1
|
Sha Z, Benkovic SJ. Purinosomes spatially co-localize with mitochondrial transporters. J Biol Chem 2024; 300:107620. [PMID: 39098527 PMCID: PMC11402301 DOI: 10.1016/j.jbc.2024.107620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/26/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024] Open
Abstract
In this study, we advance our understanding of the spatial relationship between the purinosome, a liquid condensate consisting of six enzymes involved in de novo purine biosynthesis, and mitochondria. Previous research has shown that purinosomes move along tubulin toward mitochondria, suggesting a direct uptake of glycine from mitochondria. Here, we propose that the purinosome is located proximally to the mitochondrial transporters SLC25A13 and SLC25A38, facilitating the uptake of glycine, aspartate, and glutamate, essential factors for purine synthesis. We utilized the proximity ligation assay and APEX proximity labeling to investigate the association between purinosome proteins and mitochondrial transporters. Our results indicate that purinosome assembly occurs close to the mitochondrial membrane under purine-deficient conditions, with the transporters migrating to be adjacent to the purinosome. Furthermore, both targeted and non-targeted analyses suggest that the SLC25A13-APEX2-V5 probe accurately reflects endogenous cellular status. These findings provide insights into the spatial organization of purine biosynthesis and lay the groundwork for further investigations into additional proteins involved in this pathway.
Collapse
Affiliation(s)
- Zhou Sha
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
| |
Collapse
|
2
|
Dementieva NV, Dysin AP, Shcherbakov YS, Nikitkina EV, Musidray AA, Petrova AV, Mitrofanova OV, Plemyashov KV, Azovtseva AI, Griffin DK, Romanov MN. Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study. Animals (Basel) 2024; 14:251. [PMID: 38254422 PMCID: PMC10812825 DOI: 10.3390/ani14020251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.
Collapse
Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Elena V. Nikitkina
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Artem A. Musidray
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Anna V. Petrova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | - Kirill V. Plemyashov
- Federal State Budgetary Educational Institution of Higher Education “St. Petersburg State University of Veterinary Medicine”, 196084 St. Petersburg, Russia;
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L. K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia; (A.P.D.); (Y.S.S.); (E.V.N.); (A.A.M.); (A.V.P.); (O.V.M.); (A.I.A.)
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK;
- L. K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, 142132 Podolsk, Moscow Oblast, Russia
| |
Collapse
|
3
|
Biochemical composition and adenylate energy charge shifts in longfin yellowtail (Seriola rivoliana) embryos during development under different temperatures. J Therm Biol 2023; 112:103470. [PMID: 36796915 DOI: 10.1016/j.jtherbio.2023.103470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 01/22/2023]
Abstract
The longfin yellowtail Seriola rivoliana is an emerging species for aquaculture diversification worldwide and production relies on fertilized eggs from captive broodstock. Temperature is the main factor that influences the developmental process and success during fish ontogeny. However, the effects of temperature on the utilization of the main biochemical reserves and bioenergetics are scarcely investigated in fish, whereas protein, lipid and carbohydrate metabolism have critical roles in maintaining cellular energy homeostasis. In this context, we aimed to evaluate metabolic fuels (protein, lipids, triacylglicerides, carbohydrates), adenylic nucleotides and derivates (ATP, ADP, AMP, IMP), and the adenylate energy charge (AEC) during embryogenesis and in hatched larvae in S. rivoliana at different temperatures. For this purpose, fertilized eggs were incubated at six constant (20, 22, 24, 26, 28 and 30 °C) and two oscillating (21⇄29 °C) temperatures. Biochemical analyses were made at blastula, optic vesicles, neurula, prehatch and hatch periods. Results indicated that the developmental period had a major influence on the biochemical composition at any temperature regime tested during the incubation. Protein content decreased only at hatching mainly due to the loss of the chorion, total lipids tended to increase at the neurula period and variations in carbohydrates depended on the particular spawn analyzed. Triacylglicerides were a critical egg fuel during hatching. The high AEC during embryogenesis and even in hatched larvae suggested an optimal energy balance regulation. The lack of critical biochemical changes from different temperature regimes during embryo development confirmed that this species exhibits a high adaptive capacity in response to constant and fluctuating temperatures. However, the timing of hatching was the most critical period of development, where biochemical components and energy utilization significantly changed. The oscillating temperatures tested may have physiological advantages without detrimental energetic effects that will require further research on larval quality after hatching.
Collapse
|
4
|
Shon H, Matveeva EA, Jull EC, Hu Y, Coupet TA, Lee YS. Evidence Supporting Substrate Channeling between Domains of Human PAICS: A Time-Course Analysis of 13C-Bicarbonate Incorporation. Biochemistry 2022; 61:575-582. [PMID: 35285625 PMCID: PMC8988938 DOI: 10.1021/acs.biochem.1c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human phosphoribosylaminoimidazole carboxylase phosphoribosylaminoimdiazole succinocarboxamide synthetase (PAICS) is a dual activity enzyme catalyzing two consecutive reactions in de novo purine nucleotide synthesis. Crystallographic structures of recombinant human PAICS suggested the channeling of 4-carboxy-5-aminoimidazole-1-ribose-5'-phosphate (CAIR) between two active sites of PAICS, while a prior work of an avian PAICS suggested otherwise. Here, we present time-course mass spectrometric data supporting the channeling of CAIR between domains of recombinant human PAICS. Time-course mass spectral analysis showed that CAIR added to the bulk solution (CAIRbulk) is decarboxylated and re-carboxylated before the accumulation of succinyl-5-aminoimidazole-4-carboxamide-1-ribose-5'-phosphate (SAICAR). An experiment with 13C-bicarbonate showed that SAICAR production was proportional to re-carboxylated CAIR instead of total CAIR or CAIRbulk. This result indicates that the SAICAR synthase domain selectively uses enzyme-made CAIR over CAIRbulk, which is consistent with the channeling model. This channeling between PAICS domains may be a part of a larger channeling process in de novo purine nucleotide synthesis.
Collapse
Affiliation(s)
- Hyungjoo Shon
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ella C Jull
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yijia Hu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tiffany A Coupet
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Young-Sam Lee
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| |
Collapse
|
5
|
Abstract
Over the past fifteen years, we have unveiled a new mechanism by which cells achieve greater efficiency in de novo purine biosynthesis. This mechanism relies on the compartmentalization of de novo purine biosynthetic enzymes into a dynamic complex called the purinosome. In this review, we highlight our current understanding of the purinosome with emphasis on its biophysical properties and function and on the cellular mechanisms that regulate its assembly. We propose a model for functional purinosomes in which they consist of at least ten enzymes that localize near mitochondria and carry out de novo purine biosynthesis by metabolic channeling. We conclude by discussing challenges and opportunities associated with studying the purinosome and analogous metabolons. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Anthony M Pedley
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA;
| | - Vidhi Pareek
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA; .,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA;
| |
Collapse
|
6
|
Yamamoto N, Sampei G, Kawai G. Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase. Life (Basel) 2022; 12:281. [PMID: 35207568 PMCID: PMC8880213 DOI: 10.3390/life12020281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/12/2022] [Indexed: 12/03/2022] Open
Abstract
The second step in the de novo biosynthetic pathway of purine is catalyzed by PurD, which consumes an ATP molecule to produce glycinamide ribonucleotide (GAR) from glycine and phosphoribosylamine (PRA). PurD initially reacts with ATP to produce an intermediate, glycyl-phosphate, which then reacts with PRA to produce GAR. The structure of the glycyl-phosphate intermediate bound to PurD has not been determined. Therefore, the detailed reaction mechanism at the molecular level is unclear. Here, we developed a computational protocol to analyze the free-energy profile for the glycine phosphorylation process catalyzed by PurD, which examines the free-energy change along a minimum energy path based on a perturbation method combined with the quantum mechanics and molecular mechanics hybrid model. Further analysis revealed that during the formation of glycyl-phosphate, the partial atomic charge distribution within the substrate molecules was not localized according to the formal charges, but was delocalized overall, which contributed significantly to the interaction with the charged amino acid residues in the ATP-grasp domain of PurD.
