Molecular cloning and characterization of ATP-phosphoribosyl transferase from Arabidopsis, a key enzyme in the histidine biosynthetic pathway

Making watercress (Nasturtium officinale) cropping sustainable: genomic insights into enhanced phosphorus use efficiency in an aquatic crop

Watercress (Nasturtium officinale) is a nutrient-dense salad crop with high antioxidant capacity and glucosinolate concentration and with the potential to contribute to nutrient security as a locally grown outdoor aquatic crop in northern temperate climates. However, phosphate-based fertilizers used to support plant growth contribute to the eutrophication of aquatic habitats, often pristine chalk streams, downstream of farms, increasing pressure to minimize fertilizer use and develop a more phosphorus-use efficient (PUE) crop. Here, we grew genetically distinct watercress lines selected from a bi-parental mapping population on a commercial watercress farm either without additional phosphorus (P-) or under a commercial phosphate-based fertilizer regime (P+), to decipher effects on morphology, nutritional profile, and the transcriptome. Watercress plants sustained shoot yield in P- conditions, through enhanced root biomass, but with shorter stems and smaller leaves. Glucosinolate concentration was not affected by P- conditions, but both antioxidant capacity and the concentration of sugars and starch in shoot tissue were enhanced. We identified two watercress breeding lines, with contrasting strategies for enhanced PUE: line 60, with highly plastic root systems and increased root growth in P-, and line 102, maintaining high yield irrespective of P supply, but less plastic. RNA-seq analysis revealed a suite of genes involved in cell membrane remodeling, root development, suberization, and phosphate transport as potential future breeding targets for enhanced PUE. We identified watercress gene targets for enhanced PUE for future biotechnological and breeding approaches enabling less fertilizer inputs and reduced environmental damage from watercress cultivation.

Competition co-immunoprecipitation reveals the interactors of the chloroplast CPN60 chaperonin machinery

The functionality of all metabolic processes in chloroplasts depends on a balanced integration of nuclear- and chloroplast-encoded polypeptides into the plastid's proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding under ambient and stressful conditions, with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin of Escherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of very limited knowledge about the interactors. We employed the competition immunoprecipitation method for the identification of the chaperonin's interactors in Chlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL and the expected complex partners, we revealed numerous new interactors with high confidence. Proteins that qualify as putative substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical conformation and increased aggregation propensity. Immunoprecipitations targeted against a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.

Biochemical investigation of the tryptophan biosynthetic enzyme anthranilate phosphoribosyltransferase in plants

While mammals require the essential amino acid tryptophan (Trp) in their diet, plants and microorganisms synthesize Trp de novo. The five-step Trp pathway starts with the shikimate pathway product, chorismate. Chorismate is converted to the aromatic compound anthranilate, which is then conjugated to a phosphoribosyl sugar in the second step by anthranilate phosphoribosyltransferase (PAT1). As a single-copy gene in plants, all fixed carbon flux to indole and Trp for protein synthesis, specialized metabolism, and auxin hormone biosynthesis proceeds through PAT1. While bacterial PAT1s have been studied extensively, plant PAT1s have escaped biochemical characterization. Using a structure model, we identified putative active site residues that were variable across plants and kinetically characterized six PAT1s (Arabidopsis thaliana (thale cress), Citrus sinensis (sweet orange), Pistacia vera (pistachio), Juglans regia (English walnut), Selaginella moellendorffii (spike moss), and Physcomitrium patens (spreading earth-moss)). We probed the catalytic efficiency, substrate promiscuity, and regulation of these six enzymes and found that the C. sinensis PAT1 is highly specific for its cognate substrate, anthranilate. Investigations of site-directed mutants of the A. thaliana PAT1 uncovered an active site residue that contributes to promiscuity. While Trp inhibits bacterial PAT1 enzymes, the six plant PAT1s that we tested were not modulated by Trp. Instead, the P. patens PAT1 was inhibited by tyrosine, and the S. moellendorffii PAT1 was inhibited by phenylalanine. This structure-informed biochemical examination identified variations in activity, efficiency, specificity, and enzyme-level regulation across PAT1s from evolutionarily diverse plants.

Phosphoribosyltransferases and Their Roles in Plant Development and Abiotic Stress Response

Glycosylation is a widespread glycosyl modification that regulates gene expression and metabolite bioactivity in all life processes of plants. Phosphoribosylation is a special glycosyl modification catalyzed by phosphoribosyltransferase (PRTase), which functions as a key step in the biosynthesis pathway of purine and pyrimidine nucleotides, histidine, tryptophan, and coenzyme NAD(P)⁺ to control the production of these essential metabolites. Studies in the past decades have reported that PRTases are indispensable for plant survival and thriving, whereas the complicated physiological role of PRTases in plant life and their crosstalk is not well understood. Here, we comprehensively overview and critically discuss the recent findings on PRTases, including their classification, as well as the function and crosstalk in regulating plant development, abiotic stress response, and the balance of growth and stress responses. This review aims to increase the understanding of the role of plant PRTase and also contribute to future research on the trade-off between plant growth and stress response.

