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African sleeping sickness, Chagas disease, and leishmaniasis are life-threatening diseases that together affect millions of people around the world and are caused by different members of the protozoan family Trypanosomatidae. The most studied member of the family is Trypanosoma brucei, which is spread by tsetse flies and causes African sleeping sickness. Nucleotide metabolism in T. brucei and other trypanosomatids is significantly different from that of mammals and was recognized as a target for chemotherapy already in the 1970–1980s. A more thorough investigation of the nucleotide metabolism in recent years has paved the way for identifying nucleoside analogues that can cure T. brucei brain infections in animal models. Specific features of T. brucei nucleotide metabolism include the lack of de novo purine biosynthesis, the presence of very efficient purine transporters, the lack of salvage pathways for CTP synthesis, unique enzyme localizations, and a recently discovered novel pathway for dTTP synthesis. This review describes the nucleotide metabolism of T. brucei, highlights differences and similarities to other trypanosomatids, and discusses how to exploit the parasite-specific features for drug development.

cN-II is a cytosolic 5'-nucleotidase with preference for IMP and GMP over AMP. The enzyme has been extensively studied over the last 20-30 years both for its enzymatic activity, structure, role in nucleotide metabolism and in cell biology, as well as in diseases. With the aim of highlighting the complexity of the enzyme, I will, as during PP21, present work from our group and others working on cN-II and its various roles and not give an exhaustive overview of new data.

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.

International audience; Tuberculosis claims significantly more than one million lives each year. A feasible way to face the issue of drug resistance is the development of new antibiotics. Bacterial uridine 5’-monophosphate (UMP) kinase is a promis- ing target for novel antibiotic discovery as it is essential for bacterial sur- vival and has no counterpart in human cells. The UMP kinase from M. tuberculosis is also a model of particular interest for allosteric regula- tion with two effectors, GTP (positive) and UTP (negative). In this study, using X-ray crystallography and cryo-electron microscopy, we report for the first time a detailed description of the negative effector UTP-binding site of a typical Gram-positive behaving UMP kinase. Comparison between this snapshot of low affinity for Mg-ATP with our previous 3D-structure of the GTP-bound complex of high affinity for Mg-ATP led to a better understanding of the cooperative mechanism and the allosteric regulation of UMP kinase. Thermal shift assay and circular dichroism experiments corroborate our model of an inhibition by UTP linked to higher flexibility of the Mg-ATP-binding domain. These new structural insights provide valuable knowledge for future drug discovery strategies targeting bacterial UMP kinases.

[ES] CAD es una proteína de 243 kDa dividida en cuatro dominios enzimáticos, responsables de catalizar las tres primeras reacciones de la biosíntesis de novo de pirimidinas: Glutaminasa, Carbamil fosfato sintetasa, Aspartato transcarbamilasa y Dihidroorotasa. A pesar de su importancia en el metabolismo de los nucleótidos, no existe información detallada de la estructura ni del funcionamiento de la proteína CAD entera, aunque sí de dos de sus dominios enzimáticos aislados. Estudios anteriores han demostrado que mutaciones bialélicas en CAD son la causa de un grave trastorno metabólico congénito conocido como Encefalopatía Epiléptica y del Desarrollo 50 (DEE50), tratable con suplementos dietéticos de uridina. Este trabajo de fin de grado tiene como objetivo la caracterización funcional y estructural de dos variantes patogénicas clínicas del dominio Dihidroorotasa (DHO) de CAD, p.R1810Q y p.K1556T. Subclonamos el dominio DHO de la CAD humana con la variante patogénica p.R1810Q y expresamos y purificamos la proteína recombinante. Para entender el efecto de la mutación patogénica, caracterizamos el estado oligomérico, la estabilidad y la actividad enzimática de la proteína purificada, y también intentamos su cristalización. Nuestros resultados muestran que la variante DHO p.R1810Q se produce con un rendimiento y solubilidad similares a los de la proteína silvestre y que la mutación no disminuye la actividad o la estabilidad de la proteína. Observamos que la mutación induce una disociación parcial de los dímeros de proteína, y altera las curvas de desnaturalización, lo que, sumado a la reticencia de la proteína a cristalizar, nos lleva a proponer que la mutación R1810Q aumenta la flexibilidad de la extensión C-terminal del dominio DHO que conecta con el dominio ATC. Por tanto, R1810Q podría estar afectando de forma negativa la oligomerización de CAD en una partícula hexámerica funcional. Por otro lado, para clarificar los mecanismos patogénicos de la variante p.K1556T, trazamos y refinamos con éxito la estructura cristalina del dominio DHO con esta mutación a una resolución de 1.8 Å utilizando datos de difracción de sincrotrón. El modelo estructural apoya el papel clave del residuo K1556 en la organización del centro activo y explica el efecto desfavorable de su sustitución por treonina. En general, este proyecto me ha permitido adquirir una visión amplia y práctica de los pasos necesarios para ir de la información génica a la estructura 3D de la proteína, y así comprender el impacto de las mutaciones en su estructura y función., [EN] CAD is a 243 kDa protein divided into four enzymatic domains, responsible for catalyzing the first three reactions for the de novo pyrimidine biosynthesis: Glutaminase, Carbamoyl phosphate synthetase, Aspartate transcarbamoylase and Dihydroorotase. Despite its importance in nucleotide metabolism, there is no detailed information on the structure or function of the entire CAD protein, although there is information on two of its isolated enzymatic domains. Previous studies have shown that biallelic mutations in CAD are the cause of a severe congenital metabolic disorder known as Developmental and Epileptic Encephalopathy 50 (DEE50), which is treatable with dietary uridine supplementation. This bachelor¿s thesis aims at the functional and structural characterization of two clinical pathogenic variants of the Dihydroorotase (DHO) domain of CAD, p.R1810Q and p.K1556T. We subcloned the DHO domain of human CAD containing the pathogenic variant p.R1810Q and expressed and purified the recombinant protein. To understand the effect of the pathogenic mutation, we characterized the oligomeric state, stability, and enzymatic activity of the purified protein, and we also attempted its crystallization. Our results show that the p.R1810Q DHO variant is produced in a similar yield and solubility as the wild type protein and that the mutation does not decrease the activity or stability of the protein. We observed that the mutation induces partial dissociation of protein dimers, and alters denaturation curves, which, along with the reluctance of the protein to crystallize, leads us to propose that the R1810Q mutation increases the flexibility of the C-terminal extension of the DHO domain which connects with the ATC domain. Therefore, R1810Q could be negatively affecting the oligomerization of CAD into a functional hexameric particle. In addition, to shed light on the pathogenic mechanisms of the p.K1556T variant, we successfully mapped and refined the crystal structure of the DHO domain with this mutation to a resolution of 1.8 Å using synchrotron diffraction data. The structural model supports the key role of residue K1556 in the organization of the active center and explains the unfavorable effect of the replacement by a threonine. Overall, this project has allowed me to gain a broad and practical view of the steps required to go from gene information to the 3D structure of the protein, and thus to understand the impact of mutations on its structure and function.

