The Mitochondrial Oxidative Phosphorylation Proteome of <i>Chlamydomonas reinhardtii</i> Deduced from the Genome Sequencing Project

Cardol, Pierre; González‐Halphen, Diego; Reyes‐Prieto, Adrián; Baurain, Denis; Matagne, René-Fernand; Remacle, Claire

doi:10.1104/pp.104.054148

Cited by 78 publications

(62 citation statements)

References 110 publications

(119 reference statements)

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“…In silico screening revealed the presence of several putative NDH-2 in the C. reinhardtii genome (17). One of them (Nda2) was produced as a recombinant protein and further characterized.…”

mentioning

confidence: 99%

Characterization of Nda2, a Plastoquinone-reducing Type II NAD(P)H Dehydrogenase in Chlamydomonas Chloroplasts

Desplats¹,

Mus²,

Cuiné

et al. 2009

Journal of Biological Chemistry

145

100

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Electron transfer pathways associated to oxygenic photosynthesis, including cyclic electron flow around photosystem I and chlororespiration, rely on non-photochemical reduction of plastoquinones (PQs). In higher plant chloroplasts, a bacteriallike NDH complex homologous to complex I is involved in PQ reduction, but such a complex is absent from Chlamydomonas plastids where a type II NAD(P)H dehydrogenase activity has been proposed to operate. With the aim to elucidate the nature of the enzyme-supporting non-photochemical reduction of PQs, one of the type II NAD(P)H dehydrogenases identified in the Chlamydomonas reinhardtii genome (Nda2) was produced as a recombinant protein in Escherichia coli and further characterized. As many type II NAD(P)H dehydrogenases, Nda2 uses NADH as a preferential substrate, but in contrast to the eukaryotic enzymes described so far, contains non-covalently bound FMN as a cofactor. When expressed at a low level, Nda2 complements growth of an E. coli lacking both NDH-1 and NDH-2, but is toxic at high expression levels. Using an antibody raised against the recombinant protein and based on its mass spectrometric identification, we show that Nda2 is localized in thylakoid membranes. Chlorophyll fluorescence measurements performed on thylakoid membranes show that Nda2 is able to interact with thylakoid membranes of C. reinhardtii by reducing PQs from exogenous NADH or NADPH. We discuss the possible involvement of Nda2 in cyclic electron flow around PSI, chlororespiration, and hydrogen production.

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“…In silico screening revealed the presence of several putative NDH-2 in the C. reinhardtii genome (17). One of them (Nda2) was produced as a recombinant protein and further characterized.…”

mentioning

confidence: 99%

Characterization of Nda2, a Plastoquinone-reducing Type II NAD(P)H Dehydrogenase in Chlamydomonas Chloroplasts

Desplats¹,

Mus²,

Cuiné

et al. 2009

Journal of Biological Chemistry

145

100

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show abstract

“…Being composed of multiple mitochondria, two anterior flagella, and a chloroplast, C. reinhardtii serves as an outstanding microalgae model organism, especially for analyzing eukaryotic chloroplast biology, action of flagella and basal bodies, and many biological pathways such as circadian rhythms, cell cycle control, and plant respiration (Rochaix, 2004;Wemmer and Marshall, 2004;Bisova et al, 2005;Cardol et al, 2005;Mittag et al, 2005). As a photosynthetic microalgae species, C. reinhardtii has also shown its potential in biofuel generation (Grossman et al, 2003;Beckmann et al, 2009;Langner et al, 2009;Nguyen et al, 2009).…”

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confidence: 99%

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

Ding

2012

Plant Physiology

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Chlamydomonas reinhardtii is one of the most important microalgae model organisms and has been widely studied toward the understanding of chloroplast functions and various cellular processes. Further exploitation of C. reinhardtii as a model system to elucidate various molecular mechanisms and pathways requires systematic study of gene regulation. However, there is a general lack of genome-scale gene regulation study, such as global cis-regulatory element (CRE) identification, in C. reinhardtii. Recently, large-scale genomic data in microalgae species have become available, which enable the development of efficient computational methods to systematically identify CREs and characterize their roles in microalgae gene regulation. Here, we performed in silico CRE identification at the whole genome level in C. reinhardtii using a comparative genomics-based method. We predicted a large number of CREs in C. reinhardtii that are consistent with experimentally verified CREs. We also discovered that a large percentage of these CREs form combinations and have the potential to work together for coordinated gene regulation in C. reinhardtii. Multiple lines of evidence from literature, gene transcriptional profiles, and gene annotation resources support our prediction. The predicted CREs will serve, to our knowledge, as the first large-scale collection of CREs in C. reinhardtii to facilitate further experimental study of microalgae gene regulation. The accompanying software tool and the predictions in C. reinhardtii are also made available through a Web-accessible database (http://hulab.ucf.edu/research/projects/Microalgae/sdcre/motifcomb.html).

