Mechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase

Nucleotide Limitation Results in Impaired Photosynthesis, Reduced Growth and Seed Yield Together with Massively Altered Gene Expression

Nucleotide limitation and imbalance is a well-described phenomenon in animal research but understudied in the plant field. A peculiarity of pyrimidine de novo synthesis in plants is the complex subcellular organization. Here, we studied two organellar localized enzymes in the pathway, with chloroplast aspartate transcarbamoylase (ATC) and mitochondrial dihydroorotate dehydrogenase (DHODH). ATC knock-downs were most severely affected, exhibiting low levels of pyrimidine nucleotides, a low energy state, reduced photosynthetic capacity and accumulation of reactive oxygen species. Furthermore, altered leaf morphology and chloroplast ultrastructure were observed in ATC mutants. Although less affected, DHODH knock-down mutants showed impaired seed germination and altered mitochondrial ultrastructure. Thus, DHODH might not only be regulated by respiration but also exert a regulatory function on this process. Transcriptome analysis of an ATC-amiRNA line revealed massive alterations in gene expression with central metabolic pathways being downregulated and stress response and RNA-related pathways being upregulated. In addition, genes involved in central carbon metabolism, intracellular transport and respiration were markedly downregulated in ATC mutants, being most likely responsible for the observed impaired growth. We conclude that impairment of the first committed step in pyrimidine metabolism, catalyzed by ATC, leads to nucleotide limitation and by this has far-reaching consequences on metabolism and gene expression. DHODH might closely interact with mitochondrial respiration, as seen in delayed germination, which is the reason for its localization in this organelle.

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae

Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.

Transcriptional reprogramming of nucleotide metabolism in response to altered pyrimidine availability in Arabidopsis seedlings

In Arabidopsis seedlings, inhibition of aspartate transcarbamoylase (ATC) and de novo pyrimidine synthesis resulted in pyrimidine starvation and developmental arrest a few days after germination. Synthesis of pyrimidine nucleotides by salvaging of exogenous uridine (Urd) restored normal seedling growth and development. We used this experimental system and transcriptional profiling to investigate genome-wide responses to changes in pyrimidine availability. Gene expression changes at different times after Urd supplementation of pyrimidine-starved seedlings were mapped to major pathways of nucleotide metabolism, in order to better understand potential coordination of pathway activities, at the level of transcription. Repression of de novo synthesis genes and induction of intracellular and extracellular salvaging genes were early and sustained responses to pyrimidine limitation. Since de novo synthesis is energetically more costly than salvaging, this may reflect a reduced energy status of the seedlings, as has been shown in recent studies for seedlings growing under pyrimidine limitation. The unexpected induction of pyrimidine catabolism genes under pyrimidine starvation may result from induction of nucleoside hydrolase NSH1 and repression of genes in the plastid salvaging pathway, diverting uracil (Ura) to catabolism. Identification of pyrimidine-responsive transcription factors with enriched binding sites in highly coexpressed genes of nucleotide metabolism and modeling of potential transcription regulatory networks provided new insights into possible transcriptional control of key enzymes and transporters that regulate nucleotide homeostasis in plants.

Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis

Aspartate transcarbamoylase (ATC) catalyzes the first committed step in pyrimidine de novo synthesis. As shown before, mutants with 80% reduced transcript and protein levels exhibit reduced levels of pyrimidine metabolites and thus nucleotide limitation and imbalance. Consequently, reduced photosynthetic capacity and growth, accompanied by massive transcriptional changes, were observed. Here, we show that nucleotide de novo synthesis was upregulated during cold acclimation of Arabidopsis thaliana (ecotype Columbia, Col-0) plants, but ATC knockdown mutants failed to acclimate to this condition as they did not accumulate neutral sugars and anthocyanins. A global transcriptome analysis revealed that most of the transcriptional changes observed in Col-0 plants upon cold exposure were also evident in ATC knockdown plants. However, several responses observed in cold-treated Col-0 plants could already be detected in knockdown plants when grown under standard conditions, suggesting that these mutants exhibited typical cold responses without prior cold stimulation. We believe that nucleotide signaling is involved in "cold-like priming" and "cold acclimation" in general. The observed transcript levels of genes involved in central carbon metabolism and respiration were an exception to these findings. These were upregulated in the cold but downregulated in warm-grown ATC mutants.