Abnormal cancer metabolism occurs throughout the development of tumors. Recent studies have shown that abnormal nucleotide metabolism not only accelerates the development of tumors but also inhibits the normal immune response in the tumor microenvironment. Although few relevant experiments and reports are available, study of the interaction between nucleotide metabolism and cancer development is rapidly developing. The intervention, alteration or regulation of molecular mechanisms related to abnormal nucleotide metabolism in tumor cells has become a new idea and strategy for the treatment of tumors and prevention of recurrence and metastasis. Determining how nucleotide metabolism regulates the occurrence and progression of tumors still needs long-term and extensive research and exploration.

Multiple sclerosis (MS) is an inflammatory demyelinating disease of the nervous system that primarily affects young adults. Although the exact etiology of the disease remains obscure, it is clear that alterations in the metabolome contribute to this process. As such, defining a reliable and disease-specific metabolome has tremendous potential as a diagnostic and therapeutic strategy for MS. Here, we provide an overview of studies aimed at identifying the role of metabolomics in MS. These offer new insights into disease pathophysiology and the contributions of metabolic pathways to this process, identify unique markers indicative of treatment responses, and demonstrate the therapeutic effects of drug-like metabolites in cellular and animal models of MS. By and large, the commonly perturbed pathways in MS and its preclinical model include lipid metabolism involving alpha-linoleic acid pathway, nucleotide metabolism, amino acid metabolism, tricarboxylic acid cycle, d-ornithine and d-arginine pathways with collective role in signaling and energy supply. The metabolomics studies suggest that metabolic profiling of MS patient samples may uncover biomarkers that will advance our understanding of disease pathogenesis and progression, reduce delays and mistakes in diagnosis, monitor the course of disease, and detect better drug targets, all of which will improve early therapeutic interventions and improve evaluation of response to these treatments.

The balance between oxidative phosphorylation and glycolysis is important for cancer cell growth and survival, and changes in energy metabolism are an emerging therapeutic target. Adenylate kinase (AK) regulates adenine nucleotide metabolism, maintaining intracellular nucleotide metabolic homeostasis. In this study, we focused on AK3, the isozyme localized in the mitochondrial matrix that reversibly mediates the following reaction: Mg2+ GTP + AMP ⇌ Mg2+ GDP + ADP. Additionally, we analyzed AK3-knockout (KO) HeLa cells, which showed reduced proliferation and were detected at an increased number in the G1 phase. A metabolomic analysis showed decreased ATP; increased glycolytic metabolites such as glucose 6 phosphate (G6P), fructose 6 phosphate (F6P), and phosphoenolpyruvate (PEP); and decreased levels of tricarboxylic acid (TCA) cycle metabolites in AK3KO cells. An intracellular ATP evaluation of AK3KO HeLa cells transfected with ATeam plasmid, an ATP sensor, showed decreased whole cell levels. Levels of mitochondrial DNA (mtDNA), a complementary response to mitochondrial failure, were increased in AK3KO HeLa cells. Oxidative stress levels increased with changes in gene expression, evidenced as an increase in related enzymes such as superoxide dismutase 2 (SOD2) and SOD3. Phosphoenolpyruvate carboxykinase 2 (PCK2) expression and PEP levels increased, whereas PCK2 inhibition affected AK3KO HeLa cells more than wild-type (WT) cells. Therefore, we concluded that increased PCK2 expression may be complementary to increased GDP, which was found to be deficient through AK3KO. This study demonstrated the importance of AK3 in mitochondrial matrix energy metabolism.

Methionine, through S-adenosylmethionine, activates a multifaceted growth program in which ribosome biogenesis, carbon metabolism, and amino acid and nucleotide biosynthesis are induced. This growth program requires the activity of the Gcn4 transcription factor (called ATF4 in mammals), which facilitates the supply of metabolic precursors that are essential for anabolism. However, how Gcn4 itself is regulated in the presence of methionine is unknown. Here, we discover that Gcn4 protein levels are increased by methionine, despite conditions of high cell growth and translation (in which the roles of Gcn4 are not well-studied). We demonstrate that this mechanism of Gcn4 induction is independent of transcription, as well as the conventional Gcn2/eIF2α-mediated increased translation of Gcn4. Instead, when methionine is abundant, Gcn4 phosphorylation is decreased, which reduces its ubiquitination and therefore degradation. Gcn4 is dephosphorylated by the protein phosphatase 2A (PP2A); our data show that when methionine is abundant, the conserved methyltransferase Ppm1 methylates and alters the activity of the catalytic subunit of PP2A, shifting the balance of Gcn4 toward a dephosphorylated, stable state. The absence of Ppm1 or the loss of the PP2A methylation destabilizes Gcn4 even when methionine is abundant, leading to collapse of the Gcn4-dependent anabolic program. These findings reveal a novel, methionine-dependent signaling and regulatory axis. Here methionine directs the conserved methyltransferase Ppm1 via its target phosphatase PP2A to selectively stabilize Gcn4. Through this, cells conditionally modify a major phosphatase to stabilize a metabolic master regulator and drive anabolism.

Nucleotide metabolism is the driving force of cell proliferation, and thymidylate synthase (TYMS) catalyzes a rate‐limiting step in the initial synthesis of nucleotides. Previous studies reported that TYMS activity significantly affected the proliferation of tumour cells. However, the diagnostic and prognostic significance of TYMS expression in breast cancer remains unclear. Here, we used the Breast Cancer Integrative Platform (BCIP) to investigate the relationship between progression and prognosis of breast cancer with TYMS expression, and then verified the database analysis using immunohistochemical staining. Our results indicated TYMS expression was greater in breast cancer than adjacent normal tissues and greater in triple‐negative breast cancer (TNBC) than non‐TNBC tissues. TYMS expression also had significant positive correlations with histological grade, tumour size, and ER negativity, and PR negativity. The increased copy number of the TYMS gene appears to be the reason for its upregulation in breast cancer. Breast cancer patients with higher TYMS expression had poorer prognosis. Our data suggest that TYMS has potential use as a diagnostic and prognostic marker for breast cancer patients., Thymidylate synthase expression is significant relationships with clinical parameters and survival of breast cancer patients. We suggest that TYMS might be useful as a diagnostic and prognostic indicator for breast cancer.

Background Edible mushrooms have been used as food and medicine materials for thousands of years, and the yield of cultivatable edible mushrooms has increased in recent years. The increased consumption of edible mushrooms is not only due to their nutritional value, but also to their unique taste and specific flavor. As consumer awareness of food sensory qualities increases, umami taste and aroma have become important factors affecting consumer choices. There are many factors affecting umami taste and aroma of edible mushrooms, such as cultivation conditions, species, maturity, grading, parts of mushrooms, and processing and storage methods. However, the mechanisms underlying the variations in umami taste and aroma components of different mushrooms are still unclear. Scope and approach In this review, traditional umami components, novel umami peptides, and aroma compounds are discussed, as well as the perception of umami taste and aroma. Based on a combination of human sensory evaluation and instrumental analysis, changes in the composition of these components in edible mushrooms are summarized, and the metabolic pathways and biochemical reactions involved in these changes are also discussed. Key findings and conclusions The umami taste and aroma of edible mushrooms were closely related to nucleotide metabolism, amino acid metabolism, fatty acid metabolism, and the Maillard reaction. Umami peptides and the synergy between these compounds contribute to overall umami taste. There are differences in umami taste and aroma between cultivated and wild mushrooms. The selection of processing and storage techniques is, therefore, based on the established demand for umami taste and aroma of edible mushrooms.

