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Relevant bibliographies by topics / Pyrimidine nucleotide biosynthesis

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Academic literature on the topic 'Pyrimidine nucleotide biosynthesis'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 February 2022

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Journal articles on the topic "Pyrimidine nucleotide biosynthesis"

1

West, Thomas P. "Pyrimidine nucleotide synthesis inPseudomonascitronellolis." Canadian Journal of Microbiology 50, no. 6 (June 1, 2004): 455–59. http://dx.doi.org/10.1139/w04-028.

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Pyrimidine biosynthesis was active in Pseudomonas citronellolis ATCC 13674 and appeared to be regulated by pyrimidines. When wild-type cells were grown on succinate in the presence of uracil, the de novo enzyme activities were depressed while only four enzyme activities were depressed in the glucose-grown cells. On either carbon source, orotic acid-grown cells had diminished aspartate transcarbamoylase, dihydroorotase or OMP decarboxylase activity. Pyrimidine limitation of glucose-grown pyrimidine auxotrophic cells resulted in de novo enzyme activities, except for transcarbamoyolase activity, that were elevated by more than 5-fold compared to their activities in uracil-grown cells. Since pyrimidine limitation of succinate-grown mutant cells produced less enzyme derepression, catabolite repression appeared to be a factor. At the level of enzyme activity, aspartate transcarbamoylase activity in P. citronellolis was strongly inhibited by all effectors tested. Compared to the regulation of pyrimidine biosynthesis in taxonomically-related species, pyrimidine biosynthesis in P. citronellolis appeared more highly regulated.Key words: pyrimidine biosynthesis, regulation, Pseudomonas citronellolis, auxotroph, aspartate transcarbamoylase, inhibition.

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Chunduru, Jayendra, and Thomas P. West. "Pyrimidine nucleotide synthesis in the emerging pathogen Pseudomonas monteilii." Canadian Journal of Microbiology 64, no. 6 (June 2018): 432–38. http://dx.doi.org/10.1139/cjm-2018-0015.

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Regulation of pyrimidine biosynthesis by pyrimidines in the emerging, opportunistic human pathogen Pseudomonas monteilii ATCC 700476 was evident. When wild-type cells were grown on succinate in the presence of uracil or orotic acid, the activities of all 5 pyrimidine biosynthetic enzymes were depressed while the activities of 3 of the enzymes decreased in glucose-grown cells supplemented with uracil or orotic acid compared with unsupplemented cells. Pyrimidine limitation of succinate- or glucose-grown pyrimidine auxotrophic cells lacking orotate phosphoribosyltransferase activity resulted in more than a doubling of the pyrimidine biosynthetic enzyme activities relative to their activities in uracil-grown cells. Independent of carbon source, pyrimidine-limited cells of the pyrimidine auxotrophic cells deficient for dihydroorotase activity generally resulted in a slight elevation or depression of the pyrimidine biosynthetic enzyme activities compared with their activities in cells grown under saturating uracil conditions. Aspartate transcarbamoylase activity in P. monteilii was regulated at the enzyme activity level, since the enzyme was strongly inhibited by CTP, UMP, GMP, GDP, ADP, and UTP. In summary, the regulation of pyrimidine biosynthesis in P. monteilii could be used to control its growth or to differentiate it biochemically from other related species of Pseudomonas.

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Pisithkul, Tippapha, Tyler B. Jacobson, Thomas J. O'Brien, David M. Stevenson, and Daniel Amador-Noguez. "Phenolic Amides Are Potent Inhibitors ofDe NovoNucleotide Biosynthesis." Applied and Environmental Microbiology 81, no. 17 (June 12, 2015): 5761–72. http://dx.doi.org/10.1128/aem.01324-15.

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ABSTRACTAn outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, usingEscherichia colias a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step inde novopurine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.

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Cherwinski, H. M., N. Byars, S. J. Ballaron, G. M. Nakano, J. M. Young, and J. T. Ransom. "Leflunomide interferes with pyrimidine nucleotide biosynthesis." Inflammation Research 44, no. 8 (August 1995): 317–22. http://dx.doi.org/10.1007/bf01796261.

