Michael Hodges

• BSc PhD
• Research Director at Institute of Plant Sciences - Paris-Saclay

Photosynthesis – the conversion of energy from sunlight into chemical energy – is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this...

To measure the kinetic properties of photorespiratory enzymes, it is necessary to work with purified proteins. Protocols to purify photorespiratory enzymes from leaves of various plant species require several time-consuming steps. It is now possible to produce large quantities of recombinant proteins in bacterial cells. They can be rapidly purified...

Phosphoglycolate phosphatase (PGLP) dephosphorylates 2-phosphoglycolate to glycolate that can be further metabolized to glyoxylate by glycolate oxidase (GOX) via an oxidative reaction that uses O2 and releases H2O2. The oxidation of o-dianisidine by H2O2 catalyzed by a peroxidase can be followed in real time by an absorbance change at 440 nm. Based...

Besides the historical and traditional use of nuclear magnetic resonance (NMR) spectroscopy as a structure elucidation tool for proteins and metabolites, its quantification ability allows the determination of metabolite amounts and therefore enzymatic activity measurements. For this purpose, 1H-NMR with adapted water pulse pre-saturation sequences...

Greenhouse gas (GHG) emissions have created a global climate crisis which requires immediate interventions to mitigate the negative effects on all aspects of life on this planet. As current agriculture and land use contributes up to 25% of total GHG emissions, plant scientists take center stage in finding possible solutions for a transition to sust...

Improving photosynthesis has become a strategy to increase plant productivity. Current photosynthetic targets dealing with light and CO2 capture will be briefly described and major breakthroughs dealing with photoprotection kinetics, CO2-concentrating mechanisms, and ribulose-1,5-bisphosphate regeneration will be highlighted before focusing on phot...

DspA/E is a type three effector injected by the pathogenic bacterium Erwinia amylovora inside plant cells. In non-host Arabidopsis thaliana, DspA/E inhibits seed germination, root growth, de novo protein synthesis and triggers localized cell death. To better understand the mechanisms involved, we performed EMS mutagenesis on a transgenic line, 13-1...

Salicylic acid (SA) is a plant hormone almost exclusively associated with the promotion of immunity. It is also known that SA has a negative impact on plant growth, yet only limited efforts have been dedicated to explain this facet of SA action. In this review, we focus on SA-related reduced growth and discuss whether it is a regulated process and...

Photorespiration is a metabolic process that removes toxic 2-phosphoglycolate produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase. It is essential for plant growth under ambient air, and it can play an important role under stress conditions that reduce CO2 entry into the leaf thus enhancing photorespiration. The ai...

Phosphoglycerate mutases (PGAMs) catalyse the reversible isomerisation of 3‐phosphoglycerate and 2‐phosphoglycerate, a step of glycolysis. PGAMs can be sub‐divided into 2,3‐biphosphoglycerate dependent (dPGAM) and independent (iPGAM) enzymes. In plants, phosphoglycerate isomerisation is carried out by cytosolic iPGAM. Despite its crucial role in ca...

Leaf senescence in source leaves leads to the active degradation of chloroplast components [photosystems, chlorophylls, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)] and plays a key role in the efficient remobilization of nutrients toward sink tissues. However, the progression of leaf senescence can differentially modify the photosynth...

This chapter is dedicated to the memory of Pierre Gadal a former Series Editor for Advances in Botanical Research. Its aim is to describe the research that has been done in his laboratory covering essentially the period 1970–2000 and provides first-hand testimony about how it has been done. Besides the scientific output concerning CO2 and nitrogen...

Photosynthesis is the major process leading to primary production in the Biosphere. There is a total of 7000bn tons of CO2 in the atmosphere and photosynthesis fixes more than 100bn tons annually. The CO2 assimilated by the photosynthetic apparatus is the basis of crop production and, therefore, of animal and human food. This has led to a renewed i...