A lung cancer diagnostic kit (LCDK) with the advantages of low cost, easy operation and high sensitivity for the rapid diagnosis of lung cancer was developed. The proposed LCDK is able to noninvasively discriminate lung cancer using clinical salivary and urine samples in a short period of time.

We have fabricated an ultrasensitive exosome biosensor based on a multipedal DNA walker with a core of target exosomes. Specific recognition is achieved by introducing a CD63 aptamer and facile separation is obtained with magnetic Fe3O4@Au nanoparticles. A limit of detection down to 6/μL is obtained with excellent selectivity.

Exosomes are endogenous vesicles of cells, and can be used as important biomarkers for cancers. In this work, we developed a sensitive and reliable SERS sensor for simultaneous detection of multiple cancer-related exosomes. The SERS detection probes were made of bimetallic SERS-active nanotags, gold-silver-silver core-shell-shell nanotrepangs (GSSNTs), which were composed of bumpy surface nanorod (gold nanotrepang, GNT) cores and bilayer silver shells, and decorated with linker DNAs, which were complementary to the aptamer targeting exosomes. Three kinds of SERS detection probes were designed via the adoption of different Raman reporter molecules and linker DNAs. The capture probes were prepared by modifying specific aptamers of the target exosomes on magnetic beads (MBs). In the absence of target exosomes, SERS detection probes were coupled with MBs via specific DNA hybridization for use as aptamer-based SERS sensors. In the presence of target exosomes, the aptamer specifically recognized and captured the exosomes, and GSSNTs were subsequently released into the supernatant. Therefore, attenuated SERS signals were detected on the MBs, indicating the presence of target exosomes. The proposed aptamer-based SERS sensor is expected to be a facile and sensitive method for the multiplex detection of cancer biomarkers and has potential future applications in clinical diagnosis.

Elucidation of the complex regulation of porcine muscle development is key to increasing pork output and improving pork quality. However, the molecular mechanisms involved in early porcine embryonic muscle development in different pig breeds remain largely unknown. Here, GC–MS based metabolomics and metabolomic profiling was used to examine the longissimus lumborum (LL) of the Lantang (LT) and the Landrace (LR) pig at embryonic day 35 (E35). Metabolites showed clear separation between LT and LR, with 40 metabolites having higher abundances in LT and 14 metabolites having lower abundances in LT compared with LR. In addition, these metabolic changes were mainly associated with nucleotide metabolism and energy metabolism, such as purine metabolism, pyrimidine metabolism, the pentose phosphate pathway, and the TCA cycle. More interestingly, the contents of DNA, RNA, and ATP per unit mass of LL tissues were higher in LT, indicating rapid synthesis of nucleic acids and ATP, to meet both the material and energy requirements of rapid cell proliferation and differentiation. Furthermore, enzyme activity associated with the TCA cycle and pentose phosphate pathway, including α-ketoglutaric dehydrogenase (KGDH), malate dehydrogenase (MDH), pyruvate dehydrogenase (PDH), succinate dehydrogenase (SDH), and glucose-6-phosphate dehydrogenase (G6PDH), were higher in LT. Based on these results, we conclude that there are significant differences in nucleotide metabolism and energy metabolism of LL between LT and LR, and we speculate that the enhanced nucleic acid metabolism and energy metabolism in LT can meet the material and energy requirements of rapid cell proliferation and differentiation, making myogenesis more intense in LT compared to LR which might be the metabolic mechanism underlying the distinct skeletal muscle development in the two breeds.

BACKGROUND An increasing amount of research has led to the positioning of nucleoside diphosphate kinases (NDPK/NDK) as key metabolic enzymes among all organisms. They contribute to the maintenance the intracellular di- and tri- phosphate nucleoside homeostasis, but they also are involved in widely diverse processes such as gene regulation, apoptosis, signal transduction and many other regulatory roles. OBJETIVE Examine in depth the NDPKs of trypanosomatid parasites responsible for devastating human diseases (e.g., Trypanosoma cruzi, Trypanosoma brucei and Leishmania spp.) which deserve special attention. METHODS The earliest and latest advances in the topic were explored, focusing on trypanosomatid NDPK features, multifunctionality and suitability as molecular drug targets. FINDINGS Trypanosomatid NDPKs appear to play functions different from their host counterparts. Evidences indicate that they would perform key roles in the parasite metabolism such as nucleotide homeostasis, drug resistance, DNA damage responses and gene regulation, as well as host-parasite interactions, infection, virulence and immune evasion, placing them as attractive pharmacological targets. MAIN CONCLUSIONS NDPKs are very interesting multifunctional enzymes. In the present review, the potential of trypanosomatid NDPKs was highlighted, raising awareness of their value not only with respect to parasite biology but also as molecular targets.

Nucleotide metabolism is a complex pathway regulating crucial cellular processes such as nucleic acid synthesis, DNA repair and proliferation. This study shows that impairment of the biosynthesis of one of the building blocks of DNA, dTTP, causes a severe, early-onset neurodegenerative disease. Here, we describe two unrelated children with bi-allelic variants in DTYMK, encoding dTMPK, which catalyzes the penultimate step in dTTP biosynthesis. The affected children show severe microcephaly and growth retardation with minimal neurodevelopment. Brain imaging revealed severe cerebral atrophy and disappearance of the basal ganglia. In cells of affected individuals, dTMPK enzyme activity was minimal, along with impaired DNA replication. In addition, we generated dtymk mutant zebrafish that replicate this phenotype of microcephaly, neuronal cell death and early lethality. An increase of ribonucleotide incorporation in the genome as well as impaired responses to DNA damage were observed in dtymk mutant zebrafish, providing novel pathophysiological insights. It is highly remarkable that this deficiency is viable as an essential component for DNA cannot be generated, since the metabolic pathway for dTTP synthesis is completely blocked. In summary, by combining genetic and biochemical approaches in multiple models we identified loss-of-function of DTYMK as the cause of a severe postnatal neurodegenerative disease and highlight the essential nature of dTTP synthesis in the maintenance of genome stability and neuronal survival.

