Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco

Improved salt-tolerance of transgenic soybean by stable over-expression of AhBADH gene from Atriplex hortensis

KEY MESSAGE

The salt-tolerance of transgenic soybean cleared for environmental release was improved by stable over-expression of AhBADH gene from Atriplex hortensis, which was demonstrated through molecular analysis and field experiments. An effective strategy for increasing the productivity of major crops under salt stress conditions is the development of transgenics that harbor genes responsible for salinity tolerance. Betaine aldehyde dehydrogenase (BADH) is a key enzyme involved in the biosynthesis of the osmoprotectant, glycine betaine (GB), and osmotic balance in plants, and several plants transformed with BADH gene have shown significant improvements in salt tolerance. However, very few field-tested transgenic cultivars have been reported, as most of the transgenic studies are limited to laboratory or green house experiments. In this study, we demonstrated through field experiments that AhBADH from Atriplex hortensis confers salt tolerance when transformed into soybean (Glycine max L.). AhBADH was successfully introduced into soybean by Agrobacterium mediated transformation. A total of 256 transgenic plants were obtained, out of which 47 lines showed significant enhancement of salt tolerance compared to non-transgenic control plants. Molecular analyses of the transgenic line TL2 and TL7 with the highest salt tolerance exhibited stable inheritance and expression of AhBADH in progenies with a single copy insertion. TL1, TL2 and TL7 exhibited stable enhanced salt tolerance and improved agronomic traits when subjected to 300mM NaCl treatment. Currently, the transgenic line TL2 and TL7 with stable enhanced salt tolerance, which have been cleared for environmental release, are under biosafety assessment. TL 2 and TL7 stably expressing AhBADH could then be applied in commercial breeding experiments to genetically improve salt tolerance in soybean.

Overexpression of Choline Oxidase Gene in Three Filial Generations of Rice Transgenic Lines

BACKGROUND

Glycinebetaine (GB) accumulation in many halophytic plants, animals, and microorganisms confers abiotic stress tolerance to salinity, drought, and extreme temperatures. Although there are a few genetic and biochemical pathways to synthesize GB, but isolation of a single gene Choline Oxidase (codA) from Arthrobacter spp. have opened a new hatch to engineer the susceptible plants.

OBJECTIVES

The effects of overexpressed codA gene, through multiple copy insertion and GB accumulation on salinity tolerance in rice were studied.

MATERIALS AND METHODS

Seed-derived embryogenic calli of 'Tarom Molaie' cultivar were targeted with two plasmids pChlCOD and pCytCOD both harboring the codA gene using the biolistic mediated transformation. The regenerated T₀ plants were screened by PCR analysis. A line containing three copies of codA gene and harboring pChlCOD and pCytCOD was identified by Southern blot analysis. The expression of codA gene in this transgenic line was then confirmed by RT-PCR. The Mendelian segregation pattern of the inserted sequences was accomplished by the progeny test using PCR. The effects of overexpression of codA on salinity tolerance were evaluated at germination and seedling stage using T₂-pChl transgenic line and control seeds in the presence of 0, 100, 200, and 300 mM NaCl. Finally, leaf growth dynamics of T₂-pChlCOD transgenic line and control line under hydroponic conditions in the presence of 0, 40, 80, and 120 mM NaCl were assessed.

RESULTS

The seed germination experiment results showed that the transformed seeds had a higher germination rate than the controls under all salinity treatments. But also, the leaf growth dynamics showed that the control plants had a more favorable leaf growth dynamic in all of the treatments. Although, the transgenic lines (T₀, T₁ and T₂) exhibited lower performance than the wild type, the transgenic line varied for GB and choline contents and increasing codA gene copy number led to increased GB content.

CONCLUSION

In a salinity sensitive crop such as rice, GB may not significantly contribute to the plant protection against salt stress. Also, insufficiency of choline resources as GB precursor might have affected the overall growth ability of the transgenic line and resulted in decreased leaf growth dynamics.

Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication

Betaine aldehyde dehydrogenase 1 (BADH1), a paralog of the fragrance gene BADH2, is known to be associated with salt stress through the accumulation of synthesized glycine betaine (GB), which is involved in the response to abiotic stresses. Despite the unclear association between BADH1 and salt stress, we observed the responses of eight phenotypic characteristics (germination percentage (GP), germination energy (GE), germination index (GI), mean germination time (MGT), germination rate (GR), shoot length (SL), root length (RL), and total dry weight (TDW)) to salt stress during the germination stage of 475 rice accessions to investigate their association with BADH1 haplotypes. We found a total of 116 SNPs and 77 InDels in the whole BADH1 gene region, representing 39 haplotypes. Twenty-nine haplotypes representing 27 mutated alleles (two InDels and 25 SNPs) were highly (p < 0.05) associated with salt stress, including the five SNPs that have been previously reported to be associated with salt tolerance. We observed three predominant haplotypes associated with salt tolerance, Hap_2, Hap_18, and Hap_23, which were Indica specific, indicating a comparatively high number of rice accessions among the associated haplotypes. Eight plant parameters (phenotypes) also showed clear responses to salt stress, and except for MGT (mean germination time), all were positively correlated with each other. Different signatures of domestication for BADH1 were detected in cultivated rice by identifying the highest and lowest Tajima’s D values of two major cultivated ecotypes (Temperate Japonica and Indica). Our findings on these significant associations and BADH1 evolution to plant traits can be useful for future research development related to its gene expression.

Morpho-Physiological Testing of NaCl Sensitivity of Tobacco Plants Overexpressing Choline Oxidase Gene

In this study the transgenic lines (TLs) of tobacco (Nicotianatabacum L.), which overexpress the heterologous gene encoding the bacterial enzyme choline oxidase were evaluated. The goal of our work is to study the effect of choline oxidase gene expression on the sensitivity of plant tissues to the action of NaCl. The regenerative capacity, rhizogenesis, the amount of photosynthetic pigments and osmotically active compounds (proline and glycine betaine) were assessed by in vitro cell culture methods using biochemical and morphological parameters. Transgenic lines with confirmed expression were characterized by high regeneration capacity from callus in the presence of 200 mmol NaCl, partial retention of viability at 400 mmol NaCl. These data correlated with the implicit response of regenerants and whole plants to the harmful effects of salinity. They turned out to be less sensitive to the presence of 200 mmol NaCl in the cultivation medium, in contrast to the WT plants.

Global proteomic analysis deciphers the mechanism of action of plant derived oleic acid against Candida albicans virulence and biofilm formation

Candida albicans is a commensal fungus in humans, mostly found on the mucosal surfaces of the mouth, gut, vagina and skin. Incidence of ever increasing invasive candidiasis in immunocompromised patients, alarming occurrence of antifungal resistance and insufficient diagnostic methods demand more focused research into C. albicans pathogenicity. Consequently, in the present study, oleic acid from Murraya koenigii was shown to have the efficacy to inhibit biofilm formation and virulence of Candida spp. Results of in vitro virulence assays and gene expression analysis, impelled to study the protein targets which are involved in the molecular pathways of C. albicans pathogenicity. Proteomic studies of differentially expressed proteins reveals that oleic acid induces oxidative stress responses and mainly targets the proteins involved in glucose metabolism, ergosterol biosynthesis, lipase production, iron homeostasis and amino acid biosynthesis. The current study emphasizes anti-virulent potential of oleic acid which can be used as a therapeutic agent to treat Candida infections.