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Szondy, Z., and E. A. Newsholme. "The effect of glutamine concentration on the activity of carbamoyl-phosphate synthase II and on the incorporation of [3H]thymidine into DNA in rat mesenteric lymphocytes stimulated by phytohaemagglutinin." Biochemical Journal 261, no. 3 (August 1, 1989): 979–83. http://dx.doi.org/10.1042/bj2610979.

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The maximum catalytic activities of carbamoyl-phosphate synthase II, a limiting enzyme for pyrimidine nucleotide synthesis, are very much less than those of glutaminase, a limiting enzyme for glutamine utilization, in lymphocytes and macrophages; and the flux through the pathway for pyrimidine formation de novo is only about 0.4% of the rate of glutamine utilization by lymphocytes. The Km of synthase II for glutamine is about 16 microM and the concentration of glutamine necessary to stimulate lymphocyte proliferation half-maximally is about 21 microM. This agreement suggests that the importance of glutamine for these cells is provision of nitrogen for biosynthesis of pyrimidine nucleotides (and probably purine nucleotides). However, the glutamine concentration necessary for half-maximal stimulation of glutamine utilization (glutaminolysis) by the lymphocytes is 2.5 mM. The fact that the rate of glutamine utilization by lymphocytes is markedly in excess of the rate of the pathway for pyrimidine nucleotide synthesis de novo and that the Km and ‘half-maximal concentration’ values are so different, suggests that the glutaminolytic pathway is independent of the use of glutamine nitrogen for pyrimidine synthesis.

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West, Thomas P. "Regulation of pyrimidine nucleotide biosynthesis in Pseudomonas synxantha." Antonie van Leeuwenhoek 92, no. 3 (June 20, 2007): 353–58. http://dx.doi.org/10.1007/s10482-007-9164-4.

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Pels Rijcken, W. R., B. Overdijk, D. H. van den Eijnden, and W. Ferwerda. "Pyrimidine nucleotide metabolism in rat hepatocytes: evidence for compartmentation of nucleotide pools." Biochemical Journal 293, no. 1 (July 1, 1993): 207–13. http://dx.doi.org/10.1042/bj2930207.

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Pyrimidine nucleotide metabolism in rat hepatocytes was studied by measurement of the labelling kinetics of the various intermediates after double labelling with [14C]orotic acid and [3H]cytidine, the precursors for the de novo and the salvage pathways respectively. For the uridine nucleotides, differences were found for the 14C/3H ratios in the UDP-sugars, in UMP (of RNA) and in their precursor UTP, suggesting the existence of separated flows of the radioactive precursors through the de novo and the salvage pathways. Higher ratios in the UDP-sugars, which are synthesized in the cytoplasm, and a lower ratio in UMP (of RNA) relative to the 14C/3H ratio in UTP indicated that UTP derived from orotic acid is preferentially used for the cytoplasmic biosynthesis of the UDP-sugars. Uridine, derived from cytidine, is preferentially used for the nuclear-localized synthesis of RNA. In contrast to these findings, the 14C/3H ratios in the cytidine derivatives CMP-NeuAc and CMP (of RNA), and in the liponucleotides CDP-choline and CDP-ethanolamine, were all lower than that in the precursor CTP. This indicates a preferential utilization of the salvage-derived CTP for the synthesis of the liponucleotides as well as for RNA and CMP-NeuAc. Similar conclusions could be drawn from experiments in which the intracellular amounts of several uridine- and cytidine-nucleotide-containing derivatives were increased by preincubating the hepatocytes with unlabelled pyrimidine nucleotides or ethanolamine. Based on these data, we propose a refined model for the intracellular compartmentation of pyrimidine nucleotide biosynthesis in which three pools of UTP are distinguished: a pool of de novo-derived molecules and a pool of salvage-derived molecules, both of which are channelled to the site of utilization; in addition an ‘overflow’ pool exists, consisting of molecules having escaped from channelling. An overflow pool could also be distinguished for CTP, but no discrimination between de novo and salvage-derived molecules could be made.

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Cortes, Pedro, Francis Dumler, and Nathan W. Levin. "De novo pyrimidine nucleotide biosynthesis in isolated rat glomeruli." Kidney International 30, no. 1 (July 1986): 27–34. http://dx.doi.org/10.1038/ki.1986.146.

