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Moretton A, Kourtis S, Gañez Zapater A, Calabrò C, Espinar Calvo ML, Fontaine F, Darai E, Abad Cortel E, Block S, Pascual‐Reguant L, Pardo‐Lorente N, Ghose R, Vander Heiden MG, Janic A, Müller AC, Loizou JI, Sdelci S. A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability. Mol Syst Biol 2023; 19:e11267. [PMID: 37259925 PMCID: PMC10333845 DOI: 10.15252/msb.202211267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023] Open
Abstract
While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes and processes that are essential for the resolution of DNA damage. By integrating functional genomics with chromatin proteomics and metabolomics, we provide a detailed description of the interplay between cellular metabolism and the DNA damage response. Further analysis identified that Peroxiredoxin 1, PRDX1, contributes to the DNA damage repair. During the DNA damage response, PRDX1 translocates to the nucleus where it reduces DNA damage-induced nuclear reactive oxygen species. Moreover, PRDX1 loss lowers aspartate availability, which is required for the DNA damage-induced upregulation of de novo nucleotide synthesis. In the absence of PRDX1, cells accumulate replication stress and DNA damage, leading to proliferation defects that are exacerbated in the presence of etoposide, thus revealing a role for PRDX1 as a DNA damage surveillance factor.
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Affiliation(s)
- Amandine Moretton
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Savvas Kourtis
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Antoni Gañez Zapater
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Chiara Calabrò
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | | | - Frédéric Fontaine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Evangelia Darai
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Etna Abad Cortel
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - Samuel Block
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Laura Pascual‐Reguant
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Natalia Pardo‐Lorente
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Ritobrata Ghose
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Dana‐Farber Cancer InstituteBostonMAUSA
| | - Ana Janic
- Department of Medicine and Life SciencesUniversitat Pompeu FabraBarcelonaSpain
| | - André C Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I Loizou
- Center for Cancer Research, Comprehensive Cancer CenterMedical University of ViennaViennaAustria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Sara Sdelci
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
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Fernandes J, Uppal K, Liu KH, Hu X, Orr M, Tran V, Go YM, Jones DP. Antagonistic Interactions in Mitochondria ROS Signaling Responses to Manganese. Antioxidants (Basel) 2023; 12:804. [PMID: 37107179 PMCID: PMC10134992 DOI: 10.3390/antiox12040804] [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: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Antagonistic interaction refers to opposing beneficial and adverse signaling by a single agent. Understanding opposing signaling is important because pathologic outcomes can result from adverse causative agents or the failure of beneficial mechanisms. To test for opposing responses at a systems level, we used a transcriptome-metabolome-wide association study (TMWAS) with the rationale that metabolite changes provide a phenotypic readout of gene expression, and gene expression provides a phenotypic readout of signaling metabolites. We incorporated measures of mitochondrial oxidative stress (mtOx) and oxygen consumption rate (mtOCR) with TMWAS of cells with varied manganese (Mn) concentration and found that adverse neuroinflammatory signaling and fatty acid metabolism were connected to mtOx, while beneficial ion transport and neurotransmitter metabolism were connected to mtOCR. Each community contained opposing transcriptome-metabolome interactions, which were linked to biologic functions. The results show that antagonistic interaction is a generalized cell systems response to mitochondrial ROS signaling.
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Affiliation(s)
- Jolyn Fernandes
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ken H. Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
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Peters BA, Qi Q, Usyk M, Daviglus ML, Cai J, Franceschini N, Lash JP, Gellman MD, Yu B, Boerwinkle E, Knight R, Burk RD, Kaplan RC. Association of the gut microbiome with kidney function and damage in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Gut Microbes 2023; 15:2186685. [PMID: 36882941 PMCID: PMC10012940 DOI: 10.1080/19490976.2023.2186685] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND The gut microbiome is altered in chronic kidney disease (CKD), potentially contributing to CKD progression and co-morbidities, but population-based studies of the gut microbiome across a wide range of kidney function and damage are lacking. METHODS In the Hispanic Community Health Study/Study of Latinos, gut microbiome was assessed by shotgun sequencing of stool (n = 2,438; 292 with suspected CKD). We examined cross-sectional associations of estimated glomerular filtration rate (eGFR), urinary albumin:creatinine (UAC) ratio, and CKD with gut microbiome features. Kidney trait-related microbiome features were interrogated for correlation with serum metabolites (n = 700), and associations of microbiome-related serum metabolites with kidney trait progression were examined in a prospective analysis (n = 3,635). RESULTS Higher eGFR was associated with overall gut microbiome composition, greater abundance of species from Prevotella, Faecalibacterium, Roseburia, and Eubacterium, and microbial functions related to synthesis of long-chain fatty acids and carbamoyl-phosphate. Higher UAC ratio and CKD were related to lower gut microbiome diversity and altered overall microbiome composition only in participants without diabetes. Microbiome features related to better kidney health were associated with many serum metabolites (e.g., higher indolepropionate, beta-cryptoxanthin; lower imidazole propionate, deoxycholic acids, p-cresol glucuronide). Imidazole propionate, deoxycholic acid metabolites, and p-cresol glucuronide were associated with prospective reductions in eGFR and/or increases in UAC ratio over ~6 y. CONCLUSIONS Kidney function is a significant correlate of the gut microbiome, while the relationship of kidney damage with the gut microbiome depends on diabetes status. Gut microbiome metabolites may contribute to CKD progression.
