In vivo chlorophyll fluorescence screening allows the isolation of a Chlamydomonas mutant defective for NDUFAF3, an assembly factor involved in mitochondrial complex I assembly
[en] The qualitative screening method to select complex I mutants in the microalga Chlamydomonas, based on reduced growth under heterotrophic condition, is not suited for high throughput screening. In order to develop a fast screening method based on measurements of chlorophyll fluorescence, we first demonstrated that complex I mutants displayed decreased photosystem II efficiency in the genetic background of a photosynthetic mutation leading to reduced formation of the electrochemical proton gradient in the chloroplast (pgrl1 mutation). In contrast, single mutants (complex I and pgrl1 mutants) could not be distinguished from wild type by their photosystem II efficiency in the tested conditions. We next performed an insertional mutagenesis on the pgrl1 mutant. Out of ~3000 hygromycin-resistant insertional transformants, 46 had decreased photosystem II efficiency and three were complex I mutants. One of the mutants was tagged and whole genome sequencing identified the resistance cassette in NDUFAF3, a homolog of the human NDUFAF3 gene, encoding for an assembly factor involved in complex I assembly. Complemented strains showed restored complex I activity and assembly. Overall, we described here a screening method which is fast and particularly suited for identification of Chlamydomonas complex I mutants.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Massoz, Simon; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Hanikenne, Marc ; Université de Liège - ULiège > Département des sciences de la vie > Génomique fonctionnelle et imagerie moléculaire végétale
Bailleul, Benjamin; Université Pierre et Marie Currie - Paris 6 - UPMC > Institut de Biologie Physico-Chimique (IBPC)
Coosemans, Nadine ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Radoux, Michèle ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Miranda Astudillo, Héctor Vicente ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Cardol, Pierre ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Remacle, Claire ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Language :
English
Title :
In vivo chlorophyll fluorescence screening allows the isolation of a Chlamydomonas mutant defective for NDUFAF3, an assembly factor involved in mitochondrial complex I assembly
Allen, J.F., Abrahams, J.P., Leslie, A.G. et al. (2002) Photosynthesis of ATP—Electrons, Proton Pumps, Rotors, and Poise. Cell, 110, 273–276.
Baertling, F., Sánchez-Caballero, L., Timal, S., van den Brand, M.A., Ngu, L.H., Distelmaier, F., Rodenburg, R.J. and Nijtmans, L.G. (2017) Mutations in mitochondrial complex I assembly factor NDUFAF3 cause Leigh syndrome. Hum. Mutat., 38, 692–703.
Barbieri, R., Larosa, V., Nouet, C., Subrahmanian, N., Remacle, C. and Hamel, P.P. (2011) A forward genetic screen identifies mutants deficient for mitochondrial complex I assembly in Chlamydomonas reinhardtii. Genetics, 188, 349–358.
Bell, S.A., Shen, C., Brown, A. and Hunt, A.G. (2016) Experimental genome-wide determination of RNA polyadenylation in Chlamydomonas reinhardtii. PLoS One, e0146107.
Berrisford, J.M., Baradaran, R. and Sazanov, L.A. (2016) Structure of bacterial respiratory complex I. Biochim. Biophys. Acta, 1857, 892–901.
Berthold, P., Schmitt, R. and Mages, W. (2002) Gene mediates dominant resistance against hygromycin B in Chlamydomonas reinhardtii. Protist, 153, 401–412.
Billoud, B., Jouanno, É., Nehr, Z., Carton, B., Rolland, E., Chenivesse, S. and Charrier, B. (2015) Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches to which extent can current forward genetic approaches be profitable to macroalgal localisation of a mutant locus. Front. Plant Sci., 6, 68.
Blaby, I.K., Glaesener, A.G., Mettler, T. et al. (2013) Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell, 25, 4305–4323.
Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. and Pirovano, W. (2011) Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 27, 578–579.
Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114–2120.
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.
Cardol, P. (2011) Mitochondrial NADH: ubiquinone oxidoreductase (complex I) in eukaryotes: a highly conserved subunit composition highlighted by mining of protein databases. Biochim. Biophys. Acta, 1807, 1390–1397.
Cardol, P., Matagne, R.F. and Remacle, C. (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., Gloire, G., Havaux, M., Remacle, C., Matagne, R. and Franck, F. (2003) Photosynthesis and state transitions in mitochondrial mutants of Chlamydomonas reinhardtii affected in respiration. Plant Physiol., 133, 2010–2020.
Cardol, P., Vanrobaeys, F., Devreese, B., Van Beumen, J., Matagne, R.F. and Remacle, C. (2004) Higher plant-like subunit composition of mitochondrial complex I from Chlamydomonas reinhardtii: 31 Conserved components among eukaryotes. Biochim. Biophys. Acta, 1658, 212–224.
Cardol, P., Lapaille, M., Minet, P., Franck, F., Matagne, R.F. and Remacle, C. (2006) ND3 and ND4L subunits of mitochondrial complex I, both nucleus encoded in Chlamydomonas reinhardtii, are required for activity and assembly of the enzyme. Eukaryot. Cell, 5, 1460–1467.