Accumulation of glycine betaine in transplastomic potato plants expressing choline oxidase confers improved drought tolerance

Plastid genome engineering is an effective method to generate drought-resistant potato plants accumulating glycine betaine in plastids. Glycine betaine (GB) plays an important role under abiotic stress, and its accumulation in chloroplasts is more effective on stress tolerance than that in cytosol of transgenic plants. Here, we report that the codA gene from Arthrobacter globiformis, which encoded choline oxidase to catalyze the conversion of choline to GB, was successfully introduced into potato (Solanum tuberosum) plastid genome by plastid genetic engineering. Two independent plastid-transformed lines were isolated and confirmed as homoplasmic via Southern-blot analysis, in which the mRNA level of codA was much higher in leaves than in tubers. GB accumulated in similar levels in both leaves and tubers of codA-transplastomic potato plants (referred to as PC plants). The GB content was moderately increased in PC plants, and compartmentation of GB in plastids conferred considerably higher tolerance to drought stress compared to wild-type (WT) plants. Higher levels of relative water content and chlorophyll content under drought stress were detected in the leaves of PC plants compared to WT plants. Moreover, PC plants presented a significantly higher photosynthetic performance as well as antioxidant enzyme activities during drought stress. These results suggested that biosynthesis of GB by chloroplast engineering was an effective method to increase drought tolerance.

Spatial and Temporal Profile of Glycine Betaine Accumulation in Plants Under Abiotic Stresses

Several halophytes and a few crop plants, including Poaceae, synthesize and accumulate glycine betaine (GB) in response to environmental constraints. GB plays an important role in osmoregulation, in fact, it is one of the main nitrogen-containing compatible osmolytes found in Poaceae. It can interplay with molecules and structures, preserving the activity of macromolecules, maintaining the integrity of membranes against stresses and scavenging ROS. Exogenous GB applications have been proven to induce the expression of genes involved in oxidative stress responses, with a restriction of ROS accumulation and lipid peroxidation in cultured tobacco cells under drought and salinity, and even stabilizing photosynthetic structures under stress. In the plant kingdom, GB is synthesized from choline by a two-step oxidation reaction. The first oxidation is catalyzed by choline monooxygenase (CMO) and the second oxidation is catalyzed by NAD+-dependent betaine aldehyde dehydrogenase. Moreover, in plants, the cytosolic enzyme, named N-methyltransferase, catalyzes the conversion of phosphoethanolamine to phosphocholine. However, changes in CMO expression genes under abiotic stresses have been observed. GB accumulation is ontogenetically controlled since it happens in young tissues during prolonged stress, while its degradation is generally not significant in plants. This ability of plants to accumulate high levels of GB in young tissues under abiotic stress, is independent of nitrogen (N) availability and supports the view that plant N allocation is dictated primarily to supply and protect the growing tissues, even under N limitation. Indeed, the contribution of GB to osmotic adjustment and ionic and oxidative stress defense in young tissues, is much higher than that in older ones. In this review, the biosynthesis and accumulation of GB in plants, under several abiotic stresses, were analyzed focusing on all possible roles this metabolite can play, particularly in young tissues.

Functional and expression analyses of two kinds of betaine aldehyde dehydrogenases in a glycinebetaine-hyperaccumulating graminaceous halophyte, Leymus chinensis

Glycinebetaine (GB) is an important compatible solute for salinity tolerance in many plants. In this study, we analyzed the enzymatic activity and the expression level of betaine aldehyde dehydrogenase (BADH), an important enzyme that catalyzes the last step in the GB synthesis in Leymus chinensis, a GB-hyperaccumulating graminaceous halophyte, and compared with those of barley, a graminaceous glycophyte. We have isolated cDNAs for two BADH genes, LcBADH1 and LcBADH2. LcBADH1 has a putative peroxisomal signal peptide (PTS1) at its C-terminus, while LcBADH2 does not have any typical signal peptide. Using immunofluorescent labeling, we showed that BADH proteins were localized to the cytosol and dot-shaped organelles in the mesophyll and bundle sheath cells of L.chinensis leaves. The affinity of recombinant LcBADH2 for betaine aldehyde was comparable to other plant BADHs, whereas recombinant LcBADH1 showed extremely low affinity for betaine aldehyde, indicating that LcBADH2 plays a major role in GB synthesis in L. chinensis. In addition, the recombinant LcBADH2 protein was tolerant to NaCl whereas LcBADH1 wasn't. The kinetics, subcellular and tissue localization of BADH proteins were comparable between L. chinensis and barley. The activity and expression level of BADH proteins were higher in L. chinensis compared with barley under both normal and salinized conditions, which may be related to the significant difference in the amount of GB accumulation between two plants.

The benefits of photorespiratory bypasses: how can they work?

Bypassing the photorespiratory pathway is regarded as a way to increase carbon assimilation and, correspondingly, biomass production in C3 crops. Here, the benefits of three published photorespiratory bypass strategies are systemically explored using a systems-modeling approach. Our analysis shows that full decarboxylation of glycolate during photorespiration would decrease photosynthesis, because a large amount of the released CO2 escapes back to the atmosphere. Furthermore, we show that photosynthesis can be enhanced by lowering the energy demands of photorespiration and by relocating photorespiratory CO2 release into the chloroplasts. The conductance of the chloroplast membranes to CO2 is a key feature determining the benefit of the relocation of photorespiratory CO2 release. Although our results indicate that the benefit of photorespiratory bypasses can be improved by increasing sedoheptulose bisphosphatase activity and/or increasing the flux through the bypass, the effectiveness of such approaches depends on the complex regulation between photorespiration and other metabolic pathways.

Application of metabolic flux analysis to plants

This volume compiles a series of chapters that cover the major aspects of plant metabolic flux analysis, such as but not limited to labeling of plant material, acquisition of labeling data, mathematical modeling of metabolic network at the cell, tissue, and plant level. A short revue, including methodological points and applications of flux analysis to plants, is presented in this introductory chapter.