Collapse
Affiliation(s)
- Norifumi Yamamoto
- Department of Applied Chemistry, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Chiba, Japan
| | - Genichi Sampei
- Department of Applied Physics and Chemistry, Faculty of Electro-Communications, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu 182-8585, Tokyo, Japan;
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Chiba, Japan;
| |
Collapse
|
7
|
Transcriptomic Profile of New Gene Markers Encoding Proteins Responsible for Structure of Porcine Ovarian Granulosa Cells. BIOLOGY 2021; 10:biology10111214. [PMID: 34827207 PMCID: PMC8615192 DOI: 10.3390/biology10111214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary The extracellular matrix (ECM) is involved in many physiological processes that occur in the ovary and affect reproduction in animals and humans. The ECM has been shown to significantly affect folliculogenesis, ovulation, and corpus luteum formation. This is mainly due to the involvement of ECM in intercellular signaling. In the present study, we report the gene expression profile of porcine granulosa cells during their primary in vitro culture. The genes presented are related to ECM formation but also to cadherins and integrins that influence intercellular dialogue. During the study, it was shown that most of the genes were upregulated. A detailed understanding of the expression of genes such as POSTN, CHI3L1, CAV-1, IRS1, DCN in in vitro culture of granulosa cells may provide a basis for further studies on the molecular mechanisms occurring within the ovary. Knowledge of ECM-related gene expression within granulosa cells can also be used to study the recently discovered stemness of these cells. Moreover, the presented data may serve for the development of assisted reproduction techniques, which, especially in vitro, are becoming increasingly common. Abstract The extracellular matrix (ECM) in granulosa cells is functionally very important, and it is involved in many processes related to ovarian follicle growth and ovulation. The aim of this study was to describe the expression profile of genes within granulosa cells that are associated with extracellular matrix formation, intercellular signaling, and cell–cell fusion. The material for this study was ovaries of sexually mature pigs obtained from a commercial slaughterhouse. Laboratory-derived granulosa cells (GCs) from ovarian follicles were cultured in a primary in vitro culture model. The extracted genetic material (0, 48, 96, and 144 h) were subjected to microarray expression analysis. Among 81 genes, 66 showed increased expression and only 15 showed decreased expression were assigned to 7 gene ontology groups “extracellular matrix binding”, “extracellular matrix structural constituent”, “binding, bridging”, “cadherin binding”, “cell adhesion molecule binding”, “collagen binding” and “cadherin binding involved in cell-cell adhesion”. The 10 genes with the highest expression (POSTN, ITGA2, FN1, LAMB1, ITGB3, CHI3L1, PCOLCE2, CAV1, DCN, COL14A1) and 10 of the most down-regulated (SPP1, IRS1, CNTLN, TMPO, PAICS, ANK2, ADAM23, ABI3BP, DNAJB1, IGF1) were selected for further analysis. The results were validated by RT-qPCR. The current results may serve as preliminary data for further analyses using in vitro granulosa cell cultures in assisted reproduction technologies, studies of pathological processes in the ovary as well as in the use of the stemness potential of GCs.
Collapse
|
8
|
Ruan X, Deng X, Tan M, Wang Y, Hu J, Sun Y, Yu C, Zhang M, Jiang N, Jiang R. Effect of resveratrol on the biofilm formation and physiological properties of avian pathogenic Escherichia coli. J Proteomics 2021; 249:104357. [PMID: 34450330 DOI: 10.1016/j.jprot.2021.104357] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/26/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) is widely distributed, causing great economic losses to the poultry industry. The formation of APEC biofilms causes chronic, persistent, and repeated infections in the clinic, making treatment difficult. Resveratrol is a natural product, which has good health benefits including antimicrobial, anti-inflammatory, and cardiovascular activities. Resveratrol shows efficient inhibition of bacterial biofilm formation. However, a comprehensive understanding of the proteomic properties of APEC treated resveratrol is still lacking. In this study, APEC cells treated by resveratrol were investigated using a label-free differential proteomic method. Several proteins, including those related to a two-component system and chemotaxis, were found to be implicated in APEC biofilm formation. In addition, the physiological properties were significantly changed in terms of purine, pyruvate, and glyoxylate and dicarboxylate metabolism in APEC. Data are available via ProteomeXchange with the identifier PXD025706. We speculated that pyruvate dehydrogenase might be a potential target to inhibit Escherichia coli biofilm formation. Overall, our results indicated that resveratrol inhibits APEC biofilm formation by regulating the levels of proteins in two-component systems, especially chemotaxis proteins. The results showed that resveratrol had a potential application in inhibiting the biofilm formation of APEC. SIGNIFICANCE: This study elucidated the mechanism of resveratrol inhibiting biofilm formation of avian pathogenic Escherichia coli (APEC) based on a label-free differential proteomics. It was indicated that resveratrol inhibits APEC biofilm formation by regulating the levels of proteins in two component systems, especially chemotaxis proteins. Meanwhile, we speculated that pyruvate dehydrogenase might be a potential target to inhibit Escherichia coli biofilm formation. It shows that resveratrol has a potential application prospect in inhibiting the biofilm formation of APEC.
Collapse
Affiliation(s)
- Xiangchun Ruan
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Hefei, Anhui 230036, China.
| | - Xiaoling Deng
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Meiling Tan
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Youwei Wang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jidong Hu
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ying Sun
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Chengbo Yu
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Meishi Zhang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Nuohao Jiang
- Laboratory of Veterinary Pharmacology and Toxicology, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Runshen Jiang
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei, Anhui 230036, China.
| |
Collapse
|
9
|
Abstract
The focus of this review is the human de novo purine biosynthetic pathway. The pathway enzymes are enumerated, as well as the reactions they catalyze and their physical properties. Early literature evidence suggested that they might assemble into a multi-enzyme complex called a metabolon. The finding that fluorescently-tagged chimeras of the pathway enzymes form discrete puncta, now called purinosomes, is further elaborated in this review to include: a discussion of their assembly; the role of ancillary proteins; their locus at the microtubule/mitochondria interface; the elucidation that at endogenous levels, purinosomes function to channel intermediates from phosphoribosyl pyrophosphate to AMP and GMP; and the evidence for the purinosomes to exist as a protein condensate. The review concludes with a consideration of probable signaling pathways that might promote the assembly and disassembly of the purinosome, in particular the identification of candidate kinases given the extensive phosphorylation of the enzymes. These collective findings substantiate our current view of the de novo purine biosynthetic metabolon whose properties will be representative of how other metabolic pathways might be organized for their function.
Collapse
Affiliation(s)
- Vidhi Pareek
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Anthony M Pedley
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
10
|
Wang SA, Ko Y, Zeng J, Geng Y, Ren D, Ogasawara Y, Irani S, Zhang Y, Liu HW. Identification of the Formycin A Biosynthetic Gene Cluster from Streptomyces kaniharaensis Illustrates the Interplay between Biological Pyrazolopyrimidine Formation and de Novo Purine Biosynthesis. J Am Chem Soc 2019; 141:6127-6131. [PMID: 30942582 PMCID: PMC6612245 DOI: 10.1021/jacs.9b00241] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Formycin A is a potent purine nucleoside antibiotic with a C-glycosidic linkage between the ribosyl moiety and the pyrazolopyrimidine base. Herein, a cosmid is identified from the Streptomyces kaniharaensis genome library that contains the for gene cluster responsible for the biosynthesis of formycin. Subsequent gene deletion experiments and in vitro characterization of the forBCH gene products established their catalytic functions in formycin biosynthesis. Results also demonstrated that PurH from de novo purine biosynthesis plays a key role in pyrazolopyrimidine formation during biosynthesis of formycin A. The participation of PurH in both pathways represents a good example of how primary and secondary metabolism are interlinked.
Collapse
Affiliation(s)
- Shao-An Wang
- Department of Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Yeonjin Ko
- Department of Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Jia Zeng
- Department of Molecular Biosciences, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Yujie Geng
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Daan Ren
- Department of Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Yasushi Ogasawara
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Seema Irani
- Department of Molecular Biosciences, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Yan Zhang
- Department of Molecular Biosciences, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| | - Hung-wen Liu
- Department of Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 78712
| |
Collapse
|
11
|
Tormena CD, Marcheafave GG, Rakocevic M, Bruns RE, Scarminio IS. Sequential mixture design optimization for divergent metabolite analysis: Enriched carbon dioxide effects on Coffea arabica L. leaves and buds. Talanta 2019; 191:382-389. [DOI: 10.1016/j.talanta.2018.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/31/2018] [Accepted: 09/01/2018] [Indexed: 11/28/2022]
|
12
|
Discovering novel hydrolases from hot environments. Biotechnol Adv 2018; 36:2077-2100. [PMID: 30266344 DOI: 10.1016/j.biotechadv.2018.09.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
Novel hydrolases from hot and other extreme environments showing appropriate performance and/or novel functionalities and new approaches for their systematic screening are of great interest for developing new processes, for improving safety, health and environment issues. Existing processes could benefit as well from their properties. The workflow, based on the HotZyme project, describes a multitude of technologies and their integration from discovery to application, providing new tools for discovering, identifying and characterizing more novel thermostable hydrolases with desired functions from hot terrestrial and marine environments. To this end, hot springs worldwide were mined, resulting in hundreds of environmental samples and thousands of enrichment cultures growing on polymeric substrates of industrial interest. Using high-throughput sequencing and bioinformatics, 15 hot spring metagenomes, as well as several sequenced isolate genomes and transcriptomes were obtained. To facilitate the discovery of novel hydrolases, the annotation platform Anastasia and a whole-cell bioreporter-based functional screening method were developed. Sequence-based screening and functional screening together resulted in about 100 potentially new hydrolases of which more than a dozen have been characterized comprehensively from a biochemical and structural perspective. The characterized hydrolases include thermostable carboxylesterases, enol lactonases, quorum sensing lactonases, gluconolactonases, epoxide hydrolases, and cellulases. Apart from these novel thermostable hydrolases, the project generated an enormous amount of samples and data, thereby allowing the future discovery of even more novel enzymes.
