The C3 plant Flaveria pringlei contains a plastidic NADP-malic enzyme which is orthologous to the C4 isoform of the C4 plant F. trinervia

Kinetics and functional diversity among the five members of the NADP-malic enzyme family from Zea mays, a C4 species

NADP-malic enzyme (NADP-ME) is involved in different metabolic pathways in several organisms due to the relevant physiological functions of the substrates and products of its reaction. In plants, it is one of the most important proteins that were recruited to fulfil key roles in C4 photosynthesis. Recent advances in genomics allowed the characterization of the complete set of NADP-ME genes from some C3 species, as Arabidopsis thaliana and Oryza sativa; however, the characterization of the complete NADP-ME family from a C4 species has not been performed yet. In this study, while taking advantage of the complete Zea mays genome sequence recently released, the characterization of the whole NADP-ME family is presented. The maize NADP-ME family is composed of five genes, two encoding plastidic NADP-MEs (ZmC4- and ZmnonC4-NADP-ME), and three cytosolic enzymes (Zmcyt1-, Zmcyt2-, and Zmcyt3-NADP-ME). The results presented clearly show that each maize NADP-ME displays particular organ distribution, response to stress stimuli, and differential biochemical properties. Phylogenetic footprinting studies performed with the NADP-MEs from several grasses, indicate that four members of the maize NADP-ME family share conserved transcription factor binding motifs with their orthologs, indicating conserved physiological functions for these genes in monocots. Based on the results obtained in this study, and considering the biochemical plasticity shown by the NADP-ME, it is discussed the relevance of the presence of a multigene family, in which each member encodes an isoform with particular biochemical properties, in the evolution of the C4 NADP-ME, improved to fulfil the requirements for an efficient C4 mechanism.

Carbonic anhydrase and the molecular evolution of C4 photosynthesis

C(4) photosynthesis, a biochemical CO(2)-concentrating mechanism (CCM), evolved more than 60 times within the angiosperms from C(3) ancestors. The genus Flaveria, which contains species demonstrating C(3), C(3)-C(4), C(4)-like or C(4) photosynthesis, is a model for examining the molecular evolution of the C(4) pathway. Work with carbonic anhydrase (CA), and C(3) and C(4) Flaveria congeners has added significantly to the understanding of this process. The C(4) form of CA3, a β-CA, which catalyses the first reaction in the C(4) pathway by hydrating atmospheric CO(2) to bicarbonate in the cytosol of mesophyll cells (mcs), evolved from a chloroplastic C(3) ancestor. The molecular modifications to the ancestral CA3 gene included the loss of the sequence encoding the chloroplast transit peptide, and mutations in regulatory regions that resulted in high levels of expression in the C(4) mesophyll. Analyses of the CA3 proteins and regulatory elements from Flaveria photosynthetic intermediates indicated C(4) biochemistry very likely evolved in a specific, stepwise manner in this genus. The details of the mechanisms involved in the molecular evolution of other C(4) plant β-CAs are unknown; however, comparative genetics indicate gene duplication and neofunctionalization played significant roles as they did in Flaveria.

The molecular evolution of β-carbonic anhydrase in Flaveria

Limited information exists regarding molecular events that occurred during the evolution of C(4) plants from their C(3) ancestors. The enzyme β-carbonic anhydrase (CA; EC 4.2.1.1), which catalyses the reversible hydration of CO(2), is present in multiple forms in C(3) and C(4) plants, and has given insights into the molecular evolution of the C(4) pathway in the genus Flaveria. cDNAs encoding three distinct isoforms of β-CA, CA1-CA3, have been isolated and examined from Flaveria C(3) and C(4) congeners. Sequence data, expression analyses of CA orthologues, and chloroplast import assays with radiolabelled CA precursor proteins from the C(3) species F. pringlei Gandoger and the C(4) species F. bidentis (L.) Kuntze have shown that both contain chloroplastic and cytosolic forms of the enzyme, and the potential roles of these isoforms are discussed. The data also identified CA3 as the cytosolic isoform important in C(4) photosynthesis and indicate that the C(4) CA3 gene evolved as a result of gene duplication and neofunctionalization, which involved mutations in coding and non-coding regions of the ancestral C(3) CA3 gene. Comparisons of the deduced CA3 amino acid sequences from Flaveria C(3), C(4), and photosynthetic intermediate species showed that all the C(3)-C(4) intermediates investigated and F. brownii, a C(4)-like species, have a C(3)-type CA3, while F. vaginata, another C(4)-like species, contains a C(4)-type CA3. These observations correlate with the photosynthetic physiologies of the intermediates, suggesting that the molecular evolution of C(4) photosynthesis in Flaveria may have resulted from a temporally dependent, stepwise modification of protein-encoding genes and their regulatory elements.