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So, Nellie N. C., Patrick C. L. Wong, and Ronald C. Ko. "Pathways of pyrimidine nucleotide biosynthesis in gravid Angiostrongylus cantonensis." Molecular and Biochemical Parasitology 60, no. 1 (July 1993): 45–51. http://dx.doi.org/10.1016/0166-6851(93)90027-u.

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Pal, Sharmistha, Jakub P. Kaplan, Sylwia A. Stopka, Michael S. Regan, Bradley R. Hunsel, Benjamin H. Kann, Nathalie Y. R. Agar, et al. "DDRE-32. THERAPEUTIC TARGETING OF A NOVEL METABOLIC ADDICTION IN DIFFUSE MIDLINE GLIOMA." Neuro-Oncology Advances 3, Supplement_1 (March 1, 2021): i13. http://dx.doi.org/10.1093/noajnl/vdab024.054.

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Abstract Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer that is in need of urgent “outside the box” therapeutic approaches. Recent studies show that tumor cells adapt to stresses created by oncogenic mutations and these oncogene-induced adaptations create vulnerabilities that can be exploited to therapeutic ends. To uncover these oncogene-induced vulnerabilities in DMGs we conducted a genome-wide CRIPSR knockout screen in three DMG lines. The top common DMG dependency pathway that we discovered is de novo pyrimidine biosynthesis. Under normal conditions pyrimidine nucleotide needs are met through the salvage pathway. However, in DMG tumorigenesis, pyrimidine nucleotide synthesis is rewired such that the cells become dependent on the de novo biosynthesis pathway. De novo pyrimidine synthesis is catalyzed by CAD, DHODH and UMPS; all three genes are identified as dependencies in our screen and have been validated using shRNA mediated gene knockdown. Interestingly, DMG cells did not exhibit a dependency on the de novo purine biosynthesis pathway. Using a small molecule inhibitor of DHODH, BAY2402234 [currently studied in phase I trial for myeloid malignancies (NCT03404726)], we have demonstrated and validated, (i) efficacy and specificity of de novo pyrimidine synthesis inhibition in vitro in DMG cells; (ii) de novo pyrimidine addiction is not attributable to cell proliferation; (iii) DHODH inhibition induces apoptosis by hindering replication and inciting DNA damage; (iv) DHODH and ATR inhibition act synergistically to induce DMG cell death; and (v) critical in vivo efficacy. The in vivo experiment documents that BAY2402234 crosses the blood-brain barrier, is present in the brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in intracranial DMG tumors in mice, and prolongs survival of orthotopic DMG tumor bearing mice. Taken together, our studies have identified a novel metabolic vulnerability that can be translated for the treatment of DMG patients.

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Dissertations / Theses on the topic "Pyrimidine nucleotide biosynthesis"

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蘇雅頌 and Ngar-chung Nellie So. "Pyrimidine nucleotide biosynthesis in adult angiostrongylus Cantonensis (Nematoda : Metastrongyloidea)." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1993. http://hub.hku.hk/bib/B3123320X.

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So, Ngar-chung Nellie. "Pyrimidine nucleotide biosynthesis in adult angiostrongylus Cantonensis (Nematoda : Metastrongyloidea) /." [Hong Kong : University of Hong Kong], 1993. http://sunzi.lib.hku.hk/hkuto/record.jsp?B13637745.

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Guo, Wenyue. "A study of structure and function of two enzymes in pyrimidine biosynthesis." Thesis, Boston College, 2012. http://hdl.handle.net/2345/2772.