Collapse
|
13
|
Ko Y, Wang SA, Ogasawara Y, Ruszczycky MW, Liu HW. Identification and Characterization of Enzymes Catalyzing Pyrazolopyrimidine Formation in the Biosynthesis of Formycin A. Org Lett 2017; 19:1426-1429. [PMID: 28233490 DOI: 10.1021/acs.orglett.7b00355] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Genome scanning of Streptomyces kaniharaensis, the producer of formycin A, reveals two sets of purA, purB, purC, and purH genes. The Pur enzymes catalyze pyrimidine assembly of purine nucleobases. To test whether enzymes encoded by the second set of pur genes catalyze analogous transformations in formycin biosynthesis, formycin B 5'-phosphate was synthesized and shown to be converted by ForA and ForB to formycin A 5'-phosphate. These results support that For enzymes are responsible for formycin formation.
Collapse
Affiliation(s)
- Yeonjin Ko
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Shao-An Wang
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Yasushi Ogasawara
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Mark W Ruszczycky
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
14
|
Coleto I, Trenas AT, Erban A, Kopka J, Pineda M, Alamillo JM. Functional specialization of one copy of glutamine phosphoribosyl pyrophosphate amidotransferase in ureide production from symbiotically fixed nitrogen in Phaseolus vulgaris. PLANT, CELL & ENVIRONMENT 2016; 39:1767-1779. [PMID: 27004600 DOI: 10.1111/pce.12743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
Purines are essential molecules formed in a highly regulated pathway in all organisms. In tropical legumes, the nitrogen fixed in the nodules is used to generate ureides through the oxidation of de novo synthesized purines. Glutamine phosphoribosyl pyrophosphate amidotransferase (PRAT) catalyses the first committed step of de novo purine synthesis. In Phaseolus vulgaris there are three genes coding for PRAT. The three full-length sequences, which are intron-less genes, were cloned, and their expression levels were determined under conditions that affect the synthesis of purines. One of the three genes, PvPRAT3, is highly expressed in nodules and protein amount and enzymatic activity in these tissues correlate with nitrogen fixation activity. Inhibition of PvPRAT3 gene expression by RNAi-silencing and subsequent metabolomic analysis of the transformed roots shows that PvPRAT3 is essential for the synthesis of ureides in P. vulgaris nodules.
Collapse
Affiliation(s)
- Inmaculada Coleto
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Almudena T Trenas
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Alexander Erban
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Joachim Kopka
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Josefa M Alamillo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas. Campus de Excelencia Internacional Agroalimentario, CEIA3. Campus de Rabanales, Edif. Severo Ochoa, Universidad de Córdoba, 14071, Córdoba, Spain
| |
Collapse
|
15
|
Watanabe Y, Yanai H, Kanagawa M, Suzuki S, Tamura S, Okada K, Baba S, Kumasaka T, Agari Y, Chen L, Fu ZQ, Chrzas J, Wang BC, Nakagawa N, Ebihara A, Masui R, Kuramitsu S, Yokoyama S, Sampei GI, Kawai G. Crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii. Acta Crystallogr F Struct Biol Commun 2016; 72:627-35. [PMID: 27487927 PMCID: PMC4973304 DOI: 10.1107/s2053230x1600978x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
The crystal structures of a subunit of the formylglycinamide ribonucleotide amidotransferase, PurS, from Thermus thermophilus, Sulfolobus tokodaii and Methanocaldococcus jannaschii were determined and their structural characteristics were analyzed. For PurS from T. thermophilus, two structures were determined using two crystals that were grown in different conditions. The four structures in the dimeric form were almost identical to one another despite their relatively low sequence identities. This is also true for all PurS structures determined to date. A few residues were conserved among PurSs and these are located at the interaction site with PurL and PurQ, the other subunits of the formylglycinamide ribonucleotide amidotransferase. Molecular-dynamics simulations of the PurS dimer as well as a model of the complex of the PurS dimer, PurL and PurQ suggest that PurS plays some role in the catalysis of the enzyme by its bending motion.
Collapse
Affiliation(s)
- Yuzo Watanabe
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Hisaaki Yanai
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Mayumi Kanagawa
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Sakiko Suzuki
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Satoko Tamura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
| | - Kiyoshi Okada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Seiki Baba
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kumasaka
- Structural Biology Group, SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yoshihiro Agari
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Lirong Chen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Zheng-Qing Fu
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- SER-CAT, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4861, USA
| | - John Chrzas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- SER-CAT, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439-4861, USA
| | - Bi-Cheng Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Noriko Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Akio Ebihara
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Ryoji Masui
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Gen-ichi Sampei
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan
| | - Gota Kawai
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
- RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| |
Collapse
|
16
|
Buey RM, Ledesma-Amaro R, Balsera M, de Pereda JM, Revuelta JL. Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii. Appl Microbiol Biotechnol 2015; 99:9577-89. [PMID: 26150243 DOI: 10.1007/s00253-015-6710-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 12/13/2022]
Abstract
Guanine nucleotides are the precursors of essential biomolecules including nucleic acids and vitamins such as riboflavin. The enzyme inosine-5'-monophosphate dehydrogenase (IMPDH) catalyzes the ratelimiting step in the guanine nucleotide de novo biosynthetic pathway and plays a key role in controlling the cellular nucleotide pools. Thus, IMPDH is an important metabolic bottleneck in the guanine nucleotide synthesis, susceptible of manipulation by means of metabolic engineering approaches. Herein, we report the functional and structural characterization of the IMPDH enzyme from the industrial fungus Ashbya gossypii. Our data show that the overexpression of the IMPDH gene increases the metabolic flux through the guanine pathway and ultimately enhances 40 % riboflavin production with respect to the wild type. Also, IMPDH disruption results in a 100-fold increase of inosine excretion to the culture media. Our results contribute to the developing metabolic engineering toolbox aiming at improving the production of metabolites with biotechnological interest in A. gossypii.
Collapse
Affiliation(s)
- Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | | | - Mónica Balsera
- Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, C/ Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - José María de Pereda
- Instituto de Biología Celular y Molecular del Cáncer, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| |
Collapse
|
17
|
Abstract
Chronic fatigue syndrome (CFS) is a poorly understood condition that presents as long-term physical and mental fatigue with associated symptoms of pain and sensitivity across a broad range of systems in the body. The poor understanding of the disorder comes from the varying clinical diagnostic definitions as well as the broad array of body systems from which its symptoms present. Studies on metabolism and CFS suggest irregularities in energy metabolism, amino acid metabolism, nucleotide metabolism, nitrogen metabolism, hormone metabolism, and oxidative stress metabolism. The overwhelming body of evidence suggests an oxidative environment with the minimal utilization of mitochondria for efficient energy production. This is coupled with a reduced excretion of amino acids and nitrogen in general. Metabolomics is a developing field that studies metabolism within a living system under varying conditions of stimuli. Through its development, there has been the optimisation of techniques to do large-scale hypothesis-generating untargeted studies as well as hypothesis-testing targeted studies. These techniques are introduced and show an important future direction for research into complex illnesses such as CFS.
Collapse
|
18
|
Sampei GI, Kanagawa M, Baba S, Shimasaki T, Taka H, Mitsui S, Fujiwara S, Yanagida Y, Kusano M, Suzuki S, Terao K, Kawai H, Fukai Y, Nakagawa N, Ebihara A, Kuramitsu S, Yokoyama S, Kawai G. Structures and reaction mechanisms of the two related enzymes, PurN and PurU. ACTA ACUST UNITED AC 2013; 154:569-79. [DOI: 10.1093/jb/mvt090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
19
|
Nussbaum JM, Liu LJ, Hasan SA, Schaub M, McClendon A, Stainier DY, Sakaguchi TF. Homeostatic generation of reactive oxygen species protects the zebrafish liver from steatosis. Hepatology 2013; 58:1326-38. [PMID: 23744565 PMCID: PMC3791216 DOI: 10.1002/hep.26551] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/21/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED Nonalcoholic fatty liver disease is the most common liver disease in both adults and children. The earliest stage of this disease is hepatic steatosis, in which triglycerides are deposited as cytoplasmic lipid droplets in hepatocytes. Through a forward genetic approach in zebrafish, we found that guanosine monophosphate (GMP) synthetase mutant larvae develop hepatic steatosis. We further demonstrate that activity of the small GTPase Rac1 and Rac1-mediated production of reactive oxygen species (ROS) are down-regulated in GMP synthetase mutant larvae. Inhibition of Rac1 activity or ROS production in wild-type larvae by small molecule inhibitors was sufficient to induce hepatic steatosis. More conclusively, treating larvae with hydrogen peroxide, a diffusible ROS that has been implicated as a signaling molecule, alleviated hepatic steatosis in both GMP synthetase mutant and Rac1 inhibitor-treated larvae, indicating that homeostatic production of ROS is required to prevent hepatic steatosis. We further found that ROS positively regulate the expression of the triglyceride hydrolase gene, which is responsible for the mobilization of stored triglycerides in hepatocytes. Consistently, inhibition of triglyceride hydrolase activity in wild-type larvae by a small molecule inhibitor was sufficient to induce hepatic steatosis. CONCLUSION De novo GMP synthesis influences the activation of the small GTPase Rac1, which controls hepatic lipid dynamics through ROS-mediated regulation of triglyceride hydrolase expression in hepatocytes.