Compatible solute engineering in plants for abiotic stress tolerance - role of glycine betaine

Abiotic stresses collectively are responsible for crop losses worldwide. Among these, drought and salinity are the most destructive. Different strategies have been proposed for management of these stresses. Being a complex trait, conventional breeding approaches have resulted in less success. Biotechnology has emerged as an additional and novel tool for deciphering the mechanism behind these stresses. The role of compatible solutes in abiotic stress tolerance has been studied extensively. Osmotic adjustment, at the physiological level, is an adaptive mechanism involved in drought or salinity tolerance, which permits the maintenance of turgor under conditions of water deficit, as it can counteract the effects of a rapid decline in leaf water potential. Increasing evidence from a series of in vivo and in vitro studies of the physiology, biochemistry, genetics, and molecular biology of plants suggest strongly that Glycine Betaine (GB) performs an important function in plants subjected to environmental stresses. It plays an adaptive role in mediating osmotic adjustment and protecting the sub-cellular structures in stressed plants, protection of the transcriptional and translational machineries and intervention as a molecular chaperone in the refolding of enzymes. Many important crops like rice do not accumulate glycinebetaine under stress conditions. Both the exogenous application of GB and the genetically engineered biosynthesis of GB in such crops is a promising strategy to increase stress tolerance. In this review we will discuss the importance of GB for abiotic stress tolerance in plants. Further, strategies like exogenic application and transgenic development of plants accumulating GB will be also be discussed. Work done on exogenic application and genetically engineered biosynthesis of GB will be listed and its advantages and limitations will be described.

The challenges of cellular compartmentalization in plant metabolic engineering

The complex metabolic networks in plants are highly compartmentalized and biochemical steps of a single pathway can take place in multiple subcellular locations. Our knowledge regarding reactions and precursor compounds in the various cellular compartments has increased in recent years due to innovations in tracking the spatial distribution of proteins and metabolites. Nevertheless, to date only few studies have integrated subcellular localization criteria in metabolic engineering attempts. Here, we highlight the crucial factors for subcellular-localization-based strategies in plant metabolic engineering including substrate availability, enzyme targeting, the role of transporters, and multigene transfer approaches. The availability of compartmentalized metabolic network models for plants in the near future will greatly advance the integration of localization constraints in metabolic engineering experiments and aid in predicting their outcomes.

Phosphoethanolamine methyltransferases in phosphocholine biosynthesis: functions and potential for antiparasite therapy

S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse group of enzymes that catalyze the transfer of a methyl group from a methyl donor SAM to nitrogen, oxygen, sulfur or carbon atoms of a large number of biologically active large and small molecules. These modifications play a major role in the regulation of various biological functions such as gene expression, signaling, nuclear division and metabolism. The three-step SAM-dependent methylation of phosphoethanolamine to form phosphocholine catalyzed by phosphoethanolamine N-methyltransferases (PMTs) has emerged as an important biochemical step in the synthesis of the major phospholipid, phosphatidylcholine, in some eukaryotes. PMTs have been identified in nematodes, plants, African clawed frogs, zebrafish, the Florida lancelet, Proteobacteria and human malaria parasites. Data accumulated thus far suggest an important role for these enzymes in growth and development. This review summarizes published studies on the biochemical and genetic characterization of these enzymes, and discusses their evolution and their suitability as targets for the development of therapies against parasitic infections, as well as in bioengineering for the development of nutritional and stress-resistant plants.

Glycinebetaine protects plants against abiotic stress: mechanisms and biotechnological applications

Various compatible solutes enable plants to tolerate abiotic stress, and glycinebetaine (GB) is one of the most-studied among such solutes. Early research on GB focused on the maintenance of cellular osmotic potential in plant cells. Subsequent genetically engineered synthesis of GB-biosynthetic enzymes and studies of transgenic plants demonstrated that accumulation of GB increases tolerance of plants to various abiotic stresses at all stages of their life cycle. Such GB-accumulating plants exhibit various advantageous traits, such as enlarged fruits and flowers and/or increased seed number under non-stress conditions. However, levels of GB in transgenic GB-accumulating plants are relatively low being, generally, in the millimolar range. Nonetheless, these low levels of GB confer considerable tolerance to various stresses, without necessarily contributing significantly to cellular osmotic potential. Moreover, low levels of GB, applied exogenously or generated by transgenes for GB biosynthesis, can induce the expression of certain stress-responsive genes, including those for enzymes that scavenge reactive oxygen species. Thus, transgenic approaches that increase tolerance to abiotic stress have enhanced our understanding of mechanisms that protect plants against such stress.

Identification of phosphomethylethanolamine N-methyltransferase from Arabidopsis and its role in choline and phospholipid metabolism

Three sequential methylations of phosphoethanolamine (PEA) are required for the synthesis of phosphocholine (PCho) in plants. A cDNA encoding an N-methyltransferase that catalyzes the last two methylation steps was cloned from Arabidopsis by heterologous complementation of a Saccharomyces cerevisiae cho2, opi3 mutant. The cDNA encodes phosphomethylethanolamine N-methyltransferase (PMEAMT), a polypeptide of 475 amino acids that is organized as two tandem methyltransferase domains. PMEAMT shows 87% amino acid identity to a related enzyme, phosphoethanolamine N-methyltransferase, an enzyme in plants that catalyzes all three methylations of PEA to PCho. PMEAMT cannot use PEA as a substrate, but assays using phosphomethylethanolamine as a substrate result in both phosphodimethylethanolamine and PCho as products. PMEAMT is inhibited by the reaction products PCho and S-adenosyl-l-homocysteine, a property reported for phosphoethanolamine N-methyltransferase from various plants. An Arabidopsis mutant with a T-DNA insertion associated with locus At1g48600 showed no transcripts encoding PMEAMT. Shotgun lipidomic analyses of leaves of atpmeamt and wild-type plants generated phospholipid profiles showing the content of phosphatidylmethylethanolamine to be altered relative to wild type with the content of a 34:3 lipid molecular species 2-fold higher in mutant plants. In S. cerevisiae, an increase in PtdMEA in membranes is associated with reduced viability. This raises a question regarding the role of PMEAMT in plants and whether it serves to prevent the accumulation of PtdMEA to potentially deleterious levels.

Mathematical modeling-guided evaluation of biochemical, developmental, environmental, and genotypic determinants of essential oil composition and yield in peppermint leaves

We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Menthaxpiperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a chi2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.

A kinetic model describes metabolic response to perturbations and distribution of flux control in the benzenoid network of Petunia hybrida

In recent years there has been much interest in the genetic enhancement of plant metabolism; however, attempts at genetic modification are often unsuccessful due to an incomplete understanding of network dynamics and their regulatory properties. Kinetic modeling of plant metabolic networks can provide predictive information on network control and response to genetic perturbations, which allow estimation of flux at any concentration of intermediate or enzyme in the system. In this research, a kinetic model of the benzenoid network was developed to simulate whole network responses to different concentrations of supplied phenylalanine (Phe) in petunia flowers and capture flux redistributions caused by genetic manipulations. Kinetic parameters were obtained by network decomposition and non-linear least squares optimization of data from petunia flowers supplied with either 75 or 150 mm(2)H(5)-Phe. A single set of kinetic parameters simultaneously accommodated labeling and pool size data obtained for all endogenous and emitted volatiles at the two concentrations of supplied (2)H(5)-Phe. The generated kinetic model was validated using flowers from transgenic petunia plants in which benzyl CoA:benzyl alcohol/phenylethanol benzoyltransferase (BPBT) was down-regulated via RNAi. The determined in vivo kinetic parameters were used for metabolic control analysis, in which flux control coefficients were calculated for fluxes around the key branch point at Phe and revealed that phenylacetaldehyde synthase activity is the primary controlling factor for the phenylacetaldehyde branch of the benzenoid network. In contrast, control of flux through the beta-oxidative and non-beta-oxidative pathways is highly distributed.