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Thesis advisor: Evan R. Kantrowitz
Nucleotides, the building blocks for nucleic acids, are essential for cell growth and replication. In E. coli the enzyme responsible for the regulation of pyrimidine nucleotide biosynthesis is aspartate transcarbamoylase (ATCase), which catalyzes the committed step in this pathway. ATCase is allosterically inhibited by CTP and UTP in the presence of CTP, the end products of the pyrimidine pathway. ATP, the end product of the purine biosynthetic pathway, acts as an allosteric activator. ATCase undergoes the allosteric transition from the low-activity and low-affinity T state to the high-activity and high-affinity R state upon the binding of the substrates. In this work we were able to trap an intermediate ATCase along the path of the allosteric transition between the T and R states. Both the X-ray crystallography and small-angle X-ray scattering in solution clearly demonstrated that the mutant ATCase (K164E/E239K) exists in an intermediate quaternary structure shifted about one-third toward the canonical R structure from the T structure. The structure of this intermediate ATCase is helping to understand the mechanism of the allosteric transition on a molecular basis. In this work we also discovered that a metal ion, such as Mg2+, was required for the synergistic inhibition by UTP in the presence of CTP. Therefore, the metal ion also had significant influence on how other nucleotides effect the enzyme. A more physiological relevant model was proposed involving the metal ion. To better understand the allosteric transition of ATCase, time-resolved small-angle X-ray scattering was utilized to track the conformational changes of the quaternary structure of the enzyme upon reaction with the natural substrates, PALA and nucleotide effectors. The transition rate was increased with an increasing concentration of the natural substrates but became over one order of magnitude slower with addition of PALA. Addition of ATP to the substrates increased the rate of the transition whereas CTP or the combination of CTP and UTP exhibited the opposite effect. In this work we also studied E. coli dihydroorotase (DHOase), which catalyzes the following step of ATCase in the pyrimidine biosynthetic pathway. A virtual high throughput screening system was employed to screen for inhibitors of DHOase, which may become potential anti-proliferation and anti-malarial drug candidates. Upon the discovery of the different conformations of the 100's loop of DHOase when substrate or product bound at the active site, we've genetically incorporated an unnatural fluorescent amino acid to a site on this loop in the hope of obtaining a better understanding of the catalysis that may involve the movement of the 100's loop
Thesis (PhD) — Boston College, 2012
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry

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Harris, Katharine Morse. "Studies of structure, function and mechanism in pyrimidine nucleotide biosynthesis." Thesis, Boston College, 2012. http://hdl.handle.net/2345/2594.

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Thesis advisor: Evan R. Kantrowitz
Thesis advisor: Mary F. Roberts
Living organisms depend on enzymes for the synthesis using small molecule precursors of cellular building blocks. For example, the amino acid aspartate is synthesized in one step by the amination of oxaloacetate, an intermediate compound produced in the citric acid cycle, exclusively by means of an aminotransferase enzyme. Therefore, function of this aminotransferase is critical to produce the amino acid. In the Kantrowitz Lab, we seek to understand the molecular rational for the function of enzymes that control rates for the biosynthesis of cellular building blocks. If one imagines the above aspartate-synthesis example as a single running conveyer belt, any oxaloacetate that finds its way onto that belt will be chemically transformed to give aspartate. We can extend this notion of a conveyer belt to any enzyme. Therefore, the rate at which the belt moves dictates the rate of synthesis. Now imagine many, many conveyer belts lined in a row to give analogy to a biosynthesis pathway requiring more than one enzyme for complete chemical synthesis. This is such the case for the biosynthesis of nucleotides and glucose. Nature has developed clever tricks to exquisitely control the rate of product output but means of altering the rate of one or some of the belts in the line of many, without affecting the rate of others. This type of biosynthetic rate regulation is termed allostery. Studies described in this dissertation will address questions of allosteric processes and the chemistry performed by two entirely different enzymes and biosynthetic pathways. The first enzyme of interest is fructose-1,6-bisphosphatase (FBPase) and its role in the biosynthesis of glucose. Following FBPase introduction in Chapter One, Chapter Two describes the minimal atomic scaffold necessary in a new class of allosteric type 2 diabetes drug molecules to effect catalytic inhibition of Homo sapiens FBPase. Following, is the second enzyme of interest, aspartate transcarbamoylase (ATCase) and its role in the biosynthesis of pyrimidine nucleotides. Succeeding ATCase introduction in Chapter Three, Chapter Four describes a body of work exclusively about the catalysis by ATCase. This work was inspired by the human form of the enzyme following the human genome project completion providing data that show likely Homo sapiens ATCase is not allosterically regulated. Chapter Five describes work on a allosterically-regulated, mutant ATCase and provides a biochemical model for the molecular rational for the catalytic inhibition upon cytidine triphosphate (CTP) binding to the allosteric site. The experimental techniques used for answering research questions were enzyme X-ray crystallography, in silico docking, kinetic assay experiments, genetic sub-cloning and genetic mutation
Thesis (PhD) — Boston College, 2012
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry

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Rodriguez, Rodriguez Mauricio. "Pyrimidine nucleotide de novo biosynthesis as a model of metabolic control." Texas A&M University, 2005. http://hdl.handle.net/1969.1/4425.