Collapse
Affiliation(s)
- Justin M. Nussbaum
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Liuhong J. Liu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Syeda A. Hasan
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Madeline Schaub
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Allyson McClendon
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Didier Y.R. Stainier
- Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics, and Human Genetics, and Liver Center, University of California, San Francisco, San Francisco, CA 94158
| | - Takuya F. Sakaguchi
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA,Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics, and Human Genetics, and Liver Center, University of California, San Francisco, San Francisco, CA 94158,Author for correspondence: ()
| |
Collapse
|
20
|
Stoyanov A, Petrova P, Lyutskanova D, Lahtchev K. Structural and functional analysis of PUR2,5 gene encoding bifunctional enzyme of de novo purine biosynthesis in Ogataea (Hansenula) polymorpha CBS 4732T. Microbiol Res 2013; 169:378-87. [PMID: 24135445 DOI: 10.1016/j.micres.2013.08.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 08/22/2013] [Accepted: 08/28/2013] [Indexed: 11/30/2022]
Abstract
We describe the cloning, sequencing and functional characterization of gene PUR2,5, involved in de novo purine biosynthesis of the yeast Ogataea (Hansenula) polymorpha. This gene (2369 bp) was cloned by genetic complementation of adenine requiring mutation. It encodes a bifunctional enzyme of 789 amino acids (85 kDa) that catalyzes the second and the fifth steps of de novo purine biosynthesis pathway and shows dual enzymatic activity - of glycinamide ribotide synthetase (GARS, EC 6.3.4.13) and of aminoimidazole ribotide synthetase (AIRS, EC 6.3.3.1). Nucleotide sequence analysis revealed the presence of putative regulatory elements located in the adjacent 5' region. Canonical motives that function as binding sites for BAS1 transcription activator were found at positions (-593) and (-389). The putative TAATTA-box was located at (-20) to (-14) and AT-rich heteroduplex was found in the 3'-non-translated region. We compared the amino acid sequence of OpPUR2,5p with those of the corresponding enzymes of other yeast species as well as with distant organisms like bacteria Escherichia coli and human Homo sapiens. A successful disruption of OpPUR2,5 gene was done. It was found that OpPUR2,5::LEU2 replacement affects both mating and sporulation processes. OpPUR2,5 sequence is deposited in the GenBank of NCBI with accession no. JF967633.
Collapse
Affiliation(s)
- Anton Stoyanov
- The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Penka Petrova
- The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Dimitrinka Lyutskanova
- The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Kantcho Lahtchev
- The Stefan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| |
Collapse
|
21
|
Defining the genomic signature of totipotency and pluripotency during early human development. PLoS One 2013; 8:e62135. [PMID: 23614026 PMCID: PMC3629124 DOI: 10.1371/journal.pone.0062135] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 03/19/2013] [Indexed: 11/25/2022] Open
Abstract
The genetic mechanisms governing human pre-implantation embryo development and the in vitro counterparts, human embryonic stem cells (hESCs), still remain incomplete. Previous global genome studies demonstrated that totipotent blastomeres from day-3 human embryos and pluripotent inner cell masses (ICMs) from blastocysts, display unique and differing transcriptomes. Nevertheless, comparative gene expression analysis has revealed that no significant differences exist between hESCs derived from blastomeres versus those obtained from ICMs, suggesting that pluripotent hESCs involve a new developmental progression. To understand early human stages evolution, we developed an undifferentiation network signature (UNS) and applied it to a differential gene expression profile between single blastomeres from day-3 embryos, ICMs and hESCs. This allowed us to establish a unique signature composed of highly interconnected genes characteristic of totipotency (61 genes), in vivo pluripotency (20 genes), and in vitro pluripotency (107 genes), and which are also proprietary according to functional analysis. This systems biology approach has led to an improved understanding of the molecular and signaling processes governing human pre-implantation embryo development, as well as enabling us to comprehend how hESCs might adapt to in vitro culture conditions.
Collapse
|
22
|
Transcriptional regulation of the purine de novo synthesis gene Prat in Drosophila melanogaster. Gene 2013; 518:280-6. [DOI: 10.1016/j.gene.2013.01.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 01/14/2013] [Accepted: 01/15/2013] [Indexed: 11/18/2022]
|
23
|
Batool S, Nawaz MS, Kamal MA. In silico analysis of the amido phosphoribosyltransferase inhibition by PY873, PY899 and a derivative of isophthalic acid. Invest New Drugs 2013; 31:1355-63. [PMID: 23483322 DOI: 10.1007/s10637-013-9944-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
Selectively decreasing the availability of precursors for the de novo biosynthesis of purine nucleotides is a valid approach towards seeking a cure for leukaemia. Nucleotides and deoxynucleotides are required by living cells for syntheses of RNA, DNA, and cofactors such as NADP(+), FAD(+), coenzyme A and ATP. Nucleotides contain purine and pyrimidine bases, which can be synthesized through salvage pathway as well. Amido phosphoribosyltransferase (APRT), also known as glutamine phosphoribosylpyrophosphate amidotransferase (GPAT), is an enzyme that in humans is encoded by the PPAT (phosphoribosyl pyrophosphate amidotransferase) gene. APRT catalyzes the first committed step of the de novo pathway using its substrate, phosphoribosyl pyrophosphate (PRPP). As APRT is inhibited by many folate analogues, therefore, in this study we focused on the inhibitory effects of three folate analogues on APRT activity. This is extension of our previous wet lab work to analyze and dissect molecular interaction and inhibition mechanism using molecular modeling and docking tools in the current study. Comparative molecular docking studies were carried out for three diamino folate derivatives employing a model of the human enzyme that was built using the 3D structure of Bacillus subtilis APRT (PDB ID; 1GPH) as the template. Binding orientation of interactome indicates that all compounds having nominal cluster RMSD in same active site's deep narrow polar fissure. On the basis of comparative conformational analysis, electrostatic interaction, binding free energy and binding orientation of interactome, we support the possibility that these molecules could behave as APRT inhibitors and therefore may block purine de novo biosynthesis. Consequently, we suggest that PY899 is the most active biological compound that would be a more potent inhibitor for APRT inhibition than PY873 and DIA, which also confirms previous wet lab report.
Collapse
Affiliation(s)
- Sidra Batool
- Functional Informatics Laboratory National Center for Bioinformatics, Quaid-I-Azam University, Islamabad, Pakistan
| | | | | |
Collapse
|
24
|
Manjunath K, Kanaujia SP, Kanagaraj S, Jeyakanthan J, Sekar K. Structure of SAICAR synthetase from Pyrococcus horikoshii OT3: Insights into thermal stability. Int J Biol Macromol 2013; 53:7-19. [DOI: 10.1016/j.ijbiomac.2012.10.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 10/27/2022]
|
25
|
Oh J, Lee C. Proteomic characterization of a novel structural protein ORF5a of porcine reproductive and respiratory syndrome virus. Virus Res 2012; 169:255-63. [DOI: 10.1016/j.virusres.2012.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/18/2012] [Accepted: 08/23/2012] [Indexed: 01/09/2023]
|
26
|
Iaroshenko VO, Ostrovskyi D, Petrosyan A, Mkrtchyan S, Villinger A, Langer P. Synthesis of Fluorinated Purine and 1-Deazapurine Glycosides as Potential Inhibitors of Adenosine Deaminase. J Org Chem 2011; 76:2899-903. [DOI: 10.1021/jo102579g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viktor O. Iaroshenko
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- National Taras Shevchenko University, Volodymyrska st 62., Kyiv-33, 01033, Ukraine
| | - Dmytro Ostrovskyi
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- National Taras Shevchenko University, Volodymyrska st 62., Kyiv-33, 01033, Ukraine
| | - Andranik Petrosyan
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Satenik Mkrtchyan
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Alexander Villinger
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
| | - Peter Langer
- Institut für Chemie der Universität Rostock, Albert-Einstein-Strasse 3a, D-18059 Rostock, Germany
- Leibniz Institut für Katalyse e.V. an der Universität Rostock, Albert-Einstein-Strasse 29a, D-18059 Rostock, Germany
| |
Collapse
|
27
|
Sampei GI, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G. Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria. J Biochem 2010; 148:429-38. [PMID: 20716513 DOI: 10.1093/jb/mvq088] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the β- and γ- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.
