A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the  -Proteobacterial Mitochondrial Ancestor

Atteia, Ariane; Adrait, Annie; Brugière, Sabine; Tardif, Marianne; Lis, Robert van; Deusch, Oliver; Dagan, Tal; Kuhn, Lauriane; Gontero, Brigitte; Martin, William; Garin, Jérôme; Joyard, Jacques; Rolland, Norbert

doi:10.1093/molbev/msp068

Cited by 168 publications

(149 citation statements)

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“…The absence of C4 photosynthesis is in agreement with the location of a potential C4 photosynthesis decarboxylase, PEPCK, in mitochondria ( Fig. 5; Kroth et al, 2008;Atteia et al, 2009). Furthermore, Giordano et al (2003) showed that the activity of PEPC in C. reinhardtii is influenced by nitrogen availability to a greater extent than carbon availability, which is consistent with a predominantly anaplerotic role for this enzyme.…”

Section: Focus On Differences 3 H After Ccm Inductionsupporting

confidence: 82%

“…Localization of enzymes of the photorespiratory pathway (photorespiratory carbon oxidation cycle [Tural and Moroney, 2005]) to mitochondria has been shown for Chlamydomonas (Atteia et al, 2009). These and other results on the Chlorophyceae agree with data on Eremosphaera viridis from the sister class Trebouxiophyceae (Stabenau and Winkler, 2005).…”

Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 99%

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A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

et al. 2010

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(J.A.R.) Using a gas chromatography-mass spectrometry-time of flight technique, we determined major metabolite changes during induction of the carbon-concentrating mechanism in the unicellular green alga Chlamydomonas reinhardtii. In total, 128 metabolites with significant differences between high-and low-CO 2 -grown cells were detected, of which 82 were wholly or partially identified, including amino acids, lipids, and carbohydrates. In a 24-h time course experiment, we show that the amino acids serine and phenylalanine increase transiently while aspartate and glutamate decrease after transfer to low CO 2 . The biggest differences were typically observed 3 h after transfer to low-CO 2 conditions. Therefore, we made a careful metabolomic examination at the 3-h time point, comparing low-CO 2 treatment to high-CO 2 control. Five metabolites involved in photorespiration, 11 amino acids, and one lipid were increased, while six amino acids and, interestingly, 21 lipids were significantly lower. Our conclusion is that the metabolic pattern during early induction of the carbon-concentrating mechanism fit a model where photorespiration is increasing.

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Section: Focus On Differences 3 H After Ccm Inductionsupporting

confidence: 82%

Section: Focus On Differences 3 H After Ccm Inductionmentioning

confidence: 99%

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

et al. 2010

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“…The Arabidopsis Information Resource (TAIR) (23) and SUBA assigned subcellular localizations based on GFP-hybrid protein experiments. Chlamydomonas proteins were assigned a mitochondrial localization based on their identification in purified mitochondria (39). Localizations also were assigned based on reported experimental studies.…”

Section: Methodsmentioning

confidence: 99%

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Karpowicz

Prochnik

Grossman

et al. 2011

Journal of Biological Chemistry

115

141

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The plastid is a defining structure of photosynthetic eukaryotes and houses many plant-specific processes, including the light reactions, carbon fixation, pigment synthesis, and other primary metabolic processes. Identifying proteins associated with catalytic, structural, and regulatory functions that are unique to plastid-containing organisms is necessary to fully define the scope of plant biochemistry. Here, we performed phylogenomics on 20 genomes to compile a new inventory of 597 nucleus-encoded proteins conserved in plants and green algae but not in non-photosynthetic organisms. 286 of these proteins are of known function, whereas 311 are not characterized. This inventory was validated as applicable and relevant to diverse photosynthetic eukaryotes using an additional eight genomes from distantly related plants (including Micromonas, Selaginella, and soybean). Manual curation of the known proteins in the inventory established its importance to plastid biochemistry. To predict functions for the 52% of proteins of unknown function, we used sequence motifs, subcellular localization, co-expression analysis, and RNA abundance data. We demonstrate that 18% of the proteins in the inventory have functions outside the plastid and/or beyond green tissues. Although 32% of proteins in the inventory have homologs in all cyanobacteria, unexpectedly, 30% are eukaryote-specific. Finally, 8% of the proteins of unknown function share no similarity to any characterized protein and are plant lineage-specific. We present this annotated inventory of 597 proteins as a resource for functional analyses of plant-specific biochemistry.The plastid is an organelle in plants and algae that evolved from a photosynthetic cyanobacterium after it was engulfed by an ancestral eukaryotic cell over 1.5 billion years ago (1, 2). How the endosymbiont became integral to host cell functions and evolved into a plastid is still under debate (3), but functions localized to the present day plastid depend on both plastid-and nucleus-encoded proteins. The latter are synthesized in the cytoplasm and imported into the organelle by a specific multiprotein complex composed of the translocon of the outer and inner chloroplast envelope membrane (TOC 4 and TIC, respectively) proteins (4, 5). Over 2000 proteins are estimated to be located in the plastid with the vast majority (Ͼ90%) encoded by genes in the nucleus (6 -9). Many of the nucleus-encoded proteins that function within plastids are conserved among photosynthetic organisms. These conserved proteins function in processes such as the capture and utilization of excitation energy, carbohydrate metabolism, and the synthesis of key cellular metabolites (such as lipids, isoprenoids, pigments, and amino acids). Interestingly, however, many plastid-localized proteins have not yet been assigned a specific biochemical function.The increasing availability of sequence information from diverse organisms has allowed the application of comparative genomics, or phylogenomics, to discover proteins specific to bacteria (...