Biological Calorimetry: Old Friend, New Insights

Calorimetry is an old experimental technique (first instrument developed in S. XVIII), but it is broadly used and still provides key information for understanding biological processes at the molecular level, particularly, cooperative phenomena in protein interactions. Here, we review and highlight some key aspects of biological calorimetry. Several biological systems will be described in which calorimetry was instrumental for modeling the behavior of the protein and obtaining further biological insight.

A Tailored Strategy to Crosslink the Aspartate Transcarbamoylase Domain of the Multienzymatic Protein CAD

CAD is a 1.5 MDa hexameric protein with four enzymatic domains responsible for initiating de novo biosynthesis of pyrimidines nucleotides: glutaminase, carbamoyl phosphate synthetase, aspartate transcarbamoylase (ATC), and dihydroorotase. Despite its central metabolic role and implication in cancer and other diseases, our understanding of CAD is poor, and structural characterization has been frustrated by its large size and sensitivity to proteolytic cleavage. Recently, we succeeded in isolating intact CAD-like particles from the fungus Chaetomium thermophilum with high yield and purity, but their study by cryo-electron microscopy is hampered by the dissociation of the complex during sample grid preparation. Here we devised a specific crosslinking strategy to enhance the stability of this mega-enzyme. Based on the structure of the isolated C. thermophilum ATC domain, we inserted by site-directed mutagenesis two cysteines at specific locations that favored the formation of disulfide bridges and covalent oligomers. We further proved that this covalent linkage increases the stability of the ATC domain without damaging the structure or enzymatic activity. Thus, we propose that this cysteine crosslinking is a suitable strategy to strengthen the contacts between subunits in the CAD particle and facilitate its structural characterization.

A plastid nucleoside kinase is involved in inosine salvage and control of purine nucleotide biosynthesis

In nucleotide metabolism, nucleoside kinases recycle nucleosides into nucleotides-a process called nucleoside salvage. Nucleoside kinases for adenosine, uridine, and cytidine have been characterized from many organisms, but kinases for inosine and guanosine salvage are not yet known in eukaryotes and only a few such enzymes have been described from bacteria. Here we identified Arabidopsis thaliana PLASTID NUCLEOSIDE KINASE 1 (PNK1), an enzyme highly conserved in plants and green algae belonging to the Phosphofructokinase B family. We demonstrate that PNK1 from A. thaliana is located in plastids and catalyzes the phosphorylation of inosine, 5-aminoimidazole-4-carboxamide-1-β-d-ribose (AICA ribonucleoside), and uridine but not guanosine in vitro, and is involved in inosine salvage in vivo. PNK1 mutation leads to increased flux into purine nucleotide catabolism and, especially in the context of defective uridine degradation, to over-accumulation of uridine and UTP as well as growth depression. The data suggest that PNK1 is involved in feedback regulation of purine nucleotide biosynthesis and possibly also pyrimidine nucleotide biosynthesis. We additionally report that cold stress leads to accumulation of purine nucleotides, probably by inducing nucleotide biosynthesis, but that this adjustment of nucleotide homeostasis to environmental conditions is not controlled by PNK1.

Early-stage responses to Plasmodiophora brassicae at the transcriptome and metabolome levels in clubroot resistant and susceptible oilseed Brassica napus

Clubroot, a devastating soil-borne root disease, in Brassicaceae is caused by Plasmodiophora brassicae Woronin (P. brassicae W.), an obligate biotrophic protist. Plant growth and development, as well as seed yield of Brassica crops, are severely affected due to this disease. Several reports described the molecular responses of B. napus to P. brassicae; however, information on the early stages of pathogenesis is limited. In this study, we have used transcriptomics and metabolomics to characterize P. brassicae pathogenesis at 1-, 4-, and 7-days post-inoculation (DPI) in clubroot resistant (CR) and susceptible (CS) doubled-haploid (DH) canola lines. When we compared between inoculated and uninoculated groups, a total of 214 and 324 putative genes exhibited differential expression (q-value < 0.05) at one or more time-points in the CR and CS genotypes, respectively. When the inoculated CR and inoculated CS genotypes were compared, 4765 DEGs were differentially expressed (q-value < 0.05) at one or more time-points. Several metabolites related to organic acids (e.g., citrate, pyruvate), amino acids (e.g., proline, aspartate), sugars, and mannitol, were differentially accumulated in roots in response to pathogen infection when the CR and CS genotypes were compared. Several DEGs also corresponded to differentially accumulated metabolites, including pyrroline-5-carboxylate reductase (BnaC04g11450D), citrate synthase (BnaC02g39080D), and pyruvate kinase (BnaC04g23180D) as detected by transcriptome analysis. Our results suggest important roles for these genes in mediating resistance to clubroot disease. To our knowledge, this is the first report of an integrated transcriptome and metabolome analysis aimed at characterizing the molecular basis of resistance to clubroot in canola.