Collapse
Affiliation(s)
- Gen-Ichi Sampei
- Department of Applied Physics and Chemistry, Faculty of Electro-Communications, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu-shi, Tokyo, Japan.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP. Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes. BMC PLANT BIOLOGY 2010; 10:85. [PMID: 20459672 PMCID: PMC3017814 DOI: 10.1186/1471-2229-10-85] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 05/07/2010] [Indexed: 05/11/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. This suggests that the GeneChip(R) Soybean Genome Array (soybean GeneChip) may be used for gene expression studies using common bean. RESULTS To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and accuracy of measuring differential gene expression in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and accuracy of measuring differential gene expression. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR (qRT-PCR) analysis of 20 randomly selected genes and purine-ureide pathway genes demonstrated an increased accuracy of measuring differential gene expression after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The sequence divergence pattern analysis suggested that the genes for basic cellular functions and metabolism were highly conserved between soybean and common bean. Additionally, our results show that some classes of genes, particularly those associated with environmental adaptation, are highly divergent. CONCLUSIONS The soybean GeneChip is a suitable cross-species platform for transcript profiling in common bean when used in combination with the masking protocol described. In addition to transcript profiling, CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.
Collapse
Affiliation(s)
- S Samuel Yang
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Wayne W Xu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruna Bucciarelli
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
| | - John W Gronwald
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, 62210 Cuernavaca, Mor. México
| | - Carroll P Vance
- USDA-Agricultural Research Service, Plant Science Research, St Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
29
|
Dutova TA, Mordkovich NN, Tsigankov YD. Using adaptive mutagenesis system for identification of early genes encoding de novo purine biosynthesis in methylotrophic yeast Pichia methanolica MH4. RUSS J GENET+ 2009. [DOI: 10.1134/s102279540910007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
30
|
Ng A, Uribe RA, Yieh L, Nuckels R, Gross JM. Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development. Development 2009; 136:2601-11. [PMID: 19570845 DOI: 10.1242/dev.038315] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although purines and purinergic signaling are crucial for numerous biochemical and cellular processes, their functions during vertebrate embryonic development have not been well characterized. We analyze two recessive zebrafish mutations that affect de novo purine synthesis, gart and paics. gart encodes phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase, a trifunctional enzyme that catalyzes steps 2, 3 and 5 of inosine monophosphate (IMP) synthesis. paics encodes phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase, a bifunctional enzyme that catalyzes steps 6 and 7 of this process. Zygotic gart and paics mutants have pigmentation defects in which xanthophore and iridophore pigmentation is almost completely absent, and melanin-derived pigmentation is significantly decreased, even though pigment cells are present in normal amounts and distributions. Zygotic gart and paics mutants are also microphthalmic, resulting from defects in cell cycle exit of proliferative retinoblasts within the developing eye. Maternal-zygotic and maternal-effect mutants demonstrate a crucial requirement for maternally derived gart and paics; these mutants show more severe developmental defects than their zygotic counterparts. Pigmentation and eye growth phenotypes in zygotic gart and paics mutants can be ascribed to separable biosynthetic pathways: pigmentation defects and microphthalmia result from deficiencies in a GTP synthesis pathway and an ATP synthesis pathway, respectively. In the absence of ATP pathway activity, S phase of proliferative retinoblasts is prolonged and cell cycle exit is compromised, which results in microphthalmia. These results demonstrate crucial maternal and zygotic requirements for de novo purine synthesis during vertebrate embryonic development, and identify independent functions for ATP and GTP pathways in mediating eye growth and pigmentation, respectively.
Collapse
Affiliation(s)
- Anthony Ng
- Section of Molecular Cell and Developmental Biology, Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78722, USA
| | | | | | | | | |
Collapse
|
31
|
Penney J, Bossé J, Clark DV. Expression pattern diversity and functional conservation between retroposed PRAT genes from Drosophila melanogaster and Drosophila virilis. J Mol Evol 2008; 66:457-71. [PMID: 18392760 DOI: 10.1007/s00239-008-9098-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 11/27/2007] [Accepted: 02/28/2008] [Indexed: 01/11/2023]
Abstract
Gene duplication by retrotransposition duplicates only the coding and untranslated regions of a gene and, thus, biases retroduplicated genes toward having different expression patterns from their parental genes. As such, genes duplicated by retrotransposition are more likely to develop novel expression domains. To explore this idea further, we used the Prat/Prat2 gene duplication in Drosophila as a case study to examine the aftermath of a retrotransposition event that resulted in both the parent and the child gene becoming essential for survival. We used the Gal4-UAS transgene system with EGFP as a reporter to determine the developmental expression patterns of Prat and Prat2 from D. melanogaster (DmPrat and DmPrat2) and Prat from D. virilis (DvPrat). We also tested the functional equivalence of the protein products of DmPrat and DmPrat2. We found that each of the proteins could rescue DmPrat mutations, showing that the requirement for both Prat and Prat2 in Drosophila is not simply due to differences in protein function. In contrast, we found that the DmPrat and DmPrat2 genes have developed nonoverlapping patterns of expression, which correlate with their respective loss-of-function phenotypes. We further found that DvPrat expression is similar to DmPrat during development but differs in adult gonads. Thus, the function of the Prat retrogene has not diverged in the D. melanogaster and D. virilis lineages, while some aspects of its expression pattern have evolved. Finally, we have identified promoter elements, conserved upstream of DmPrat and DvPrat, that this retrogene has acquired to drive its expression.
Collapse
Affiliation(s)
- Jay Penney
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
| | | | | |
Collapse
|
32
|
Pimkin M, Markham GD. The CBS subdomain of inosine 5'-monophosphate dehydrogenase regulates purine nucleotide turnover. Mol Microbiol 2008; 68:342-59. [PMID: 18312263 DOI: 10.1111/j.1365-2958.2008.06153.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyses the rate-limiting step in guanine nucleotide biosynthesis. IMPDH has an evolutionary conserved CBS subdomain of unknown function. The subdomain can be deleted without impairing the in vitro IMPDH catalytic activity and is the site for mutations associated with human retinitis pigmentosa. A guanine-prototrophic Escherichia coli strain, MP101, was constructed with the subdomain sequence deleted from the chromosomal gene for IMPDH. The ATP content was substantially elevated in MP101 whereas the GTP content was slighty reduced. The activities of IMPDH, adenylosuccinate synthetase and GMP reductase were two to threefold lower in MP101 crude extracts compared with the BW25113 wild-type strain. Guanine induced a threefold reduction in the MP101 ATP pool and a fourfold increase in the GTP pool within 10 min of addition to growing cells; this response does not result from the reduced IMPDH activity or starvation for guanylates. In vivo kinetic analysis using 14-C tracers and 33-P pulse-chasing revealed mutation-associated changes in purine nucleotide fluxes and turnover rates. We conclude that the CBS subdomain of IMPDH may coordinate the activities of the enzymes of purine nucleotide metabolism and is essential for maintaining the normal ATP and GTP pool sizes in E. coli.
Collapse
Affiliation(s)
- Maxim Pimkin
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
| | | |
Collapse
|
33
|
Grochowski LL, White RH. Promiscuous anaerobes: new and unconventional metabolism in methanogenic archaea. Ann N Y Acad Sci 2007; 1125:190-214. [PMID: 18096851 DOI: 10.1196/annals.1419.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The development of an oxygenated atmosphere on earth resulted in the polarization of life into two major groups, those that could live in the presence of oxygen and those that could not-the aerobes and the anaerobes. The evolution of aerobes from the earliest anaerobic prokaryotes resulted in a variety of metabolic adaptations. Many of these adaptations center on the need to sustain oxygen-sensitive reactions and cofactors to function in the new oxygen-containing atmosphere. Still other metabolic pathways that were not sensitive to oxygen also diverged. This is likely due to the physical separation of the organisms, based on their ability to live in the presence of oxygen, which allowed for the independent evolution of the pathways. Through the study of metabolic pathways in anaerobes and comparison to the more established pathways from aerobes, insight into metabolic evolution can be gained. This, in turn, can allow for extra- polation to those metabolic pathways occurring in the Last Universal Common Ancestor (LUCA). Some of the unique and uncanonical metabolic pathways that have been identified in the archaea with emphasis on the biochemistry of an obligate anaerobic methanogen, Methanocaldococcus jannaschii are reviewed.