Once considered a waste product of anaerobic cellular metabolism, lactate has been identified as a critical regulator of tumorigenesis, maintenance, and progression. The putative primary function of lactate dehydrogenase B (LDHB) is to catalyze the conversion of lactate to pyruvate; however, its role in regulating metabolism during tumorigenesis is largely unknown. To determine whether LDHB plays a pivotal role in tumorigenesis, we performed 2D and 3D in vitro experiments, utilized a conventional xenograft tumor model, and developed a novel genetically engineered mouse model (GEMM) of non-small cell lung cancer (NSCLC), in which we combined an LDHB deletion allele with an inducible model of lung adenocarcinoma driven by the concomitant loss of p53 (also known as Trp53) and expression of oncogenic KRAS (G12D) (KP). Here, we show that epithelial-like, tumor-initiating NSCLC cells feature oxidative phosphorylation (OXPHOS) phenotype that is regulated by LDHB-mediated lactate metabolism. We show that silencing of LDHB induces persistent mitochondrial DNA damage, decreases mitochondrial respiratory complex activity and OXPHOS, resulting in reduced levels of mitochondria-dependent metabolites, e.g., TCA intermediates, amino acids, and nucleotides. Inhibition of LDHB dramatically reduced the survival of tumor-initiating cells and sphere formation in vitro, which can be partially restored by nucleotide supplementation. In addition, LDHB silencing reduced tumor initiation and growth of xenograft tumors. Furthermore, we report for the first time that homozygous deletion of LDHB significantly reduced lung tumorigenesis upon the concomitant loss of Tp53 and expression of oncogenic KRAS without considerably affecting the animal’s health status, thereby identifying LDHB as a potential target for NSCLC therapy. In conclusion, our study shows for the first time that LDHB is essential for the maintenance of mitochondrial metabolism, especially nucleotide metabolism, demonstrating that LDHB is crucial for the survival and proliferation of NSCLC tumor-initiating cells and tumorigenesis., Cellular and Molecular Life Sciences, 79 (8), ISSN:1420-682X, ISSN:1420-9071

Nucleotide metabolism is vital for plant development and dependent on the support of various enzymes including the phosphofructokinase B-type (PfkB) sugar kinases. Although some PfkB kinases such as adenosine kinase (ADK), ribokinase (RBSK), and pseudouridine kinase (PUKI) have been successfully identified and characterized in recent years, much is still unknown about these kinases. In this study, PfkB kinases from Arabidopsis thaliana were functionally screened leading to the identification of a plastid inosine kinase (PINK) that is involved in the feedback regulation of de novo purine synthesis and of kinase 6-2 (K6-2), which may be involved in negative regulation of purine synthesis. According to bioinformatic analyses, PINK is highly conserved in the plant kingdom, Subcellular localization and in vitro kinase activity analyses revealed that PINK is a plastid kinase that phosphorylates inosine, uridine, and 5-aminoimidazole-4-carboxamide ribonucleoside (AICAr). Furthermore, metabolite analysis was performed of Arabidopsis seedlings in which PINK expression was varied, which showed that PINK is not only involved in the inosine salvage but also likely contributes to feedback inhibition of de novo purine biosynthesis by regulating the plastid IMP pool. Moreover, PINK is possibly involved in pyrimidine nucleotide synthesis, at least in the context of defective uridine degradation. Additionally, another member of the PfkB family, kinase 6-2 (K6-2) was partially characterized in this work. K6-2 is localized in the chloroplast and in vitro biochemical analysis showed that K6-2 can phosphorylate AICAr, inosine, and guanosine. Furthermore, an in vivo functional study suggested that K6-2 is a negative regulator of purine de novo biosynthesis, as the biosynthesis of purine nucleotides was enhanced in the knock-down mutant of K6-2. Moreover, the reduced expression of K6-2 in Arabidopsis led to a phenotype that involved yellowing and suppressed leaf growth.

Glyceraldehyde (GA) is a 3-carbon monosaccharide that is present in cells as byproduct of fructose metabolism. The phosphorylated form, glyceraldehyde-3-phosphate is a key metabolite in central carbon metabolism. Bruno Mendel and Otto Warburg proved that the application of glyceraldehyde to cancer cells inhibits glycolysis and their growth. This phenomenon was extensively studied up until the 1970's. The consensus reached was that the L-isomer of glyceraldehyde is a more effective glycolytic inhibitor than the D-isomer. However, the mechanism by which this occurred was not clarified. This thesis describes a novel mechanism by which L-GA inhibits cancer cell growth. The work describes how L-GA induces significant changes in the metabolic profile and hinders nucleotide biosynthesis. Gas chromatography–mass spectrometry and 13C-labelling was employed to measure the flow of carbon through glycolytic intermediates under L-GA treatment. The data in this thesis recapitulated previous research on the inhibitory efficacy of L-GA and D-GA. It was found that L-GA is a more potent inhibitor of glycolysis due to its targeting of NADH-dependent reactions, leading to a redox crisis in the cancer cell. Through proteomics analysis it was confirmed that redox mechanisms were modulated via L-GA. This elucidated a specific subset of proteins harbouring oxidoreductase and anti-oxidant activity. Further bioinformatic and molecular biology analysis suggested that the generation of reactive oxygen species via L-GA activates the KEAP1-NRF2 pathway, to drive the expression of anti-oxidant proteins. Analysis of nucleotide pools in L-GA treated cells depicted a remarkable and previously unreported phenotype. Nucleotide biosynthesis in neuroblastoma cells is significantly inhibited upon L-GA treatment, yet the D-isomer showed minimal inhibition. Critically, this evidence could be linked to findings in the proteome and metabolome. Through the application of the antioxidant N-acetyl-cysteine in conjunction with L-GA, inhibition was relieved. This work presents significant novel evidence for the mechanism of L-GA action in neuroblastoma cells. Specifically, a simple sugar that inhibits the growth of cancer via dysregulating the fragile homeostatic environment inherent to the nature of the cancerous cell., Glyzerinaldehyd (GA) ist ein Dreifachzucker und entsteht als Nebenprodukt im zellulären Fruktosestoffwechsel. Die phosphorylierte Form, Glyzerinaldehyd-3-Phosphat, ist ein zentraler Metabolit in der Glykolyse. Bruno Mendel und Otto Warburg konnten nachweisen, dass Glyzerinaldehyd das Wachstum und die Glykolyse in Krebszellen hemmen kann. Forschungen zu dieser Fragestellung gab es bis in die 70er Jahre des 20. Jahrhunderts. Es konnte zweifelsfrei nachgewiesen werden, dass die L-Konformation des Glyzerinaldehyds den Stoffwechsel und das Wachstum von Krebszellen effektiver inhibiert als die D-Konformation, die Gründe hierfür blieben aber unaufgeklärt. Im Rahmen dieser Arbeit wird ein neuer Mechanismus beschrieben, auf welche Weise L-Glyzerinaldehyd (L-GA) das Wachstum von Krebszellen inhibiert. Die Arbeit beschreibt, wie L-GA signifikante Änderungen im zellulären Stoffwechsel herbeiführt und die Nukleotidbiosynthese beeinflusst. Mittels GC-MS basierten Isotopen-unterstützten Stoffwechselanalysen konnten die Änderungen des Kohlenstoffflusses in der Glykolyse bestimmt werden. Die Daten, welche in dieser Arbeit gezeigt werden, spiegeln bisher veröffentlichte Daten über die Wirkung von L-GA wider. Weiterführend wurde gezeigt, dass L-GA ein stärkerer Inhibitor der Glykolyse ist als D-GA, weil ein dominanter Einfluss auf NADH abhängige Reaktionen vorliegt. Schließlich wird eine Änderung des zellulären RedOx Zustandes in der Zelle provoziert. Dies konnte mit Hilfe von ungerichteten Proteomanalysen bestätigt werden. Weitergehende bioinformatische und molekularbiologische Analysen deuten darauf hin, dass die Entstehung von freien Radikalen durch L-GA Behandlung den KEAP1-NRF2 Signalweg beeinflusst. Die Analyse der zellulären Nukleotidmengen unter L-GA Behandlung zeigte bemerkenswerte und bis dahin unbekannte Änderungen des Nukleotidstoffwechsels. Die Neusynthese von Nukleotiden wird durch Behandlung mit L-GA stark inhibiert. D-GA provozierte dem gegenüber nur eine mäßige Veränderung in den Nukleotidmengen. Das konnte durch die gefundenen Änderungen im Metabolome und Proteom bestätigt werden. In dieser Arbeit werden neue Aspekte der Wirkweise von L-GA in Neuroblastomzellen aufgezeigt. Letztendlich kann ein einfacher Zucker das Wachstum von Krebszellen vermindern, indem das fragile zelluläre Gleichgewicht von Krebszellen gezielt gestört wird.

