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Abdelrahman HA, Akawi N, Al-Shamsi AM, Al-Gazali L, Ali BR. Pontocerebellar Hypoplasia Type 9: A New Case with a Novel Mutation and Review of Literature. J Pediatr Genet 2024; 13:215-222. [PMID: 39086442 PMCID: PMC11288706 DOI: 10.1055/s-0042-1748018] [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: 05/31/2021] [Accepted: 03/07/2022] [Indexed: 10/18/2022]
Abstract
Pontocerebellar hypoplasia type 9 (PCH-9) is a very rare autosomal recessive neurodegenerative disorder. Affected infants present early with severe developmental delay, spasticity, with the unique magnetic resonance imaging picture of thin corpus callosum, atrophied pons, and cerebellum. It is caused by loss of function mutations in the AMPD2 gene, encoding for the adenosine monophosphate deaminase enzyme-paralog 2. This gene is expressed in different somatic tissues with high level of expression in cerebellum and its encoded enzyme catalyzes a critical step in de novo biosynthesis of purines and its deficiency in the developing neurons severely affects neuronal differentiation and cell viability. We clinically evaluated an Emirati patient presented with severe developmental and growth delay, as well as corpus callosum agenesis and atrophy of brainstem and cerebellum. We performed exome sequencing, Sanger sequencing, and segregation analysis to identify the genetic cause of the phenotype, followed by in silico and in vitro analysis. We identified the novel variant (NM_004037.9:c.1471G > A) in AMPD2 gene leading to a single amino acid substitution (p.Gly491Arg) in adenosine monophosphate deaminase-2 enzyme. This variant is predicted to be pathogenic using several in silico tools, and resulted in a decrease in the enzyme function in the patient's polymorphonuclear cells by 82% (95% confidence interval: 73.3-91.7%, p = 0.029) compared with the control. This data establishes that the affected child is affected by PCH-9. Furthermore, we review all reported cases in literature to summarize the main clinical features of this rare disease.
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Affiliation(s)
- Hanadi A. Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Nadia Akawi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
- Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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2
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Sun M, Dai P, Cao Z, Dong J. Purine metabolism in plant pathogenic fungi. Front Microbiol 2024; 15:1352354. [PMID: 38384269 PMCID: PMC10879430 DOI: 10.3389/fmicb.2024.1352354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
In eukaryotic cells, purine metabolism is the way to the production of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and plays key roles in various biological processes. Purine metabolism mainly consists of de novo, salvage, and catabolic pathways, and some components of these pathways have been characterized in some plant pathogenic fungi, such as the rice blast fungus Magnaporthe oryzae and wheat head blight fungus Fusarium graminearum. The enzymatic steps of the de novo pathway are well-conserved in plant pathogenic fungi and play crucial roles in fungal growth and development. Blocking this pathway inhibits the formation of penetration structures and invasive growth, making it essential for plant infection by pathogenic fungi. The salvage pathway is likely indispensable but requires exogenous purines, implying that purine transporters are functional in these fungi. The catabolic pathway balances purine nucleotides and may have a conserved stage-specific role in pathogenic fungi. The significant difference of the catabolic pathway in planta and in vitro lead us to further explore and identify the key genes specifically regulating pathogenicity in purine metabolic pathway. In this review, we summarized recent advances in the studies of purine metabolism, focusing on the regulation of pathogenesis and growth in plant pathogenic fungi.
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Affiliation(s)
- Manli Sun
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
| | | | | | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology/College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China
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Effects of different expression systems on characterization of adenylate deaminase from Aspergillus oryzae. Bioprocess Biosyst Eng 2020; 43:919-926. [PMID: 32020448 DOI: 10.1007/s00449-020-02288-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 01/13/2020] [Indexed: 10/25/2022]
Abstract
Adenylate deaminase (AMPD) is an amino hydrolase that catalyzes the irreversible hydrolysis of adenosine monophosphate (AMP) to inosine monophosphate (IMP) and ammonia. In this study, the effect of different hosts on the enzymatic properties of AMPD from Aspergillus oryzae GX-08 was investigated and showed that Bacillus subtilis WB600 was more suitable for producing AMPD with a higher activity of 2540 U/mL. After purification, the optimal temperature and pH of recombinant AMPD were 55 °C and pH 6.0, respectively, and its activity was significantly enhanced by 10 mM Fe3+ with an increase of 236%. More importantly, the recombinant AMPD specifically and effectively catalyzed the conversion between AMP and IMP, in which 10 mL of crude AMPD achieved a conversion ratio of 76.4% after 40 min. Therefore, B. subtilis WB600 provides a potential platform for producing AMPD with excellent catalytic ability and catalytic specificity.
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Li S, Qian Y, Liang Y, Chen X, Zhao M, Guo Y, Pang Z. Overproduction, Purification and Characterization of Adenylate Deaminase from Aspergillus oryzae. Appl Biochem Biotechnol 2016; 180:1635-1643. [PMID: 27539573 DOI: 10.1007/s12010-016-2192-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 07/12/2016] [Indexed: 12/01/2022]
Abstract
Adenylate deaminase (AMPD, EC 3.5.4.6) is an aminohydrolase that widely used in the food and medicine industries. In this study, the gene encoding Aspergillus oryzae AMPD was cloned and expressed in Escherichia coli. Induction with 0.75 mM isopropyl β-D-l-thiogalactopyranoside resulted in an enzyme activity of 1773.9 U/mL. Recombinant AMPD was purified to electrophoretic homogeneity using nickel affinity chromatography, and its molecular weight was calculated as 78.6 kDa. Purified AMPD exhibited maximal activity at 35 °C, pH 6.0 and 30 mM K+, with apparent K m and V max values of 2.7 × 10-4 M and 77.5 μmol/mg/min under these conditions. HPLC revealed that recombinant AMPD could effectively catalyse the synthesis of inosine-5'-monophosphate (IMP) with minimal by-products, indicating high specificity and suggesting that it could prove useful for IMP production.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Yi Qian
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Yunlong Liang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Xinkuan Chen
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Mouming Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning, 530004, China
| | - Yuan Guo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, 530004, China.