Transcriptome and protein networks to elucidate the mechanism underlying nitrite degradation by Lactiplantibacillus plantarum

Excessive nitrite residue is one of the bottlenecks in the production of many fermented foods. Lactiplantibacillus plantarum PK25 obtained from traditional Chinese pickles exhibited excellent nitrite degradation ability. Here, transcriptome, protein-protein interaction networks, and phenotype were performed to evaluate systematically the mechanism of nitrite degradation of L. plantarum PK25. The results demonstrated that genes expression varied considerably at key time points for nitrite degradation. 553 (upregulated: 366, downregulated: 187) and 767 (upregulated: 425, downregulated: 342) differentially expressed genes were identified at 6 h and 24 h, respectively. The hub genes were mainly enriched in carbohydrate metabolism, energy metabolism, and nucleotide synthesis. PK25 expanded its carbon source utilizing profile and improved glycolysis to produce more ATP to counteract environmental stress. The related enzymes including glycoside hydrolase, sugar ABC transporter protein, and PTS sugar transporter were 5.714, 5.885, and 3.578-fold upregulated at the transcriptional level. For strain to sustain energy levels and acid generation, pyruvate metabolism was critical, with the result that phosphoenolpyruvate synthase and pyruvate oxidase were up-regulated to accelerate the pyruvate transition. To repair DNA lesions induced by nitrite, both base excision repair mechanism and recombinational DNA repair pathway were exploited, such as endodeoxyribonuclease upregulated 5.314 and 19.687-fold at the two moments. The results provided a theoretical reference and practical possibility to reduce nitrite residue and improve safety during food fermented products.

Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration

Multidrug-resistant pathogens constitute a serious global issue and, therefore, novel antimicrobials with new modes of action are urgently needed. Here, we investigated the effect of a phenothiazine derivative (JBC 1847) with high antimicrobial activity on Staphylococcus aureus, using a wide range of in vitro assays, flow cytometry, and RNA transcriptomics. The flow cytometry results showed that JBC 1847 rapidly caused depolarization of the cell membrane, while the macromolecule synthesis inhibition assay showed that the synthesis rates of DNA, RNA, cell wall, and proteins, respectively, were strongly decreased. Transcriptome analysis of S. aureus exposed to sub-inhibitory concentrations of JBC 1847 identified a total of 78 downregulated genes, whereas not a single gene was found to be significantly upregulated. Most importantly, there was downregulation of genes involved in adenosintrifosfat (ATP)-dependent pathways, including histidine biosynthesis, which is likely to correlate with the observed lower level of intracellular ATP in JBC 1847-treated cells. Furthermore, we showed that JBC 1847 is bactericidal against both exponentially growing cells and cells in a stationary growth phase. In conclusion, our results showed that the antimicrobial properties of JBC 1847 were primarily caused by depolarization of the cell membrane resulting in dissipation of the proton motive force (PMF), whereby many essential bacterial processes are affected. JBC 1847 resulted in lowered intracellular levels of ATP followed by decreased macromolecule synthesis rate and downregulation of genes essential for the amino acid metabolism in S. aureus. Bacterial compensatory mechanisms for this proposed multi-target activity of JBC 1847 seem to be limited based on the observed very low frequency of resistance toward the compound.

Low-molecular-weight ligands in plants: role in metal homeostasis and hyperaccumulation

Mineral nutrition is one of the key factors determining plant productivity. In plants, metal homeostasis is achieved through the functioning of a complex system governing metal uptake, translocation, distribution, and sequestration, leading to the maintenance of a regulated delivery of micronutrients to metal-requiring processes as well as detoxification of excess or non-essential metals. Low-molecular-weight ligands, such as nicotianamine, histidine, phytochelatins, phytosiderophores, and organic acids, play an important role in metal transport and detoxification in plants. Nicotianamine and histidine are also involved in metal hyperaccumulation, which determines the ability of some plant species to accumulate a large amount of metals in their shoots. In this review we extensively summarize and discuss the current knowledge of the main pathways for the biosynthesis of these ligands, their involvement in metal uptake, radial and long-distance transport, as well as metal influx, isolation and sequestration in plant tissues and cell compartments. It is analyzed how diverse endogenous ligand levels in plants can determine their different tolerance to metal toxic effects. This review focuses on recent advances in understanding the physiological role of these compounds in metal homeostasis, which is an essential task of modern ionomics and plant physiology. It is of key importance in studying the influence of metal deficiency or excess on various physiological processes, which is a prerequisite to the improvement of micronutrient uptake efficiency and crop productivity and to the development of a variety of applications in phytoremediation, phytomining, biofortification, and nutritional crop safety.