Metabolomics for functional genomics, systems biology, and biotechnology

Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

Metabolic flux analysis in plants: coping with complexity

Theory and experience in metabolic engineering both show that metabolism operates at the network level. In plants, this complexity is compounded by a high degree of compartmentation and the synthesis of a very wide array of secondary metabolic products. A further challenge to understanding and predicting plant metabolic function is posed by our ignorance about the structure of metabolic networks even in well-studied systems. Metabolic flux analysis (MFA) provides tools to measure and model the functioning of metabolism, and is making significant contributions to coping with their complexity. This review gives an overview of different MFA approaches, the measurements required to implement them and the information they yield. The application of MFA methods to plant systems is then illustrated by several examples from the recent literature. Next, the challenges that plant metabolism poses for MFA are discussed together with ways that these can be addressed. Lastly, new developments in MFA are described that can be expected to improve the range and reliability of plant MFA in the coming years.

Isolation, identification and expression analysis of salt-induced genes in Suaeda maritima, a natural halophyte, using PCR-based suppression subtractive hybridization

BACKGROUND

Despite wealth of information generated on salt tolerance mechanism, its basics still remain elusive. Thus, there is a need of continued effort to understand the salt tolerance mechanism using suitable biotechnological techniques and test plants (species) to enable development of salt tolerant cultivars of interest. Therefore, the present study was undertaken to generate information on salt stress responsive genes in a natural halophyte, Suaeda maritima, using PCR-based suppression subtractive hybridization (PCR-SSH) technique.

RESULTS

Forward and reverse SSH cDNA libraries were constructed after exposing the young plants to 425 mM NaCl for 24 h. From the forward SSH cDNA library, 429 high quality ESTs were obtained. BLASTX search and TIGR assembler programme revealed overexpression of 167 unigenes comprising 89 singletons and 78 contigs with ESTs redundancy of 81.8%. Among the unigenes, 32.5% were found to be of special interest, indicating novel function of these genes with regard to salt tolerance. Literature search for the known unigenes revealed that only 17 of them were salt-inducible. A comparative analysis of the existing SSH cDNA libraries for NaCl stress in plants showed that only a few overexpressing unigenes were common in them. Moreover, the present study also showed increased expression of phosphoethanolamine N-methyltransferase gene, indicating the possible accumulation of a much studied osmoticum, glycinebetaine, in halophyte under salt stress. Functional categorization of the proteins as per the Munich database in general revealed that salt tolerance could be largely determined by the proteins involved in transcription, signal transduction, protein activity regulation and cell differentiation and organogenesis.

CONCLUSION

The study provided a clear indication of possible vital role of glycinebetaine in the salt tolerance process in S. maritima. However, the salt-induced expression of a large number of genes involved in a wide range of cellular functions was indicative of highly complex nature of the process as such. Most of the salt inducible genes, nonetheless, appeared to be species-specific. In light of the observations made, it is reasonable to emphasize that a comparative analysis of ESTs from SSH cDNA libraries generated systematically for a few halophytes with varying salt exposure time may clearly identify the key salt tolerance determinant genes to a minimum number, highly desirable for any genetic manipulation adventure.

Dynamics of Positional Enrichment: Theoretical Development and Application to Carbon Labeling in Zymomonas mobilis

Positional enrichment analysis has become an important technique for assessing detailed flux distributions and the fates of specific atoms in metabolic pathway systems. The typical approach to positional enrichment analysis is performed by supplying specifically labeled substrate to a cell system, letting the system reach steady state, and measuring where label had arrived and accumulated. The data are then evaluated mathematically with the help of a linear stoichiometric flux distribution model. While this procedure has proven to yield new and valuable insights, it does not address the transient dynamics between providing label and its ultimate steady-state distribution, which is often of great interest to the experimentalist (pulse labeling experiments). We show here that an extension of a recent mathematical method for dynamic labeling analysis is able to shed light on these transitions, thereby revealing insights not obtained with traditional positional enrichment analyses. The method traces the dynamics of one or more carbons through fully regulated metabolic pathways, which, in principle, may be arbitrarily complex. After a brief review of the earlier method and description of the theoretical extension, we illustrate the method with an analysis of the pentose phosphate pathway in Zymomonas mobilis, which has been used for traditional positional enrichment analyses in the past. We show how different labeling schemes result in distinctly different transients, which nevertheless eventually lead to a steady-state labeling profile that coincides exactly with the corresponding profile from traditional analysis. Thus, over the domain of commonality, the proposed method leads to results equivalent to those from state-of-the-art existing methods. However, these steady-state results constitute only a small portion of the insights obtainable with the proposed method. Our method can also be used as an "inverse" technique for elucidating the topology and regulation of pathway systems, if appropriate time series data are available. While such dynamic data are still rather rare, they are now being generated with increasing frequency and we believe it is desirable, and indeed necessary, to accompany this trend with an adequate, rigorous method of analysis.

Towards salinity tolerance in Brassica: an overview

Among the various abiotic stresses limiting the crop productivity, salinity stress is a major problem, which needs to be addressed and answered urgently. Since members of Brassicaceae are important contributor to total oilseed production, there is an immediate need being felt to raise Brassica plants which would be more suitable for saline and dry lands in years to come. One of the suggested way to develop salinity tolerant Brassica plants is to make use of the broad gene pool available within the family. Efforts of breeders have been successful in such endeavors to a large extent and several salinity tolerant Brassica genotypes have been developed within India and elsewhere. On the other hand, transgenic technology will undoubtedly continue to aid the search for the cellular mechanisms that confer tolerance, but the complexity of the trait is likely to mean that the road to engineer such tolerance into sensitive species will not be easy. However, with increasing number of reports available for suitable genetic transformation for various Brassica genotypes, there is a hope that salinity tolerance can be improved in this important crop plant. In this direction, the complete genome sequence of related wild plants such as Arabidopsis or crop plants such as rice can also serve as a platform for identification of "candidate genes". Recently, complete genome sequencing of the Brassica genomes has also been initiated with the view that availability of such useful information can pave way towards raising Brassica with improved tolerance towards these stresses. In the present paper, we discuss the success obtained so far; in raising brassica genotypes with improved salinity tolerance employing both plant breeding and/or genetic engineering tools.

Getting to grips with the plant metabolic network

Research into plant metabolism has a long history, and analytical approaches of ever-increasing breadth and sophistication have been brought to bear. We now have access to vast repositories of data concerning enzymology and regulatory features of enzymes, as well as large-scale datasets containing profiling information of transcripts, protein and metabolite levels. Nevertheless, despite this wealth of data, we remain some way off from being able to rationally engineer plant metabolism or even to predict metabolic responses. Within the past 18 months, rapid progress has been made, with several highly informative plant network interrogations being discussed in the literature. In the present review we will appraise the current state of the art regarding plant metabolic network analysis and attempt to outline what the necessary steps are in order to further our understanding of network regulation.