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning, 530004, China. .,College of Life Science and Technology, Guangxi University, Nanning, 530005, China.
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5
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Li S, Chen L, Hu Y, Fang G, Zhao M, Guo Y, Pang Z. Enzymatic production of 5'-inosinic acid by AMP deaminase from a newly isolated Aspergillus oryzae. Food Chem 2016; 216:275-81. [PMID: 27596420 DOI: 10.1016/j.foodchem.2016.07.171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 07/22/2016] [Accepted: 07/28/2016] [Indexed: 11/28/2022]
Abstract
5'-adenylic acid deaminase (AMP deaminase), an important enzyme for the food industry, can catalyze the irreversible hydrolysis of adenosine monophosphate (AMP) to inosine monophosphate (IMP) and ammonia. In this study, a new strain was screened that efficiently produces 3191.6U/g of AMP deaminase at 32°C. After purification, the optimal temperature and pH of the AMP deaminase were found to be 40°C and 6.0, respectively, but it was partially inhibited by Fe(3+), Cu(2+), Al(3+), and Zn(2+). With amplification of the AMP deaminase production system, 6mL of crude enzyme could produce 2.00mg/g of IMP from 2.04mg/g of dried yeast with an 84.8% molar yield after 40min. These results provide a new insight into AMP deaminase production and offer a potential platform for producing 5'-IMP.
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Affiliation(s)
- Shubo Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Leitao Chen
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yangjun Hu
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Guohui Fang
- College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Mouming Zhao
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yuan Guo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning 530007, China.
| | - Zongwen Pang
- College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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Akizu N, Cantagrel V, Schroth J, Cai N, Vaux K, McCloskey D, Naviaux RK, Van Vleet J, Fenstermaker AG, Silhavy JL, Scheliga JS, Toyama K, Morisaki H, Sonmez FM, Celep F, Oraby A, Zaki MS, Al-Baradie R, Faqeih EA, Saleh MAM, Spencer E, Rosti RO, Scott E, Nickerson E, Gabriel S, Morisaki T, Holmes EW, Gleeson JG. AMPD2 regulates GTP synthesis and is mutated in a potentially treatable neurodegenerative brainstem disorder. Cell 2013; 154:505-17. [PMID: 23911318 DOI: 10.1016/j.cell.2013.07.005] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 05/10/2013] [Accepted: 07/01/2013] [Indexed: 01/03/2023]
Abstract
Purine biosynthesis and metabolism, conserved in all living organisms, is essential for cellular energy homeostasis and nucleic acid synthesis. The de novo synthesis of purine precursors is under tight negative feedback regulation mediated by adenosine and guanine nucleotides. We describe a distinct early-onset neurodegenerative condition resulting from mutations in the adenosine monophosphate deaminase 2 gene (AMPD2). Patients have characteristic brain imaging features of pontocerebellar hypoplasia (PCH) due to loss of brainstem and cerebellar parenchyma. We found that AMPD2 plays an evolutionary conserved role in the maintenance of cellular guanine nucleotide pools by regulating the feedback inhibition of adenosine derivatives on de novo purine synthesis. AMPD2 deficiency results in defective GTP-dependent initiation of protein translation, which can be rescued by administration of purine precursors. These data suggest AMPD2-related PCH as a potentially treatable early-onset neurodegenerative disease.
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Affiliation(s)
- Naiara Akizu
- Neurogenetics Laboratory, Institute for Genomic Medicine, Rady Children's Hospital, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA
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7
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Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae. Genetics 2012; 190:885-929. [PMID: 22419079 DOI: 10.1534/genetics.111.133306] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ever since the beginning of biochemical analysis, yeast has been a pioneering model for studying the regulation of eukaryotic metabolism. During the last three decades, the combination of powerful yeast genetics and genome-wide approaches has led to a more integrated view of metabolic regulation. Multiple layers of regulation, from suprapathway control to individual gene responses, have been discovered. Constitutive and dedicated systems that are critical in sensing of the intra- and extracellular environment have been identified, and there is a growing awareness of their involvement in the highly regulated intracellular compartmentalization of proteins and metabolites. This review focuses on recent developments in the field of amino acid, nucleotide, and phosphate metabolism and provides illustrative examples of how yeast cells combine a variety of mechanisms to achieve coordinated regulation of multiple metabolic pathways. Importantly, common schemes have emerged, which reveal mechanisms conserved among various pathways, such as those involved in metabolite sensing and transcriptional regulation by noncoding RNAs or by metabolic intermediates. Thanks to the remarkable sophistication offered by the yeast experimental system, a picture of the intimate connections between the metabolomic and the transcriptome is becoming clear.