Photorespiration is an essential process in oxygenic photosynthetic organisms triggered by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase. In peroxisomes, photorespiratory HYDROXYPYRUVATE REDUCTASE 1 (HPR1) catalyzes the conversion of hydroxypyruvate to glycerate together with the oxidation of a pyridine nucleotide cofact...

In photosynthetic organisms, the photorespiratory cycle is an essential pathway leading to the recycling of 2-phosphoglycolate, produced by the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase, to 3-phosphoglycerate. Although photorespiration is a widely studied process, its regulation remains poorly understood. In this context...

The photorespiratory cycle is a crucial pathway in photosynthetic organisms since it removes toxic 2‐phosphoglycolate made by the oxygenase activity of ribulose‐1,5‐bisphosphate carboxylase/oxygenase and retrieves its carbon as 3‐phosphoglycerate. Mitochondrial serine hydroxymethyltransferase 1 (SHMT1) is an essential photorespiratory enzyme conver...

The analysis of complex mixtures by NMR is a challenge in (bio)chemistry due to signal overcrowding making the analysis difficult. Thus, new advanced quantitative 2D NMR techniques that lead to better resolved and more intense signals have been applied to extracts of plants for tracking biomarkers of the photosynthesis and photorespiration cycles.

Arabidopsis thaliana SNF1-Related-Kinase1 (SnRK1)-Activating Kinase 1 and 2 (AtSnAK1 and 2) have been shown to phosphorylate in vitro and activate the energy signalling integrator, SnRK1. To clarify this signalling cascade in planta, a genetic- and molecular-based approach was developed. Homozygous single AtSnAK1 and AtSnAK2 T-DNA insertional mutan...

Considerable efforts are currently devoted to understand the regulation of primary carbon metabolism in plant leaves, which is known to change dramatically with environmental conditions, e.g., along light/dark transitions. Protein phosphorylation is believed to be a key factor in such a metabolic control. In fact, some studies have suggested modifi...

Photorespiration is an essential high flux metabolic pathway that is found in all oxygen-producing photosynthetic organisms. It is often viewed as a closed metabolic repair pathway that serves to detoxify 2-phosphoglycolic acid and to recycle carbon to fuel the Calvin-Benson cycle. However, this view is too simplistic since the photorespiratory cyc...

Photorespiration is one of the major carbon metabolism pathways in oxygen-producing photosynthetic organisms. This pathway recycles 2-phosphoglycolate (2-PG), a toxic metabolite, to 3-phosphoglycerate when ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) uses oxygen instead of carbon dioxide. The photorespiratory cycle is in competition wi...

Metabolic and physiological analyses of Arabidopsis thaliana glycolate oxidase (GOX) mutant leaves were performed to understand the development of the photorespiratory phenotype after transfer from high CO2 to air. We show that two Arabidopsis genes, GOX1 and GOX2, share a redundant photorespiratory role. Air-grown single gox1 and gox2 mutants grew...

Metabolic and physiological analyses of glutamate:glyoxylate aminotransferase 1 (GGT1) mutants were performed at the global leaf scale to elucidate the mechanisms involved in their photorespiratory growth phenotype. Air-grown ggt1 mutants showed retarded growth and development, that was not observed at high CO2 (3000 μL.L(-1) ). When compared to wi...

In plants, glycolate oxidase is involved in the photorespiratory cycle, one of the major fluxes at the global scale. To clarify both the nature of the mechanism and possible differences in glycolate oxidase enzyme chemistry from C3 and C4 plant species, we analyzed kinetic parameters of purified recombinant C3 (Arabidopsis thaliana) and C4 (Zea may...

Phototropin-dependent chloroplast movement is essential to the photosynthetic acclimation of mesophyll cells to incident light. Chloroplast movement involves many cellular actors, such as chloroplast-associated actin filaments and proteins that mediate signalling between phototropins and chloroplast motion. In the past few years, genetic approaches...