Evolutionary insights on C4 photosynthetic subtypes in grasses from genomics and phylogenetics

In plants, an oligogene family encodes NADP-malic enzymes (NADP-me), which are responsible for various functions and exhibit different kinetics and expression patterns. In particular, a chloroplast isoform of NADP-me plays a key role in one of the three biochemical subtypes of C(4) photosynthesis, an adaptation to warm environments that evolved several times independently during angiosperm diversification. By combining genomic and phylogenetic approaches, this study aimed at identifying the molecular mechanisms linked to the recurrent evolutions of C(4)-specific NADP-me in grasses (Poaceae). Genes encoding NADP-me (nadpme) were retrieved from genomes of model grasses and isolated from a large sample of C(3) and C(4) grasses. Genomic and phylogenetic analyses showed that 1) the grass nadpme gene family is composed of four main lineages, one of which is expressed in plastids (nadpme-IV), 2) C(4)-specific NADP-me evolved at least five times independently from nadpme-IV, and 3) some codons driven by positive selection underwent parallel changes during the multiple C(4) origins. The C(4) NADP-me being expressed in chloroplasts probably constrained its recurrent evolutions from the only plastid nadpme lineage and this common starting point limited the number of evolutionary paths toward a C(4) optimized enzyme, resulting in genetic convergence. In light of the history of nadpme genes, an evolutionary scenario of the C(4) phenotype using NADP-me is discussed.

Cloning, identification, expression analysis and phylogenetic relevance of two NADP-dependent malic enzyme genes from hexaploid wheat

The NADP-dependent malic enzyme (NADP-ME; EC1.1.1.40) found in many metabolic pathways catalyzes the oxidative decarboxylation of L-malate, producing pyruvate, CO(2) and NADPH. The NADP-MEs have been well studied in C4 plants but not well in C3 plants. In this study, we identified the NADP-ME isoforms from hexaploid wheat (Triticum aestivum L). Two different NADP-ME transcripts were first identified in this C3 plant. The first is named TaNADP-ME1 [NCBI: EU170134] and encodes a putative plastidic isoform, while the second is named TaNADP-ME2 [NCBI: EU082065] and encodes a cytosolic counterpart. Sequence alignment shows that the two NADP-ME isoforms share an identity of 73.26% in whole amino acids and 64.08% in nucleotide sequences. The phylogenetic analysis deciphers the two NADP-MEs as belonging to the monocots (Group II), which closely resemble OschlME6 and OscytME2, respectively. Tissue-specific analyses indicate that the two NADP-ME genes are both expressed in root, stem and leaf, and that TaNADP-ME1 is a leaf-abundant isoform. Semi-quantitative RT-PCR analysis show that the two NADP-ME transcripts in wheat leaves respond differently to low temperature, salt, dark and drought stresses stimuli and to exogenous abscisic acid (ABA) and salicylic acid (SA). Our results demonstrate that exogenous hormones (ABA and SA), as well as salt, low temperature, dark and drought stresses can regulate the expressions of TaNADP-ME1 and TaNADP-ME2 in wheat. This indicates that the two NADP-ME genes may play an important role in the response of wheat to ABA, SA, low temperature, salt, dark and drought stress.