Nitrate-responsive NIN-like protein transcription factors perform unique and redundant roles in Arabidopsis

Upon sensing nitrate, NODULE INCEPTION (NIN)-like protein (NLP) transcription factors alter gene expression to promote nitrate uptake and utilization. Of the nine NLPs in Arabidopsis, the physiological roles of only three NLPs (NLP6-NLP8) have been characterized to date. To evaluate the unique and redundant roles of Arabidopsis NLPs, we assessed the phenotypes of single and higher order nlp mutants. Unlike other nlp single mutants, nlp2 and nlp7 single mutants showed a reduction in shoot fresh weight when grown in the presence of nitrate as the sole nitrogen source, indicating that NLP2, like NLP7, plays a major role in vegetative growth. Interestingly, the growth defect of nlp7 recovered upon the supply of ammonium or glutamine, whereas that of nlp2 did not. Furthermore, complementation assays using chimeric constructs revealed that the coding sequence, but not the promoter region, of NLP genes was responsible for the differences between nlp2 and nlp7 single mutant phenotypes, suggesting differences in protein function. Importantly, nitrate utilization was almost completely abolished in the nlp septuple mutant (nlp2 nlp4 nlp5 nlp6 nlp7 nlp8 nlp9), suggesting that NLPs other than NLP2 and NLP7 also assist in the regulation of nitrate-inducible gene expression and nitrate-dependent promotion of vegetative growth in Arabidopsis.

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme–HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively. The calculated sequence similarity networks between HISN2 analogs from prokaryotes and eukaryotes suggest that the plant enzymes are closest relatives of those in the class of Deltaproteobacteria. In this work, we obtained crystal structures of HISN2 enzyme from Medicago truncatula (MtHISN2) and described its architecture and interactions with AMP. The AMP molecule bound to the PRA-PH domain shows positioning of the N1-phosphoribosyl relevant to catalysis. AMP bound to the PRA-CH domain mimics a part of the substrate, giving insights into the reaction mechanism. The latter interaction also arises as a possible second-tier regulatory mechanism of the HBP flux, as indicated by inhibition assays and isothermal titration calorimetry.

Metabolic and physiological responses to progressive drought stress in bread wheat

Wheat (Tritium aestivum) is vulnerable to future climate change because it is predominantly grown under rain-fed conditions in drought-prone areas. Thus, in-depth understanding of drought effect on wheat metabolism is essential for developing drought-tolerant wheat varieties. Here, we exposed wheat 'Norin 61' plants to progressive drought stress [0 (before drought), 2, 4, 6, 8, and 10 days after withholding water] during the flowering stage to investigate physiological and metabolomic responses. Transcriptional analyses of key abscisic acid-responsive genes indicated that abscisic acid signalling played a major role in the adaptation of wheat to water deficit. Carbon isotope composition had a higher value than the control while canopy temperature (CT) increased under drought stress. The CT depression was tightly correlated with soil water potential (SWP). Additionally, SWP at - 517 kPa was identified as the critical point for increasing CT and inducing reactive oxygen species. Metabolome analysis identified four potential drought-responsive biomarkers, the enhancement of nitrogen recycling through purine and pyrimidine metabolism, drought-induced senescence based on 1-aminocyclopropane-1-carboxylic acid and Asn accumulation, and an anti-senescence response through serotonin accumulation under severe drought stress. Our findings provide in-depth insight into molecular, physiological and metabolite changes involved in drought response which are useful for wheat breeding programs to develop drought-tolerant wheat varieties.

Dynamic resource allocation drives growth under nitrogen starvation in eukaryotes

Cells can sense changes in their extracellular environment and subsequently adapt their biomass composition. Nutrient abundance defines the capability of the cell to produce biomass components. Under nutrient-limited conditions, resource allocation dramatically shifts to carbon-rich molecules. Here, we used dynamic biomass composition data to predict changes in growth and reaction flux distributions using the available genome-scale metabolic models of five eukaryotic organisms (three heterotrophs and two phototrophs). We identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion. Surprisingly, our calculations of model sensitivity and biosynthetic cost showed that free energy of biomass metabolites is the main driver of biosynthetic cost and not molecular weight, thus explaining the high costs of arginine and histidine. We demonstrated how metabolic models can accurately predict the complexity of interwoven mechanisms in response to stress over the course of growth.

Guarding the gateway to histidine biosynthesis in plants: Medicago truncatula ATP-phosphoribosyltransferase in relaxed and tense states

In the first committed step of histidine biosynthesis, adenosine 5'-triphosphate (ATP) and 5-phosphoribosyl-α1-pyrophosphate (PRPP), in the presence of ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17), yield phosphoribosyl-ATP. ATP-PRTs are subject to feedback inhibition by histidine that allosterically binds between the regulatory domains. Histidine biosynthetic pathways of bacteria, lower eukaryotes, and plants are considered promising targets for the design of antibiotics, antifungal agents, and herbicides because higher organisms are histidine heterotrophs. Plant ATP-PRTs are similar to one of the two types of their bacterial counterparts, the long-type ATP-PRTs. A biochemical and structural study of ATP-PRT from the model legume plant, Medicago truncatula (MedtrATP-PRT1) is reported herein. Two crystal structures, presenting homohexameric MedtrATP-PRT1 in its relaxed (R-) and histidine-bound, tense (T-) states allowed to observe key features of the enzyme and provided the first structural insights into an ATP-PRT from a eukaryotic organism. In particular, they show pronounced conformational reorganizations during R-state to T-state transition that involves substantial movements of domains. This rearrangement requires a trans- to cis- switch of a peptide backbone within the hinge region of MedtrATP-PRT1. A C-terminal α-helix, absent in bacteria, reinforces the hinge that is constituted by two peptide strands. As a result, conformations of the R- and T-states are significantly different from the corresponding states of prokaryotic enzymes with known 3-D structures. Finally, adenosine 5'-monophosphate (AMP) bound at the active site is consistent with a competitive (and synergistic with histidine) nature of AMP inhibition.