Metabolic flux analysis in plants: from intelligent design to rational engineering

Metabolic flux analysis (MFA) is a rapidly developing field concerned with the quantification and understanding of metabolism at the systems level. The application of MFA has produced detailed maps of flow through metabolic networks of a range of plant systems. These maps represent detailed metabolic phenotypes, contribute significantly to our understanding of metabolism in plants, and have led to the discovery of new metabolic routes. The presentation of thorough statistical evaluation with current flux maps has set a new standard for the quality of quantitative flux studies. In microbial systems, powerful methods have been developed for the reconstruction of metabolic networks from genomic and transcriptomic data, pathway analysis, and predictive modeling. This review brings together the recent developments in quantitative MFA and predictive modeling. The application of predictive tools to high quality flux maps in particular promises to be important in the rational metabolic engineering of plants.

Metabolic flux analysis in plants using dynamic labeling technique: application to tryptophan biosynthesis in cultured rice cells

The concept and methodology of using dynamic labeling for the MFA of plant metabolic pathways are described, based on a case study to develop a method for the MFA of the tryptophan biosynthetic pathway in cultured rice cells. Dynamic labeling traces the change in the labeling level of a metabolite in a metabolic pathway after the application of a stable isotope-labeled compound. In this study, [1-(13)C] l-serine was fed as a labeling precursor and the labeling level of Trp was determined by using the LC-MS/MS. The value of metabolic flux is determined by fitting a model describing the labeling dynamics of the pathway to the observed labeling data. The biosynthetic flux of Trp in rice suspension cultured cell was determined to be 6.0+/-1.1 nmol (gFWh)(-1). It is also demonstrated that an approximately sixfold increase in the biosynthetic flux of Trp in transgenic rice cells expressing the feedback-insensitive version of anthranilate synthase alpha-subunit gene (OASA1D) resulted in a 45-fold increase in the level of Trp. In this article, the basic workflow for the experiment is introduced and the details of the actual experimental procedures are explained. Future perspectives are also discussed by referring recent advances in the dynamic labeling approach.

Experimental and mathematical approaches to modeling plant metabolic networks

To support their sessile and autotrophic lifestyle higher plants have evolved elaborate networks of metabolic pathways. Dynamic changes in these metabolic networks are among the developmental forces underlying the functional differentiation of organs, tissues and specialized cell types. They are also important in the various interactions of a plant with its environment. Further complexity is added by the extensive compartmentation of the various interconnected metabolic pathways in plants. Thus, although being used widely for assessing the control of metabolic flux in microbes, mathematical modeling approaches that require steady-state approximations are of limited utility for understanding complex plant metabolic networks. However, considerable progress has been made when manageable metabolic subsystems were studied. In this article, we will explain in general terms and using simple examples the concepts underlying stoichiometric modeling (metabolic flux analysis and metabolic pathway analysis) and kinetic approaches to modeling (including metabolic control analysis as a special case). Selected studies demonstrating the prospects of these approaches, or combinations of them, for understanding the control of flux through particular plant pathways are discussed. We argue that iterative cycles of (dry) mathematical modeling and (wet) laboratory testing will become increasingly important for simulating the distribution of flux in plant metabolic networks and deriving rational experimental designs for metabolic engineering efforts.

Glycinebetaine accumulation is more effective in chloroplasts than in the cytosol for protecting transgenic tomato plants against abiotic stress

Tomato (Lycopersicon esculentum Mill. cv. Moneymaker) plants were transformed with a gene for choline oxidase (codA) from Arthrobacter globiformis. The gene product (CODA) was targeted to the chloroplasts (Chl-codA), cytosol (Cyt-codA) or both compartments simultaneously (ChlCyt-codA). These three transgenic plant types accumulated different amounts and proportions of glycinebetaine (GB) in their chloroplasts and cytosol. Targeting CODA to either the cytosol or both compartments simultaneously increased total GB content by five- to sixfold over that measured from the chloroplast targeted lines. Accumulation of GB in codA transgenic plants was tissue dependent, with the highest levels being recorded in reproductive organs. Despite accumulating, the lowest amounts of GB, Chl-codA plants exhibited equal or higher degrees of enhanced tolerance to various abiotic stresses. This suggests that chloroplastic GB is more effective than cytosolic GB in protecting plant cells against chilling, high salt and oxidative stresses. Chloroplastic GB levels were positively correlated with the degree of oxidative stress tolerance conferred, whereas cytosolic GB showed no such a correlation. Thus, an increase in total GB content does not necessarily lead to enhanced stress tolerance, but additional accumulation of chloroplastic GB is likely to further raise the level of stress tolerance beyond what we have observed.

Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation

In this paper we present a method that allows dynamic flux analysis without a priori kinetic knowledge. This method was developed and validated using the pulse-feeding experimental data obtained in our previous study (Matsuda et al., 2005), in which incorporation of exogenously applied l-phenylalanine-d(5) into seven phenylpropanoid metabolites in potato tubers was determined. After identification of the topology of the metabolic network of these biosynthetic pathways, the system was described by dynamic mass balances in combination with power-law kinetics. After the first simulations, some reactions were removed from the network because they were not contributing significantly to network behaviour. As a next step, the exponents of the power-law kinetics were identified and then kept at fixed values during further analysis. The model was tested for statistical reliability using Monte Carlo simulations. Most fluxes could be identified with high accuracy. The two test cases, control and after elicitation, were clearly distinguished, and with elicitation fluxes to N-p-coumaroyloctopamine (pCO) and N-p-coumaroyltyramine (pCT) increased significantly, whereas those for chlorogenic acid (CGA) and p-coumaroylshikimate decreased significantly. According to the model, increases in the first two fluxes were caused by induction/derepression mechanisms. The decreases in the latter two fluxes were caused by decreased concentrations of their substrates, which in turn were caused by increased activity of the pCO- and pCT-producing enzymes. Flux-control analysis showed that, in most cases, flux control was changed after application of elicitor. Thus the results revealed potential targets for improving actions against tissue wounding and pathogen attack.

Metabolic flux analysis: recent advances in carbon metabolism in plants

Isotopic tracers are used to both trace metabolic pathways and quantify fluxes through these pathways. The use of different labeling methods recently led to profound changes in our views of plant metabolism. Examples are taken from primary metabolism, with sugar interconversions, carbon partitioning between glycolysis and the pentose phosphate pathway, or metabolite inputs into the tricarboxylic acid (TCA) cycle, as well as from secondary metabolism with the relative contribution of the plastidial and cytosolic pathways to the biosynthesis of terpenoids. While labeling methods are often distinguished according to the instruments used for label detection, emphasis is put here on labeling duration. Short time labeling is adequate to study limited areas of the metabolic network. Long-term labeling, when designed to obtain metabolic and isotopic steady-state, allows to calculate various fluxes in large areas ofcentral metabolism. After longer labeling periods, large amounts of label accumulate in structural or storage compounds: their detailed study through the retrobiosynthetic method gives access to the biosynthetic pathways of otherwise undetectable precursors. This chapter presents the power and limits of the different methods, and illustrates how they can be associated with each other and with other methods of cell biology, to provide the information needed for a rational approach of metabolic engineering.