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This manuscript presents a thorough investigation and description of metabolic control dynamics in vivo and in silico using as a model de novo pyrimidine biosynthesis. Metabolic networks have been studied intensely for decades, helping develop a detailed understanding of the way cells carry out their biosynthetic and catabolic functions. Biochemical reactions have been defined, pathway structures have been proposed, networks of genetic control have been examined, and mechanisms of enzymatic activity and regulation have been elucidated. In parallel with these types of traditional biochemical analysis, there has been increasing interest in engineering cellular metabolism for commercial and medical applications. Several different mathematical approaches have been developed to model biochemical pathways by combining stoichiometric and/or kinetic information with probabilistic analysis, or deciphering the comparative logic of metabolic networks using genomic-derived data. However, most of the research performed to date has relied on theoretical analyses and non-dynamic physiological states. The studies described in this dissertation provide a unique effort toward combining mathematical analysis with dynamic transition experimental data. Most importantly these studies emphasize the significance of providing a quantitative framework for understanding metabolic control. The pathway of de novo biosynthesis of pyrimidines in Escherichia coli provides an ideal model for the study of metabolic control, as there is extensive documentation available on each gene and enzyme involved as well as on their corresponding mechanisms of regulation. Biochemical flux through the pathway was analyzed under dynamic conditions using middle-exponential growth and steady state cultures. The fluctuations of the biochemical pathway intermediates and end products transitions were quantified in response to physiological perturbation. Different growth rates allowed the comparison of rapid versus long-term equilibrium shifts in metabolic adaptation. Finally, monitoring enzymatic activity levels during metabolic transitions provided insight into the interaction of genetic and biochemical mechanisms of regulation. Thus, it was possible to construct a robust mathematical model that faithfully represented, with a remarkable predictability, the nature of the metabolic response to specific environmental perturbations. These studies constitute a significant contribution to the fields of quantitative biochemistry and metabolic control, which can be extended to other cellular processes as well as different organisms.

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Cockrell, Gregory Mercer. "New Insights into Catalysis and Regulation of the Allosteric Enzyme Aspartate Transcarbamoylase." Thesis, Boston College, 2013. http://hdl.handle.net/2345/3156.

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Thesis advisor: Evan R. Kantrowitz
The enzyme aspartate transcarbamoylase (ATCase) is an enzyme in the pyrimidine nucleotide biosynthetic pathway. It was once an attractive target for anti-proliferation drugs but has since become a teaching model due to kinetic properties such as cooperativity and allostery exhibited by the Escherichia coli form of the enzyme. ATCase from E. coli has been extensively studied over that last 60 years and is the textbook example of allosteric enzymes. Through this past research it is understood that ATCase is allosterically inhibited by CTP, the end product of pyrimidine biosynthesis, and allosterically activated by ATP, the end product of the parallel purine biosynthetic pathway. Part of the work discussed in this dissertation involves further understanding the catalytic properties of ATCase by examining an unregulated trimeric form from Bacillus subtilis, a bacterial ATCase that more closely resembles the mammalian form than E. coli ATCase. Through X-ray crystallography and molecular modeling, the complete catalytic cycle of B. subtilis ATCase was visualized, which provided new insights into the manifestation of properties such as cooperativity and allostery in forms of ATCase that are regulated. Most of the work described in the following chapters involves understanding allostery in E. coli ATCase. The work here progressively builds a new model of allostery through new X-ray structures of ATCase*NTP complexes. Throughout these studies it has been determined that the allosteric site is bigger than previously thought and that metal ions play a significant role in the kinetic response of the enzyme to nucleotide effectors. This work proves that what is known about ATCase regulation is inaccurate and that currently accepted, and taught, models of allostery are wrong. This new model of allostery for E. coli ATCase unifies all old and current data for ATCase regulation, and has clarified many previously unexplainable results
Thesis (PhD) — Boston College, 2013
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Chemistry

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Montigny, Jacky de. "Ura5 et ura10, deux genes codant pour deux isoenzymes a activite omp pyrophosphorylase chez la levure saccharomyces cerevisiae : structure, expression et regulation." Strasbourg 1, 1988. http://www.theses.fr/1988STR13198.