A comprehensive analysis of the NADP-malic enzyme gene family of Arabidopsis

The Arabidopsis (Arabidopsis thaliana) genome contains four genes encoding putative NADP-malic enzymes (MEs; AtNADP-ME1-ME4). NADP-ME4 is localized to plastids, whereas the other three isoforms do not possess any predicted organellar targeting sequence and are therefore expected to be cytosolic. The plant NADP-MEs can be classified into four groups: groups I and II comprising cytosolic and plastidic isoforms from dicots, respectively; group III containing isoforms from monocots; and group IV composed of both monocots and dicots, including AtNADP-ME1. AtNADP-MEs contained all conserved motifs common to plant NADP-MEs and the recombinant isozymes showed different kinetic and structural properties. NADP-ME2 exhibits the highest specific activity, while NADP-ME3 and NADP-ME4 present the highest catalytic efficiency for NADP and malate, respectively. NADP-ME4 exists in equilibrium of active dimers and tetramers, while the cytosolic counterparts are present as hexamers or octamers. Characterization of T-DNA insertion mutant and promoter activity studies indicates that NADP-ME2 is responsible for the major part of NADP-ME activity in mature tissues of Arabidopsis. Whereas NADP-ME2 and -ME4 are constitutively expressed, the expression of NADP-ME1 and NADP-ME3 is restricted by both developmental and cell-specific signals. These isoforms may play specific roles at particular developmental stages of the plant rather than being involved in primary metabolism.

NADP-malic enzyme and Hsp70: co-purification of both proteins and modification of NADP-malic enzyme properties by association with Hsp70

Different preparations of antibodies against 62 kDa NADP-malic enzyme (NADP-ME) from purified maize leaves cross-react with a 72 kDa protein from diverse tissues in many species. A 72 kDa protein, suggested to be a non-photosynthetic NADP-ME, has been purified from several plant species. However, to date, a cDNA coding for this putative 72 kDa NADP-ME has not been isolated. The screening of maize and tobacco leaf expression libraries using antibodies against purified 62 kDa NADP-ME allowed the identification of a heat shock protein (Hsp70). In addition, tandem mass spectrometry (MS/MS) studies indicate that along with NADP-ME, a 72 kDa protein, identified as an Hsp70 and reacting with the antibodies, is also purified from maize roots. On the other hand, the screening of a maize root cDNA library revealed the existence of a cDNA that encodes a mature 66 kDa NADP-ME. These results suggest that the 72 kDa protein is not actually an NADP-ME but in fact an Hsp70, at least in maize and tobacco. Probably, NADP-ME-Hsp70 association, taking place at least when preparing crude extracts, can lead to a co-purification of the proteins and can thus explain the cross-reaction of the antibodies. In the present work, we analyse and discuss a probable interaction of NADP-ME with Hsp70.

Overexpression of C(4)-cycle enzymes in transgenic C(3) plants: a biotechnological approach to improve C(3)-photosynthesis

The process of photorespiration diminishes the efficiency of CO(2) assimilation and yield of C(3)-crops such as wheat, rice, soybean or potato, which are important for feeding the growing world population. Photorespiration starts with the competitive inhibition of CO(2) fixation by O(2) at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and can result in a loss of up to 50% of the CO(2) fixed in ambient air. By contrast, C(4) plants, such as maize, sugar cane and Sorghum, possess a CO(2) concentrating mechanism, by which atmospheric CO(2) is bound to C(4)-carbon compounds and shuttled from the mesophyll cells where the prefixation of bicarbonate occurs via phosphoenolpyruvate carboxylase (PEPC) into the gas-tight bundle-sheath cells, where the bound carbon is released again as CO(2) and enters the Calvin cycle. However, the anatomical division into mesophyll and bundle-sheaths cells ("Kranz"-anatomy) appears not to be a prerequisite for the operation of a CO(2) concentrating mechanism. Submerged aquatic macrophytes, for instance, can induce a C(4)-like CO(2) concentrating mechanism in only one cell type when CO(2) becomes limiting. A single cell C(4)-mechanism has also been reported recently for a terrestrial chenopod. For over 10 years researchers in laboratories around the world have attempted to improve photosynthesis and crop yield by introducing a single cell C(4)-cycle in C(3) plants by a transgenic approach. In the meantime, there has been substantial progress in overexpressing the key enzymes of the C(4) cycle in rice, potato, and tobacco. In this review there will be a focus on biochemical and physiological consequences of the overexpression of C(4)-cycle genes in C(3) plants. Bearing in mind that C(4)-cycle enzymes are also present in C(3) plants, the pitfalls encountered when C(3) metabolism is perturbed by the overexpression of individual C(4) genes will also be discussed.