Measuring multiple fluxes through plant metabolic networks

Fluxes through metabolic networks are crucial for cell function, and a knowledge of these fluxes is essential for understanding and manipulating metabolic phenotypes. Labeling provides the key to flux measurement, and in network flux analysis the measurement of multiple fluxes allows a flux map to be superimposed on the metabolic network. The principles and practice of two complementary methods, dynamic and steady-state labeling, are described, emphasizing best practice and illustrating their contribution to network flux analysis with examples taken from the plant and microbial literature. The principal analytical methods for the detection of stable isotopes are also described, as well as the procedures for obtaining flux maps from labeling data. A series of boxes summarizing the key concepts of network flux analysis is provided for convenience.

Revealing metabolic phenotypes in plants: inputs from NMR analysis

Assessing the performance of the plant metabolic network, with its varied biosynthetic capacity and its characteristic subcellular compartmentation, remains a considerable challenge. The complexity of the network is such that it is not yet possible to build large-scale predictive models of the fluxes it supports, whether on the basis of genomic and gene expression analysis or on the basis of more traditional measurements of metabolites and their interconversions. This limits the agronomic and biotechnological exploitation of plant metabolism, and it undermines the important objective of establishing a rational metabolic engineering strategy. Metabolic analysis is central to removing this obstacle and currently there is particular interest in harnessing high-throughput and/or large-scale analyses to the task of defining metabolic phenotypes. Nuclear magnetic resonance (NMR) spectroscopy contributes to this objective by providing a versatile suite of analytical techniques for the detection of metabolites and the fluxes between them. The principles that underpin the analysis of plant metabolism by NMR are described, including a discussion of the measurement options for the detection of metabolites in vivo and in vitro, and a description of the stable isotope labelling experiments that provide the basis for metabolic flux analysis. Despite a relatively low sensitivity, NMR is suitable for high-throughput system-wide analyses of the metabolome, providing methods for both metabolite fingerprinting and metabolite profiling, and in these areas NMR can contribute to the definition of plant metabolic phenotypes that are based on metabolic composition. NMR can also be used to investigate the operation of plant metabolic networks. Labelling experiments provide information on the operation of specific pathways within the network, and the quantitative analysis of steady-state labelling experiments leads to the definition of large-scale flux maps for heterotrophic carbon metabolism. These maps define multiple unidirectional fluxes between branch-points in the metabolic network, highlighting the existence of substrate cycles and discriminating in favourable cases between fluxes in the cytosol and plastid. Flux maps can be used to define a functionally relevant metabolic phenotype and the extensive application of such maps in microbial systems suggests that they could have important applications in characterising the genotypes produced by plant genetic engineering.

Understanding in vivo benzenoid metabolism in petunia petal tissue

In vivo stable isotope labeling and computer-assisted metabolic flux analysis were used to investigate the metabolic pathways in petunia (Petunia hybrida) cv Mitchell leading from Phe to benzenoid compounds, a process that requires the shortening of the side chain by a C(2) unit. Deuterium-labeled Phe ((2)H(5)-Phe) was supplied to excised petunia petals. The intracellular pools of benzenoid/phenylpropanoid-related compounds (intermediates and end products) as well as volatile end products within the floral bouquet were analyzed for pool sizes and labeling kinetics by gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry. Modeling of the benzenoid network revealed that both the CoA-dependent, beta-oxidative and CoA-independent, non-beta-oxidative pathways contribute to the formation of benzenoid compounds in petunia flowers. The flux through the CoA-independent, non-beta-oxidative pathway with benzaldehyde as a key intermediate was estimated to be about 2 times higher than the flux through the CoA-dependent, beta-oxidative pathway. Modeling of (2)H(5)-Phe labeling data predicted that in addition to benzaldehyde, benzylbenzoate is an intermediate between l-Phe and benzoic acid. Benzylbenzoate is the result of benzoylation of benzyl alcohol, for which activity was detected in petunia petals. A cDNA encoding a benzoyl-CoA:benzyl alcohol/phenylethanol benzoyltransferase was isolated from petunia cv Mitchell using a functional genomic approach. Biochemical characterization of a purified recombinant benzoyl-CoA:benzyl alcohol/phenylethanol benzoyltransferase protein showed that it can produce benzylbenzoate and phenylethyl benzoate, both present in petunia corollas, with similar catalytic efficiencies.

Cloning and salt-induced, ABA-independent expression of choline mono-oxygenase in Atriplex prostrata

Certain plants accumulate glycinebetaine, a type of osmoprotectant, in response to salinity. Glycinebetaine is synthesized in these plants via the two-step oxidation of choline, and the first step is catalysed by choline mono-oxygenase (CMO; EC 1.14.15.7). Cloned by RT-PCR and 3'-RACE, the cDNA of Atriplex prostrata CMO (ApCMO) is 1669 bp in length and encodes a full-length protein of 438 amino acids. The deduced amino acid sequence of ApCMO revealed a Rieske-type [2Fe-2S] cluster motif and a mononuclear non-heme Fe binding motif, and shares 82.9% identity and 87.2% similarity with the deduced amino acid sequence of spinach CMO. Accumulation of CMO transcript and glycinebetaine both increased in response to NaCl treatment. Without salt treatment, CMO mRNA was detected in stems and 5-day-old seedlings, but not in leaves, roots and older seedlings. With salt treatment, CMO mRNA accumulated dramatically in stems, leaves and roots, with the most abundant accumulation occurring in young stems. Although abscisic acid may initiate global physiological reactions in response to osmotic stress, it did not induce the expression of CMO in A. prostrata. In summary, salt-induction of CMO mRNA in A. prostrata is more substantial than that reported in spinach and sugar beet, and the plant may serve as a useful model to study regulation of glycinebetaine synthesis by environmental stress.

Evidence from engineering that decarboxylation of free serine is the major source of ethanolamine moieties in plants

Plants form ethanolamine (Etn) moieties by decarboxylating serine or phosphatidylserine (PtdSer), and use them to make phosphatidylethanolamine, phosphatidylcholine, choline, and glycine betaine. Serine decarboxylation is mediated by a serine decarboxylase (SDC) that is unique to plants and has a characteristic N-terminal extension. This extension was shown to have little influence on function of the enzyme in vitro. To explore the importance of SDC and its extension in vivo, native or truncated versions of the Arabidopsis enzyme were expressed in tobacco. Transgene expression increased SDC activity by up to 10-fold and free Etn level up to 6-fold, but did not change levels of serine, choline, phosphocholine, or phosphatidyl bases. The truncated enzyme gave significantly higher Etn levels. These results show that SDC activity exerts substantial control over flux to Etn, and suggest that the enzyme's N-terminus may have a regulatory role. In complementary studies with Arabidopsis, we showed that a mutant with 9-fold elevated mitochondrial PtdSer decarboxylase activity had normal pools of serine, Etn, and Etn metabolites. Taken together, these data indicate that serine decarboxylation is the main source of Etn moieties in plants. The ability to enhance serine --> Etn flux should advance engineering of choline and glycine betaine accumulation.