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Walther T, Novo M, Rössger K, Létisse F, Loret MO, Portais JC, François JM. Control of ATP homeostasis during the respiro-fermentative transition in yeast. Mol Syst Biol 2010; 6:344. [PMID: 20087341 PMCID: PMC2824524 DOI: 10.1038/msb.2009.100] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 11/07/2009] [Indexed: 11/09/2022] Open
Abstract
Respiring Saccharomyces cerevisiae cells respond to a sudden increase in glucose concentration by a pronounced drop of their adenine nucleotide content ([ATP]+[ADP]+[AMP]=[AXP]). The unknown fate of 'lost' AXP nucleotides represented a long-standing problem for the understanding of the yeast's physiological response to changing growth conditions. Transient accumulation of the purine salvage pathway intermediate, inosine, accounted for the apparent loss of adenine nucleotides. Conversion of AXPs into inosine was facilitated by AMP deaminase, Amd1, and IMP-specific 5'-nucleotidase, Isn1. Inosine recycling into the AXP pool was facilitated by purine nucleoside phosphorylase, Pnp1, and joint action of the phosphoribosyltransferases, Hpt1 and Xpt1. Analysis of changes in 24 intracellular metabolite pools during the respiro-fermentative growth transition in wild-type, amd1, isn1, and pnp1 strains revealed that only the amd1 mutant exhibited significant deviations from the wild-type behavior. Moreover, mutants that were blocked in inosine production exhibited delayed growth acceleration after glucose addition. It is proposed that interconversion of adenine nucleotides and inosine facilitates rapid and energy-cost efficient adaptation of the AXP pool size to changing environmental conditions.
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Affiliation(s)
- Thomas Walther
- Université de Toulouse, INSA, UPS, INP, Toulouse, France.
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9
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Phenotypic consequences of purine nucleotide imbalance in Saccharomyces cerevisiae. Genetics 2009; 183:529-38, 1SI-7SI. [PMID: 19635936 DOI: 10.1534/genetics.109.105858] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Coordinating homeostasis of multiple metabolites is a major task for living organisms, and complex interconversion pathways contribute to achieving the proper balance of metabolites. AMP deaminase (AMPD) is such an interconversion enzyme that allows IMP synthesis from AMP. In this article, we show that, under specific conditions, lack of AMPD activity impairs growth. Under these conditions, we found that the intracellular guanylic nucleotide pool was severely affected. In vivo studies of two AMPD homologs, Yjl070p and Ybr284p, indicate that these proteins have no detectable AMP, adenosine, or adenine deaminase activity; we show that overexpression of YJL070c instead mimics a loss of AMPD function. Expression of the yeast transcriptome was monitored in a AMPD-deficient mutant in a strain overexpressing YJL070c and in cells treated with the immunosuppressive drug mycophenolic acid, three conditions that lead to severe depletion of the guanylic nucleotide pool. These three conditions resulted in the up- or downregulation of multiple transcripts, 244 of which are common to at least two conditions and 71 to all three conditions. These transcriptome results, combined with specific mutant analysis, point to threonine metabolism as exquisitely sensitive to the purine nucleotide balance.
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Gauthier S, Coulpier F, Jourdren L, Merle M, Beck S, Konrad M, Daignan-Fornier B, Pinson B. Co-regulation of yeast purine and phosphate pathways in response to adenylic nucleotide variations. Mol Microbiol 2008; 68:1583-94. [PMID: 18433446 DOI: 10.1111/j.1365-2958.2008.06261.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenylate kinase (Adk1p) is a pivotal enzyme in both energetic and adenylic nucleotide metabolisms. In this paper, using a transcriptomic analysis, we show that the lack of Adk1p strongly induced expression of the PHO and ADE genes involved in phosphate utilization and AMP de novo biosynthesis respectively. Isolation and characterization of adk1 point mutants affecting PHO5 expression revealed that all these mutations also severely affected Adk1p catalytic activity, as well as PHO84 and ADE1 transcription. Furthermore, overexpression of distantly related enzymes such as human adenylate kinase or yeast UMP kinase was sufficient to restore regulation. These results demonstrate that adenylate kinase catalytic activity is critical for proper regulation of the PHO and ADE pathways. We also establish that adk1 deletion and purine limitation have similar effects on both adenylic nucleotide pool and PHO84 or ADE17 expression. Finally, we show that, in the adk1 mutant, upregulation of ADE1 depends on synthesis of the previously described effector(s) (S)AICAR ((N-succinyl)-5-aminoimidazol-4-carboxamide ribotide), while upregulation of PHO84 necessitates the Spl2p positive regulator. This work reveals that adenylic nucleotide availability is a key signal used by yeast to co-ordinate phosphate utilization and purine synthesis.
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Affiliation(s)
- Sébastien Gauthier
- Université Victor Segalen/Bordeaux 2, Institut de Biochimie et Génétique Cellulaires, Bordeaux, France
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Xu J, Zhang HY, Xie CH, Xue HW, Dijkhuis P, Liu CM. EMBRYONIC FACTOR 1 encodes an AMP deaminase and is essential for the zygote to embryo transition in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 42:743-56. [PMID: 15918887 DOI: 10.1111/j.1365-313x.2005.02411.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fusion of the egg and the sperm cells in plants produces a zygote that develops into an embryo. Screening of ethyl methanesulfonate-mutagenized populations of Arabidopsis led to the identification of EMBRYONIC FACTOR 1 (FAC1), a locus that gives a zygote-lethal phenotype when mutated. The FAC1 gene was identified by positional cloning and confirmed by a genetic complementation test against a T-DNA insertion allele. It encodes an AMP deaminase (AMPD) that is known in human and yeast to convert AMP to IMP to maintain the energy potential. Expression of FAC1 in a yeast AMPD mutant after removal of its N-terminal putative transmembrane domain complemented the mutant phenotype, suggesting a functional conservancy but a structural divergence through evolution. Although a low level of FAC1 expression was observed in all organs tested, using a reporter construct we observed a significantly increased FAC1 expression in the zygote, early embryo and endosperm. Furthermore, during somatic embryogenesis, a high level of FAC1 expression was observed in developing embryos including putative embryogenic cells. FAC1, therefore, represents one of the earliest expressed genes known in plants. It may act through AMP depletion to provide sufficient energy for the zygote to proceed through development.
