero-length cross-linking. Biochemistry 43:3750-3755.
Kao, M. C., E. Nakamaru-Ogiso, A. Matsuno-Yagi, and T. Yagi. 2005. Characterization of the membrane domain subunit NuoK (ND4L) of the NADH-quinone oxidoreductase from Escherichia coli. Biochemistry 44:9545-9554.
Karpova, O. V., and K. J. Newton. 1999. A partially assembled complex I in ND4-deficient mitochondria of maize. Plant J. 17:511-521.
Kashani-Poor, N., K. Zwicker, S. Kerscher, and U. Brandt. 2001. A central functional role for the 49-kDa subunit within the catalytic core of mitochondrial complex I. J. Biol. Chem. 276:24082-24087.
Kervinen, M., J. Patsi, M. Finel, and I. E. Hassinen. 2004. A pair of membrane-embedded acidic residues in the NuoK subunit of Escherichia coli NDH-1, a counterpart of the ND4L subunit of the mitochondrial complex I, are required for high ubiquinone reductase activity. Biochemistry 43:773-781.
Kindle, K. L. 1990. High frequency nuclear transformation of Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA 87:1228-1232.
Kuffner, R., A. Rohr, A. Schmiede, C. Krull, and U. Schulte. 1998. Involvement of two novel chaperones in the assembly of mitochondrial NADH: ubiquinone oxidoreductase (complex I). J. Mol. Biol. 283:409-417.
Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
Loppes, R., and M. Radoux. 2001. Identification of short promoter regions involved in the transcriptional expression of the nitrate reductase gene in Chlamydomonas reinhardtii. Plant Mol. Biol. 45:215-227.
Loppes, R., and M. Radoux. 2002. Two short regions of the promoter are essential for activation and repression of the nitrate reductase gene in Chlamydomonas reinhardtii. Mol. Genet. Genomics 268:42-48.
Marienfeld, J. R., and K. J. Newton. 1994. The maize NCS2 abnormal growth mutant has a chimeric nad4-nad7 mitochondrial gene and is associated with reduced complex I function. Genetics 138:855-863.
Marques, I., M. Duarte, J. Assuncao, A. V. Ushakova, and A. Videira. 2005. Composition of complex I from Neurospora crassa and disruption of two "accessory" subunits. Biochim. Biophys. Acta 1707:211-220.
Matagne, R. F., M. R. Michel-Wolwertz, C. Munaut, C. Duyckaerts, and F. Sluse. 1989. Induction and characterization of mitochondrial DNA mutants in Chlamydomonas reinhardtii. J. Cell Biol. 108:1221-1226.
Mathiesen, C., and C. Hagerhall. 2002. Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters. Biochim. Biophys. Acta 1556:121-132.
Mathiesen, C., and C. Hagerhall. 2003. The "antiporter module" of respiratory chain complex I includes the MrpC/NuoK subunit - a revision of the modular evolution scheme. FEBS Lett. 549:7-13.
McFarland, R., D. M. Kirby, K. J. Fowler, A. Ohtake, M. T. Ryan, D. J. Amor, J. M. Fletcher, J. W. Dixon, F. A. Collins, D. M. Turnbull, R. W. Taylor, and D. R. Thorburn. 2004. De novo mutations in the mitochondrial ND3 gene as a cause of infantile mitochondrial encephalopathy and complex I deficiency. Ann. Neurol. 55:58-64.
Michaelis, G., C. Vahrenholz, and E. Pratje. 1990. Mitochondrial DNA of Chlamydomonas reinhardtii: the gene for apocytochrome b and the complete functional map of the 15.8 kb DNA. Mol. Gen. Genet. 223:211-216.
Newman, S. M., J. E. Boynton, N. W. Gillham, B. L. Randolph-Andersen, A. M. Johnson, and E. H. Harris,. 1990. Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events. Genetics 126:875-888.
Pazour, G. J., and G. B. Witman. 2000. Forward and reverse genetic analysis of microtubule motors in Chlamydomonas. Methods 22:285-298.
Perez-Martinez, X., M. Vazquez-Acevedo, E. Tolkunova, S. Funes, M. G. Claros, E. Davidson, M. P. King, and D. González-Halphen. 2000. Unusual location of a mitochondrial gene. Subunit III of cytochrome c oxidase is encoded in the nucleus of chlamydomonad algae. J. Biol. Chem. 275:30144-30152.