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Affiliation(s)
- Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mykhaylo Usyk
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Martha L. Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, USA
| | - Jianwen Cai
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Lash
- Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Marc D. Gellman
- Department of Psychology, University of Miami, Miami, FL, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Rob Knight
- Departments of Pediatrics, Computer Science and Engineering, Bioengineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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Kim NY, Kim OB. The ybcF Gene of Escherichia coli Encodes a Local Orphan Enzyme, Catabolic Carbamate Kinase. J Microbiol Biotechnol 2022; 32:1527-1536. [PMID: 36384810 PMCID: PMC9843812 DOI: 10.4014/jmb.2210.10037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022]
Abstract
Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA-ylbE-ylbF-ybcF that is located downstream of the allDCE-operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA, ylbE, ylbF, and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The Vmax is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the KM value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK.
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Affiliation(s)
- Nam Yeun Kim
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Ok Bin Kim
- Department of Life Science, Division of EcoScience, Ewha Womans University, Seoul 03760, Republic of Korea
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5
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Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid. Sci Rep 2022; 12:19178. [PMID: 36357418 PMCID: PMC9649776 DOI: 10.1038/s41598-022-21272-7] [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: 07/18/2022] [Accepted: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.
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6
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Pinna S, Kunz C, Halpern A, Harrison SA, Jordan SF, Ward J, Werner F, Lane N. A prebiotic basis for ATP as the universal energy currency. PLoS Biol 2022; 20:e3001437. [PMID: 36194581 PMCID: PMC9531788 DOI: 10.1371/journal.pbio.3001437] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 08/30/2022] [Indexed: 11/07/2022] Open
Abstract
ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.
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Affiliation(s)
- Silvana Pinna
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Cäcilia Kunz
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Aaron Halpern
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Stuart A. Harrison
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - Sean F. Jordan
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
| | - John Ward
- Department of Biochemical Engineering, University College London, London, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, University College London, Darwin Building, London, United Kingdom
| | - Nick Lane
- Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, Darwin Building, London, United Kingdom
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7
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Zarlenga D, Thompson P, Mitreva M, Rosa BA, Hoberg E. Horizontal gene transfer provides insights into the deep evolutionary history and biology of Trichinella. Food Waterborne Parasitol 2022; 27:e00155. [PMID: 35542181 PMCID: PMC9079694 DOI: 10.1016/j.fawpar.2022.e00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
Evolution involves temporal changes in the characteristics of a species that are subsequently propagated or rejected through natural selection. In the case of parasites, host switching also plays a prominent role in the evolutionary process. These changes are rooted in genetic variation and gene flow where genes may be deleted, mutated (sequence), duplicated, rearranged and/or translocated and then transmitted through vertical gene transfer. However, the introduction of new genes is not driven only by Mendelian inheritance and mutation but also by the introduction of DNA from outside a lineage in the form of horizontal gene transfer between donor and recipient organisms. Once introduced and integrated into the biology of the recipient, vertical inheritance then perpetuates the newly acquired genetic factor, where further functionality may involve co-option of what has become a pre-existing physiological capacity. Upon sequencing the Trichinella spiralis (Clade I) genome, a cyanate hydratase (cyanase) gene was identified that is common among bacteria, fungi, and plants, but rarely observed among other eukaryotes. The sequence of the Trichinella cyanase gene clusters with those derived from the Kingdom Plantae in contrast to the genes found in some Clade III and IV nematodes that cluster with cyanases of bacterial origin. Phylogenetic analyses suggest that the Trichinella cyanase was acquired during the Devonian period and independently from those of other nematodes. These data may help inform us of the deep evolutionary history and ecological connectivity of early ancestors within the lineage of contemporary Trichinella. Further, in many extant organisms, cyanate detoxification has been largely superseded by energy requirements for metabolism. Thus, deciphering the function of Trichinella cyanase may provide new avenues for treatment and control.