Distinct but conserved functions for two chloroplastic NADP-malic enzyme isoforms in C3 and C4 Flaveria species

In the most common C4 pathway for carbon fixation, an NADP-malic enzyme (NADP-ME) decarboxylates malate in the chloroplasts of bundle sheath cells. Isoforms of plastidic NADP-ME are encoded by two genes in all species of Flaveria, including C3, C3-C4 intermediate, and C4 types. However, only one of these genes, ChlMe1, encodes the enzyme that functions in the C4 pathway. We compared the expression patterns of the ChlMe1 and ChlMe2 genes in developing leaves of Flaveria pringlei (C3) and Flaveria trinervia (C4) and in transgenic Flaveria bidentis (C4). ChlMe1 expression in C4 species increases in leaves with high C4 pathway activity. In the C3 species F. pringlei, ChlMe1 expression is transient and limited to early leaf development. In contrast, ChlMe2 is expressed in C3 and C4 species concurrent with stages in chloroplast biogenesis. Because previous studies suggest that NADP-ME activities generally reflect the level of its mRNA abundance, we discuss possible roles of ChlMe1 and ChlMe2 based on these expression patterns.

Differential regulation of transcripts encoding cytosolic NADP-malic enzyme in C3 and C4 Flaveria species

A cytosolic NADP-malic enzyme (CYTME) has been described previously in several plants, all C3 species. CYTME is distinct from the chloroplastic NADP-malic enzyme (CHLME) that is highly active in C4 species. We show that at least one CytMe gene is present in all Flaveria spp., including C3, C4, and C3-C4 intermediate types. Based on the CytMe expression patterns in Flaveria pringlei (C3) and Flaveria trinervia (C4), we suggest CYTME has several distinct roles, including the supplying of NADPH for cytosolic metabolism, the supporting of wound response or repair, and the balancing of cellular pH in illuminated leaves. These three roles are likely correlated with CytMe mRNAs of apparent sizes 2.0, 2.2, and 2.4 kb, respectively, which differ in the length of the 5' untranslated regions. Various regulatory mechanisms involving RNA processing and translational efficiency are discussed.

NADP-malic enzyme from plants: a ubiquitous enzyme involved in different metabolic pathways

NADP-malic enzyme (NADP-ME) is a widely distributed enzyme that catalyzes the oxidative decarboxylation of L-malate. Photosynthetic NADP-MEs are found in C4 bundle sheath chloroplasts and in the cytosol of CAM plants, while non-photosynthetic NADP-MEs are either plastidic or cytosolic in various plants. We propose a classification of plant NADP-MEs based on their physiological function and localization and we describe recent advances in the characterization of each isoform. Based on the alignment of amino acid sequences of plant NADP-MEs, we identify putative binding sites for the substrates and analyze the phylogenetic origin of each isoform, revealing several features of the molecular evolution of this ubiquitous enzyme.

High level expression of C4-specific NADP-malic enzyme in leaves and impairment of photoautotrophic growth in a C3 plant, rice

The chloroplastic NADP-malic enzyme (NADP-ME) is a key enzyme of the C4 photosynthesis pathway in NADP-ME type C4 plants such as maize. To express the chloroplastic NADP-ME in leaves of a C3 plant, rice, full-length cDNAs encoding the rice C3-specific isoform and the maize C4-specific isoform of the enzyme were expressed under the control of the rice CAB: promoter. Transformants carrying the rice cDNA showed the NADP-ME activities in the leaves less than several-fold that of non-transformants, while those carrying the maize cDNA showed activities up to 30-fold that of non-transformants or about 60% of the NADP-ME activity of maize leaves. These results indicate that expression of the rice C3-specific NADP-ME is suppressed at co- and/or post-transcriptional levels by some regulation mechanisms intrinsic to rice, while that of the foreign C4-specific isoform can escape from such suppression. The accumulation of the maize C4-specific NADP-ME led to bleaching of leaf color and growth hindrance in rice plants under natural light. These deteriorative effects resulted from enhanced photoinhibition of photosynthesis due to an increase in the level of NADPH inside the chloroplast by the action of the maize enzyme.