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Affiliation(s)
- Jun Xu
- Cluster of Plant Developmental Systems, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
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Haas AL, Sabina RL. N-terminal extensions of the human AMPD2 polypeptide influence ATP regulation of isoform L. Biochem Biophys Res Commun 2003; 305:421-7. [PMID: 12745092 DOI: 10.1016/s0006-291x(03)00787-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Human tissues and cells express three AMP deaminase (AMPD) isoforms containing divergent N-terminal domains, and each member of the multigene family encoding these enzymes produces alternative transcripts that confer additional N-terminal divergence through extensions and cassette-type substitutions. Available data suggest that divergent N-terminal domains can influence AMPD isoform behavior, but the functional significance for additional divergence within each enzyme is unknown. Three isoform L (AMPD2) variants, 1A/2, 1B/2, and 1B/3, contain N-terminal extensions of 47, 128, and 53 amino acids, respectively. This study has determined the kinetic and regulatory behaviors of these three isoform L enzymes in the presence of positive (ATP) and negative (phosphate) allosteric effectors. All display nearly identical kinetic parameters and regulatory responses in the presence of phosphate alone, or in combination with ATP. Regulation by ATP is biphasic and the three isoform L enzymes also exhibit similar activation profiles and maximum initial velocities at 2-3mM in the presence of 1mM phosphate, whereas higher concentrations of phosphate suppress this activation. However, maximum initial velocities are achieved at lower ATP concentrations (0.8-1.5mM) in the absence of phosphate and under these conditions 1B/2 is less active, 1B/3 is more active, and 1A/2 is similarly active when compared to 1mM phosphate over the range of ATP concentrations found in non-muscle cells (0.8-3.7mM). These combined results suggest that isoform L enzymes are designed to function under different metabolic conditions encountered in the non-striated muscle environments where they are expressed.
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Affiliation(s)
- Amy Louise Haas
- Department of Biochemistry, The Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-4801, USA
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13
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Haas AL, Sabina RL. Expression, purification, and inhibition of in vitro proteolysis of human AMPD2 (isoform L) recombinant enzymes. Protein Expr Purif 2003; 27:293-303. [PMID: 12597889 DOI: 10.1016/s1046-5928(02)00636-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
AMP deaminase (AMPD) is a multigene family in higher eukaryotes whose three members encode tetrameric isoforms that catalyze the deamination of AMP to IMP. AMPD polypeptides share conserved C-terminal catalytic domains of approximately 550 amino acids, whereas divergent N-terminal domains of approximately 200-330 amino acids may confer isoform-specific properties to each enzyme. However, AMPD polypeptides are subject to limited N-terminal proteolysis during purification and subsequent storage at 4 degrees C. This presents a technical challenge to studies aimed at determining the structural and functional significance of these divergent sequences. This study describes the recombinant overexpression of three naturally occurring human AMPD2 proteins, 1A/2, 1B/2, and 1B/3, that differ by N-terminal extensions of 47-128 amino acids, resulting from the use of multiple promoters and alternative splicing events. A survey of protease inhibitors reveals that E-64 and leupeptin are able to maintain the subunit structure of each AMPD2 protein when they are included in extraction and storage buffers. Gel filtration chromatography of these three purified AMPD2 enzymes comprised of intact subunits reveals that each migrates faster than expected, resulting in observed molecular masses significantly greater than those predicted for native tetrameric structures. However, chemical crosslinking analysis indicates four subunits per AMPD2 molecule, confirming that these enzymes have a native tetrameric structure. These combined results suggest that AMPD2 N-terminal extensions may exist as extended structures in solution.
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Affiliation(s)
- Amy Louise Haas
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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14
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Chae SC, Fuller D, Loomis WF. Altered cell-type proportioning in Dictyostelium lacking adenosine monophosphate deaminase. Dev Biol 2002; 241:183-94. [PMID: 11784104 DOI: 10.1006/dbio.2001.0491] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The proportions of prespore and prestalk cells in Dictyostelium discoideum are regulated so that they are size invariant and can adjust when the ratio is perturbed. We have found that disruption of the gene amdA that encodes AMP deaminase results in a significantly increased proportion of prestalk cells. Strains lacking AMP deaminase form short, thick stalks and glassy sori with less than 5% the normal number of spores. The levels of prestalk-specific mRNAs in amdA(-) cells are more than twice as high as those in wild-type strains and prespore-specific mRNAs are reduced. Using an ecmA::lacZ construct to mark prestalk cells, we found that amdA(-) null slugs have twice the normal number of prestalk cells. The number of cells expressing an ecmO::lacZ construct was not affected by loss of AmdA, indicating that the mutation results in an increase in PST-A prestalk cells rather than PST-O cells. This alteration in cell-type proportioning is a cell-autonomous consequence of the loss of AMP deaminase since mutant cells developed together with wild-type cells still produced excess prestalk cells and wild-type cells carrying the ecmA::lacZ construct formed normal numbers of prestalk cells when developed together with an equal number of amdA(-) mutant cells.