Genome and transcriptome-wide study of carbamoyltransferase genes in major fleshy fruits: A multi-omics study of evolution and functional significance

The carbamoyltransferase or aspartate carbamoyltransferase (ATCase)/ornithine carbamoyltransferase (OTCase) is an evolutionary conserved protein family, which contains two genes, ATCase and OTCase. The ATCase catalyzes the committed step in the synthesis of UMP from which all pyrimidine molecules are synthesized. The second member, OTCase, catalytically regulates the conversion of ornithine to citrulline. This study traces the evolution of the carbomoyltransferase genes in the plant kingdom and their role during fruit ripening in fleshy fruits. These genes are highly conserved throughout the plant kingdom and, except for melon and watermelon, do not show gene expansion in major fleshy fruits. In this study, 393 carbamoyltransferase genes were identified in the plant kingdom, including 30 fleshy fruit representatives. Their detailed phylogeny, evolutionary patterns with their expression during the process of fruit ripening, was analyzed. The ATcase and OTcase genes were conserved throughout the plant kingdom and exhibited lineage-specific signatures. The expression analysis of the ATcase and OTcase genes during fruit development and ripening in climacteric and non-climacteric fruits showed their involvement in fruit ripening irrespective of the type of fruits. No direct role in relation to ethylene-dependent or -independent ripening was identified; however, the co-expression network suggests their involvement in the various ripening processes.

Microbial induced phosphate precipitation accelerate lead mineralization to alleviate nucleotide metabolism inhibition and alter Penicillium oxalicum's adaptive cellular machinery

Microbial-induced phosphate (P) precipitation (MIPP) based on P-solubilizing microorganisms (PSM) is regarded as a promising approach to bioimmobilize environmental lead (Pb). Nevertheless, the underlying changes of Pb²⁺ biotoxicity in PSM during MIPP process were rarely discussed. The current study explored the Pb²⁺ immobilization and metabolic changes in PSM Penicillium oxalicum postexposure to Pb²⁺ and/or tricalcium phosphate (TCP). TCP addition significantly increased soluble P concentrations, accelerated extracellular Pb mineralization, and improved antioxidative enzyme activities in P. oxalicum during MIPP process. Secondary Pb²⁺ biomineralization products were measured as hydroxypyromorphite [Pb₁₀(PO₄)₆(OH)₂]. Using untargeted metabolomic and transcriptomics, we found that Pb²⁺ exposure stimulated the membrane integrity deterioration and nucleotide metabolism obstruction of P. oxalicum. Correspondingly, P. oxalicum could produce higher levels of gamma-aminobutyric acid (GABA) to enhance the adaptive cellular machineries under Pb²⁺ stress. While the MIPP process improved extracellular Pb²⁺ mineralization, consequently alleviating the nucleotide metabolism inhibition and membrane deterioration. Multi-omics results suggested that GABA degradation pathway was stimulated for arginine biosynthesis and TCA cycle after Pb²⁺ mineralization. These results provided new biomolecular information underlying the Pb²⁺ exposure biotoxicities to microorganisms in MIPP before the application of this approach in environmental Pb²⁺ remediation.

New Insight into Aspartate Metabolic Pathways in Populus: Linking the Root Responsive Isoenzymes with Amino Acid Biosynthesis during Incompatible Interactions of Fusarium solani