Histidine Regulates Seed Oil Deposition through Abscisic Acid Biosynthesis and β-Oxidation

The storage compounds are deposited into plant seeds during maturation. As the model oilseed species, Arabidopsis (Arabidopsis thaliana) has long been studied for seed oil deposition. However, the regulation of this process remains unclear. Through genetic screen with a seed oil body-specific reporter, we isolated low oil1 (loo1) mutant. LOO1 was mapped to HISTIDINE BIOSYNTHESIS NUMBER 1A (HISN1A). HISN1A catalyzes the first step of His biosynthesis. Oil significantly decreased, and conversely proteins markedly increased in hisn1a mutants, indicating that HISN1A regulates both oil accumulation and the oil-protein balance. HISN1A was predominantly expressed in embryos and root tips. Accordingly, the hisn1a mutants exhibited developmental phenotype especially of seeds and roots. Transcriptional profiling displayed that β-oxidation was the major metabolic pathway downstream of HISN1A β-Oxidation was induced in hisn1a mutants, whereas it was reduced in 35S:HISN1A-transgenic plants. In plants, seed storage oil is broken-down by β-oxidation, which is controlled by abscisic acid (ABA). We found that His activated genes of ABA biosynthesis and correspondingly advanced ABA accumulation. Exogenous ABA rescued the defects of hisn1a mutants, whereas mutation of ABA DEFICIENT2, a key enzyme in ABA biosynthesis, blocked the effect of His on β-oxidation, indicating that ABA mediates His regulation in β-oxidation. Intriguingly, structural analysis showed that a potential His-binding domain was present in the general amino acid sensors GENERAL CONTROL NON-DEREPRESSIBLE2 and PII, suggesting that His may serve as a signal molecule. Taken together, our study reveals that His promotes plant seed oil deposition through ABA biosynthesis and β-oxidation.

Campylobacter jejuni adenosine triphosphate phosphoribosyltransferase is an active hexamer that is allosterically controlled by the twisting of a regulatory tail

Adenosine triphosphate phosphoribosyltransferase (ATP-PRT) catalyzes the first committed step of the histidine biosynthesis in plants and microorganisms. Here, we present the functional and structural characterization of the ATP-PRT from the pathogenic ε-proteobacteria Campylobacter jejuni (CjeATP-PRT). This enzyme is a member of the long form (HisGL ) ATP-PRT and is allosterically inhibited by histidine, which binds to a remote regulatory domain, and competitively inhibited by AMP. In the crystalline form, CjeATP-PRT was found to adopt two distinctly different hexameric conformations, with an open homohexameric structure observed in the presence of substrate ATP, and a more compact closed form present when inhibitor histidine is bound. CjeATP-PRT was observed to adopt only a hexameric quaternary structure in solution, contradicting previous hypotheses favoring an allosteric mechanism driven by an oligomer equilibrium. Instead, this study supports the conclusion that the ATP-PRT long form hexamer is the active species; the tightening of this structure in response to remote histidine binding results in an inhibited enzyme.

The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants

Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.

Proteome Analysis of Poplar Seed Vigor

Seed vigor is a complex property that determines the seed’s potential for rapid uniform emergence and subsequent growth. However, the mechanism for change in seed vigor is poorly understood. The seeds of poplar (Populus × Canadensis Moench), which are short-lived, were stored at 30°C and 75±5% relative humidity for different periods of time (0–90 days) to obtain different vigor seeds (from 95 to 0% germination). With decreasing seed vigor, the temperature range of seed germination became narrower; the respiration rate of the seeds decreased markedly, while the relative electrolyte leakage increased markedly, both levelling off after 45 days. A total of 81 protein spots showed a significant change in abundance (≥ 1.5-fold, P < 0.05) when comparing the proteomes among seeds with different vigor. Of the identified 65 proteins, most belonged to the groups involved in metabolism (23%), protein synthesis and destination (22%), energy (18%), cell defense and rescue (17%), and storage protein (15%). These proteins accounted for 95% of all the identified proteins. During seed aging, 53 and 6 identified proteins consistently increased and decreased in abundance, respectively, and they were associated with metabolism (22%), protein synthesis and destination (22%), energy (19%), cell defense and rescue (19%), storage proteins (15%), and cell growth and structure (3%). These data show that the decrease in seed vigor (aging) is an energy-dependent process, which requires protein synthesis and degradation as well as cellular defense and rescue.