We determine that type I interferon (IFN) response biomarkers are enriched in a subset of pancreatic ductal adenocarcinoma (PDAC) tumors; however, actionable vulnerabilities associated with IFN signaling have not been systematically defined. Integration of a phosphoproteomic analysis and a chemical genomics synergy screen reveals that IFN activates the replication stress response kinase ataxia telangiectasia and Rad3-related protein (ATR) in PDAC cells and sensitizes them to ATR inhibitors. IFN triggers cell-cycle arrest in S-phase, which is accompanied by nucleotide pool insufficiency and nucleoside efflux. In combination with IFN, ATR inhibitors induce lethal DNA damage and downregulate nucleotide biosynthesis. ATR inhibition limits the growth of PDAC tumors in which IFN signaling is driven by stimulator of interferon genes (STING). These results identify a cross talk between IFN, DNA replication stress response networks, and nucleotide metabolism while providing the rationale for targeted therapeutic interventions that leverage IFN signaling in tumors.

13 páginas, 5 figuras, 1 tabla, 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., This work was supported by grant RTI2018-098084-B-I00 financed by MCIN/AEI/10.13039/ 501100011033/ and “FEDER Una manera de hacer Europa”, by grant PID2021-128468NB-I00 financed by MCIN/AEI /10.13039/501100011033, and by Fundación Ramón Areces, XX National Call. F.d.C.-O. is a postdoctoral fellow of the Generalitat Valenciana (APOSTD 2021). AR-d-C is supported by salary from the European Commission–Next Generation EU through the CSIC Global Health Platform (PTI+ Salud Global) established by EU Council Regulation 2020/2094. X-ray diffraction experiments at ALBA were performed as part of the BAG proposal 2018082950.

Simple Summary Korat is a new chicken breed with high-protein meat, low fat, and low purine content. However, the effects of improving the breed’s feed efficiency, which would enhance production, on meat quality are unknown. Hence, understanding the genetic architecture underlying feed efficiency and meat quality traits in chicken offers new opportunities toward genetic improvement. Through a weighted gene co-expression network analysis on Korat chickens, the presented results provide new information on the molecular pathways that play important roles in FE and meat quality that could help achieve the optimum feed efficiency while maintaining meat quality in Korat chickens. Abstract Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes.

14 páginas, 6 figuras, 1 tabla., 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., Fundación Ramón Areces, Grant/AwardNumber: XX National Call; area of RareDiseases; Ministerio de Ciencia eInnovación, Grant/Award Number:RTI2018-098084-B-100; AEI/FEDER; UE

Resveratrol belongs to the Bioactive Food Component (BFC) family. It seems admitted that its cytotoxic action impacts tumor cells and spares healthy cells, but the published proofs remain rare. We hypothesized that cells may differentially metabolize resveratrol and lead to different systemic impacts. For this, resveratrol metabolization was evaluated by ultra-high-performance liquid chromatography (UHPLC) coupled with diode array detection (DAD), and correlated with the expression of Uridyl-diphosphate-Glucuronosyl Transferase 1A (UGT1A) genes. The expression of UGT1A genes in human colorectal tissues was studied with RNAseq databases. Functional validation of UGT1A enzymes implication in resveratrol sensitivity of colorectal cells established by UGT1A expression modulation. As resveratrol impacts the S phase of the cell cycle, nucleotide metabolic balance was assessed. We found that resveratrol was more cytotoxic in cells with downregulation of UGTs, i.e. tumor cells. Conversely, overexpression of the UGT1A10 gene in an initial resveratrol-sensitive tumor cell line restored the metabolization accompanied by cytotoxicity diminution. Resveratrol affected intestinal sensitive tumor cell homeostasis with a cell growth/proliferation decoupling, cell-cycle modulation, and UXP/AXP nucleotide imbalance resulting in a global reduction of transcription and translation. This impact on global cell activity was restricted to tumor cells. This study improves resveratrol’s general knowledge and explains how its antitumor action can spare non-tumor cells. It also paves the way to select colorectal tumors eligible for resveratrol treatment potentiation without additional toxicity to healthy digestive tissues.

Type I interferons (IFNs) are critical effectors of emerging cancer immunotherapies designed to activate pattern recognition receptors (PRRs). A challenge in the clinical translation of these agents is the lack of noninvasive pharmacodynamic biomarkers that indicate increased intratumoral IFN signaling following PRR activation. Positron emission tomography (PET) imaging enables the visualization of tissue metabolic activity, but whether IFN signaling-induced alterations in tumor cell metabolism can be detected using PET has not been investigated. We found that IFN signaling augments pancreatic ductal adenocarcinoma (PDAC) cell nucleotide metabolism via transcriptional induction of metabolism-associated genes including thymidine phosphorylase (TYMP). TYMP catalyzes the first step in the catabolism of thymidine, which competitively inhibits intratumoral accumulation of the nucleoside analog PET probe 3'-deoxy-3'-[18F]fluorothymidine ([18F]FLT). Accordingly, IFN treatment up-regulates cancer cell [18F]FLT uptake in the presence of thymidine, and this effect is dependent upon TYMP expression. In vivo, genetic activation of stimulator of interferon genes (STING), a PRR highly expressed in PDAC, enhances the [18F]FLT avidity of xenograft tumors. Additionally, small molecule STING agonists trigger IFN signaling-dependent TYMP expression in PDAC cells and increase tumor [18F]FLT uptake in vivo following systemic treatment. These findings indicate that [18F]FLT accumulation in tumors is sensitive to IFN signaling and that [18F]FLT PET may serve as a pharmacodynamic biomarker for STING agonist-based therapies in PDAC and possibly other malignancies characterized by elevated STING expression.