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Lortet, Sylviane. "Les mécanismes de synthèse des nucléotides pyrimidiques myocardiques à partir de la cytidine." Grenoble 1, 1987. http://www.theses.fr/1987GRE10056.

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La synthese des nucleotides pyrimidiques du tissu myocardique a ete mesuree sur une preparation de coeur isole et perfuse. Les constantes cinetiques sont determinees a partir des extraits acellulaires, une forte activite kinasique est notee vis a vis de l'uridine et de la cytidine. L'ensemble des resultats montre que la phosphorylation de la cytidine plasmatique pourrait representer la voie essentielle de synthese des nucleotides pyrimidiques myocardiques

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Kumar, Alan P. "Structure-Function Studies on Aspartate Transcarbamoylase and Regulation of Pyrimidine Biosynthesis by a Positive Activator Protein, PyrR in Pseudomonas putida." Thesis, University of North Texas, 2003. https://digital.library.unt.edu/ark:/67531/metadc4362/.

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The regulation of pyrimidine biosynthesis was studied in Pseudomonas putida. The biosynthetic and salvage pathways provide pyrimidine nucleotides for RNA, DNA, cell membrane and cell wall biosynthesis. Pyrimidine metabolism is intensely studied because many of its enzymes are targets for chemotheraphy. Four aspects of pyrimidine regulation are described in this dissertation. Chapter I compares the salvage pathways of Escherichia coli and P. putida. Surprisingly, P. putida lacks several salvage enzymes including nucleoside kinases, uridine phosphorylase and cytidine deaminase. Without a functional nucleoside kinase, it was impossible to feed exogenous uridine to P. putida. To obviate this problem, uridine kinase was transferred to P. putida from E. coli and shown to function in this heterologous host. Chapter II details the enzymology of Pseudomonas aspartate transcarbamoylase (ATCase), its allosteric regulation and how it is assembled. The E. coli ATCase is a dodecamer of two different polypeptides, encoded by pyrBI. Six regulatory (PyrI) and six catalytic (PyrB) polypeptides assemble from two preformed trimers (B3) and three preformed regulatory dimers (I2) in the conserved 2B3:3I2 molecular structure. The Pseudomonas ATCase also assembles from two different polypeptides encoded by pyrBC'. However, a PyrB polypeptide combines with a PyrC. polypeptide to form a PyrB:PyrC. protomer; six of these assemble into a dodecamer of structure 2B3:3C'2. pyrC' encodes an inactive dihydroorotase with pyrB and pyrC' overlapping by 4 bp. Chapter III explores how catabolite repression affects pyrimidine metabolism. The global catabolite repression control protein, Crc, has been shown to affect pyrimidine metabolism in a number of ways. This includes orotate transport for use as pyrimidine, carbon and nitrogen sources. Orotate is important because it interacts with PyrR in repressing the pyr genes. Chapter IV describes PyrR, the positive activator of the pyrimidine pathway. As with other positive activator proteins, when pyrimidine nucleotides are depleted, PyrR binds to DNA thereby enhancing expression of pyrD, pyrE and pyrF genes. When pyrimidine nucleotides are in excess, the PyrR apoprotein binds to orotate, its co-repressor, to shut down all the pyrimidine genes. Like many positive activators, PyrR is subject to autoregulation and has catalytic activity for uracil phosphoribosyltransferase inducible by orotate.

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Brichta, Dayna Michelle. "Construction of a Pseudomonas aeruginosa Dihydroorotase Mutant and the Discovery of a Novel Link between Pyrimidine Biosynthetic Intermediates and the Ability to Produce Virulence Factors." Thesis, University of North Texas, 2003. https://digital.library.unt.edu/ark:/67531/metadc4344/.