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Affiliation(s)
- Dante Zarlenga
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Peter Thompson
- U.S. Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, B1180 BARC-East Beltsville, MD 20705, USA
| | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Bruce A. Rosa
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnel Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Eric Hoberg
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
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8
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Wang Q, Guan K, Lv Y, Zhang Y, Yu Z, Kan Q. Disturbance of hepatocyte growth and metabolism in a hyperammonemia microenvironment. Arch Biochem Biophys 2021; 716:109109. [PMID: 34932992 DOI: 10.1016/j.abb.2021.109109] [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: 05/06/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND We found through previous research that hyperammonemia can cause secondary liver damage. However, whether hepatocytes are target cells of ammonia toxicity and whether hyperammonemia affects hepatocyte metabolism remain unknown. AIMS The purpose of the current study is to examine whether the hepatocyte is a specific target cell of ammonia toxicity and whether hyperammonemia can interfere with hepatocyte metabolism. METHODS Cell viability and apoptosis were analyzed in primary hepatocytes and other cells that had been exposed to ammonium chloride. Western blotting was adopted to examine the expression of proteins related to ammonia transport. We also established a metabolomics method based on gas chromatography-mass spectrometry to understand the characteristics of the hepatocyte metabolic spectrum in a hyperammonemia microenvironment, to screen and identify differential metabolites, and to determine the differential metabolic pathway. Different technologies were used to verify the differential metabolic pathways. RESULTS Hepatocytes are target cells of ammonia toxicity. The mechanism is related to the ammonia transporter. Hyperammonemia interferes with hepatocyte metabolism, which leads to TCA cycle, urea cycle, and RNA synthesis disorder. CONCLUSIONS This study demonstrates that hepatocyte growth and metabolism are disturbed in a hyperammonemia microenvironment, which further deteriorates hepatocyte function.
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Affiliation(s)
- Qiongye Wang
- Departments of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kelei Guan
- Department of Pharmacology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuanjun Lv
- Department of Respiratory. the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingxuan Zhang
- Department of Hepatobiliary and Pancreatic Surgery. the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Departments of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Quancheng Kan
- Department of Pharmacology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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9
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Couchet M, Breuillard C, Corne C, Rendu J, Morio B, Schlattner U, Moinard C. Ornithine Transcarbamylase - From Structure to Metabolism: An Update. Front Physiol 2021; 12:748249. [PMID: 34658931 PMCID: PMC8517447 DOI: 10.3389/fphys.2021.748249] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Ornithine transcarbamylase (OTC; EC 2.1.3.3) is a ubiquitous enzyme found in almost all organisms, including vertebrates, microorganisms, and plants. Anabolic, mostly trimeric OTCs catalyze the production of L-citrulline from L-ornithine which is a part of the urea cycle. In eukaryotes, such OTC localizes to the mitochondrial matrix, partially bound to the mitochondrial inner membrane and part of channeling multi-enzyme assemblies. In mammals, mainly two organs express OTC: the liver, where it is an integral part of the urea cycle, and the intestine, where it synthesizes citrulline for export and plays a major role in amino acid homeostasis, particularly of L-glutamine and L-arginine. Here, we give an overview on OTC genes and proteins, their tissue distribution, regulation, and physiological function, emphasizing the importance of OTC and urea cycle enzymes for metabolic regulation in human health and disease. Finally, we summarize the current knowledge of OTC deficiency, a rare X-linked human genetic disorder, and its emerging role in various chronic pathologies.