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“…Among algae in general, the only proteome to be studied is that of Chlmaydomonas reinhardtii, with even with sub-cellular proteome investigations (Stauber and Hippler 2004, Atteia et al 2009, Wienkoop et al 2010. Recently, C. reinhardtii proteome, transcriptome and metabolome have been studied under varying CO 2 concentration.…”

Section: Image Analysismentioning

confidence: 99%

Influence of CO₂concentration on carbon concentrating mechanisms in cyanobacteria and green algae: a proteomic approach

Ramanan¹,

Vinayagamoorthy²,

Sivanesan³

et al. 2012

ALGAE

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Carbon concentrating mechanisms play a vital role in photosynthesis in microalgae and cyanobacteria especially in the proper functioning of Rubisco and assimilation of carbon via the Calvin cycle. This study evaluates the role of carbon dioxide on carbon concentrating mechanism (CCM) in a cynaobacteria, Spirulina platensis and a microalga, Chlorella sp. 786. The study organisms were grown in both atmospheric (control sample, 0.035%) and high (exposed sample, 10%) CO 2 concentrations. Second dimension (2D) electrophoresis revealed a huge difference in the protein profiles of both organisms suggesting the induction of CCM related proteins in the sample maintained at atmospheric CO 2 concentration and the repression of CCM related proteins in the sample maintained at 10% CO 2 . Liquid chromatography-mass spectroscopy analysis revealed the presence of two important C i transporter proteins in the control sample of S. platensis, namely ferredoxin-NADP + reductase and ATP binding cassette (ABC) transport system protein. These proteins were only expressed in the control sample and were downregulated or not expressed at all in the exposed sample. Consequently, this study conclusively proves that CCMs are only inducted at low CO 2 concentrations and are not functional at high CO 2 concentration.Key Words: carbon concentrating mechanism (CCM); Chlorella sp.; cyanobacteria; proteomics; Rubisco; Spirulina platensis INTRODUCTIONNatural photosynthesis in green plants achieves carbon dioxide (CO 2 ) fixation on a global scale. The incorporation of CO 2 into the biosphere by the photosynthetic action of plants and microorganisms has been estimated to amount to about 10 11 tons of CO 2 per year Somanchi 1999, Prentice 2001). However, the efficiency of solar energy conversion in plant production under optimal growth conditions is only 5-6%. The global average efficiency has been estimated as 0.15% (Price et al. 2008). Photosynthesis is much more efficient in single celled organisms such as microalgae and cyanobacteria than in terrestrial C 3 and C 4 plants ( Kaplan and Reinhold 1999). This high efficiency is primarily due to two factors: the action of carbonic anhydrase (CA), both extracellular and intracellular, and the CO 2 concentrating mechanisms (CCM) ( Van et al. 2001, Spalding et al. 2002, Vance and Spalding 2005. CO 2 concentration plays a vital role in the induction or repression of CCM in microalgae and cyanobacteria. It has been proven that CCM is induced in low CO 2 concentrations, however, there is little informa- 296exposed sample was maintained at a CO 2 concentration of 10% (10,000 ppm). Both the cultures were grown for a period of 15-20 days in the reactor (Ramanan et al. 2010).The algal cells were centrifuged at 5,000 ×g for 5 min and to 0.5 g of algal pellet, 10 mL of algal culture medium with 2% Triton X-100 was added. The algal pellet was resuspended and pelleted. Supernatant which had greenish-yellow tint was poured off. The pellet was once again rinsed with culture medium and centrifuged again. The super...

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A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the -Proteobacterial Mitochondrial Ancestor

Cited by 168 publications

References 106 publications

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Influence of CO₂concentration on carbon concentrating mechanisms in cyanobacteria and green algae: a proteomic approach

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A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the -Proteobacterial Mitochondrial Ancestor

Cited by 168 publications

References 106 publications

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

A Metabolomic Approach to Study Major Metabolite Changes during Acclimation to Limiting CO2 in Chlamydomonas reinhardtii

The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage

Influence of CO2concentration on carbon concentrating mechanisms in cyanobacteria and green algae: a proteomic approach

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Influence of CO₂concentration on carbon concentrating mechanisms in cyanobacteria and green algae: a proteomic approach