Immune checkpoint inhibitors (ICIs), Ipilimumab, Nivolumab, Pembrolizumab and Atezolizumab, have been applied in anti-tumor therapy and demonstrated exciting performance compared to conventional treatments. However, the unsatisfactory response rates, high recurrence and adaptive resistance limit their benefits. Metabolic reprogramming appears to be one of the crucial barriers to immunotherapy. The deprivation of required nutrients and altered metabolites not only promote tumor progression but also confer dysfunction on immune cells in the tumor microenvironment (TME). Glycolysis plays a central role in metabolic reprogramming and immunoregulation in the TME, and many therapies targeting glycolysis have been developed, and their combinations with ICIs are in preclinical and clinical trials. Additional attention has been paid to the role of amino acids, lipids, nucleotides and mitochondrial biogenesis in metabolic reprogramming and clinical anti-tumor therapy. This review attempts to describe reprogramming metabolisms within tumor cells and immune cells, from the aspects of glycolysis, amino acid metabolism, lipid metabolism, nucleotide metabolism and mitochondrial biogenesis and their impact on immunity in the TME, as well as the significance of targeting metabolism in anti-tumor therapy, especially in combination with ICIs. In particular, we highlight the expression mechanism of programmed cell death (ligand) 1 [PD-(L)1] in tumor cells and immune cells under reprogramming metabolism, and discuss in detail the potential of targeting key metabolic pathways to break resistance and improve the efficacy of ICIs based on results from current preclinical and clinical trials. Besides, we draw out biomarkers of potential predictive value in ICIs treatment from a metabolic perspective.

The mechanisms of epigenetic gene regulation—histone modifications, chromatin remodeling, DNA methylation, and noncoding RNA—use metabolites as enzymatic cofactors and substrates in reactions that allow chromatin formation, nucleotide biogenesis, transcription, RNA processing, and translation. Gene expression responds to demands from cellular processes that use specific metabolites and alters or maintains cellular metabolic status. However, the roles of metabolites—particularly nucleotides—as regulatory molecules in epigenetic regulation and biological processes remain largely unknown. Here we review the crosstalk between gene expression, nucleotide metabolism, and cellular processes, and explore the role of metabolism in epigenetics as a critical regulator of biological events.

Host innate immunity is fundamental to the resistance against Candida albicans and Candida glabrata infection, two of the most important agents contributing to human fungal infections. Phagocytic cells, such as neutrophils, constitute the first line of host defense mechanisms, and the release of neutrophil extracellular traps (NETs) represent an important strategy to immobilize and to kill invading microorganisms, arresting the establishment of infection. The purinergic system operates an important role in the homeostasis of immunity and inflammation, and ectophosphatase and ectonucleotidase activities are recognized as essential for survival strategies and infectious potential of several pathogens. The expression and unique activity of a 3′-nucleotidase/nuclease (3′NT/NU), able to hydrolyze not only AMP but also nucleic acids, has been considered as part of a possible mechanism of microbes to escape from NETs. The aim of the present study was to evaluate if yeasts escape from the NET-mediated killing through their 3′NT/NU enzymatic activity contributing to NET-hydrolysis. After demonstrating the presence of 3′NT/NU activity in C. albicans, C. glabrata, and Saccharomyces cerevisiae, we show that, during neutrophils-Candida interaction, when NETs formation and release are triggered, NETs digestion occurs and this process of NETs disruption promoted by yeast cells was prevented by ammonium tetrathiomolybdate (TTM), a 3′NT/NU inhibitor. In conclusion, although the exact nature and specificity of yeasts ectonucleotidases are not completely unraveled, we highlight the importance of these enzymes in the context of infection, helping yeasts to overcome host defenses, whereby C. albicans and C. glabrata can escape NET-mediate killing through their 3′NT/NU activity.

Nucleotides are essential for life. It is easy to validate this statement—one just needs to recall that nucleotides are the building blocks of DNA and RNA, and that many molecules that are central for metabolism, for example ATP, NADH, Co-A, and UDP-Glc, are nucleotides or contain nucleotide

The shift between a proliferating and a nonproliferating state is associated with significant changes in metabolic needs. Proliferating cells tend to have higher metabolic rates, and their metabolic profiles facilitate biosynthesis, as compared to those of non-dividing cells of the same sort. Recent studies have elucidated specific molecules that control metabolic changes while cells shift between proliferation and quiescence. Embryonic stem cells, which are rapidly proliferating, tend to have metabolic patterns that are similar to those of non-stem cells in a proliferative state. Moreover, although adult stem cells tend to be quiescent, their metabolic profiles have been reported in multiple organs to more closely resemble those of proliferating than those of nondividing cells in some respects. The findings raise questions about whether there are metabolic profiles that are required for stemness, and whether these profiles relate to the metabolic properties that may be required for quiescence. Here, we review the literature on how metabolism changes upon commitment to proliferation, and compare the proliferating and nonproliferating metabolic states of differentiated cells, and embryonic and adult stem cells.

Changes in the ecto-5′-nucleotidase activity—an extracellular nucleotide catabolic enzyme may lead to the inflammation and endothelial dysfunction. We investigated the effect of CD73 deletion on the endothelial function and l-arginine metabolism in various age groups of mice. 1-,3-,6-, and 12-month-old, male C57BL/6 J wild type (WT) and C57BL/6 J CD73−/− (CD73−/−) mice were used. Blood samples were used for the analysis of adenine nucleotide concentrations. Serum samples were analyzed for the concentration of amino acids, Interleukin 6 (IL-6), Intercellular Adhesion Molecule 1 (ICAM-1), Vascular Cell Adhesion Molecule 1 (VCAM-1), and endothelial nitric oxide synthase (eNOS) level. Serum and aortic nitrate/nitrite, as well as aortic arginase and NOS activity in endothelial cells (EC) were evaluated. CD73 deletion led to age-dependent increase in IL-6, ICAM-1, and VCAM-1 concentration compared to WT. All CD73−/− mice age groups were characterized by reduced l-Arginine concentration and eNOS level. Significantly lower NOS activity was noticed in EC isolated from CD73−/− mice lungs in comparison to EC isolated from WT lungs. The l-Arginine/ADMA ratio in the CD73−/− decreased in age-dependent manner in comparison to WT. The nitrate/nitrite ratio was reduced in serum and in aortas of 6-month-old CD73−/− mice as compared to WT. The ornithine/arginine and ornithine/citrulline ratios were increased in CD73−/− compared to controls. Blood (erythrocyte) Adenosine-5′-triphosphate and Adenosine-5′-diphosphate levels were reduced in favor to higher blood Adenosine-5′-monophosphate concentration in CD73−/− mice in comparison to WT. The CD73 deletion leads to the development of age-dependent endothelial dysfunction in mice, associated with impaired l-arginine metabolism. CD73 activity seems to protect endothelium. Electronic supplementary material The online version of this article (10.1007/s11010-019-03537-4) contains supplementary material, which is available to authorized users.

The metabolic mechanism of excessive exopolysaccharide (BMPS) synthesis by Bacillus mucilaginosus CGMCC5766 under CaCO3 addition was investigated. Under CaCO3 (5 g/L), the maximum BMPS concentration reached 28.4 g/L, which was 11.2 folds higher than that of the control. Proteomics was then used to analyze the proteins with substantial differences expressed by B. mucilaginosus with and without CaCO3 addition. The proteomic results revealed that the enzymes related to the central metabolic pathway, amino acid biosynthesis, and nucleotide metabolism were depressed. By contrast, the UDP–glucose pyrophosphorylase involved in BMPS biosynthesis was overexpressed and converted metabolic flux from the biomass accumulation to the biosynthesis of BMPS. This research provides a new and widened perspective into understanding the mechanism of BMPS biosynthesis and applying theoretical and practical significance for the improvement of BMPS production from B. mucilaginosus.