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Affiliation(s)
- Soo-Cheon Chae
- Division of Biology, University of California San Diego, La Jolla, California 92093, USA
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15
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Martini D, Ranieri-Raggi M, Sabbatini AR, Raggi A. Regulation of skeletal muscle AMP deaminase: lysine residues are critical for the pH-dependent positive homotropic cooperativity behaviour of the rabbit enzyme. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1544:123-32. [PMID: 11341922 DOI: 10.1016/s0167-4838(00)00211-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction of rabbit skeletal muscle AMP deaminase with a low molar excess of trinitrobenzene sulfonic acid (TNBS) results in conversion of the enzyme into a species with about six trinitrophenylated lysine residues per molecule which no longer manifests positive homotropic cooperativity at pH 7.1 or at the optimal pH value of 6.5 in the presence of low K+ concentrations. Substitution of the reactive thiol groups with 5,5'-dithiobis-(2-nitrobenzoic acid) does not protect the enzyme from the TNBS-induced changes of the catalytic properties, indicating that cysteine residues modification is not at the basis of the effects of TNBS treatment on AMP deaminase and strongly suggesting the obligatory participation of lysine residues to the constitution of a regulatory anionic site to which AMP must bind to stimulate the enzyme at alkaline pH. The TNBS-treated enzyme is also completely desensitized to inhibition by ATP, but not to inhibition by GTP and stimulation by ADP. This observation suggests a connection between the operation of the hypothesized anionic activating site, responsible for positive homotropic cooperativity, and the inhibition exerted by anionic compounds that compete for the same site, among them the most efficient metabolite being probably ATP.
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Affiliation(s)
- D Martini
- Dipartimento di Scienze dell'Uomo e dell'Ambiente, Chimica e Biochimica Medica, Università di Pisa, via Roma 55, 56126, Pisa, Italy
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Sabina RL, Mahnke-Zizelman DK. Towards an understanding of the functional significance of N-terminal domain divergence in human AMP deaminase isoforms. Pharmacol Ther 2000; 87:279-83. [PMID: 11008004 DOI: 10.1016/s0163-7258(00)00040-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human AMP deaminase (AMPD; EC 3.5.4.6) isoforms are encoded by a multigene family and have conserved C-terminal domains that contain catalytic residues and an ATP-binding site. N-terminal domains diverge dramatically, yet are conserved when compared across mammalian species. Cross-species conservation of entire gene-specific polypeptides (e.g., rat versus human AMPD1) suggests that divergent N-terminal domains may play a role in isoform-specific properties of the enzyme. It now has become evident that the majority of published data used to characterize purified AMPD isoforms were likely derived from preparations lacking significant portions of their N-terminal domains (up to nearly 100 residues). Accumulating evidence indicates that divergent N-terminal sequences do influence catalytic behavior, protein-protein interactions, and intracellular distributions of this enzyme.
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Affiliation(s)
- R L Sabina
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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17
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Affiliation(s)
- V L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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18
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Sims B, Mahnke-Zizelman DK, Profit AA, Prestwich GD, Sabina RL, Theibert AB. Regulation of AMP deaminase by phosphoinositides. J Biol Chem 1999; 274:25701-7. [PMID: 10464307 DOI: 10.1074/jbc.274.36.25701] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AMP deaminase (AMPD) converts AMP to IMP and is a diverse and highly regulated enzyme that is a key component of the adenylate catabolic pathway. In this report, we identify the high affinity interaction between AMPD and phosphoinositides as a mechanism for regulation of this enzyme. We demonstrate that endogenous rat brain AMPD and the human AMPD3 recombinant enzymes specifically bind inositide-based affinity probes and to mixed lipid micelles that contain phosphatidylinositol 4,5-bisphosphate. Moreover, we show that phosphoinositides specifically inhibit AMPD catalytic activity. Phosphatidylinositol 4,5-bisphosphate is the most potent inhibitor, effecting pure noncompetitive inhibition of the wild type human AMPD3 recombinant enzyme with a K(i) of 110 nM. AMPD activity can be released from membrane fractions by in vitro treatment with neomycin, a phosphoinositide-binding drug. In addition, in vivo modulation of phosphoinositide levels leads to a change in the soluble and membrane-associated pools of AMPD activity. The predicted human AMPD3 sequence contains pleckstrin homology domains and (R/K)X(n)(R/K)XKK sequences, both of which are characterized phosphoinositide-binding motifs. The interaction between AMPD and phosphoinositides may mediate membrane localization of the enzyme and function to modulate catalytic activity in vivo.
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Affiliation(s)
- B Sims
- Departments of Neurobiology and Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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19
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Noskov VN, Staak K, Shcherbakova PV, Kozmin SG, Negishi K, Ono BC, Hayatsu H, Pavlov YI. HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Yeast 1998. [DOI: 10.1002/(sici)1097-0061(199601)12:1<17::aid-yea875>3.0.co;2-i] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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20
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Abstract
N-ribohydrolases and transferases act on nucleosides, nucleotides and oligonucleotides to effect base removal. Advances in mechanistic and structural analysis have established that enzymes of N-riboside scission act by combinations of leaving-group and ribosyl activation. Alternative O-riboside substrates have been developed for mechanistic diagnosis. Transition-state structures have been determined, and powerful inhibitors have been designed from structural and transition-state information.
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Affiliation(s)
- V L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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21
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Naidoo KJ, Brady J. Molecular dynamics simulations of a glycoprotein: the lectin from Erythrina corallodendron. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(96)04868-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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22
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Nygaard P, Duckert P, Saxild HH. Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis. J Bacteriol 1996; 178:846-53. [PMID: 8550522 PMCID: PMC177734 DOI: 10.1128/jb.178.3.846-853.1996] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The isolation of mutants defective in adenine metabolism in Bacillus subtilis has provided a tool that has made it possible to investigate the role of adenine deaminase in adenine metabolism in growing cells. Adenine deaminase is the only enzyme that can deaminate adenine compounds in B. subtilis, a reaction which is important for adenine utilization as a purine and also as a nitrogen source. The uptake of adenine is strictly coupled to its further metabolism. Salvaging of adenine is inhibited by the stringent response to amino acid starvation, while the deamination of adenine is not. The level of adenine deaminase was reduced when exogenous guanosine served as the purine source and when glutamine served as the nitrogen source. The enzyme level was essentially the same whether ammonia or purines served as the nitrogen source. Reduced levels were seen on poor carbon sources. The ade gene was cloned, and the nucleotide sequence and mRNA analyses revealed a single-gene operon encoding a 65-kDa protein. By transductional crosses, we have located the ade gene to 130 degrees on the chromosomal map.