Cellulose is one of the most important organic compounds in terrestrial ecosystems and represents a major plant structural polymer. However, knowledge of the regulation of cellulose biosynthesis is still rather limited. Recent studies have shown that the phosphorylation of cellulose synthases (CESAs) may represent a key regulatory event in cellulos...

As sessile organisms, plants must adapt to changing environmental conditions that affect their optimal growth and development. Recent studies have highlig hted the importance of a central molecule in redox and respiratory metabolism, nicotinamide aden ine dinucleotide (NAD), in the metabolic signaling in plants and animals. They suggest that NAD pl...

Rubisco activase (RCA) is an ancillary photosynthetic protein essential for Rubisco activity. Some data suggest that post-translational modifications (such as reduction of disulphide bridges) are involved in the regulation of RCA activity. However, despite the key role of protein phosphorylation in general metabolic regulation, RCA phosphorylation...

Photosynthetic CO2 assimilation is the carbon source for plant anabolism, including amino acid production and protein synthesis. The biosynthesis of leaf proteins is known for decades to correlate with photosynthetic activity but the mechanisms controlling this effect are not documented. The cornerstone of the regulation of protein synthesis is bel...

Phosphopeptides identified using nanoLC-MS/MS. (DOCX)

Eukaryotic initiation factors and ribosomal proteins indentified by nanoLC-MS/MS. (DOCX)

The cornerstone of carbon ( C ) and nitrogen ( N ) metabolic interactions – respiration – is presently not well understood in plant cells: the source of the key intermediate 2‐oxoglutarate (2 OG ), to which reduced N is combined to yield glutamate and glutamine, remains somewhat unclear . We took advantage of combined mutations of NAD ‐ and NADP ‐d...

SNF1-Related protein Kinase-1 (SnRK1), the plant kinase homolog of mammalian AMP-activated protein Kinase (AMPK), is a sensor maintaining cellular energy homeostasis via the control of anabolism/catabolism balance. It was previously described that AMPK-dependent phosphorylation of p27(KIP) (1) impacts on cell cycle progression, autophagy and apopto...

Photorespiration allows the recycling of carbon atoms of 2-phosphoglycolate produced by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenase activity, as well as the removal of potentially toxic metabolites. The photorespiratory pathway takes place in the light, encompasses four cellular compartments and interacts with several other...

Nitrogen isotope composition (δ(15) N) in plant organic matter is currently used as a natural tracer of nitrogen acquisition efficiency. However, the δ(15) N value of whole leaf material does not properly reflect the way in which N is assimilated because isotope fractionations along metabolic reactions may cause substantial differences among leaf c...

Leaf respiration is a major metabolic process that drives energy production and growth. Earlier works in this field were focused on the measurement of respiration rates in relation to carbohydrate content, photosynthesis, enzymatic activities or nitrogen content. Recently, several studies have shed light on the mechanisms describing the regulation...

Natural (13)C abundance is now an unavoidable tool to study ecosystem and plant carbon economies. A growing number of studies take advantage of isotopic fractionation between carbon pools or (13)C abundance in respiratory CO(2) to examine the carbon source of respiration, plant biomass production or organic matter sequestration in soils. (12)C/(13)...

Considerable advances in our understanding of the control of mitochondrial metabolism and its interactions with nitrogen metabolism and associated carbon/nitrogen interactions have occurred in recent years, particularly highlighting important roles in cellular redox homeostasis. The tricarboxylic acid (TCA) cycle is a central metabolic hub for the...

The PII protein is an integrator of central metabolism and energy levels. In Arabidopsis, allosteric sensing of cellular energy and carbon levels alters the ability of PII to interact with target enzymes such as N-acetyl-l-glutamate kinase and heteromeric acetyl-coenzyme A carboxylase, thereby modulating the biological activity of these plastidial...

*Nitrogen assimilation in leaves requires primary NH(2) acceptors that, in turn, originate from primary carbon metabolism. Respiratory metabolism is believed to provide such acceptors (such as 2-oxoglutarate), so that day respiration is commonly seen as a cornerstone for nitrogen assimilation into glutamate in illuminated leaves. However, both glyc...