HISN3 mediates adaptive response of Chlamydomonas reinhardtii to excess nickel

Investigation of genes for heavy metal [e.g. nickel (Ni) and zinc (Zn)] absorption and detoxification in green algae is of great importance because some of the metals have become one of the major contaminants in the aquatic ecosystem. In plants, overload of heavy metals modifies many aspects of biological processes. However, the mechanisms by which heavy metals exert detrimental effects are not fully understood. The present study identified a biological role for HISN3 (the gene coding for phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide isomerase) in regulating the response of Chlamydomonas reinhardtii, a unicellular green alga, to Ni toxicity. In higher plants, HISN3 encodes an enzyme catalyzing the fourth step in the histidine biosynthesis pathway, but its functional importance is yet to be identified. Transgenic algae overexpressing HISN3 in C. reinhardtii showed high tolerance to excess Ni, with a 48.3-57.4% increase in cell population and moderate histidine accumulation compared with the wild type. HISN3 overexpression improved accumulation of Chl and photosynthesis efficiency, but suppressed Ni-induced generation of reactive oxygen species and lipid peroxides. Interestingly, more Ni and other metals [Zn, iron (Fe), copper (Cu), manganese (Mn) and magnesium (Mg)] were accumulated in HISN3-overexpressing cells than in the wild type. In contrast, RNA interference of HISN3 depressed Ni accumulation but caused cellular sensitivity to Ni. The elevated metal absorption in the HISN3-overexpressing algae implies that the metals can be removed from water media. Thus, our work presents an example for algae genetically designed to improve tolerance to metal toxicity and environmental restoration of metal-contaminated aquatic ecosystems.

Histidine biosynthesis

Histidine (His) is one of the standard amino acids in proteins, and plays a critical role in plant growth and development. The chemical properties of the imidazole side group allow His to participate in acid-base catalysis, and in the co-ordination of metal ions. Despite the biological importance of this molecule, His biosynthesis has been somewhat neglected in plants, in stark contrast to micro-organisms where the study of this pathway was fundamental in the discovery of operon structure and regulation by attenuation. With the recent isolation of histidinol-phosphate phosphatase, all the enzymes of His biosynthesis have now been identified in Arabidopsis, and several lines of evidence have implicated ATP-phosphoribosyl transferase (which catalyses the first committed step of the pathway) as playing an important role in the regulation of this pathway. However, little is known about the transcriptional regulation of the His biosynthetic genes, nor how demand for this amino acid is balanced with other metabolic requirements in plants. Similarly, the pathway of His catabolism has yet to be determined.

The missing link in plant histidine biosynthesis: Arabidopsis myoinositol monophosphatase-like2 encodes a functional histidinol-phosphate phosphatase

Histidine (His) plays a critical role in plant growth and development, both as one of the standard amino acids in proteins, and as a metal-binding ligand. While genes encoding seven of the eight enzymes in the pathway of His biosynthesis have been characterized from a number of plant species, the identity of the enzyme catalyzing the dephosphorylation of histidinol-phosphate to histidinol has remained elusive. Recently, members of a novel family of histidinol-phosphate phosphatase proteins, displaying significant sequence similarity to known myoinositol monophosphatases (IMPs) have been identified from several Actinobacteria. Here we demonstrate that a member of the IMP family from Arabidopsis (Arabidopsis thaliana), myoinositol monophosphatase-like2 (IMPL2; encoded by At4g39120), has histidinol-phosphate phosphatase activity. Heterologous expression of IMPL2, but not the related IMPL1 protein, was sufficient to rescue the His auxotrophy of a Streptomyces coelicolor hisN mutant. Homozygous null impl2 Arabidopsis mutants displayed embryonic lethality, which could be rescued by supplying plants heterozygous for null impl2 alleles with His. In common with the previously characterized HISN genes from Arabidopsis, IMPL2 was expressed in all plant tissues and throughout development, and an IMPL2:green fluorescent protein fusion protein was targeted to the plastid, where His biosynthesis occurs in plants. Our data demonstrate that IMPL2 is the HISN7 gene product, and suggest a lack of genetic redundancy at this metabolic step in Arabidopsis, which is characteristic of the His biosynthetic pathway.