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Affiliation(s)
- P Nygaard
- Department of Biological Chemistry, University of Copenhagen, Denmark
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23
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Noskov VN, Staak K, Shcherbakova PV, Kozmin SG, Negishi K, Ono BC, Hayatsu H, Pavlov YI. HAM1, the gene controlling 6-N-hydroxylaminopurine sensitivity and mutagenesis in the yeast Saccharomyces cerevisiae. Yeast 1996; 12:17-29. [PMID: 8789257 DOI: 10.1002/(sici)1097-0061(199601)12:1%3c17::aid-yea875%3e3.0.co;2-i] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The ham1 mutant of yeast Saccharomyces cerevisiae is sensitive to the mutagenic and lethal effects of the base analog, 6-N-hydroxylaminopurine (HAP). We have isolated a clone from a centromere-plasmid-based genomic library complementing HAP sensitivity of the ham1 strain. After subcloning, a 3.4 kb functional fragment was sequenced. It contained three open reading frames (ORFs) corresponding to proteins 353, 197 and 184 amino acids long. LEU2+ disruptions of the promoter and N-terminal part of the gene coding 197 amino acids long protein led to moderate and strong sensitivity to HAP, respectively, and were allelic to the original ham1-1 mutation. Thus this ORF represents the HAM1 gene. The deduced amino acid sequence of HAM1 protein was not similar to any protein sequence of the SwissProt database. The HAM1 gene was localized on the right arm of chromosome X between cdc8 and cdc11. Spontaneous mutagenesis was not affected by the ham1::LEU2 disruption mutation.
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Affiliation(s)
- V N Noskov
- Department of Genetics, Sankt-Petersburg University, Russia
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24
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Ranieri-Raggi M, Ronca F, Sabbatini A, Raggi A. Regulation of skeletal-muscle AMP deaminase: involvement of histidine residues in the pH-dependent inhibition of the rabbit enzyme by ATP. Biochem J 1995; 309 ( Pt 3):845-52. [PMID: 7639701 PMCID: PMC1135709 DOI: 10.1042/bj3090845] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Reaction of rabbit skeletal-muscle AMP deaminase with a low molar excess of diethyl pyrocarbonate results in conversion of the enzyme into a species with one or two carbethoxylated histidine residues per subunit that retains sensitivity to ATP at pH 7.1 but, unlike the native enzyme, it is not sensitive to regulation by ATP at pH 6.5. This effect mimics that exerted on the enzyme by limited proteolysis with trypsin, which removes the 95-residue N-terminal region from the 80 kDa enzyme subunit. These observations suggest involvement of some histidine residues localized in the region HHEMQAHILH (residues 51-60) in the regulatory mechanism which stabilizes the binding of ATP to its inhibitory site at acidic pH. Carbethoxylation of two histidine residues per subunit abolishes the inhibition by ATP of the proteolysed enzyme at pH 7.1, suggesting the obligatory participation of a second class of histidine residues, localized in the 70 kDa subunit core, in the mechanism of the pH-dependent inhibition of the enzyme by ATP. At a slightly acidic pH, these histidine residues would be positively charged, resulting in a desensitized form of the enzyme similar to that obtained with the carbethoxylation reaction.
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Affiliation(s)
- M Ranieri-Raggi
- Istituto di Chimica Biologica dell'Università di Pisa, Italy
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25
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Kline P, Schramm V. Electrostatic potential surfaces of the transition state for AMP deaminase and for (R)-coformycin, a transition state inhibitor. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)31801-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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26
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Holmstrøm K, Brandt T, Kallesøe T. The sequence of a 32,420 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae. Yeast 1994; 10 Suppl A:S47-62. [PMID: 8091861 DOI: 10.1002/yea.320100007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The sequence of a 32,420 bp segment of Saccharomyces cerevisiae chromosome II has been deduced. The sequence data revealed 19 potential new genes covering 83.5% of the sequence. Four genes had already been cloned and sequenced: part of RIF1, DPB3, MRP-L27 and SNF5. Besides these four genes, 15 open reading frames (ORFs) of at least 100 amino acids encoding potential new genes were identified. Two of these ORFs are overlapping and a third is located within another ORF. The putative gene product of ORF YBR2039 was homologous to the group of uncoupling proteins involved in the mitochondrial energy transfer system. We propose a remapping of the MRP-L27 gene encoding the mitoribosomal protein YmL27 as it previously has been mapped on chromosome X. The ORF YBR2020 has a strong homology with a 31.9% identity in a 473 amino acid region to the yeast gene SEC61, suggesting that YBR2020 is a new gene encoding a protein involved in translocation of proteins in the yeast cell. Six of the potential genes do not exhibit any significant homology to previously sequenced genes as predicted in the Fast A analysis.