Evolution of C4 photosynthesis in flaveria species. Isoforms Of nadp-malic enzyme

NADP-malic enzyme (NADP-ME, EC 1.1.1.40), a key enzyme in C4 photosynthesis, provides CO2 to the bundle-sheath chloroplasts, where it is fixed by ribulose-1,5-bisphosphate carboxylase/oxygenase. We characterized the isoform pattern of NADP-ME in different photosynthetic species of Flaveria (C3, C3-C4 intermediate, C4-like, C4) based on sucrose density gradient centrifugation and isoelectric focusing of the native protein, western-blot analysis of the denatured protein, and in situ immunolocalization with antibody against the 62-kD C4 isoform of maize. A 72-kD isoform, present to varying degrees in all species examined, is predominant in leaves of C3 Flaveria spp. and is also present in stem and root tissue. By immunolabeling, NADP-ME was found to be mostly localized in the upper palisade mesophyll chloroplasts of C3 photosynthetic tissue. Two other isoforms of the enzyme, with molecular masses of 62 and 64 kD, occur in leaves of certain intermediates having C4 cycle activity. The 62-kD isoform, which is the predominant highly active form in the C4 species, is localized in bundle-sheath chloroplasts. Among Flaveria spp. there is a 72-kD constitutive form, a 64-kD form that may have appeared during evolution of C4 metabolism, and a 62-kD form that is necessary for the complete functioning of C4 photosynthesis.

NADP-malic enzyme from the C4 plant Flaveria bidentis: nucleotide substrate specificity

NADP-malic enzyme (NADP-ME, EC 1.1.1.40) was purified to near-homogeneity from leaves of the C4 dicot Flaveria bidentis and shown to possess intrinsic NAD-dependent malic enzyme activity. The NAD-dependent activity is optimal at pH 7.5 and in the presence of Mn2+. The Km for NAD is very high (20 mM), while the Vmax is 50% greater than the Vmax with NADP under the same conditions. The NAD-dependent activity is competitively inhibited by micromolar concentrations of NADP and NADPH (Ki approximately 2 microM). This very low Ki reflects the high affinity of malic enzyme for NADP(H) under these conditions. When utilizing NADP, the Km for NADP is 1.5 microM while the Ki for NADPH is 2 microM. Chicken liver NADP-ME also has NAD-dependent activity that is inhibited by low concentrations of NADPH. These results indicate that the NAD- and NADP-dependent activities are likely catalyzed by the same active site. The use of NAD as an alternative coenzyme revealed interactions between the binding of coenzyme and metal ions on the Km values of each of the other participants in the malic enzyme reaction. Thus, the affinity of malic enzyme for the divalent metal ions Mg2+ and particularly Mn2+ as well as the other substrate L-malate is also dependent on the nucleotide coenzyme substrate. In turn, the divalent metal ion influences the affinity of the enzyme for the coenzyme as well as L-malate. With NADP as substrate the Km for Mn2+ is 4 microM, whereas with NAD the Km is 300 microM. The relatively high affinity of the enzyme for Mn2+ and low affinity for NAD required the use of metal ion buffers when determining these values because of the substantial depletion of free Mn2+ caused by binding to NADP.

Genomic structure and expression of the pyruvate, orthophosphate dikinase gene of the dicotyledonous C4 plant Flaveria trinervia (Asteraceae)

Pyruvate orthophosphate dikinase (PPDK) is a key enzyme of C4 photosynthesis providing the acceptor molecule for the primary CO2 fixation in the mesophyll cells. Here we present the isolation and characterisation of the corresponding gene (termed pdk) from the C4 plant Flaveria trinervia (Asteraceae). Southern analysis indicates that in contrast to maize pdk sequences in F. trinervia are present as single copy. Sequence analysis of the entire gene reveals that its coding sequence is identical to the previous isolated PPDK-cDNA from this species. The gene spans about 13 kb and consists of 21 exons, it thus contains two additional exons compared to the maize gene. As in maize, a long intervening sequence of 6.1 kb is positioned at the boundary of the transit peptide segment and the mature protein region. Pdk transcripts accumulate abundantly in leaves, but are also detectable in stems and roots. While the leaf and stem transcripts are 3.4 kb in size and encode the chloroplastic PPDK isoform, a 3.0 kb transcript lacking the region encoding the plastidic transit peptide accumulates in roots. Thus two different transcripts can be produced from a single pdk gene most likely by use of alternative promoters and not by alternative splicing. The accumulation of the 3.4 kb transcript is under light control. Darkening leads to a drastic depletion of this transcript in both leaves and stems. Instead, the 3.0 kb transit peptide-lacking pdk transcript accumulates, but only in stems and roots, not in leaves.