Collapse
Affiliation(s)
- Laura L Grochowski
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | | |
Collapse
|
34
|
Jezewski S, von der Heide M, Poltermann S, Härtl A, Künkel W, Zipfel PF, Eck R. Role of the Vps34p-interacting protein Ade5,7p in hyphal growth and virulence of Candida albicans. Microbiology (Reading) 2007; 153:2351-2362. [PMID: 17600079 DOI: 10.1099/mic.0.2006/004028-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phosphatidylinositol (PtdIns) 3-kinase Vps34p of the human pathogenic yeast Candida albicans participates in virulence and in protein transport. In order to dissect these two functions, a search for proteins interacting with C. albicans Vps34p was performed using a yeast two-hybrid system. This study demonstrates the physical interaction between Vps34p and Ade5,7p, which is the bifunctional enzyme of the de novo purine nucleotide biosynthetic pathway. The interaction initially observed in a yeast two-hybrid system was confirmed in vitro with recombinant proteins. Given the complex formation between Ade5,7p and the virulence-regulating Vps34p, it was of interest to characterize the function of Ade5,7p in C. albicans. To this end, ade5,7 null mutants were generated. The resulting mutants were adenine deficient, and sensitive to the presence of metal ions. In addition, the ade5,7 null mutants were avirulent in a mouse model of systemic candidiasis, and showed reduced hyphal growth in an agar matrix under embedded conditions. In summary, Ade5,7p interacts with the multifunctional virulence regulator PtdIns 3-kinase Vps34p, and ade5,7 and vps34 null mutant strains show similar phenotypes regarding sensitivity to metal ions, hyphal growth and virulence.
Collapse
Affiliation(s)
- Susann Jezewski
- Leibniz Institute for Natural Products Research and Infection Biology/Hans Knöll Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Monika von der Heide
- Leibniz Institute for Natural Products Research and Infection Biology/Hans Knöll Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Sophia Poltermann
- Leibniz Institute for Natural Products Research and Infection Biology/Hans Knöll Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Albert Härtl
- Leibniz Institute for Natural Products Research and Infection Biology/Hans Knöll Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Waldemar Künkel
- University of Applied Sciences, Carl-Zeiss-Promenade 2, D-07745 Jena, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Products Research and Infection Biology/Hans Knöll Institute, Beutenbergstrasse 11, D-07745 Jena, Germany
| | - Raimund Eck
- University of Applied Sciences, Carl-Zeiss-Promenade 2, D-07745 Jena, Germany
| |
Collapse
|
35
|
Zrenner R, Stitt M, Sonnewald U, Boldt R. Pyrimidine and purine biosynthesis and degradation in plants. ANNUAL REVIEW OF PLANT BIOLOGY 2006; 57:805-36. [PMID: 16669783 DOI: 10.1146/annurev.arplant.57.032905.105421] [Citation(s) in RCA: 359] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Nucleotide metabolism operates in all living organisms, embodies an evolutionarily ancient and indispensable complex of metabolic pathways and is of utmost importance for plant metabolism and development. In plants, nucleotides can be synthesized de novo from 5-phosphoribosyl-1-pyrophosphate and simple molecules (e.g., CO(2), amino acids, and tetrahydrofolate), or be derived from preformed nucleosides and nucleobases via salvage reactions. Nucleotides are degraded to simple metabolites, and this process permits the recycling of phosphate, nitrogen, and carbon into central metabolic pools. Despite extensive biochemical knowledge about purine and pyrimidine metabolism, comprehensive studies of the regulation of this metabolism in plants are only starting to emerge. Here we review progress in molecular aspects and recent studies on the regulation and manipulation of nucleotide metabolism in plants.
Collapse
Affiliation(s)
- Rita Zrenner
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam OT Golm, Germany.
| | | | | | | |
Collapse
|
36
|
Long H, Cameron S, Yu L, Rao Y. De novo GMP synthesis is required for axon guidance in Drosophila. Genetics 2005; 172:1633-42. [PMID: 16322525 PMCID: PMC1456273 DOI: 10.1534/genetics.105.042911] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Guanine nucleotides are key players in mediating growth-cone signaling during neural development. The supply of cellular guanine nucleotides in animals can be achieved via the de novo synthesis and salvage pathways. The de novo synthesis of guanine nucleotides is required for lymphocyte proliferation in animals. Whether the de novo synthesis pathway is essential for any other cellular processes, however, remains unknown. In a search for genes required for the establishment of neuronal connectivity in the fly visual system, we identify the burgundy (bur) gene as an essential player in photoreceptor axon guidance. The bur gene encodes the only GMP synthetase in Drosophila that catalyzes the final reaction of de novo GMP synthesis. Loss of bur causes severe defects in axonal fasciculation, retinotopy, and growth-cone morphology, but does not affect photoreceptor differentiation or retinal patterning. Similar defects were observed when the raspberry (ras) gene, encoding for inosine monophosphate dehydrogenase catalyzing the IMP-to-XMP conversion in GMP de novo synthesis, was mutated. Our study thus provides the first in vivo evidence to support an essential and specific role for de novo synthesis of guanine nucleotides in axon guidance.
Collapse
Affiliation(s)
- Hong Long
- McGill Centre for Research in Neuroscience and Department of Neurology and Neurosurgery, McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
| | | | | | | |
Collapse
|
37
|
Ji Y, Clark DV. The purine synthesis gene Prat2 is required for Drosophila metamorphosis, as revealed by inverted-repeat-mediated RNA interference. Genetics 2005; 172:1621-31. [PMID: 16322507 PMCID: PMC1456287 DOI: 10.1534/genetics.105.045641] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PRAT (phosphoribosylamidotransferase; E.C. 2.4.2.14) catalyzes the first reaction in de novo purine nucleotide biosynthesis. In Drosophila melanogaster, the Prat and Prat2 genes are both highly conserved with PRAT sequences from prokaryotes and eukaryotes. However, Prat2 organization and expression during development is different from Prat. We used RNA interference (RNAi) to knock down expression of both Prat and Prat2 to investigate their functions. Using the GAL4-UAS system, Prat RNAi driven by Act5c-GAL4 or tubP-GAL4 causes variable pupal lethality (48-100%) and approximately 50% female sterility, depending on the transgenic strains and drivers used. This observation agrees with the phenotype previously observed for Prat EMS-induced mutations. Prat2 RNAi driven by Act5C-GAL4 or tubP-GAL4 also results in variable pupal lethality (61-93%) with the different transgenic strains, showing that Prat2 is essential for fly development. However, Prat2 RNAi-induced arrested pupae have a head eversion defect reminiscent of the "cryptocephal" phenotype, whereas Prat RNAi-induced arrested pupae die later as pharate adults. We conclude that Prat2 is required during the prepupal stage while Prat is more important for the pupal stage. In addition, Prat and Prat2 double RNAi results in more severe pupal lethal phenotypes, suggesting that Prat and Prat2 have partially additive functions during Drosophila metamorphosis.
Collapse
Affiliation(s)
- Yingbiao Ji
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick E3B 5A3, Canada
| | | |
Collapse
|
38
|
Bussell JD, Hall DJ, Mann AJ, Goggin DE, Atkins CA, Smith PMC. Alternative splicing of the Vupur3 transcript in cowpea produces multiple mRNA species with a single protein product that is present in both plastids and mitochondria. FUNCTIONAL PLANT BIOLOGY : FPB 2005; 32:683-693. [PMID: 32689167 DOI: 10.1071/fp05044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 04/28/2005] [Indexed: 06/11/2023]
Abstract
A heterogeneous population of cDNAs (designated Vupur3) encoding phosphoribosylglycinamide formyltransferase (GART; EC 2.1.2.2) was isolated from a cowpea (Vigna unguiculata L. Walp.) nodule library. Three classes of cDNA with the same ORF, but differing in their 3'-UTRs, were identified. Southern analysis and sequencing of genomic DNA confirmed that these differences result from alternative splicing of the primary transcript of a single Vupur3 gene. Alternative splicing does not appear to play a role in the production of soybean (Glycine max Merrill.) pur3 transcripts. The presence of the protein product of the Vupur3 gene, GART, in plastids and mitochondria was confirmed by immunoblotting with antibodies raised against the recombinant protein. The antibodies recognised two proteins with apparent molecular masses of 27 and 27.5 kDa in both mitochondria and plastids. All Vupur3 transcripts have two in-frame start codons that are active in wheatgerm in vitro transcription / translation experiments suggesting a mechanism by which the gene product could be targeted to two organelles. Like other genes encoding enzymes for purine synthesis, Vupur3 is expressed in nodules before nitrogen fixation begins but in contrast to these genes its expression does not increase markedly after nitrogen fixation begins.