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The ability to synthesize pyrimidine nucleotides is essential for most organisms. Pyrimidines are required for RNA and DNA synthesis, as well as cell wall synthesis and the metabolism of certain carbohydrates. Recent findings, however, indicate that the pyrimidine biosynthetic pathway and its intermediates maybe more important for bacterial metabolism than originally thought. Maksimova et al., 1994, reported that a P. putida M, pyrimidine auxotroph in the third step of the pathway, dihydroorotase (DHOase), failed to produce the siderophore pyoverdin. We created a PAO1 DHOase pyrimidine auxotroph to determine if this was also true for P. aeruginosa. Creation of this mutant was a two-step process, as P. aeruginosa has two pyrC genes (pyrC and pyrC2), both of which encode active DHOase enzymes. The pyrC gene was inactivated by gene replacement with a truncated form of the gene. Next, the pyrC2 gene was insertionally inactivated with the aacC1 gentamicin resistance gene, isolated from pCGMW. The resulting pyrimidine auxotroph produced significantly less pyoverdin than did the wild type. In addition, the mutant produced 40% less of the phenazine antibiotic, pyocyanin, than did the wild type. As both of these compounds have been reported to be vital to the virulence response of P. aeruginosa, we decided to test the ability of the DHOase mutant strain to produce other virulence factors as well. Here we report that a block in the conversion of carbamoyl aspartate (CAA) to dihydroorotate significantly impairs the ability of P. aeruginosa to affect virulence. We believe that the accumulation of CAA in the cell is the root cause of this observed defect. This research demonstrates a potential role for pyrimidine intermediates in the virulence response of P. aeruginosa and may lead to novel targets for chemotherapy against P. aeruginosa infections.

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Book chapters on the topic "Pyrimidine nucleotide biosynthesis"

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Bein, Kiflai, and David R. Evans. "de novo Pyrimidine Nucleotide Biosynthesis in Synchronized Chinese Hamster Ovary Cells." In Purine and Pyrimidine Metabolism in Man VIII, 545–48. Boston, MA: Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-2584-4_115.

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Forsgren, A. "Effect of 4-Quinolone Antibiotics on Cell Function, Cell Growth, and Pyrimidine Nucleotide Biosynthesis in Human Lymphocytes In Vitro." In The Influence of Antibiotics on the Host-Parasite Relationship III, 255–62. Berlin, Heidelberg: Springer Berlin Heidelberg, 1989. http://dx.doi.org/10.1007/978-3-642-73653-7_35.

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Löffler, Monika, Johannes Jöckel, Gertrud Schuster, and Cornelia Becker. "Dihydroorotat-ubiquinone oxidoreductase links mitochondria in the biosynthesis of pyrimidine nucleotides." In Detection of Mitochondrial Diseases, 125–29. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4615-6111-8_19.

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Marinaki, Anthony M., Lynette D. Fairbanks, and Richard W. E. Watts. "Disorders of purine and pyrimidine metabolism." In Oxford Textbook of Medicine, edited by Timothy M. Cox, 2015–31. Oxford University Press, 2020. http://dx.doi.org/10.1093/med/9780198746690.003.0230.

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Disorders of purine and pyrimidine metabolism are due to abnormalities in the biosynthesis, interconversion, and degradation of the purines—adenine and guanine—and of the pyrimidines—cytosine, thymine, and uracil. The purine nucleotides, their cyclic derivatives (cAMP and cGMP), and their more highly phosphorylated derivatives have functions in many aspects of intermediary metabolism. Purine compounds also function as signal transducers, neurotransmitters, vasodilators, and mediators of platelet aggregation. Disorders of purine metabolism—the end point of purine metabolism in humans is uric acid. When uric acid levels become supersaturated in body fluids, uric acid and sodium urate monohydrate crystallize, causing gout. This results from either overproduction or underexcretion of urate, or from a combination of these defects. Decreased net tubular urate secretion is most often due to genetic polymorphism in uric acid transporters and is the commonest cause of primary (‘idiopathic’) gout. Gout may be secondary to a wide variety of renal disorders. Gout is also a consequence of enzymatic defects that accelerate de novo purine synthesis. Acute attacks of gout are treated with nonsteroidal anti-inflammatory drugs, colchicine, or steroids. Hypouricaemia may be caused by inherited disorders of uric acid biosynthesis or may be due to inherited or acquired renal tubule transport defects. Disorders of pyrimidine metabolism—the de novo synthesis of pyrimidine nucleotides involves a series of six reactions beginning with the formation of carbamyl phosphate and concluding with orotidine monophosphate, which then undergoes a series of interconversion and salvage reactions. The inherited disorders of pyrimidine metabolism, which can present in a wide variety of ways, are much less common and/or much less easily recognized than disorders of purine metabolism.