Cardol, P., Boutaffala, L., Memmi, S., Devresse, B., Matagne, R.F. and Remacle, C. (2008) In Chlamydomonas, the loss of ND5 subunit prevents the assembly of whole mitochondrial complex I and leads to the formation of a low abundant 700 kDa subcomplex. Biochim. Biophys. Acta, 1777, 388–396.
Cardol, P., Alric, J., Girard-Bascou, J., Franck, F., Wollman, F.A. and Finazzi, G. (2009) Impaired respiration discloses the physiological significance of state transitions in Chlamydomonas. Proc. Natl Acad. Sci. USA, 106, 15979–15984.
Dang, K., Plet, J., Tolleter, D. et al. (2014) Combined increases in mitochondrial cooperation and oxygen photoreduction compensate for deficiency in cyclic electron flow in Chlamydomonas reinhardtii. Plant Cell, 26, 3036–3050.
Dent, R.M., Haglund, C.M., Chin, B.L., Kobayashi, M.C. and Niyogi, K.K. (2005) Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiol., 137, 545–556.
Depège, N., Bellafiore, S. and Rochaix, J.D. (2003) Role of chloroplast protein kinase Stt7 in LHCII phosphorylation and state transition in Chlamydomonas. Science, 299, 1572–1575.
Duby, F. and Matagne, R.F. (1999) Alteration of dark respiration and reduction of phototrophic growth in a mitochondrial DNA deletion mutant of Chlamydomonas lacking cob, nd4, and the 3′ end of nd5. Plant Cell, 11, 115–125.
Fiedorczuk, K., Letts, J.A., Degliesposti, G., Kaszuba, K., Skehel, M. and Sazanov, L.A. (2016) Atomic structure of the entire mammalian mitochondrial complex I. Nature, 538, 406–410.
Fromm, S., Braun, H.P. and Peterhansel, C. (2016) Mitochondrial gamma carbonic anhydrases are required for complex I assembly and plant reproductive development. New Phytol., 211, 194–207.
Gawryluk, R.M. and Gray, M.W. (2010) Evidence for an early evolutionary emergence of gamma-type carbonic anhydrases as components of mitochondrial respiratory complex I. BMC Evol. Biol., 10, 176.
Genty, B., Briantais, J. and Baker, N.R. (1989) Electron transport and quenching of chlorophyll fluorescence. Biochim. Biophys. Acta, 990, 87–92.
Giovannoni, J.J., Wing, R., Ganal, M.W. and Tanksley, S.D. (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Res., 19, 6553–6558.
Guerrero-Castillo, S., Baertling, F., Kownatzki, D., Wessels, H.J., Arnold, S., Brandt, U. and Nijtmans, L. (2017) The assembly pathway of mitochondrial respiratory chain complex I. Cell Metab., 25, 128–139.
Hirst, J. (2013) Mitochondrial complex I. Annu. Rev. Biochem., 82, 551–575.
Hoefs, S.J.G., van Spronsen, F.J., Lenssen, E.W.H., Nijtmans, L., Rodenburg, R.J., Smeitink, J.A. and van den Heuvel, L.P. (2011) NDUFA10 mutations cause complex I deficiency in a patient with Leigh disease. Eur. J. Hum. Genet., 19, 270–274.
Johnson, X., Vandystadt, G., Bujaldon, S., Wollman, F.A., Dubois, R., Roussel, P., Alric, J. and Béal, D. (2009) A new setup for in vivo fluorescence imaging of photosynthetic activity. Photosynthesis Res., 102, 85–93.
Kitajima, M. and Butler, W.L. (1975) Quenching of chlorophyll fluorescence and primary photochemistry in chloroplasts by dibromothymoquinone. Biochim. Biophys. Acta, 376, 105–115.
Klodmann, J., Sunderhaus, S., Nimtz, M., Jänsch, L. and Braun, H.P. (2010) Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell, 22, 797–810.
Kmita, K., Wirth, C., Warnau, J., Guerrero-Castillo, S., Hunte, C., Hummer, G., Kaila, V.R., Zwicker, K., Brandt, U. and Zickermann, V. (2015) Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proc. Natl Acad. Sci. USA, 112, 5685–5690.
Lecler, R., Cardol, P., Remacle, C., Emonds-Alt, B., Cardol, P. and Remacle, C. (2012) Characterization of an internal type-II NADH dehydrogenase from Chlamydomonas reinhardtii mitochondria. Curr. Genet., 58, 205–216.
Letts, J.A. and Sazanov, L.A. (2015) Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Curr. Opin. Struct. Biol., 33, 135–145.
Liu, Y.G., Mitsukawa, N., Oosumi, T. and Whittier, R.F. (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J., 8, 457–463.
Massoz, S., Larosa, V., Horrion, B., Matagne, R.F., Remacle, C. and Cardol, P. (2015) Isolation of Chlamydomonas reinhardtii mutants with altered mitochondrial respiration by chlorophyll fluorescence measurement. J. Biotechnol., 215, 27–34.