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Affiliation(s)
- Morgane Couchet
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Charlotte Breuillard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - John Rendu
- Centre Hospitalier Université Grenoble Alpes, Grenoble, France
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Lyon, France
| | - Uwe Schlattner
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France.,Institut Universitaire de France, Paris, France
| | - Christophe Moinard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
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10
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Carbamoyl phosphate and its substitutes for the uracil synthesis in origins of life scenarios. Sci Rep 2021; 11:19356. [PMID: 34588537 PMCID: PMC8481487 DOI: 10.1038/s41598-021-98747-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/06/2021] [Indexed: 11/29/2022] Open
Abstract
The first step of pyrimidine synthesis along the orotate pathway is studied to test the hypothesis of geochemical continuity of protometabolic pathways at the origins of life. Carbamoyl phosphate (CP) is the first high-energy building block that intervenes in the in vivo synthesis of the uracil ring of UMP. Thus, the likelihood of its occurrence in prebiotic conditions is investigated herein. The evolution of carbamoyl phosphate in water and in ammonia aqueous solutions without enzymes was characterised using ATR-IR, 31P and 13C spectroscopies. Carbamoyl phosphate initially appears stable in water at ambient conditions before transforming to cyanate and carbamate/hydrogenocarbonate species within a matter of hours. Cyanate, less labile than CP, remains a potential carbamoylating agent. In the presence of ammonia, CP decomposition occurs more rapidly and generates urea. We conclude that CP is not a likely prebiotic reagent by itself. Alternatively, cyanate and urea may be more promising substitutes for CP, because they are both “energy-rich” (high free enthalpy molecules in aqueous solutions) and kinetically inert regarding hydrolysis. Energy-rich inorganic molecules such as trimetaphosphate or phosphoramidates were also explored for their suitability as sources of carbamoyl phosphate. Although these species did not generate CP or other carbamoylating agents, they exhibited energy transduction, specifically the formation of high-energy P–N bonds. Future efforts should aim to evaluate the role of carbamoylating agents in aspartate carbamoylation, which is the following reaction in the orotate pathway.
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11
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Wang Q, Xu Z, Ai Q. Arginine metabolism and its functions in growth, nutrient utilization, and immunonutrition of fish. ACTA ACUST UNITED AC 2021; 7:716-727. [PMID: 34466676 PMCID: PMC8379419 DOI: 10.1016/j.aninu.2021.03.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/30/2022]
Abstract
Fish have limited ability in endogenous biosynthesis of arginine. Arginine is an indispensable amino acid for fish, and the arginine requirement varies with fish species and fish size. Recent studies on fish have demonstrated that arginine influences nutrient metabolism, stimulates insulin release, is involved in nonspecific immune responses and antioxidant responses, and elevates disease resistance. Specifically, arginine can regulate energy homeostasis via modulating the adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK) pathway, and also regulate protein synthesis via activating the target of rapamycin (TOR) signaling pathway. The present article reviews pertinent knowledge of arginine in fish, including dietary quantitative requirements, endogenous anabolism and catabolism, regulation of the endocrine and metabolic systems, and immune-regulatory functions under pathogenic challenge. Our findings showed that further data about the distribution of arginine after intake into specific cells, its sub-cellular sensor to initiate downstream signaling pathways, and its effects on fish mucosal immunity, especially the adaptive immune response against pathogenic infection in different species, are urgently needed.
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Affiliation(s)
- Qingchao Wang
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhen Xu
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qinghui Ai
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Aquaculture Nutrition and Feed (Ministry of Agriculture), Ocean University of China, Qingdao, China
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Aron O, Wang M, Mabeche AW, Wajjiha B, Li M, Yang S, You H, Cai Y, Zhang T, Li Y, Wang B, Zhang D, Wang Z, Tang W. MoCpa1-mediated arginine biosynthesis is crucial for fungal growth, conidiation, and plant infection of Magnaporthe oryzae. Appl Microbiol Biotechnol 2021; 105:5915-5929. [PMID: 34292355 DOI: 10.1007/s00253-021-11437-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/16/2021] [Accepted: 06/19/2021] [Indexed: 12/01/2022]
Abstract
Arginine is an important amino acid involved in processes such as cell signal transduction, protein synthesis, and sexual reproduction. To understand the biological roles of arginine biosynthesis in pathogenic fungi, we used Cpa1, the carbamoyl phosphate synthase arginine-specific small chain subunit in Saccharomyces cerevisiae as a query to identify its ortholog in the Magnaporthe oryzae genome and named it MoCpa1. MoCpa1 is a 471-amino acid protein containing a CPSase_sm_chain domain and a GATase domain. MoCpa1 transcripts were highly expressed at the conidiation, early-infection, and late-infection stages of the fungus. Targeted deletion of the MoCPA1 gene resulted in a ΔMocpa1 mutant exhibiting arginine auxotrophy on minimum culture medium (MM), confirming its role in de novo arginine biosynthesis. The ΔMocpa1 mutant presented significantly decreased sporulation with some of its conidia being defective in morphology. Furthermore, the ΔMocpa1 mutant was nonpathogenic on rice and barley leaves, which was a result of defects in appressorium-mediated penetration and restricted invasive hyphal growth within host cells. Addition of exogenous arginine partially rescued conidiation and pathogenicity defects on the barley and rice leaves, while introduction of the MoCPA1 gene into the ΔMocpa1 mutant fully complemented the lost phenotype. Further confocal microscopy examination revealed that MoCpa1 is localized in the mitochondria. In summary, our results demonstrate that MoCpa1-mediated arginine biosynthesis is crucial for fungal development, conidiation, appressorium formation, and infection-related morphogenesis in M. oryzae, thus serving as an attractive target for mitigating obstinate fungal plant pathogens. KEY POINTS: • MoCpa1 is important for aerial hyphal growth and arginine biosynthesis. • MoCpa1 is pivotal for conidial morphogenesis and appressorium formation. • MoCpa1 is crucial for full virulence in M. oryzae.