Cytosolic NADP-dependent isocitrate dehydrogenase (cICDH) produces 2-oxoglutarate (2-OG) and NADPH, and is encoded by a single gene in Arabidopsis thaliana. Three allelic lines carrying T-DNA insertions in this gene showed less than 10% extractable leaf ICDH activity, but only relatively small decreases in growth compared to wild-type Col0. Metabol...

Arabidopsis thaliana sucrose nonfermenting 1-related protein kinase 1 complexes belong to the SNF1/AMPK/SnRK1 protein kinase family that shares an ancestral function as central regulators of metabolism. In A. thaliana, the products of AtSnAK1 and AtSnAK2, orthologous to yeast genes, have been shown to autophosphorylate and to phosphorylate/activate...

Transgenic tomato (Solanum lycopersicum) plants were generated expressing a fragment of the mitochondrial NAD-dependent isocitrate dehydrogenase gene (SlIDH1) in the antisense orientation. The transgenic plants displayed a mild reduction in the activity of the target enzyme in the leaves but essentially no visible alteration in growth from the wild...

The PII protein is a signal integrator involved in the regulation of nitrogen metabolism in bacteria and plants. Upon sensing of cellular carbon and energy availability, PII conveys the signal by interacting with target proteins, thereby modulating their biological activity. Plant PII is located to plastids; therefore, to identify new PII target pr...

While the possible importance of the tricarboxylic acid (TCA) cycle reactions for leaf photosynthesis operation has been recognized, many uncertainties remain on whether TCA cycle biochemistry is similar in the light compared with the dark. It is widely accepted that leaf day respiration and the metabolic commitment to TCA decarboxylation are down-...

The metabolic control of the interaction between ArabidopsisN-acetyl-l-glutamate kinase (NAGK) and the PII protein has been studied. Both gel exclusion and affinity chromatography analyses of recombinant, affinity-purified PII (trimeric complex) and NAGK (hexameric complex) showed that NAGK strongly interacted with PII only in the presence of Mg-AT...

Two phosphoenolpyruvate carboxylase (PEPC) kinase genes (PPCk1 and PPCk2) are present in the Arabidopsis genome; only PPCk1 is expressed in rosette leaves. Homozygous lines of two independent PPCk1 T-DNA-insertional mutants showed very little (dln1), or no (csi8) light-induced PEPC phosphorylation and a clear retard in growth under our greenhouse c...

In higher plants, the PII protein is a nuclear-encoded plastid protein that regulates the activity of a key enzyme of arginine biosynthesis. We have previously observed that Arabidopsis PII mutants are more sensitive to nitrite toxicity. Using intact chloroplasts isolated from Arabidopsis leaves and (15)N-labelled nitrite we show that a light-depen...

Screening of the Arabidopsis thaliana genome revealed three potential homologues of mammalian and yeast mitochondrial DICs (dicarboxylate carriers) designated as DIC1, DIC2 and DIC3, each belonging to the mitochondrial carrier protein family. DIC1 and DIC2 are broadly expressed at comparable levels in all the tissues investigated. DIC1-DIC3 have be...

Day respiration is the process by which nonphotorespiratory CO2 is produced by illuminated leaves. The biological function of day respiratory metabolism is a major conundrum of plant photosynthesis research: because the rate of CO2 evolution is partly inhibited in the light, it is viewed as either detrimental to plant carbon balance or necessary fo...

Intense efforts are currently devoted to elucidate the metabolic networks of plants, in which nitrogen assimilation is of particular importance because it is strongly related to plant growth. In addition, at the leaf level, primary nitrogen metabolism interacts with photosynthesis, day respiration, and photorespiration, simply because nitrogen assi...