The current molecular understanding of Alzheimer’s disease (AD) has still not resulted in successful interventions. Mitochondrial dysfunction of the AD brain is currently emerging as a hallmark of this disease. One mitochondrial function often affected in AD is oxidative phosphorylation responsible for ATP production, but also for production of reactive oxygen species (ROS) and for the de novo synthesis of pyrimidines. This paper reviews the role of mitochondrial produced ROS and pyrimidines in the aetiology of AD and their proposed role in oxidative degeneration of macromolecules, synthesis of essential phospholipids and maintenance of mitochondrial viability in the AD brain.

Glycans - simple or complex carbohydrates - play key roles as recognition determinants and modulators of numerous physiological and pathological processes. Thus, many biotechnological, diagnostic and therapeutic opportunities abound for molecular recognition entities that can bind glycans with high selectivity and affinity. This review begins with an overview of the current biologically and synthetically derived glycan-binding scaffolds that include antibodies, lectins, aptamers and boronic acid-based entities. It is followed by a more detailed discussion on various aspects of their generation, structure and recognition properties. It serves as the basis for highlighting recent key developments and technical challenges that must be overcome in order to fully deal with the specific recognition of a highly diverse and complex range of glycan structures.

In a recent issue of Science Advances, Srivastava et al. report a novel nucleotide biosynthesis regulatory role for UBR7 in NOTCH1-driven T-ALL. Here we will discuss their key findings and the implications for using cancer metabolism to understand the development and progression of T-ALL.

Nucleotide metabolism plays a central role in bacterial physiology, producing the nucleic acids necessary for DNA replication and RNA transcription. Recent studies demonstrate that nucleotide metabolism also proactively contributes to antibiotic-induced lethality in bacterial pathogens and that disruptions to nucleotide metabolism contributes to antibiotic treatment failure in the clinic. As antimicrobial resistance continues to grow unchecked, new approaches are needed to study the molecular mechanisms responsible for antibiotic efficacy. Here we review emerging technologies poised to transform understanding into why antibiotics may fail in the clinic. We discuss how these technologies led to the discovery that nucleotide metabolism regulates antibiotic drug responses and why these are relevant to human infections. We highlight opportunities for how studies into nucleotide metabolism may enhance understanding of antibiotic failure mechanisms.

Nucleoside hydrolases (NSH; nucleosidases) catalyze the cleavage of nucleosides into ribose and free nucleobases. These enzymes have been postulated as key elements controlling the ratio between nucleotide salvage and degradation. Moreover, they play a pivotal role in ureidic legumes by providing the substrate for the synthesis of ureides. Furthermore, nucleotide metabolism has a crucial role during germination and early seedling development, since the developing seedlings require high amount of nucleotide simultaneously to the mobilization of nutrient in cotyledons. In this study, we have cloned two nucleosidases genes from Phaseolus vulgaris, PvNSH1 and PvNSH2, expressed them as recombinant proteins, and characterized their catalytic activities. Both enzymes showed a broad range of substrate affinity; however, PvNSH1 exhibited the highest activity with uridine, followed by xanthosine, whereas PvNSH2 hydrolyses preferentially xanthosine and shows low activity with uridine. The study of the regulation of nucleosidases during germination and early postgerminative development indicated that nucleosidases are induced in cotyledons and embryonic axes just after the radicle emergence, coincident with the induction of nucleases activity and the synthesis of ureides in the embryonic axes, with no remarkable differences in the level of expression of both nucleosidase genes. In addition, nucleosides and nucleobase levels were determined as well in cotyledons and embryonic axes. Our results suggest that PvNSH1 and PvNSH2 play an important role in the mobilization of nutrients during this crucial stage of plant development.

Understanding the dependence of cancers and virus-infected and immune cells on nucleotides can tilt the balance to benefit therapy., Virus-infected cells and cancers share metabolic commonalities that stem from their insatiable need to replicate while evading the host immune system. These similarities include hijacking signaling mechanisms that induce metabolic rewiring in the host to up-regulate nucleotide metabolism and, in parallel, suppress the immune response. In both cancer and viral infections, the host immune cells and, specifically, lymphocytes augment nucleotide synthesis to support their own proliferation and effector functions. Consequently, established treatment modalities targeting nucleotide metabolism against cancers and virally infected cells may result in restricted immune response. Encouragingly, following the introduction of immunotherapy against cancers, multiple studies improved our understanding for improving antigen presentation to the immune system. We propose here that understanding the immune consequences of targeting nucleotide metabolism against cancers may be harnessed to optimize therapy against viral infections.

Epstein-Barr virus (EBV) is associated with 200,000 cancers annually, including B-cell lymphomas in immunosuppressed hosts. Hypomorphic mutations of the de novo pyrimidine synthesis pathway enzyme cytidine 5’ triphosphate synthase 1 (CTPS1) suppress cell mediated immunity, resulting in fulminant EBV infection and EBV+ central nervous system (CNS) lymphomas. Since CTP is a critical precursor for DNA, RNA and phospholipid synthesis, this observation raises the question of whether the isozyme CTPS2 or cytidine salvage pathways help meet CTP demand in EBV-infected B-cells. Here, we found that EBV upregulated CTPS1 and CTPS2 with distinct kinetics in newly infected B-cells. While CRISPR CTPS1 knockout caused DNA damage and proliferation defects in lymphoblastoid cell lines (LCL), which express the EBV latency III program observed in CNS lymphomas, double CTPS1/2 knockout caused stronger phenotypes. EBNA2, MYC and non-canonical NF-□B positively regulated CTPS1 expression. CTPS1 depletion impaired EBV lytic DNA synthesis, suggesting that latent EBV may drive pathogenesis with CTPS1 deficiency. Cytidine rescued CTPS1/2 deficiency phenotypes in EBV-transformed LCL and Burkitt B-cells, highlighting CTPS1/2 as a potential therapeutic target for EBV-driven lymphoproliferative disorders. Collectively, our results suggest that CTPS1 and CTPS2 have partially redundant roles in EBV-transformed B-cells and provide insights into EBV pathogenesis with CTPS1 deficiency.