Relative contributions of nine genes in the pathway of histidine biosynthesis to the control of free histidine concentrations in Arabidopsis thaliana

Despite the functional importance of histidine (His) as an essential amino acid in proteins and as a metal-coordinating ligand, comparatively little is known about the regulation of its biosynthesis in plants and the potential for metabolic engineering of this pathway. To investigate the contribution of different steps in the pathway to overall control of His biosynthesis, nine His biosynthetic genes were individually over-expressed in Arabidopsis thaliana to determine their effects on free amino acid pools. Constitutive, CaMV 35S-driven over-expression of the cDNAs encoding either isoform of ATP-phosphoribosyltransferase (ATP-PRT), the first enzyme in the pathway, was sufficient to increase the pool of free His by up to 42-fold in shoot tissue of Arabidopsis, with negligible effect on any other amino acid. In contrast, over-expression of cDNAs for seven other enzymes in the biosynthetic pathway had no effect on His content, suggesting that control of the pool of free His resides largely with ATP-PRT activity. Over-expression of ATP-PRT and increased His content had a negative pleiotropic effect on plant biomass production in 35S:PRT1 lines, but this effect was not observed in 35S:PRT2 lines. In the presence of 100 microM Ni, which was inhibitory to wild-type plants, a strong positive correlation was observed between free His content and biomass production, indicating that the metabolic cost of His overproduction was outweighed by the benefit of increased tolerance to Ni. His-overproducing plants also displayed somewhat elevated tolerance to Co and Zn, but not to Cd or Cu, indicating chemical selectivity in intracellular metal binding by His.

CYP710A genes encoding sterol C22-desaturase in Physcomitrella patens as molecular evidence for the evolutionary conservation of a sterol biosynthetic pathway in plants

We have characterized cytochromes P450, CYP710A13, and CYP710A14, as the sterol C22-desaturase in the moss Physcomitrella patens. GC-MS analyses demonstrated that P. patens accumulated stigmasterol as the major sterol (56-60% of total sterol) and sitosterol to a lesser extent (8-12%); this sterol profile contrasts with those in higher plants accumulating stigmasterol as a minor component. Recombinant CYP710A13 and CYP710A14 proteins prepared using a baculovirus/insect cell system exhibited the C22-desaturase activity with beta-sitosterol to produce stigmasterol, while campesterol and 24-epi-campesterol were not accepted as the substrates. The K(m) values for beta-sitosterol of CYP710A13 (1.0 +/- 0.043 microM) and CYP710A14 (2.1 +/- 0.17 microM) were at comparable levels of those reported with higher plant CYP710A proteins. In Arabidopsis T87 cells over-expressing CYP710A14, stigmasterol contents reached a level 20- to 72-fold higher than those in the basal level of T87 cells, confirming the C22-desaturase activity of this P450 enzyme. The occurrence of the end-products together with the enzymes involved in the last step of the pathway substantiated the presence of an entire sterol biosynthetic pathway in P. patens, providing evidence for the conservation of the sterol biosynthetic pathway through the evolutionary process of land plants.

Genetic dissection of histidine biosynthesis in Arabidopsis

The biosynthesis of histidine (His) in microorganisms, long studied through the isolation and characterization of auxotrophic mutants, has emerged as a paradigm for the regulation of metabolism and gene expression. Much less is known about His biosynthesis in flowering plants. One limiting factor has been the absence of large collections of informative auxotrophs. We describe here the results of a systematic screen for His auxotrophs of Arabidopsis (Arabidopsis thaliana). Ten insertion mutants disrupted in four different biosynthetic genes (HISN2, HISN3, HISN4, HISN6A) were identified through a combination of forward and reverse genetics and were shown to exhibit an embryo-defective phenotype that could be rescued by watering heterozygous plants with His. Male transmission of the mutant allele was in several cases reduced. Knockouts of two redundant genes (HISN1B and HISN5A) had no visible phenotype. Another mutant blocked in the final step of His biosynthesis (hisn8) and a double mutant altered in the redundant first step of the pathway (hisn1a hisn1b) exhibited a combination of gametophytic and embryonic lethality in heterozygotes. Homozygous mutant seedlings and callus tissue produced from rescued seeds appeared normal when grown in the presence of His but typically senesced after continued growth in the absence of His. These knockout mutants document the importance of His biosynthesis for plant growth and development, provide valuable insights into amino acid transport and source-sink relationships during seed development, and represent a significant addition to the limited collection of well-characterized auxotrophs in flowering plants.

Substrate recognition by the hetero-octameric ATP phosphoribosyltransferase from Lactococcus lactis

Two families of ATP phosphoribosyl transferases (ATP-PRT) join ATP and 5-phosphoribosyl-1 pyrophosphate (PRPP) in the first reaction of histidine biosynthesis. These consist of a homohexameric form found in all three kingdoms and a hetero-octameric form largely restricted to bacteria. Hetero-octameric ATP-PRTs consist of four HisGS catalytic subunits related to periplasmic binding proteins and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. To clarify the relationship between the two families of ATP-PRTs and among phosphoribosyltransferases in general, we determined the steady state kinetics for the hetero-octameric form and characterized the active site by mutagenesis. The KmPRPP (18.4 +/- 3.5 microM) and kcat (2.7 +/- 0.3 s-1) values for the PRPP substrate are similar to those of hexameric ATP-PRTs, but the Km for ATP (2.7 +/- 0.3 mM) is 4-fold higher, suggestive of tighter regulation by energy charge. Histidine and AMP were determined to be noncompetitive (Ki = 81.1 microM) and competitive (Ki = 1.44 mM) inhibitors, respectively, with values that approximate their intracellular concentrations. Mutagenesis experiments aimed at investigating the side chains recognizing PRPP showed that 5'-phosphate contacts (T159A and T162A) had the largest (25- and 155-fold, respectively) decreases in kcat/Km, while smaller decreases were seen with mutants making cross subunit contacts (K50A and K8A) to the pyrophosphate moiety or contacts to the 2'-OH group. Despite their markedly different quaternary structures, hexameric and hetero-octameric ATRP-PRTs exhibit similar functional parameters and employ mechanistic strategies reminiscent of the broader PRT superfamily.

Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum)

PPi has previously been implicated specifically in the co-ordination of the sucrose-starch transition and in the broader context of its role as co-factor in heterotrophic plant metabolism. In order to assess the compartmentation of pyrophosphate (PPi) metabolism in the potato tuber we analysed the effect of expressing a bacterial pyrophosphatase in the amyloplast of wild type tubers or in the cytosol or amyloplast of invertase-expressing tubers. The second and third approaches were adopted since we have previously characterized the invertase expressing lines to both exhibit highly altered sucrose metabolism and to contain elevated levels of PPi (Farré et al. (2000a) Plant Physiol 123:681) and therefore this background rendered questions concerning the level of communication between the plastidic and cytosolic pyrophosphate pools relatively facile. In this study we observed that the increase in PPi in the invertase expressing lines was mainly confined to the cytosol. Accordingly, the expression of a bacterial pyrophosphatase in the plastid of either wild type or invertase-expressing tubers did not lead to a decrease in total PPi content. However, the expression of the heterologous pyrophosphatase in the cytosol of cytosolic invertase-expressing tubers led to strong metabolic changes. These results are discussed both with respect to our previous hypotheses and to current models of the compartmentation of potato tuber metabolism.

Subcellular pyrophosphate metabolism in developing tubers of potato (Solanum tuberosum)

PPi has previously been implicated specifically in the co-ordination of the sucrose-starch transition and in the broader context of its role as co-factor in heterotrophic plant metabolism. In order to assess the compartmentation of pyrophosphate (PPi) metabolism in the potato tuber we analysed the effect of expressing a bacterial pyrophosphatase in the amyloplast of wild type tubers or in the cytosol or amyloplast of invertase-expressing tubers. The second and third approaches were adopted since we have previously characterized the invertase expressing lines to both exhibit highly altered sucrose metabolism and to contain elevated levels of PPi (Farré et al. (2000a) Plant Physiol 123:681) and therefore this background rendered questions concerning the level of communication between the plastidic and cytosolic pyrophosphate pools relatively facile. In this study we observed that the increase in PPi in the invertase expressing lines was mainly confined to the cytosol. Accordingly, the expression of a bacterial pyrophosphatase in the plastid of either wild type or invertase-expressing tubers did not lead to a decrease in total PPi content. However, the expression of the heterologous pyrophosphatase in the cytosol of cytosolic invertase-expressing tubers led to strong metabolic changes. These results are discussed both with respect to our previous hypotheses and to current models of the compartmentation of potato tuber metabolism.

Histidine biosynthesis in plants

The study of histidine metabolism has never been at the forefront of interest in plant systems despite the significant role that the analysis of this pathway has played in development of the field of molecular genetics in microbes. With the advent of methods to analyze plant gene function by complementation of microbial auxotrophic mutants and the complete analysis of plant genome sequences, strides have been made in deciphering the histidine pathway in plants. The studies point to a complex evolutionary origin of genes for histidine biosynthesis. Gene regulation studies have indicated novel regulatory networks involving histidine. In addition, physiological studies have indicated novel functions for histidine in plants as chelators and transporters of metal ions. Recent investigations have revealed intriguing connections of histidine in plant reproduction. The exciting new information suggests that the study of plant histidine biosynthesis has finally begun to flower.

ALBINO AND PALE GREEN 10 Encodes BBMII Isomerase Involved in Histidine Biosynthesis in Arabidopsis thaliana

We isolated an Arabidopsis albino and pale green 10 (apg10) mutant which exhibits pale green cotyledons and true leaves at the juvenile stage. We identified a valine to leucine change in BBMII (N'-[(5'-phosphoribosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide) isomerase involved in histidine biosynthesis. The morphological abnormality of apg10 was recovered by histidine supplementation. The histidine limitation induced by apg10 mutation causes dynamic changes of the free amino acid profile, suggesting the existence of a cross-pathway regulatory mechanism of amino acid biosynthesis in plants. We also revealed that the APG10 knockout mutant exhibited embryo lethality, indicating the essential role of the Arabidopsis BBMII isomerase for plant growth.