Michelmore, R.W., Paran, I. and Kesseli, R.V. (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis - a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl Acad. Sci. USA, 88, 9828–9832.
Mitchell, P. (1961) Coupling of phosphorylation to electron and hydrogen transfer by chemi-osmotic type of mechanism. Nature, 191, 144–148.
Newman, S.M., Boynton, J.E., Gillham, N.W., Randolph-Anderson, B.L., Johnson, A.M. and Harris, E.H. (1990) Transformation of chloroplast ribosomal RNA genes in Chlamydomonas: molecular and genetic characterization of integration events. Genetics, 126, 875–888.
Perez, E., Lapaille, M., Degand, H. et al. (2014) The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae. Mitochondrion, 19 (Pt B), 338–349.
Rak, M. and Rustin, P. (2014) Supernumerary subunits NDUFA3, NDUFA5 and NDUFA12 are required for the formation of the extramembrane arm of human mitochondrial complex I. FEBS Lett., 588, 1832–1838.
Remacle, C., Baurain, D., Cardol, P. and Matagne, F. (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., Cardol, P., Coosemans, N., Gaisne, M. and Bonnefoy, N. (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.
Saada, A., Vogel, R.O., Hoefs, S.J. et al. (2009) Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease. Am. J. Hum. Genet., 84, 718–727.
Salinas, T., Larosa, V., Cardol, P., Maréchal-Drouard, L. and Remacle, C. (2014) Respiratory deficient mutants of the unicellular green alga Chlamydomonas: a review. Biochimie, 100, 207–218.
Sánchez-Caballero, L., Guerrero-Castillo, S. and Nijtmans, L. (2016) Unraveling the complexity of mitochondrial complex I assembly; a dynamic process. Biochim. Biophys. Acta, 1857, 980–990.
Schimmeyer, J., Bock, R. and Meyer, E.H. (2016) l-Galactono-1,4-lactone dehydrogenase is an assembly factor of the membrane arm of mitochondrial complex I in Arabidopsis. Plant Mol. Biol., 90, 117–126.
Sheftel, A.D., Stehling, O., Pierik, A.J., Netz, D.J., Kerscher, S., Elsässer, H.P., Wittig, I., Balk, J., Brandt, U. and Lill, R. (2009) Human ind1, an iron-sulfur cluster assembly factor for respiratory complex I. Mol. Cell. Biol., 29, 6059–6073.
Stroud, D., Formosa, L.E., Wijeyeratne, X.W., Nguyen, T.N. and Ryan, M.T. (2013) Gene knockout using transcription activator-like effector nucleases (TALENs) reveals that human ndufa9 protein is essential for stabilizing the junction between membrane and matrix arms of complex I. J. Biol. Chem., 288, 1685–1690.
Subrahmanian, N., Remacle, C. and Hamel, P.P. (2016) Plant mitochondrial complex I composition and assembly: a review. Biochim. Biophys. Acta, 1857, 1001–1014.
Sunderhaus, S., Dudkina, N.V., Jänsch, L., Klodmann, J., Heinemeyer, J., Perales, M., Zabaleta, E., Boekema, E.J. and Braun, H.P. (2006) Carbonic anhydrase subunits form a matrix-exposed domain attached to the membrane arm of mitochondrial complex I in plants. J. Biol. Chem., 281, 6482–6488.
Szklarczyk, R., Wanschers, B.F.J., Nabuurs, S.B., Nouws, J., Nijtmans, L.G. and Huynen, M.A. (2011) NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I. FEBS Lett., 585, 737–743.
Terashima, M., Specht, M., Naumann, B. and Hippler, M. (2010) Characterizing the anaerobic response of Chlamydomonas reinhardtii by quantitative proteomics. Mol. Cell Proteomics, 9, 1514–1532.
Tolleter, D., Reiter, I.M., Genty, B. et al. (2011) Control of hydrogen photoproduction by the proton gradient generated by cyclic electron flow in Chlamydomonas reinhardtii. Plant Cell, 23, 2619–2630.
Van Den Ecker, D., Van Den Brand, M.A., Ariaans, G., Hoffmann, M., Bossinger, O., Mayatepek, E., Nijtmans, L.G. and Distelmaier, F. (2012) Identification and functional analysis of mitochondrial complex I assembly factor homologues in C. elegans. Mitochondrion, 12, 399–405.
Vinothkumar, K.R., Zhu, J. and Hirst, J. (2014) Architecture of mammalian respiratory complex I. Nature, 515, 80–84.
Wydro, M.M., Sharma, P., Foster, J.M., Bych, K., Meyer, E.H. and Balk, J. (2013) The evolutionarily conserved iron-sulfur protein INDH is required for complex I assembly and mitochondrial translation in Arabidopsis. Plant Cell, 25, 4014–4027.
Zerbino, D.R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821–829.
Zhu, J., Vinothkumar, K.R. and Hirst, J. (2016) Structure of mammalian respiratory complex I. Nature, 536, 354–358.
Zickermann, V., Wirth, C., Nasiri, H., Siegmund, K., Schwalbe, H., Hunte, C. and Brandt, U. (2015) Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science, 347, 44–49.