Integrating amino acid metabolic pathways into plant defense and immune systems provides the building block for stress acclimation and host-pathogen interactions. Recent progress in L-aspartate (Asp) and its deployed metabolic pathways highlighted profound roles in plant growth and defense modulation. Nevertheless, much remains unknown concerning the multiple isoenzyme families involved in Asp metabolic pathways in Populus trichocarpa, a model tree species. Here, we present comprehensive features of 11 critical isoenzyme families, representing biological significance in plant development and stress adaptation. The in silico prediction of the molecular and genetic patterns, including phylogenies, genomic structures, and chromosomal distribution, identify 44 putative isoenzymes in the Populus genome. Inspection of the tissue-specific expression demonstrated that approximately 26 isogenes were expressed, predominantly in roots. Based on the transcriptomic atlas in time-course experiments, the dynamic changes of the genes transcript were explored in Populus roots challenged with soil-borne pathogenic Fusarium solani (Fs). Quantitative expression evaluation prompted 12 isoenzyme genes (PtGS2/6, PtGOGAT2/3, PtAspAT2/5/10, PtAS2, PtAspg2, PtAlaAT1, PtAK1, and PtAlaAT4) to show significant induction responding to the Fs infection. Using high-performance liquid chromatography (HPLC) and non-target metabolomics assay, the concurrent perturbation on levels of Asp-related metabolites led to findings of free amino acids and derivatives (e.g., Glutamate, Asp, Asparagine, Alanine, Proline, and α-/γ-aminobutyric acid), showing marked differences. The multi-omics integration of the responsive isoenzymes and differential amino acids examined facilitates Asp as a cross-talk mediator involved in metabolite biosynthesis and defense regulation. Our research provides theoretical clues for the in-depth unveiling of the defense mechanisms underlying the synergistic effect of fine-tuned Asp pathway enzymes and the linked metabolite flux in Populus.

Chloroplasts are key players to cope with light and temperature stress

Under natural environmental conditions, changes in light intensity and temperature are closely interwoven, and of all organelles, only chloroplasts react strongly upon alterations of these two parameters. We review increasing evidence indicating that changes in chloroplast metabolism are critical for the comprehensive cellular answer in a challenging environment. This cellular answer starts with rapid modifications of thylakoid-located processes, followed by modifications in the stroma and transport activities across the chloroplast envelope. We propose that the 'modulators' involved contribute to plant stress tolerance and that deciphering of their characteristics is essential to understand 'acclimation'. Especially in times of climatic changes, we must gain knowledge on physiological reactions that might become instrumental for directed breeding strategies aiming to develop stress-tolerant crop plants.

Cytidine Triphosphate Synthase Four From Arabidopsis thaliana Attenuates Drought Stress Effects

Cytidine triphosphate synthase (CTPS) catalyzes the final step in pyrimidine de novo synthesis. In Arabidopsis, this protein family consists of five members (CTPS1-5), and all of them localize to the cytosol. Specifically, CTPS4 showed a massive upregulation of transcript levels during abiotic stress, in line with increased staining of CTPS4 promoter:GUS lines in hypocotyl, root and to lesser extend leaf tissues. In a setup to study progressive drought stress, CTPS4 knockout mutants accumulated less fresh and dry weight at days 5-7 and showed impaired ability to recover from this stress after 3 days of rewatering. Surprisingly, a thorough physiological characterization of corresponding plants only revealed alterations in assimilation and accumulation of soluble sugars including those related to drought stress in the mutant. Bimolecular fluorescence complementation (BiFC) studies indicated the interaction of CTPS4 with other isoforms, possibly affecting cytoophidia (filaments formed by CTPS formation. Although the function of these structures has not been thoroughly investigated in plants, altered enzyme activity and effects on cell structure are reported in other organisms. CTPS activity is required for cell cycle progression and growth. Furthermore, drought can lead to the accumulation of reactive oxygen species (ROS) and by this, to DNA damage. We hypothesize that effects on the cell cycle or DNA repair might be relevant for the observed impaired reduced drought stress tolerance of CTPS4 mutants.

Cytosolic CTP Production Limits the Establishment of Photosynthesis in Arabidopsis

CTP synthases (CTPS) comprise a protein family of the five members CTPS1-CTPS5 in Arabidopsis, all located in the cytosol. Specifically, downregulation of CTPS2 by amiRNA technology results in plants with defects in chlorophyll accumulation and photosynthetic performance early in development. CTP and its deoxy form dCTP are present at low levels in developing seedlings. Thus, under conditions of fast proliferation, the synthesis of CTP (dCTP) can become a limiting factor for RNA and DNA synthesis. The higher sensitivity of ami-CTPS2 lines toward the DNA-Gyrase inhibitor ciprofloxacin, together with reduced plastid DNA copy number and 16S and 23S chloroplast ribosomal RNA support this view. High expression and proposed beneficial biochemical features render CTPS2 the most important isoform for early seedling development. In addition, CTPS2 was identified as an essential enzyme in embryo development before, as knock-out mutants were embryo lethal. In line with this, ami-CTPS2 lines also exhibited reduced seed numbers per plant.

Deciphering CAD: Structure and function of a mega-enzymatic pyrimidine factory in health and disease

CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD's architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.