Constitutively high expression of the histidine biosynthetic pathway contributes to nickel tolerance in hyperaccumulator plants

Plants that hyperaccumulate Ni exhibit an exceptional degree of Ni tolerance and the ability to translocate Ni in large amounts from root to shoot. In hyperaccumulator plants in the genus Alyssum, free His is an important Ni binding ligand that increases in the xylem proportionately to root Ni uptake. To determine the molecular basis of the His response and its contribution to Ni tolerance, transcripts representing seven of the eight enzymes involved in His biosynthesis were investigated in the hyperaccumulator species Alyssum lesbiacum by RNA gel blot analysis. None of the transcripts changed in abundance in either root or shoot tissue when plants were exposed to Ni, but transcript levels were constitutively higher in A. lesbiacum than in the congeneric nonaccumulator A. montanum, especially for the first enzyme in the biosynthetic pathway, ATP-phosphoribosyltransferase (ATP-PRT). Comparison with the weak hyperaccumulator A. serpyllifolium revealed a close correlation between Ni tolerance, root His concentration, and ATP-PRT transcript abundance. Overexpression of an A. lesbiacum ATP-PRT cDNA in transgenic Arabidopsis thaliana increased the pool of free His up to 15-fold in shoot tissue, without affecting the concentration of any other amino acid. His-overproducing lines also displayed elevated tolerance to Ni but did not exhibit increased Ni concentrations in either xylem sap or shoot tissue, suggesting that additional factors are necessary to recapitulate the complete hyperaccumulator phenotype. These results suggest that ATP-PRT expression plays a major role in regulating the pool of free His and contributes to the exceptional Ni tolerance of hyperaccumulator Alyssum species.

Enhancing the first enzymatic step in the histidine biosynthesis pathway increases the free histidine pool and nickel tolerance inArabidopsis thaliana

Naturally selected nickel (Ni) tolerance in Alyssum lesbiacum has been proposed to involve constitutively high levels of endogenous free histidine. Transgenic Arabidopsis thaliana expressing a Salmonella typhimurium ATP phosphoribosyl transferase enzyme (StHisG) resistant to feedback inhibition by histidine contained approximately 2-fold higher histidine concentrations than wild type plants. Under exposure to a toxic Ni concentration, biomass production in StHisG expressing lines was between 14- and 40-fold higher than in wild-type plants. This suggested that enhancing the first step in the histidine biosynthesis pathway is sufficient to increase the endogenous free histidine pool and Ni tolerance in A. thaliana.

A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos

Developing oilseeds synthesize large quantities of triacylglycerol from sucrose and hexose. To understand the fluxes involved in this conversion, a quantitative metabolic flux model was developed and tested for the reaction network of glycolysis and the oxidative pentose phosphate pathway (OPPP). Developing Brassica napus embryos were cultured with [U-13C6]glucose, [1-13C]glucose, [6-13C]glucose, [U-13C12]sucrose, and/or [1,2-13C2]glucose and the labeling patterns in amino acids, lipids, sucrose, and starch were measured by gas chromatography/mass spectrometry and NMR. Data were used to verify a reaction network of central carbon metabolism distributed between the cytosol and plastid. Computer simulation of the steady state distribution of isotopomers in intermediates of the glycolysis/OPPP network was used to fit metabolic flux parameters to the experimental data. The observed distribution of label in cytosolic and plastidic metabolites indicated that key intermediates of glycolysis and OPPP have similar labeling in these two compartments, suggesting rapid exchange of metabolites between these compartments compared with net fluxes into end products. Cycling between hexose phosphate and triose phosphate and reversible transketolase velocity were similar to net glycolytic flux, whereas reversible transaldolase velocity was minimal. Flux parameters were overdetermined by analyzing labeling in different metabolites and by using data from different labeling experiments, which increased the reliability of the findings. Net flux of glucose through the OPPP accounts for close to 10% of the total hexose influx into the embryo. Therefore, the reductant produced by the OPPP accounts for at most 44% of the NADPH and 22% of total reductant needed for fatty acid synthesis.

Molecular characterization and expression study of a histidine auxotrophic mutant (his1-) of Nicotiana plumbaginifolia

The histidine auxotroph mutant his 1(-) isolated from Nicotiana plumbaginifolia haploid protoplasts was first characterized to be deficient for the enzyme histidinol phosphate aminotransferase that is responsible for one of the last steps of histidine biosynthesis. Expression of the mutated gene at the RNA level was assessed by northern analysis of various tissues. Transcriptional activity was unimpaired by the mutation and, in contrast, a higher level of expression was obtained when compared to the wild-type. The cDNA sequence encoding the mutated gene was isolated by RT-PCR and compared to the wild-type gene. A single point mutation corresponding to the substitution of a G nucleotide by A was identified at position 1212 starting from the translation site. The alignment of the deduced amino acid sequences from the mutated and wild-type gene showed that this mutation resulted in the substitution of an Arg by a His residue at position 381. This Arg residue is a conserved amino acid for histidinol phosphate aminotransferase of many species. These results indicate that the identified mutation results in an altered histidinol phosphate aminotransferase enzyme that is unable to convert the substrate imidazole acetol phosphate to histidinol phosphate and thereby leads to the blockage of histidine biosynthesis. Possible consequences of this blockage on the expression of other amino acid biosynthesis genes were evaluated by analysing the expression of the dhdps gene encoding dihydrodipicolinate synthase, the first key enzyme of the lysine pathway.