NAD-dependent isocitrate dehydrogenase (IDH) is a tricarboxylic acid cycle enzyme that produces 2-oxoglutarate, an organic acid required by the glutamine synthetase/glutamate synthase cycle to assimilate ammonium. Three Arabidopsis (Arabidopsis thaliana) IDH mutants have been characterized, corresponding to an insertion into a different IDH gene (A...

NAD-dependent isocitrate dehydrogenase (IDH) is a Krebs cycle enzyme situated in mitochondria. In Arabidopsis thaliana, five genes encode functional IDH subunits that can be classed into two groups based on gene structure and subunit amino acid sequence. Arabidopsis contains two 'catalytic' and three 'regulatory' subunits according to their homolog...

In higher plants, PII is a nuclear-encoded plastid protein which is homologous to bacterial PII signalling proteins known to be involved in the regulation of nitrogen metabolism. A reduced ornithine, citrulline and arginine accumulation was observed in two Arabidopsis PII knock-out mutants in response to NH4+ resupply after N starvation. This diffe...

Phosphoenolpyruvate carboxylase (PEPc) is a multifaceted enzyme that serves different physiological functions in plants. In C3 plants, an important role is in the anaplerotic supply of carbon skeletons for biosynthetic functions such as amino acid synthesis, whereas C4 and crassulacean acid metabolism (CAM) species also have a specific, highly acti...

The PII signal transducing protein is involved in carbon/nitrogen (C/N) sensing in bacteria and cyanobacteria. In higher plants the function of the PII homolog GLB1 is not known. GLB1 transcripts were found in all plant organs tested, while in Arabidopsis leaves GLB1 expression and PII protein levels were not significantly affected by either the da...

The four phosphoenolpyruvate carboxylase encoding genes (1–4) of Arabidopsis thaliana were found to be expressed in rosette leaves, with PEPC2 mRNA being the major species. The enzyme activity was sensitive to feedback inhibition by malate, aspartate and glutamate and this effect was antagonized by glucose-6-phosphate and modulated after a dark–lig...

In rice roots, transient and cell-type-specific accumulation of both mRNA and protein for NADH-dependent glutamate synthase (NADH-GOGAT) occurs after the supply of NH4 + ions. In order to better understand the origin of 2-oxoglutarate for this reaction, we focused on mitochondrial NAD-dependent isocitrate dehydrogenase (IDH) and glutamate dehydrog...

Plant mitochondria maintain metabolic communication with the cytosol through a family of carrier proteins that share several structural features. Early studies led to the recognition of several mitochondrial transport activities but the proteins responsible for these activities had not been identified. The in silico analysis of the complete Arabido...

Like many other soluble chloroplastic enzymes, thioredoxin f is nuclear-encoded and expressed as a precursor protein. After synthesis in the cytosol, it is imported into the chloroplast with subsequent cleavage of the transit sequence in the stroma. We report the expression and the partial purification of the recombinant precursor thioredoxin f pro...

The metabolic communication between plant mitochondria and the cytosol requires the flux of metabolites, nucleotides and cofactors across the inner mitochondrial membrane. This is accomplished by a family of mitochondrial carrier pro-teins (better characterized in animal and yeast) that span the inner membrane lipid bilayer and share distinct commo...

The assimilation of ammonium into glutamate is mainly achieved by the GS/GOGAT pathway and requires carbon skeletons in the form of 2-oxoglutarate. To date, the exact enzymatic origin of this organic acid for plant ammonium assimilation is unknown. NADP+-dependent isocitrate dehydrogenases can carry out this function and the recent efforts concentr...

This review examines the current understanding of the structural, functional and regulatory properties of C4 and C3 forms of higher plant phosphoenolpyruvate carboxylase. The emphasis is on the interactive metabolic and post‐translational controls acting on the enzyme in the physiological context of C4 photosynthesis and the anaplerotic pathway. A...

A cDNA from Arabidopsis thalianaand four related cDNAs from Nicotiana tabacum that we have isolated encode hitherto unidentified members of the mitochondrial carrier family. These proteins have been overexpressed in bacteria and reconstituted into phospholipid vesicles. Their transport properties demonstrate that they are orthologs/isoforms of a no...