Collapse
Affiliation(s)
- John D Bussell
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Doug J Hall
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Anthea J Mann
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Danica E Goggin
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Craig A Atkins
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Penelope M C Smith
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| |
Collapse
|
39
|
Malmanche N, Clark DV. Drosophila melanogaster Prat, a purine de novo synthesis gene, has a pleiotropic maternal-effect phenotype. Genetics 2005; 168:2011-23. [PMID: 15611171 PMCID: PMC1448727 DOI: 10.1534/genetics.104.033134] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Drosophila melanogaster, two genes, Prat and Prat2, encode the enzyme, amidophosphoribosyltransferase, that performs the first and limiting step in purine de novo synthesis. Only Prat mRNA is present in the female germline and 0- to 2-hr embryos prior to the onset of zygotic transcription. We studied the maternal-effect phenotype caused by Prat loss-of-function mutations, allowing us to examine the effects of decreased purine de novo synthesis during oogenesis and the early stages of embryonic development. In addition to the purine syndrome previously characterized, we found that Prat mutant adult females have a significantly shorter life span and are conditionally semisterile. The semisterility is associated with a pleiotropic phenotype, including egg chamber defects and later effects on embryonic and larval viability. Embryos show mitotic synchrony and/or nuclear content defects at the syncytial blastoderm stages and segmentation defects at later stages. The semisterility is partially rescued by providing Prat mutant females with an RNA-enriched diet as a source of purines. Our results suggest that purine de novo synthesis is a limiting factor during the processes of cellular or nuclear proliferation that take place during egg chamber and embryonic development.
Collapse
Affiliation(s)
- Nicolas Malmanche
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick E3B 6E1, Canada
| | | |
Collapse
|
40
|
Bønsdorff T, Gautier M, Farstad W, Rønningen K, Lingaas F, Olsaker I. Mapping of the bovine genes of the de novo AMP synthesis pathway. Anim Genet 2005; 35:438-44. [PMID: 15566465 DOI: 10.1111/j.1365-2052.2004.01201.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Summary The purine nucleotides adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are critical for energy metabolism, cell signalling and cell reproduction. Despite their essential function, little is known about the regulation and in vivo expression pattern of the genes involved in the de novo purine synthesis pathway. The complete coding region of the bovine phosphoribosylaminoimidazole carboxylase gene (PAICS), which catalyses steps 6 and 7 of the de novo purine biosynthesis pathway, as well as bovine genomic sequences of the six other genes in the pathway producing inosine monophosphate (IMP) and AMP [phosphoribosyl pyrophosphate amidotransferase (PPAT), phosphoribosylglycinamide formyltransferase (GART), phosphoribosylformylglycinamidine synthase (PFAS), adenylosuccinate lyase (ADSL), 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC) and adenylosuccinate synthase (ADSS)], were identified. The genes were mapped to segments of six different bovine chromosomes using a radiation hybrid (RH) cell panel. The gene PPAT, coding for the presumed rate-limiting enzyme of the purine de novo pathway was closely linked to PAICS on BTA6. These, and the other bovine locations i.e. GART at BTA1, PFAS at BTA19, ADSL at BTA5, ATIC at BTA2 and ADSS at BTA16, are in agreement with published comparative maps of cattle and man. PAICS and PPAT genes are known to be closely linked in human, rat and chicken. Previously, an expressed sequence fragment of PAICS (Bos taurus corpus luteum, BTCL9) was mapped to BTA13. By isolation and characterization of a BAC clone, we have now identified a PAICS processed pseudogene sequence (psiPAICS) on BTA13. Processed pseudogene sequences of PAICS and other genes of the purine biosynthesis pathway were identified in several mammalian species, indicating that the genes of this pathway have been susceptible to retrotransposition. The seven bovine genes are expressed at a higher level in testicular and ovary tissues compared with skeletal muscle.
Collapse
Affiliation(s)
- T Bønsdorff
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, PO Box 8146 Dep., 0033 Oslo, Norway
| | | | | | | | | | | |
Collapse
|
41
|
Kolberg M, Logan DT, Bleifuss G, Pötsch S, Sjöberg BM, Gräslund A, Lubitz W, Lassmann G, Lendzian F. A new tyrosyl radical on Phe208 as ligand to the diiron center in Escherichia coli ribonucleotide reductase, mutant R2-Y122H. Combined x-ray diffraction and EPR/ENDOR studies. J Biol Chem 2005; 280:11233-46. [PMID: 15634667 DOI: 10.1074/jbc.m414634200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R2 protein subunit of class I ribonucleotide reductase (RNR) belongs to a structurally related family of oxygen bridged diiron proteins. In wild-type R2 of Escherichia coli, reductive cleavage of molecular oxygen by the diferrous iron center generates a radical on a nearby tyrosine residue (Tyr122), which is essential for the enzymatic activity of RNR, converting ribonucleotides into deoxyribonucleotides. In this work, we characterize the mutant E. coli protein R2-Y122H, where the radical site is substituted with a histidine residue. The x-ray structure verifies the mutation. R2-Y122H contains a novel stable paramagnetic center which we name H, and which we have previously proposed to be a diferric iron center with a strongly coupled radical, Fe(III)Fe(III)R.. Here we report a detailed characterization of center H, using 1H/2H -14N/15N- and 57Fe-ENDOR in comparison with the Fe(III)Fe(IV) intermediate X observed in the iron reconstitution reaction of R2. Specific deuterium labeling of phenylalanine residues reveals that the radical results from a phenylalanine. As Phe208 is the only phenylalanine in the ligand sphere of the iron site, and generation of a phenyl radical requires a very high oxidation potential, we propose that in Y122H residue Phe208 is hydroxylated, as observed earlier in another mutant (R2-Y122F/E238A), and further oxidized to a phenoxyl radical, which is coordinated to Fe1. This work demonstrates that small structural changes can redirect the reactivity of the diiron site, leading to oxygenation of a hydrocarbon, as observed in the structurally similar methane monoxygenase, and beyond, to formation of a stable iron-coordinated radical.
Collapse
Affiliation(s)
- Matthias Kolberg
- Max-Volmer-Laboratory, Institute for Chemistry, PC 14, Technical University Berlin, D-10623 Berlin, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Malmanche N, Clark DV. Identification of trans-dominant modifiers of Prat expression in Drosophila melanogaster. Genetics 2003; 164:1419-33. [PMID: 12930749 PMCID: PMC1462663 DOI: 10.1093/genetics/164.4.1419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The first committed step in the purine de novo synthesis pathway is performed by amidophosphoribosyltransferase (EC 2.4.2.14) or Prat. Drosophila melanogaster Prat is an essential gene with a promoter that lacks a TATA-box and initiator element and has multiple transcription start sites with a predominant start site. To study the regulation of Prat expression in the adult eye, we used the Prat:bw reporter gene, in which the Prat coding region was replaced with the brown (bw) coding region. The pale-orange eye color of a single copy of Prat:bw prompted us to use a multicopy array of Prat:bw that was derived using P transposase mutagenesis and produces a darker-orange eye color in a bw(D); st genetic background. We used a 13-copy array of Prat:bw as a tool to recover dominant EMS-induced mutations that affect the expression of the transgene. After screening 21,000 F(1)s for deviation from the orange eye color, we isolated 23 dominant modifiers: 21 suppressors (1 Y-linked, 5 X-linked, 4 2-linked, and 11 3-linked) and 2 enhancers (1 2-linked and 1 3-linked). Quantification of their effect on endogenous Prat gene expression, using RT-PCR in young adult fly heads, identifies a subset of modifiers that are candidates for genes involved in regulating Prat expression.
Collapse
Affiliation(s)
- Nicolas Malmanche
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick E3B 6E1, Canada
| | | |
Collapse
|
43
|
Schwoebel ED, Ho TH, Moore MS. The mechanism of inhibition of Ran-dependent nuclear transport by cellular ATP depletion. J Cell Biol 2002; 157:963-74. [PMID: 12058015 PMCID: PMC2174045 DOI: 10.1083/jcb.200111077] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Rran-dependent nuclear transport requires a nuclear pool of RanGTP both for the assembly of export complexes and the disassembly of import complexes. Accordingly, in order for these processes to proceed, Ran-dependent nuclear import and export assays in vitro require the addition of GTP to produce RanGTP. Notably, no ATP requirement can be detected for these transport processes in vitro. But in vivo, when cells are depleted of ATP by the addition of sodium azide and 2-deoxyglucose to block ATP production by oxidative phosphorylation and glycolysis, respectively, Ran-dependent nuclear import and export are rapidly inhibited. This raised the question of whether there is an ATP requirement for these nuclear transport pathways in an intact cell that has remained undetected in vitro. Here we report that the free (but not total) GTP concentration rapidly drops to an undetectable level upon ATP depletion as does the availability of RanGTP. Our conclusion is that the inhibition of Ran-dependent nuclear transport observed upon ATP depletion in vivo results from a shortage of RanGTP rather than the inhibition of some ATP-dependent process.