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“…Chlamydomonas reinhardtii allowed the construction of a comprehensive catalog of its OXPHOS components [1]. Here, we present as an introduction an update of the inventory set up in that review, with special focus on assembly factors that have been identified in mammals or fungi since that time.…”

Section: The Mitochondrial Respiratory Chain Of Chlamydomonasmentioning

confidence: 99%

“…All of them are conserved in Chlamydomonas. Cytochrome c is nucleus-encoded and the type-III maturation system is used, like in mammal and fungi [1].…”

Section: Main Components Of the Respiratory Chainmentioning

confidence: 99%

“…This process comprises an electron-transfer chain that is driven by substrate oxidation and is coupled to the synthesis of ATP through an electrochemical transmembrane gradient. Therefore, the mitochondrial respiratory-chain proteome comprises protein components participating in this process (complexes I-V and additional oxidoreductases) and in its biogenesis (assembly factors).The release of the complete genome sequence of the unicellular green algaChlamydomonas reinhardtii allowed the construction of a comprehensive catalog of its OXPHOS components [1]. Here, we present as an introduction an update of the inventory set up in that review, with special focus on assembly factors that have been identified in mammals or fungi since that time.…”

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confidence: 99%

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Respiratory-deficient mutants of the unicellular green alga Chlamydomonas: A review

et al. 2014

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Genetic manipulation of the unicellular green alga Chlamydomonas reinhardtii is straightforward. Nuclear genes can be interrupted by insertional mutagenesis or targeted by RNA interference whereas random or site-directed mutagenesis allows the introduction of mutations in the mitochondrial genome. This, combined with a screen that easily allows discriminating respiratorydeficient mutants, makes Chlamydomonas a model system of choice to study mitochondria biology in photosynthetic organisms. Since the first description of Chlamydomonas respiratory-deficient mutants in 1977 by random mutagenesis, many other mutants affected in mitochondrial components have been characterized. These respiratory-deficient mutants increased our knowledge on function and assembly of the respiratory enzyme complexes. More recently some of these mutants allowed the study of mitochondrial gene expression processes poorly understood in Chlamydomonas. In this review, we update the data concerning the respiratory components with a special focus on the assembly factors identified on other organisms. In addition, we make an inventory of different mitochondrial respiratory mutants that are inactivated either on mitochondrial or nuclear genes. Opposed Reviewers:Claire Remacle -Génétique des microorganismes -Institut de Botanique B22 Boulevard du Rectorat, 27 -Université de Liège-B-4000 Liège, Belgique Tel +32 4 3663812 -Fax +32 4 3663840 e-mail: c.remacle@ulg.ac.be First, we wish to thank the two anonymous reviewers for their constructive comments. We found their suggestions very helpful to improve the quality of our manuscript. We have addressed all the points they raised and have modified the text accordingly. A detailed response to reviewers' comments is included below.We believe we have addressed all referees' comments and we hope this revised version is now suitable for publication in Biochimie.We are looking forward to hearing from you, With best regards, Cover LetterResponse to reviewers The text has been modified in order to give more background details on the methodology used to create and screen respiratory mutants in Chlamydomonas. The main modifications correspond to: Paragraph 2.3: -p8. A figure (Fig. 4) has been added in order to provide more information on dark-dier/slow growth screens for different classes of mutant.-p9. The mitochondrial transformation method used in Chlamydomonas has been detailed.Paragraph 2.4: -p10. The TTC-based screen has been explained.Finally, all along the text the methods used to create nuclear and mitochondrial mutants has been indicated. Also, the text could benefit from being proof-read by a native English speaker as the grammar is a little awkward in places. I highlight a couple of points below, but there are a number of other places where the English could be improved for clarity.The text has been proof-read by a good English speaker as requested and the text has been modified according to the comments.Minor points:1. Abstract, line 1: "the genetics" have been replaced by "genetic manipu...

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The Mitochondrial Oxidative Phosphorylation Proteome of Chlamydomonas reinhardtii Deduced from the Genome Sequencing Project

Cited by 78 publications

References 110 publications

Characterization of Nda2, a Plastoquinone-reducing Type II NAD(P)H Dehydrogenase in Chlamydomonas Chloroplasts

Characterization of Nda2, a Plastoquinone-reducing Type II NAD(P)H Dehydrogenase in Chlamydomonas Chloroplasts

Systematic Prediction of cis-Regulatory Elements in the Chlamydomonas reinhardtii Genome Using Comparative Genomics

Respiratory-deficient mutants of the unicellular green alga Chlamydomonas: A review

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