The metabolic cross-talk associated with re-assimilation of photorespiratory NH4+ was analysed in transformed tobacco (Nicotiana tabacum L.) plants with low activities of ferredoxin-dependent glutamine-alpha-ketoglutarate aminotransferase (Fd-GOGAT; EC 1.4.7.1). Amounts of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco; EC 4.1.1.39) prote...

Ammonium is the reduced nitrogen form available to plants for assimilation into amino acids. This is achieved by the GS/GOGAT pathway that requires carbon skeletons in the form of 2‐oxoglutarate. To date, the exact enzymatic origin of this organic acid for plant ammonium assimilation is unknown. Isocitrate dehydrogenases and aspartate aminotransfer...

The metabolic cross-talk associated with re-assimilation of photorespiratory NH4+ was analysed in transformed tobacco (Nicotiana tabacum L.) plants with low activities of ferredoxin-dependent glutamine-alpha-ketoglutarate aminotransferase (Fd-GOGAT; EC 1.4.7.1). Amounts of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco; EC 4.1.1.39) prote...

Related sequence: EST Z26469.

In plants, nitrogen assimilation into amino acids relies on the availability of the reduced form of nitrogen, ammonium. The glutamine synthetase-glutamate synthase pathway, which requires carbon skeletons in the form of 2-oxoglutarate, achieves this. To date, the exact enzymatic origin of 2-oxoglutarate for plant ammonium assimilation is unknown. I...

Mitochondrial NAD-dependent (IDH) and cytosolic NADP-dependent isocitrate dehydrogenases have been considered as candidates for the production of 2-oxoglutarate required by the glutamine synthetase/glutamate synthase cycle. The increase in IDH transcripts in leaf and root tissues, induced by nitrate or NH4+ resupply to short-term N-starved tobacco...

NAD-dependent isocitrate dehydrogenase (IDH) is a key enzyme controlling the activity of the citric acid cycle. Despite more than 30 years of work, the plant enzyme remains poorly characterized. In this paper, a molecular characterization of the plant IDH is presented. Starting from probes defined according to sequence comparisons, three full-lengt...

Expression of a transgene is rarely analysed in the androgenetic progenies of the transgenic plants. Here, we report differential transgene expression in androgenetic haploid and doubled haploid (DH) tobacco plants as compared to the diploid parental lines, thus demonstrating a gene dosage effect. Using Agrobacterium-mediated transformation, and ba...

NADP-dependent isocitrate dehydrogenase (NADP-ICDH) activity is increased in roots of Eucalyptus globulus subsp. bicostata ex Maiden Kirkp. during colonization by the ectomycorrhizal fungus Pisolithus tinctorius Coker and Couch. To investigate the regulation of the enzyme expression, a cDNA (EgIcdh) encoding the NADP-ICDH was isolated from a cDNA l...

In this work, we describe the isolation of a new cDNA encoding an NADP-dependent isocitrate dehydrogenase (ICDH). The nucleotide sequence in its 5' region gives a deduced amino acid sequence indicative of a targeting peptide. However, even if this cDNA clearly encodes a noncytosolic ICDH, it is not possible to say from the targeting peptide sequenc...

In this work, we describe the isolation of a new cDNA encoding an NADP-dependent isocitrate dehydrogenase (ICDH). The nucleotide sequence in its 5' region gives a deduced amino acid sequence indicative of a targeting peptide. However, even if this cDNA clearly encodes a noncytosolic ICDH, it is not possible to say from the targeting peptide sequenc...

A cDNA which encodes a specific member of the NADP-dependent isocitrate dehydrogenase (ICDH) multi-isoenzyme family has been isolated from a tobacco cell suspension library, and the expression pattern of ICDH transcripts examined in various plant tissues. To assign this cDNA to a specific ICDH isoenzyme, the major, cytosolic ICDH isoenzyme of tobac...