Enhanced formation of flowers in salt-stressed Arabidopsis after genetic engineering of the synthesis of glycine betaine

Previously, we showed that transformation with the codA gene for choline oxidase allows plants to synthesize glycine betaine (GB) and enhances their ability to tolerate various kinds of stress during germination and vegetative growth. In this study, we examined the tolerance of transformed plants to salt stress at the reproductive stage, which is the stage at which plants are most sensitive to environmental stress. Salt-shock treatment of wild-type plants for 3 days resulted in the abortion of flower buds and decreased the number of seeds per silique. These deleterious effects were clearly visible 6 days after the termination of salt-shock treatment. Microscopic examination of floral structures revealed that salt stress inhibited the development of anthers, pistils, and petals. In particular, the production of pollen grains and ovules was dramatically inhibited. These effects of salt stress were significantly reduced by transformation with the codA gene, and our observations suggested that the enhanced tolerance of the transgenic plants was a result of the accumulation of GB in the reproductive organs. Indeed, levels of GB in flowers, siliques, and inflorescence apices were about five times higher than in leaves.

beta-alanine N-methyltransferase of Limonium latifolium. cDNA cloning and functional expression of a novel N-methyltransferase implicated in the synthesis of the osmoprotectant beta-alanine betaine

Beta-alanine (Ala) betaine, an osmoprotectant suitable under saline and hypoxic environments, is found in most members of the halophytic plant family Plumbaginaceae. In Limonium latifolium (Plumbaginaceae), it is synthesized via methylation of beta-Ala by the action of a trifunctional S-adenosyl L-methionine (Ado-Met): beta-Ala N-methyltransferase (NMTase). Peptide sequences from purified beta-Ala NMTase were used to design primers for reverse transcriptase-PCR, and several cDNA clones were isolated. The 5' end of the cDNA was cloned using a 5'-rapid amplification of cDNA ends protocol. A 500-bp cDNA was used as a probe to screen a lambda-gt10 L. latifolium leaf cDNA library. Partial cDNA clones represented two groups, NMTase A and NMTase B, differing only in their 3'-untranslated regions. The full-length NMTase A cDNA was 1,414 bp and included a 1128-bp open reading frame and a 119-bp 5'-untranslated region. The deduced amino acid sequence of 375 residues had motifs known to be involved in the binding of Ado-Met. The NMTase mRNA was expressed in L. latifolium leaves but was absent in Limonium sinuatum, a member of the genus that lacks the synthetic pathway for beta-Ala betaine. NMTase mRNA expression was high in young and mature leaves and was enhanced by light. NMTase cDNA was expressed in yeast (Saccharomyces cerevisiae) under the control of a galactose-inducible promoter. Protein extracts of galactose-induced recombinant yeast had Ado-Met-specific NMTase activities that were highly specific to beta-Ala, N-methyl beta-Ala, and N,N-dimethyl beta-Ala as methyl acceptors. NMTase activities were not detectable in comparable protein extracts of yeast, transformed with vector control. The NMTase protein sequence shared homology with plant caffeic acid O-methyltransferases and related enzymes. Phylogenetic analyses suggested that beta-Ala NMTase represents a novel family of N-methyltransferases that are evolutionarily related to O-methyltransferases.

Purification and properties of betaine aldehyde dehydrogenase from Avena sativa

Betaine aldehyde dehydrogenase (BADH; EC 1.2.1.8) is the enzyme that catalyzes the second step in the synthesis of the osmoprotectant, glycine betaine. NAD-dependent BADH was purified from Avena sativa shoots by DEAE Sephacel, hydroxyapatite, 5'-AMP Sepharose 4B, Mono Q and TSK-GEL column chromatographies to homogeneity by the criterion of native PAGE, and the properties of BADH were compared with those of aminoaldehyde dehydrogenase purified to homogeneity from A. sativa. The molecular mass estimated by both gel filtration using TSK-GEL column and Sephacryl S-200 was 120 and 115, kDa, respectively. The enzyme is a homodimer with a subunit molecular mass of 61 kDa as shown by SDS-PAGE. The pI value of the enzyme was found to be 6.3. The purified enzyme catalyzed not only the oxidation of betaine aldehyde (BAL), but also that of aminoaldehydes, 3-aminopropionaldehyde (APAL), 4-aminobutyraldehyde (ABAL), and 4-guanidinobutyraldehyde (GBAL). The K(m) values for BAL, APAL, ABAL and GBAL were 5x10(-6), 5.4x10(-7), 2.4x10(-5) and 5x10(-5) M, respectively. APAL showed substrate inhibition at a concentration of 0.1 mM. A fragment of BADH cleaved by V8 protease shared homology with other plant BADHs.

The metabolic architecture of plant cells. Stability of central metabolism and flexibility of anabolic pathways during the growth cycle of tomato cells

The changes in the intermediary metabolism of plant cells were quantified according to growth conditions at three different stages of the growth cycle of tomato cell suspension. Eighteen fluxes of central metabolism were calculated from (13)C enrichments after near steady-state labeling by a metabolic model similar to that described in Dieuaide-Noubhani et al. (Dieuaide-Noubhani, M., Raffard, G., Canioni, P., Pradet, A., and Raymond, P. (1995) J. Biol. Chem. 270, 13147-13159), and 10 net fluxes were obtained directly from end-product accumulation rates. The absolute flux values of central metabolic pathways gradually slowed down with the decrease of glucose influx into the cells. However, the relative fluxes of glycolysis, the pentose-P pathway, and the tricarboxylic acid cycle remained unchanged during the culture cycle at 70, 28, and 40% of glucose influx, respectively, and the futile cycle of sucrose remained high at about 6-fold the glucose influx, independently from carbon nutritional conditions. This natural resistance to flux alterations is referred to as metabolic stability. The numerous anabolic pathways, including starch synthesis, hexose accumulation, biosynthesis of wall polysaccharides, and amino and organic acid biosynthesis were comparatively low and variable. The phosphoenolpyruvate carboxylase flux decreased 5-fold in absolute terms and 2-fold in relation to the glucose influx rate during the culture cycle. We conclude that anabolic fluxes constitute the flexible part of plant cell metabolism that can fluctuate in relation to cell demands for growth.