BACKGROUND An effective therapeutic method still hasn’t been devised for lethal high grade glioma. Thus, a method with high anti-tumoral efficiency, tumoral targeting, and acceptable side effect needs to be designed. Oncolytic virotherapy which can specifically lyse tumor cells via mass replication and deleting nucleotide metabolism related gene, like TK, required in viral replication and overexpressed in tumor cells, provides hope for patients. However, the virus only contained TK deletion is unable to show sufficient specificity of anti-tumoral response in tumor cells. Here, the adapted strain of vaccinia virus with high tumoral specificity due to TK and RR deletion and FUC1 insertion, named T601, is chosen in this project. In clinical application, intra-tumoral injection showed improved anti-tumoral efficiency and acceptable side effect. However, intra-tumoral viral injection in orthotropic glioma model is rare. In this project, various biosafety and antitumoral efficiency parameter would be tested for confirming the biosafety and reliability of intra-tumoral T601 viral injection for future clinical trials. MATERIAL AND METHODS For measuring the IC50 of T601, 10 different amounts of virus was tested in vitro via calculating cell viability with CCK-8(cell counting kit-8). For measuring the further antitumoral response of FCU1, different concentration of the 5-FC was added into the medium with IC50 viral amount. To ensure the biosafety of T601, MTD (maximum tolerance dose) was measured. Based on the MTD result, for evaluating the anti-tumoral efficiency, 106 pfu,105 pfu,104 pfu of virus was intra-tumoral injected in orthotopic GBM bearing mice. Tumor size was measured once a week through in vivo bioimaging system. RESULTS 0.022 MOI, the IC50 of T601, showed high cytotoxicity of T601. Moreover, the significantly decreased cell viability under the combined treatment of 5-FC and 0.22MOI T601 showed intact anti-tumoral function. In MTD assay, except for 107 group, no significant weight loss was found. However, in 107 pfu group, mean body weight decreased around 10% and animal fatality happened on day 9. According to the MTD result, certain amount of virus was intra-tumorally injected. In all treatment group, the tumor size was significantly shrined. At the same time, the survival rate of mice under viral treatment was significantly extended. CONCLUSION In summary, T601 exhibited efficient anti-tumoral function and acceptable side effect. T601 treatment prolonged the survival period of GBM mice with acceptable neurotoxicity, demonstrating that T601 contains necessary criterial for intra-tumoral injection. Ultimately, this project provided basic reference information of dose for future clinical trial.

The nucleotide metabolism has been targeted for many years and in various clinical settings, including cancer. The increased knowledge of certain enzymes involved in this metabolism and in associated cellular processes accumulated over the last few years, gives important information to the druggability of certain proteins and to the use of inhibitors for others. Here, we review recent data on such enzymes with major interest in drug development, i.e. SAMHD1 and the proteins of the NUDIX family. These include information on their roles in cancer progression, correlations with clinical outcome in cancer patients, and development and study of enzymatic inhibitors.

Iron deprivation activates mitophagy and extends lifespan in nematodes. In patients suffering from Parkinson&rsquo, s disease (PD), PINK1-PRKN mutations via deficient mitophagy trigger iron accumulation and reduce lifespan. To evaluate molecular effects of iron chelator drugs as a potential PD therapy, we assessed fibroblasts by global proteome profiles and targeted transcript analyses. In mouse cells, iron shortage decreased protein abundance for iron-binding nucleotide metabolism enzymes (prominently XDH and ferritin homolog RRM2). It also decreased the expression of factors with a role for nucleotide surveillance, which associate with iron-sulfur-clusters (ISC), and are important for growth and survival. This widespread effect included prominently Nthl1-Ppat-Bdh2, but also mitochondrial Glrx5-Nfu1-Bola1, cytosolic Aco1-Abce1-Tyw5, and nuclear Dna2-Elp3-Pold1-Prim2. Incidentally, upregulated Pink1-Prkn levels explained mitophagy induction, the downregulated expression of Slc25a28 suggested it to function in iron export. The impact of PINK1 mutations in mouse and patient cells was pronounced only after iron overload, causing hyperreactive expression of ribosomal surveillance factor Abce1 and of ferritin, despite ferritin translation being repressed by IRP1. This misregulation might be explained by the deficiency of the ISC-biogenesis factor GLRX5. Our systematic survey suggests mitochondrial ISC-biogenesis and post-transcriptional iron regulation to be important in the decision, whether organisms undergo PD pathogenesis or healthy aging.

SummaryWhile the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly-growing bacteria, DNA replication and cell division are temporally-resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine if cell-cycle dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the IMP dehydrogenase guaB2 dedicated to guanosine synthesis displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division, and identify periodically regulated genes that can be related to specific cell biological functions.

Dihydrofolate reductase (DHFR) is an essential enzyme for nucleotide metabolism used to obtain energy and structural nucleic acids. Schistosoma mansoni has all the pathways for pyrimidine biosynthesis, which include the thymidylate cycle and, consequentially, the DHFR enzyme. Here, we describe the characterization of Schistosoma mansoni DHFR (SmDHFR) using isothermal titration calorimetry for the enzymatic activity and thermodynamic determination, also the folate analogs inhibition. Moreover, X-ray crystallography was used to determine the enzyme atomic model at 1.95 A.

Treatment of pediatric acute leukemia might involve combined therapies targeting the FMS-like tyrosine kinase 3 (FLT3) receptor (i.e. quizartinib - AC220) and nucleotide metabolism (cytarabine - AraC). This study addressed the possibility of FLT3 modulating nucleoside salvage processes and, eventually, cytarabine action. Bone marrow samples from 108 pediatric leukemia patients (B-cell precursor acute lymphoblastic leukemia, BCP-ALL: 83; T-ALL: 9; acute myeloid leukemia, AML: 16) were used to determine the mRNA expression levels of FLT3, the cytarabine activating kinase dCK, and the nucleotidases cN-II and SAMHD1. FLT3 mRNA levels positively correlated with dCK, cN-II and SAMHD1 in the studied cohort. FLT3 inhibition using AC220 promoted the expression of cN-II in MV4-11 cells. Indeed, inhibition of cN-II with anthraquinone-2,6-disulfonic acid (AdiS) further potentiated the synergistic action of AC220 and cytarabine, at low concentrations of this nucleoside analog. FLT3 inhibition also down-regulated phosphorylated forms of SAMHD1 in MV4-11 and SEM cells. Thus, inhibition of FLT3 may also target the biochemical machinery associated with nucleoside salvage, which may modulate the ability of nucleoside-derived drugs. In summary, this contribution highlights the need to expand current knowledge on the mechanistic events linking tyrosine-kinase receptors, likely to be druggable in cancer treatment, and nucleotide metabolism, particularly considering tumor cells undergo profound metabolic reprogramming.

SUMMARYRibulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for catalytic activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a nucleotide-based, CO2-incorporating pathway. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham Cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.

International audience; Nucleotide biosynthesis proceeds through a de novo pathway and a salvage route. In the salvage route, free bases and/or nucleosides are recycled to generate the corresponding nucleotides. Thymidine kinase (TK) is the first enzyme in the salvage pathway to recycle thymidine nucleosides as it phosphorylates thymidine to yield thymidine monophosphate. The Arabidopsis genome contains two TK genes -TK1a and TK1b- that show similar expression patterns during development. In this work, we studied the respective roles of the two genes during early development and in response to genotoxic agents targeting the organellar or the nuclear genome. We found that the pyrimidine salvage pathway is crucial for chloroplast development and genome replication, as well as for the maintenance of its integrity, and is thus likely to play a crucial role during the transition from heterotrophy to autotrophy after germination. Interestingly, defects in TK activity could be partially compensated by supplementation of the medium with sugar, and this effect resulted from both the availability of a carbon source and the activation of the nucleotide de novo synthesis pathway, providing evidence for a compensation mechanism between two routes of nucleotide biosynthesis that depend on nutrient availability. Finally, we found differential roles of the TK1a and TK1b genes during the plant response to genotoxic stress, suggesting that different pools of nucleotides exist within the cells and are required to respond to different types of DNA damage. Altogether, our results highlight the importance of the pyrimidine salvage pathway, both during plant development and in response to genotoxic stress.