Collapse
Affiliation(s)
- Eric D Schwoebel
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | |
Collapse
|
44
|
Iancu CV, Borza T, Choe JY, Fromm HJ, Honzatko RB. Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure. J Biol Chem 2001; 276:42146-52. [PMID: 11560929 DOI: 10.1074/jbc.m106294200] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vertebrates possess two isozymes of adenylosuccinate synthetase. The acidic isozyme is similar to the synthetase from bacteria and plants, being involved in the de novo biosynthesis of AMP, whereas the basic isozyme participates in the purine nucleotide cycle. Reported here is the first instance of overexpression and crystal structure determination of a basic isozyme of adenylosuccinate synthetase. The recombinant mouse muscle enzyme purified to homogeneity in milligram quantities exhibits a specific activity comparable with that of the rat muscle enzyme isolated from tissue and K(m) parameters for GTP, IMP, and l-aspartate (12, 45, and 140 microm, respectively) similar to those of the enzyme from Escherichia coli. The mouse muscle and E. coli enzymes have similar polypeptide folds, differing primarily in the conformation of loops, involved in substrate recognition and stabilization of the transition state. Residues 65-68 of the muscle isozyme adopt a conformation not observed in any previous synthetase structure. In its new conformation, segment 65-68 forms intramolecular hydrogen bonds with residues essential for the recognition of IMP and, in fact, sterically excludes IMP from the active site. Observed differences in ligand recognition among adenylosuccinate synthetases may be due in part to conformational variations in the IMP pocket of the ligand-free enzymes.
Collapse
Affiliation(s)
- C V Iancu
- Department of Biochemistry, Biophysics, and Molecular Biology, Molecular Biology Building, Iowa State University, Ames, Iowa 5011, USA
| | | | | | | | | |
Collapse
|
45
|
McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res 2001; 29:774-82. [PMID: 11160901 PMCID: PMC30389 DOI: 10.1093/nar/29.3.774] [Citation(s) in RCA: 198] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.
Collapse
Affiliation(s)
- L McCue
- The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Anderson PM. Urea and glutamine synthesis: Environmental influences on nitrogen excretion. FISH PHYSIOLOGY 2001. [DOI: 10.1016/s1546-5098(01)20008-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
47
|
Clark DV, MacAfee N. The purine biosynthesis enzyme PRAT detected in proenzyme and mature forms during development of Drosophila melanogaster. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2000; 30:315-323. [PMID: 10727898 DOI: 10.1016/s0965-1748(00)00005-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Glutamine phosphoribosylpyrophosphate amidotransferase (PRAT; EC 2.4. 2.14) is the first and rate-limiting enzyme of de novo purine biosynthesis. PRAT expression in Drosophila development was examined to determine if it is correlated with cell proliferation and/or nutritional isolation. An antiserum, raised against the 16 carboxyl-terminal amino acids of PRAT, detects two proteins corresponding to a 60 kDa proenzyme and 55 kDa mature enzyme, consistent with a 53 amino acid propeptide predicted from the gene sequence. Mature enzyme is maternally expressed, and proenzyme appears in embryos at 2-8 h, corresponding to the interval during which zygotic transcription is initiated. Upon hatching of first instar larvae, proenzyme levels are reduced and remain low relative to mature enzyme. Adult females have higher levels of both proteins relative to males, consistent with maternal expression. Maternal expression reflects a requirement for the enzyme during embryogenesis, while reduction in expression following hatching reflects a switch to an exogenous source of purines. Prat mRNA levels follow a similar overall pattern in the same developmental stages examined for the protein. Discovery of a second gene encoding PRAT with 78% amino acid identity leads to the possibility that the antiserum raised against the carboxyl-terminus detects two enzymes.
Collapse
Affiliation(s)
- D V Clark
- Department of Biology, University of New Brunswick, Fredericton, Canada.
| | | |
Collapse
|
48
|
O'Donnell AF, Tiong S, Nash D, Clark DV. The Drosophila melanogaster ade5 gene encodes a bifunctional enzyme for two steps in the de novo purine synthesis pathway. Genetics 2000; 154:1239-53. [PMID: 10757766 PMCID: PMC1460979 DOI: 10.1093/genetics/154.3.1239] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Steps 6 and 7 of de novo purine synthesis are performed by 5-aminoimidazole ribonucleotide carboxylase (AIRc) and 4-[(N-succinylamino)carbonyl]-5-aminoimidazole ribonucleotide synthetase (SAICARs), respectively. In vertebrates, a single gene encodes AIRc-SAICARs with domains homologous to Escherichia coli PurE and PurC. We have isolated an AIRc-SAICARs cDNA from Drosophila melanogaster via functional complementation with an E. coli purC purine auxotroph. This cDNA encodes AIRc yet is unable to complement an E. coli purE mutant, suggesting functional differences between Drosophila and E. coli AIRc. In vertebrates, the AIRc-SAICARs gene shares a promoter region with the gene encoding phosphoribosylamidotransferase, which performs the first step in de novo purine synthesis. In Drosophila, the AIRc-SAICARs gene maps to section 11B4-14 of the X chromosome, while the phosphoribosylamidotransferase gene (Prat) maps to chromosome 3; thus, the close linkage of these two genes is not conserved in flies. Three EMS-induced X-linked adenine auxotrophic mutations, ade4(1), ade5(1), and ade5(2), were isolated. Two gamma-radiation-induced (ade5(3) and ade5(4)) and three hybrid dysgenesis-induced (ade5(5), ade5(6), and ade5(8)) alleles were also isolated. Characterization of the auxotrophy and the finding that the hybrid dysgenesis-induced mutations all harbor P transposon sequences within the AIRc-SAICARs gene show that ade5 encodes AIRc-SAICARs.
Collapse
Affiliation(s)
- A F O'Donnell
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick E3B 6E1, Canada
| | | | | | | |
Collapse
|
49
|
Gassmann MG, Stanzel A, Werner S. Growth factor-regulated expression of enzymes involved in nucleotide biosynthesis: a novel mechanism of growth factor action. Oncogene 1999; 18:6667-76. [PMID: 10597272 DOI: 10.1038/sj.onc.1203120] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Keratinocyte growth factor (KGF) is a potent and specific mitogen for epithelial cells, including the keratinocytes of the skin. We investigated the mechanisms of action of KGF by searching for genes which are regulated by this growth factor in cultured human keratinocytes. Using the differential display RT-PCR technology we identified the gene encoding adenylosuccinate lyase [EC 4.3.2.2] as a novel KGF-regulated gene. Adenylosuccinate lyase plays an important role in purine de novo synthesis. To gain further insight into the potential role of nucleotide biosynthesis in the mitogenic effect of KGF, we cloned cDNA fragments of the key regulatory enzymes involved in purine and pyrimidine metabolism (adenylosuccinate synthetase [EC 6.3.4.4], phosphoribosyl pyrophosphate synthetase [EC 2.7.6.1], amidophosphoribosyl transferase [EC 2.4.2.14], hypoxanthine guanine phosphoribosyl transferase [EC 2.4.2.8] and the multifunctional protein CAD which includes the enzymatic activities of carbamoyl-phosphate synthetase II [EC 6.3.5.59], aspartate transcarbamylase [EC 2.1.3.2] and dihydroorotase [EC 3.5.2.3]). Expression of all of these enzymes was upregulated after treatment with KGF and also with epidermal growth factor (EGF), indicating that these mitogens stimulate nucleotide production by induction of these enzymes. To determine a possible in vivo correlation between the expression of KGF, EGF and the enzymes mentioned above, we analysed the expression of the enzymes during cutaneous wound repair, where high levels of these mitogens are present. Indeed, we found a strong mRNA expression of all of these enzymes in the EGF- and KGF-responsive keratinocytes of the hyperproliferative epithelium at the wound edge, indicating that their expression might also be regulated by growth factors during wound healing.
Collapse
Affiliation(s)
- M G Gassmann
- Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | | | | |
Collapse
|
50
|
Patterson D, Bleskan J, Gardiner K, Bowersox J. Human phosphoribosylformylglycineamide amidotransferase (FGARAT): regional mapping, complete coding sequence, isolation of a functional genomic clone, and DNA sequence analysis. Gene 1999; 239:381-91. [PMID: 10548741 DOI: 10.1016/s0378-1119(99)00378-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Purines play essential roles in many cellular functions, including DNA replication, transcription, intra- and extra-cellular signaling, energy metabolism, and as coenzymes for many biochemical reactions. The de-novo synthesis of purines requires 10 enzymatic steps for the production of inosine monophosphate (IMP). Defects in purine metabolism are associated with human diseases. Further, many anticancer agents function as inhibitors of the de-novo biosynthetic pathway. Genes or cDNAs for most of the enzymes comprising this pathway have been isolated from humans or other mammals. One notable exception is the phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway. This gene has been cloned from numerous microorganisms and from Drosophila melanogaster and C. elegans. We report here the identification of a human cDNA containing the coding region of the FGARAT mRNA and the isolation of a P1 clone that contains an intact human FGARAT gene. The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the protein for FGARAT. The P1 clone was used to regionally map the FGARAT gene to chromosome region 17p13, a location consistent with our prior assignment of this gene to chromosome 17. A comparison of the DNA sequence of the human FGARAT and FGARAT DNA sequence from 17 other organisms is reported. The isolation of this gene means that DNA clones for all the 10 steps of IMP synthesis have been isolated from humans or other mammals.
Collapse
Affiliation(s)
- D Patterson
- Eleanor Roosevelt Institute, 1899 Gaylord Street, Denver, CO 80206, USA.
| | | | | | | |
Collapse
|