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Affiliation(s)
- Osakina Aron
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Min Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Anjago Wilfred Mabeche
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Batool Wajjiha
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meiqin Li
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuai Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haixia You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Cai
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Zhang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yunxi Li
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baohua Wang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongmei Zhang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
| | - Wei Tang
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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13
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Del Caño-Ochoa F, Ramón-Maiques S. Deciphering CAD: Structure and function of a mega-enzymatic pyrimidine factory in health and disease. Protein Sci 2021; 30:1995-2008. [PMID: 34288185 PMCID: PMC8442968 DOI: 10.1002/pro.4158] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein divided into different enzymatic domains, each catalyzing one of the initial reactions for de novo biosynthesis of pyrimidine nucleotides: glutaminase‐dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase, and Dihydroorotase. The pathway for de novo pyrimidine synthesis is essential for cell proliferation and is conserved in all living organisms, but the covalent linkage of the first enzymatic activities into a multienzymatic CAD particle is unique to animals. In other organisms, these enzymatic activities are encoded as monofunctional proteins for which there is abundant structural and biochemical information. However, the knowledge about CAD is scarce and fragmented. Understanding CAD requires not only to determine the three‐dimensional structures and define the catalytic and regulatory mechanisms of the different enzymatic domains, but also to comprehend how these domains entangle and work in a coordinated and regulated manner. This review summarizes significant progress over the past 10 years toward the characterization of CAD's architecture, function, regulatory mechanisms, and cellular compartmentalization, as well as the recent finding of a new and rare neurometabolic disorder caused by defects in CAD activities.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
| | - Santiago Ramón-Maiques
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,Group 739, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) - Instituto de Salud Carlos III, Valencia, Spain
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14
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Enhanced production of L-arginine by improving carbamoyl phosphate supply in metabolically engineered Corynebacterium crenatum. Appl Microbiol Biotechnol 2021; 105:3265-3276. [PMID: 33837829 DOI: 10.1007/s00253-021-11242-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
Carbamoyl phosphate is an important precursor for L-arginine and pyrimidines biosynthesis. In view of this importance, the cell factory should enhance carbamoyl phosphate synthesis to improve related compound production. In this work, we verified that carbamoyl phosphate is essential for L-arginine production in Corynebacterium sp., followed by engineering of carbamoyl phosphate synthesis for further strain improvement. First, carAB encoding carbamoyl phosphate synthetase II was overexpressed to improve the synthesis of carbamoyl phosphate. Second, the regulation of glutamine synthetase increases the supply of L-glutamine, providing an effective substrate for carbamoyl phosphate synthetase II. Third, carbamate kinase, which catalyzes inorganic ammonia synthesis carbamoyl phosphate, was screened and selected to assist in carbamoyl phosphate supply. Finally, we disrupted ldh (encoding lactate dehydrogenase) to decrease by-production formation and save NADH to regenerate ATP through the electron transport chain. Subsequently, the resulting strain allowed a dramatically increased L-arginine production of 68.6 ± 1.2 g∙L-1, with an overall productivity of 0.71 ± 0.01 g∙L-1∙h-1 in 5-L bioreactor. Stepwise rational metabolic engineering based on an increase in the supply of carbamoyl phosphate resulted in a gradual increase in L-arginine production. The strategy described here can also be implemented to improve L-arginine and pyrimidine derivatives. KEY POINTS: • The L-arginine production strongly depended on the supply of carbamoyl phosphate. • The novel carbamoyl phosphate synthesis pathway for C. crenatum based on carbamate kinase was first applied to L-arginine synthesis. • ATP was regenerated followed with the disruption of lactate formation.