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27
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Functionally distinct elements are required for expression of the AMPD1 gene in myocytes. Mol Cell Biol 1993. [PMID: 8355716 DOI: 10.1128/mcb.13.9.5854] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AMP deaminase (AMPD) is an enzyme found in all eukaryotic cells. Tissue-specific and stage-specific isoforms of this enzyme are found in vertebrates, and expression of these different isoforms is determined by selective expression of the multiple genes. The AMPD1 gene is expressed predominantly in skeletal muscle, in which transcript abundance is controlled by stage-specific and fiber type-specific signals. This enzyme activity is presumed to be important in skeletal muscle because a metabolic myopathy develops in individuals with an inherited deficiency of AMPD1. In the present study, cis- and trans-acting factors that control expression of AMPD1 have been identified. Two cis-acting elements located within 100 nucleotides of the transcriptional start site are required for muscle-specific expression of AMPD1. One element (-100 to -79) behaves like a tissue-specific enhancer, and it interacts with protein(s) found predominantly in nuclei of myoblasts and myotubes. This element is similar in sequence to an MEF2 binding motif, and it contains an A/T core that is essential for enhancer activity and binding of a nuclear protein(s). The second element (-60 to -40) has properties of a stage-specific promoter in that it is essential for muscle-specific expression of the AMPD1 promoter, does not confer muscle-specific expression on a heterologous promoter construct, and interacts with a protein(s) restricted to nuclei of differentiated myotubes. Interaction between these functionally distinct elements may be required for regulating the expression of AMPD1 during myocyte differentiation and in different muscle fiber types.
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28
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Morisaki T, Holmes EW. Functionally distinct elements are required for expression of the AMPD1 gene in myocytes. Mol Cell Biol 1993; 13:5854-60. [PMID: 8355716 PMCID: PMC360332 DOI: 10.1128/mcb.13.9.5854-5860.1993] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AMP deaminase (AMPD) is an enzyme found in all eukaryotic cells. Tissue-specific and stage-specific isoforms of this enzyme are found in vertebrates, and expression of these different isoforms is determined by selective expression of the multiple genes. The AMPD1 gene is expressed predominantly in skeletal muscle, in which transcript abundance is controlled by stage-specific and fiber type-specific signals. This enzyme activity is presumed to be important in skeletal muscle because a metabolic myopathy develops in individuals with an inherited deficiency of AMPD1. In the present study, cis- and trans-acting factors that control expression of AMPD1 have been identified. Two cis-acting elements located within 100 nucleotides of the transcriptional start site are required for muscle-specific expression of AMPD1. One element (-100 to -79) behaves like a tissue-specific enhancer, and it interacts with protein(s) found predominantly in nuclei of myoblasts and myotubes. This element is similar in sequence to an MEF2 binding motif, and it contains an A/T core that is essential for enhancer activity and binding of a nuclear protein(s). The second element (-60 to -40) has properties of a stage-specific promoter in that it is essential for muscle-specific expression of the AMPD1 promoter, does not confer muscle-specific expression on a heterologous promoter construct, and interacts with a protein(s) restricted to nuclei of differentiated myotubes. Interaction between these functionally distinct elements may be required for regulating the expression of AMPD1 during myocyte differentiation and in different muscle fiber types.
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Affiliation(s)
- T Morisaki
- Seymour Gray Molecular Medicine Laboratory, Department of Medicine and Human Genetics, University of Pennsylvania, Philadelphia 19104-4283
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29
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Tanfani F, Kossowska E, Purzycka-Preis J, Zydowo MM, Wozniak M, Tartaglini E, Bertoli E. The interaction of phospholipid bilayers with pig heart AMP deaminase: Fourier-transform infrared spectroscopic and kinetic studies. Biochem J 1993; 291 ( Pt 3):921-6. [PMID: 8489518 PMCID: PMC1132457 DOI: 10.1042/bj2910921] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The interaction of pig heart AMP deaminase with different chemical species of phosphatidylcholine and with natural plasma membranes has been investigated. Phospholipids added to the system either as natural biological membranes (plasma membrane vesicles) or in the form of liposomes containing unsaturated phosphatidylcholine considerably enhanced AMP deaminase activity. The secondary structure of pig heart AMP deaminase in the absence and in the presence of dioleoyl phosphatidylcholine and dipalmitoyl phosphatidylcholine liposomes was investigated by Fourier-transform infrared spectroscopy. Quantitative analysis of the amide I band showed that the enzyme contains 45% beta-sheets, 28% alpha-helix, 16% turns and 11% non-ordered structure. In the presence of dioleoyl phosphatidylcholine liposomes, the beta/alpha content ratio decreased; this decrease was dependent on the amount of lipid added. This phenomenon was not observed in the case of dipalmitoyl phosphatidylcholine liposomes. These data suggest a possible role for membrane phospholipids in the regulation of AMP deaminase activity.
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Affiliation(s)
- F Tanfani
- Istituto di Biochimica, Facoltà di Medicina, Università di Ancona, Italy
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30
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Kvalnes-Krick K, Labdon J, Ma X, Nieves E, Schramm V. Mutagenic analysis of AMP nucleosidase from Escherichia coli. Deletion of a region similar to AMP deaminase and peptide characterization by mass spectrometry. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)52934-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Yeast AMP deaminase. Catalytic activity in Schizosaccharomyces pombe and chromosomal location in Saccharomyces cerevisiae. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53645-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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32
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Mossé MO, Linder P, Lazowska J, Slonimski PP. A comprehensive compilation of 1001 nucleotide sequences coding for proteins from the yeast Saccharomyces cerevisiae (= ListA2). Curr Genet 1993; 23:66-91. [PMID: 8428384 DOI: 10.1007/bf00336752] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The amount of nucleotide sequence data is increasing exponentially. We therefore continued our effort to make a comprehensive database for the yeast Saccharomyces cerevisiae. In this database (ListA2) we have compiled 1001 protein coding sequences from this organism. Each sequence has been attributed a single genetic name and in the case of allelic duplicated sequences, synonyms are given, if necessary. For the nomenclature we have introduced a standard principle for naming gene sequences based on priority rules. We have also applied a simple method to distinguish duplicated sequences of one and the same gene from non-allelic sequences of duplicated genes. By using these principles we have sorted out a lot of confusion in the literature and databanks. Along with the genetic name, the mnemonic from the EMBL databank, the codon bias, reference of the publication of the sequence and the EMBL accession numbers are included for each entry. The database is available on request.