Functional characterization of choline monooxygenase, an enzyme for betaine synthesis in plants

In plants, the first step in betaine synthesis was shown to be catalyzed by a novel Rieske-type iron-sulfur enzyme, choline monooxygenase (CMO). Although CMO so far has been found only in Chenopodiaceae and Amaranthaceae, the recent genome sequence suggests the presence of a CMO-like gene in Arabidopsis, a betaine non-accumulating plant. Here, we examined the functional properties of CMO expressed in Escherichia coli, cyanobacterium, and Arabidopsis thaliana. We found that E. coli cells in which choline dehydrogenase (CDH) was replaced with spinach CMO accumulate betaine and complement the salt-sensitive phenotype of the CDH-deleted E. coli mutant. Changes of Cys-181 in spinach CMO to Ser, Thr, and Ala and His-287 to Gly, Val, and Ala abolished the accumulation of betaine. The Arabidopsis CMO-like gene was transcribed in Arabidopsis, but its protein was not detected. When the Arabidopsis CMO-like gene was expressed in E. coli, the protein was detected but was found not to promote betaine sysnthesis. Overexpression of spinach CMO in E. coli, Synechococcus sp. PCC7942, and Arabidopsis conferred resistance to abiotic stress. These facts clearly indicate that CMO, but not the CMO-like protein, could oxidize choline and that Cys-181 and His-287 are involved in the binding of Fe-S cluster and Fe, respectively.

Glycerophosphocholine metabolism in higher plant cells. Evidence of a new glyceryl-phosphodiester phosphodiesterase

Glycerophosphocholine (GroPCho) is a diester that accumulates in different physiological processes leading to phospholipid remodeling. However, very little is known about its metabolism in higher plant cells. (31)P-Nuclear magnetic resonance spectroscopy and biochemical analyses performed on carrot (Daucus carota) cells fed with GroPCho revealed the existence of an extracellular GroPCho phosphodiesterase. This enzymatic activity splits GroPCho into sn-glycerol-3-phosphate and free choline. In vivo, sn-glycerol-3-phosphate is further hydrolyzed into glycerol and inorganic phosphate by acid phosphatase. We visualized the incorporation and the compartmentation of choline and observed that the major choline pool was phosphorylated and accumulated in the cytosol, whereas a minor fraction was incorporated in the vacuole as free choline. Isolation of plasma membranes, culture medium, and cell wall proteins enabled us to localize this phosphodiesterase activity on the cell wall. We also report the existence of an intracellular glycerophosphodiesterase. This second activity is localized in the vacuole and hydrolyzes GroPCho in a similar fashion to the cell wall phosphodiesterase. Both extra- and intracellular phosphodiesterases are widespread among different plant species and are often enhanced during phosphate deprivation. Finally, competition experiments on the extracellular phosphodiesterase suggested a specificity for glycerophosphodiesters (apparent K(m) of 50 microM), which distinguishes it from other phosphodiesterases previously described in the literature.

Enhancement of tolerance of abiotic stress by metabolic engineering of betaines and other compatible solutes

The accumulation of compatible solutes, such as betaines, proline and sugar alcohols, is a widespread response that may protect plants against environmental stress. It is not yet fully understood how these compounds are involved in the stress tolerance of whole plants. Some plants have been genetically engineered to express enzymes that catalyze the synthesis of various compatible solutes. Some interventions have increased the tolerance of some crop plants to abiotic stress. Furthermore, analysis of such transgenic plants has begun to clarify the roles of compatible solutes in stress tolerance.

Nuclear magnetic resonance and plant metabolic engineering

Nuclear magnetic resonance (NMR) can be used to measure metabolite levels and metabolic fluxes, to probe the intracellular environment, and to follow transport and energetics nondestructively. NMR methods are therefore powerful aids to understanding plant metabolism and physiology. Both spectroscopy and imaging can help overcome the unique challenges that plants present to the metabolic engineer by detecting, identifying, quantifying, and localizing novel metabolites in vivo and in extracts; revealing the composition and physical state of cell wall and other polymers; allowing the identification of active pathways; providing quantitative measures of metabolic flux; and testing hypotheses about the effects of engineered traits on plant physiological function. The aim of this review is to highlight recent studies in which NMR has contributed to metabolic engineering of plants and to illustrate the unique characteristics of NMR measurements that give it the potential to make greater contributions in the future.

Mathematical modeling of plant metabolic pathways

The understanding of the control of metabolic flux in plants requires integrated mathematical formulations of gene and protein expression, enzyme kinetics, and developmental biology. Plants have a large number of metabolically active compartments, and non-steady-state conditions are frequently encountered. Consequently steady-state metabolic flux balance and isotopic flux balance modeling approaches have limited utility in probing plant metabolic systems. Transient isotopic flux analysis and kinetic modeling are powerful proven techniques for the quantification of metabolic fluxes in compartmentalized, dynamic metabolic systems. These tools are now widely used to address metabolic flux responses to environmental and genetic perturbations in plant metabolism. Continued developments in isotopic and kinetic modeling, quantifying metabolite exchange between compartments, and transcriptional and posttranscriptional regulatory mechanisms governing enzyme level and activity will enable simulation of large sections of plant metabolism under non-steady-state conditions. Metabolic control analysis will continue to make substantial contributions to the understanding of quantitative distribution of control of flux. From the synergy between mathematical models and experiments, creative methods for controlling the distribution of flux by genetic or environmental means will be discovered and rationally implemented.

Metabolic engineering of osmoprotectant accumulation in plants

Drought and salinity are among the worst scourges of agriculture. One effective mechanism to reduce damage from these stresses is the accumulation of high intracellular levels of osmoprotectant compounds. These compounds include proline, ectoine, betaines, polyols, and trehalose and have evolved in many different organisms. Since some crop plants have low levels of these osmoprotectants or none at all, engineering osmoprotectant biosynthesis pathways is a potential way to improve stress tolerance. First-generation engineering work--much of it with single genes--has successfully introduced osmoprotectant pathways into plants that lack them naturally, and this has often improved stress tolerance. However, the engineered osmoprotectant levels are generally low and the increases in tolerance commensurately small. To get beyond trace levels of osmoprotectants and marginal tolerance increments we need to use flux measurements to diagnose what limits osmoprotectant levels in engineered plants and to use iterative cycles of engineering to overcome these limitations.

Information transfer in metabolic pathways. Effects of irreversible steps in computer models

Various metabolic models have been studied by computer simulation in an effort to understand why allowing for the reversibility of the reaction catalysed by pyruvate kinase, normally considered as irreversible for all practical purposes, significantly altered the behaviour of the model of glycolysis in Trypanosoma brucei [Eisenthal, R. & Cornish-Bowden, A. (1998) J. Biol. Chem. 273, 5500-5505]. Studies of several much simpler models indicate that the enzymes catalysing early steps in a pathway must receive information about the concentrations of the metabolites at the end of the pathway if a model is to be able to reach a steady state; treating all internal steps as reversible is just one way of ensuring this. Feedback inhibition provides a much better way, and as long as feedback loops are present in a model it makes almost no difference to the behaviour whether the intermediate steps with large equilibrium constants are treated as irreversible. In the absence of feedback loops, ordinary product inhibition of all the enzymes in the chain can also transfer information; this is efficient for regulating fluxes but very inefficient for regulating intermediate concentrations. More complicated patterns of regulation, such as activation of a competing branch or forcing flux through a parallel route, can also serve to some degree as ways of passing information around an irreversible step. However, they normally do so less efficiently than inhibition, because the extent to which an enzyme or a pathway can be activated always has an upper limit (which may be below what is required), whereas most enzymes are inhibited completely at saturating concentrations of inhibitor.