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Watts, Richard W. E. "Disorders of purine and pyrimidine metabolism." In Oxford Textbook of Medicine, 1619–35. Oxford University Press, 2010. http://dx.doi.org/10.1093/med/9780199204854.003.1204.

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Abstract:

These disorders are due to abnormalities in the biosynthesis, interconversion and degradation of the purines—adenine and guanine—and of the pyrimidines—cytosine, thymine and uracil. All are heterocyclic bases which exist in tri-, di-, and mono-phosphorylated forms, and as either deoxyribosylated or ribosylated derivatives (deoxyribose and ribose are pentose carbohydrates). The phosphorylated deoxyribosylated and ribosylated derivatives are termed ‘nucleotides’, and the purely ribosylated derivatives, which lack the phosphate group, are ‘nucleosides’....

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Conference papers on the topic "Pyrimidine nucleotide biosynthesis"

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Matherly, Larry H., Xin Zhang, Adrianne Wallace, Zhanjun Hou, Christina George, Xilin Zhou, and Aleem Gangjee. "Abstract 4481: Tumor-targeting with novel 6-substituted thienoyl[2,3-d]pyrimidine antifolates via cellular uptake by folate receptor α, and inhibition of de novopurine nucleotide biosynthesis." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4481.

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Cherian, Christina, Yiqiang Wang, Shermaine Mitchell-Ryan, Steven Orr, Zhanjun Hou, Aleem Gangjee, and Larry H. Matherly. "Abstract 5493: Tumor-targeting with novel non-benzoyl 6-substituted pyrrolo[2,3-d]pyrimidine antifolates via cellular uptake by folate receptor α and inhibition ofde novopurine nucleotide biosynthesis." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5493.

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Mitchell-Ryan, Shermaine K., Lei Wang, Steven Orr, Sita Kugel, Christina Cherian, Aleem Gangjee, and Larry H. Matherly. "Abstract 5494: Novel 6-substituted pyrrolo[2,3-d]pyrimidine thienoyl antifolate regioisomers target folate receptor alpha positive ovarian cancer cells via inhibition of de novo purine nucleotide biosynthesis." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-5494.

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Wallace-Povirk, Adrianne, Nian Tong, Carrie O'Connor, Zhanjun Hou, Aleem Gangjee, Larry Matherly, and Xilin Zhou. "Abstract 3983: Tumor-targeting with novel dual-targeted 6-substituted thieno[2,3-d]pyrimidine antifolates via cellular uptake by folate receptor α, and inhibition of de novo purine nucleotide biosynthesis." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-3983.

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Mitchell-Ryan, Shermaine K., Yiqiang Wang, Christina Cherian, Erika Etnyre, Zhanjun Hou, Aleem Gangjee, and Larry H. Matherly. "Abstract 3822: A tumor-targeted 5-pyrrolo[2,3-d]pyrimidine antifolate is a selective substrate for folate receptor ≤ and potent inhibitor of 5-amino-4-carboxamide formyltransferase inde novopurine nucleotide biosynthesis." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-3822.

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Cherian, Christina, Lei Wang, Adrianne Wallace, Steven Orr, Zhanjun Hou, Aleem Gangjee, and Larry H. Matherly. "Abstract 2706: Tumor-targeting with novel pyridyl 6-substituted pyrrolo[2,3-d]pyrimidine antifolates via cellular uptake by folate receptor (FR) α and the proton-coupled folate transporter (PCFT) and inhibition ofde novopurine nucleotide biosynthesis." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-2706.

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