Perez-Martinez, X., A. Antaramian, M. Vazquez-Acevedo, S. Funes, E. Tolkunova, J. d'Alayer, M. G. Claros, E. Davidson, M. P. King, and D. González-Halphen. 2001. Subunit II of cytochrome c oxidase in chlamydomonad algae is a heterodimer encoded by two independent nuclear genes. J. Biol. Chem. 276:11302-11309.
Perez-Martinez, X., S. Funes, E. Tolkunova, E. Davidson, M. P. King, and D. González-Halphen. 2002. Structure of nuclear-localized cox3 genes in Chlamydomonas reinhardtii and in its colorless close relative Polytomella sp. Curr. Genet. 40:399-404.
Pineau, B., C. Mathieu, C. Gerard-Hirne, R. De Paepe, and P. Chetrit. 2005. Targeting the NAD7 subunit to mitochondria restores a functional complex I and a wild type phenotype in the Nicotiana sylvestris CMS II mutant lacking nad7. J. Bio. Chem. 280:25994-26001.
Prieur, I., J. Lunardi, and A. Dupuis. 2001. Evidence for a quinone binding site close to the interface between NUOD and NUOB subunits of complex I. Biochim. Biophys. Acta 1504:173-178.
Pröschold, T., B. Marin, U. G. Schlosser, and M. Melkonian. 2001. Molecular phytogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist 152:265-300.
Race, H. L., R. G. Herrmann, and W. Martin. 1999. Why have organelles retained genomes? Trends Genet. 15:364-370.
Reddy, A. S. N. 2001. Nuclear pre-mRNA splicing in plants. Crit. Rev. Plant Sci. 20:523-571.
Remacle, C., D. Baurain, P. Cardol, and R. F. Matagne. 2001. Mutants of Chlamydomonas reinhardtii deficient in mitochondrial complex I. Characterization of two mutations affecting the nd1 coding sequence. Genetics 158:1051-1060.
Remacle, C., F. Duby, P. Cardol, and R. F. Matagne. 2001. Mutations inactivating mitochondrial genes in Chlamydomonas reinhardtii. Biochem. Soc. Trans. 29:442-446.
Remacle, C., P. Cardol, N. Coosemans, M. Gaisne, and N. Bonnefoy. 2006. High-efficiency biolistic transformation of Chlamydomonas mitochondria can be used to insert mutations in complex I genes. Proc. Natl. Acad. Sci. USA 103:4771-4776.
Rexroth, S., J. M. Meyer zu Tittingdorf, F. Krause, N. A. Dencher, and H. Seelen. 2003. Thylakoid membrane at altered metabolic state: challenging the forgotten realms of the proteome. Electrophoresis 24:2814-2823.
Sazanov, L. A., S. Y. Peak-Chew, I. M. Fearnley, and J. E. Walker. 2000. Resolution of the membrane domain of bovine complex I into subcomplexes: implications for the structural organization of the enzyme. Biochemistry 39:7229-7235.
Schägger, H., and G. Von Jago. 1991. Blue native electrophoresis for isolation of membrane protein complexes in enzymatically active form. Anal. Biochem. 199:223-231.
Schapira, A. H. 1998. Human complex I defects in neurodegenerative diseases. Biochim. Biophys. Acta 1364:261-270.
Schroda, M. 2006. RNA silencing in Chlamydomonas: mechanisms and tools. Curr. Genet. 49:69-84.
Silflow, C. D. 1998. Organization of the nuclear genome, p. 25-40. In J. D. Rochaix, M. Goldschmidt-Clermont, and S. Merchant (ed.), The molecular biology of chloroplasts and mitochondria in Chlamydomonas. Kluwer Academic Publishers, Dordrecht, The Netherlands.
Taylor, R. W., R. Singh-Kler, C. M. Hayes, P. E. Smith, and D. M. Turnbull. 2001. Progressive mitochondrial disease resulting from a novel missense mutation in the mitochondrial DNA ND3 gene. Ann. Neurol. 50:104-107.
van Lis, R., A. Atteia, G. Mendoza-Hernández, and D. González-Halphen. 2003. Identification of novel mitochondrial protein components of Chlamydomonas reinhardtii. A proteomic approach. Plant Physiol. 132:318-330.
Videira, A., and M. Duarte. 2002. From NADH to ubiquinone in Neurospora mitochondria. Biochim. Biophys. Acta 1555:187-191.