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Affiliation(s)
- M O Mossé
- Centre de Génétique Moléculaire, Université Pierre et Marie Curie, Gif-sur Yvette, France
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33
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Molecular cloning of AMP deaminase isoform L. Sequence and bacterial expression of human AMPD2 cDNA. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41686-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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34
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Cloning of human AMP deaminase isoform E cDNAs. Evidence for a third AMPD gene exhibiting alternatively spliced 5'-exons. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(19)36768-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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35
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Wächtershäuser G. Groundworks for an evolutionary biochemistry: the iron-sulphur world. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1992; 58:85-201. [PMID: 1509092 DOI: 10.1016/0079-6107(92)90022-x] [Citation(s) in RCA: 359] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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36
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Chang ZY, Nygaard P, Chinault AC, Kellems RE. Deduced amino acid sequence of Escherichia coli adenosine deaminase reveals evolutionarily conserved amino acid residues: implications for catalytic function. Biochemistry 1991; 30:2273-80. [PMID: 1998686 DOI: 10.1021/bi00222a033] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The goal of the research reported here is to identify evolutionarily conserved amino acid residues associated with enzymatic deamination of adenosine. To do this, we isolated molecular clones of the Escherichia coli adenosine deaminase gene by functional complementation of adenosine deaminase deficient bacteria and deduced the amino acid sequence of the enzyme from the nucleotide sequence of the gene. Nucleotide sequence analysis revealed the presence of a 996-nucleotide open reading frame encoding a protein of 332 amino acids having a molecular weight of 36,345. The deduced amino acid sequence of the E. coli enzyme has approximately 33% identity with those of the mammalian adenosine deaminases. With conservative amino acid substitutions the overall sequence homology approaches 50%, suggesting that the structures and functions of the mammalian and bacterial enzymes are similar. Additional amino acid sequence analysis revealed specific residues that are conserved among all three adenosine deaminases and four AMP deaminases for which sequence information is currently available. In view of previously published enzymological data and the conserved amino acid residues identified in this study, we propose a model to account for the enzyme-catalyzed hydrolytic deamination of adenosine. Potential catalytic roles are assigned to the conserved His 214, Cys 262, Asp 295, and Asp 296 residues of mammalian adenosine deaminases and the corresponding conserved amino acid residues in bacterial adenosine deaminase and the eukaryotic AMP deaminases.
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Affiliation(s)
- Z Y Chang
- Verna and Marrs McLean Department of Biochemistry, Baylor College of Medicine, Houston, Texas 77030
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37
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A novel pathway for alternative splicing: identification of an RNA intermediate that generates an alternative 5' splice donor site not present in the primary transcript of AMPD1. Mol Cell Biol 1990. [PMID: 2398891 DOI: 10.1128/mcb.10.10.5271] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AMP deaminase (AMPD) is a central enzyme in eucaryotic energy metabolism, and tissue-specific as well as stage-specific isoforms are found in many vertebrates. This study demonstrates the AMPD1 gene product in rat is alternatively spliced. The second exon, a 12-base miniexon, was found to be excluded or included in a tissue-specific and stage-specific pattern. This example of cassette splicing utilizes a unique pathway through an RNA intermediate that generates an alternative 5' splice donor site at the point where exon 2 is ligated to exon 1. In the analogous intermediate of human AMPD1, the potential 5' splice donor site created at the boundary of exon 1 and exon 2 was a poor substrate for splicing because of differences in exon 2 sequences, and human AMPD1 was not alternatively spliced. These results demonstrate that in some cases alternative splicing may proceed through an RNA intermediate that generates an alternative splice donor site not present in the primary transcript. Discrimination between alternative 5' splice donor sites in the RNA intermediate of AMPD1 is apparently controlled by tissue-specific and stage-specific signals.
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38
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A novel pathway for alternative splicing: identification of an RNA intermediate that generates an alternative 5' splice donor site not present in the primary transcript of AMPD1. Mol Cell Biol 1990; 10:5271-8. [PMID: 2398891 PMCID: PMC361213 DOI: 10.1128/mcb.10.10.5271-5278.1990] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AMP deaminase (AMPD) is a central enzyme in eucaryotic energy metabolism, and tissue-specific as well as stage-specific isoforms are found in many vertebrates. This study demonstrates the AMPD1 gene product in rat is alternatively spliced. The second exon, a 12-base miniexon, was found to be excluded or included in a tissue-specific and stage-specific pattern. This example of cassette splicing utilizes a unique pathway through an RNA intermediate that generates an alternative 5' splice donor site at the point where exon 2 is ligated to exon 1. In the analogous intermediate of human AMPD1, the potential 5' splice donor site created at the boundary of exon 1 and exon 2 was a poor substrate for splicing because of differences in exon 2 sequences, and human AMPD1 was not alternatively spliced. These results demonstrate that in some cases alternative splicing may proceed through an RNA intermediate that generates an alternative splice donor site not present in the primary transcript. Discrimination between alternative 5' splice donor sites in the RNA intermediate of AMPD1 is apparently controlled by tissue-specific and stage-specific signals.
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40
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41
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Merkler DJ, Schramm VL. Catalytic and regulatory site composition of yeast AMP deaminase by comparative binding and rate studies. Resolution of the cooperative mechanism. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39581-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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42
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