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The carB Gene of Escherichia coli BL21(DE3) is Associated with Nematicidal Activity against the Root-Knot Nematode Meloidogyne javanica. Pathogens 2021; 10:pathogens10020222. [PMID: 33670696 PMCID: PMC7923116 DOI: 10.3390/pathogens10020222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022] Open
Abstract
Biological nematicides have been widely used to lower the losses generated by phytoparasitic nematodes. The purpose of this study was to evaluate the nematicidal effects of Escherichia coli BL21(DE3) against Meloidogyne javanica and to identify nematicide-related genes. Culture filtrates of BL21(DE3) caused juvenile mortality and inhibited egg hatching in a dose-dependent manner. In the greenhouse, treatment of tomato seedlings with BL21(DE3) culture filtrates at 50 and 100% concentrations not only reduced the amount of M. javanica egg masses and galls, but improved plant root and shoot fresh weight. Culture filtrate analysis indicated that the nematicidal active ingredients of strain BL21(DE3) were non-proteinaceous, heat and cold resistant, sensitive to pH and volatile. To identify the genes associated with nematicidal activity, a BL21(DE3) library of 5000 mutants was produced using Tn5 transposase insertion. The culture filtrate of the MB12 mutant showed no nematicidal activity after 72 h of treatment and thermal asymmetrical interlaced PCR demonstrated that the carB gene was disrupted. Nematicidal activity was restored when the pH of the MB12 culture filtrate was adjusted to the original pH value (4.15) or following MB12 complementation with the carB gene, confirming a role for carB in mediating pH value and nematicidal activity. The outcomes of this pilot study indicate that BL21(DE3) is a potential microorganism for the continuable biological control of root-knot nematode in tomato and that carB affects the nematicidal activity of BL21(DE3) by modulating the pH environment.
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Nitzahn M, Lipshutz GS. CPS1: Looking at an ancient enzyme in a modern light. Mol Genet Metab 2020; 131:289-298. [PMID: 33317798 PMCID: PMC7738762 DOI: 10.1016/j.ymgme.2020.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 02/06/2023]
Abstract
The mammalian urea cycle (UC) is responsible for siphoning catabolic waste nitrogen into urea for excretion. Disruptions of the functions of any of the enzymes or transporters lead to elevated ammonia and neurological injury. Carbamoyl phosphate synthetase 1 (CPS1) is the first and rate-limiting UC enzyme responsible for the direct incorporation of ammonia into UC intermediates. Symptoms in CPS1 deficiency are typically the most severe of all UC disorders, and current clinical management is insufficient to prevent the associated morbidities and high mortality. With recent advances in basic and translational studies of CPS1, appreciation for this enzyme's essential role in the UC has been broadened to include systemic metabolic regulation during homeostasis and disease. Here, we review recent advances in CPS1 biology and contextualize them around the role of CPS1 in health and disease.
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Affiliation(s)
- Matthew Nitzahn
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gerald S Lipshutz
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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Nitzahn M, Allegri G, Khoja S, Truong B, Makris G, Häberle J, Lipshutz GS. Split AAV-Mediated Gene Therapy Restores Ureagenesis in a Murine Model of Carbamoyl Phosphate Synthetase 1 Deficiency. Mol Ther 2020; 28:1717-1730. [PMID: 32359471 DOI: 10.1016/j.ymthe.2020.04.011] [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: 10/25/2019] [Revised: 02/25/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
The urea cycle enzyme carbamoyl phosphate synthetase 1 (CPS1) catalyzes the initial step of the urea cycle; bi-allelic mutations typically present with hyperammonemia, vomiting, ataxia, lethargy progressing into coma, and death due to brain edema if ineffectively treated. The enzyme deficiency is particularly difficult to treat; early recognition is essential to minimize injury to the brain. Even under optimal conditions, therapeutic interventions are of limited scope and efficacy, with most patients developing long-term neurologic sequelae. One significant encumberment to gene therapeutic development is the size of the CPS1 cDNA, which, at 4.5 kb, nears the packaging capacity of adeno-associated virus (AAV). Herein we developed a split AAV (sAAV)-based approach, packaging the large transgene and its regulatory cassette into two separate vectors, thereby delivering therapeutic CPS1 by a dual vector system with testing in a murine model of the disorder. Cps1-deficient mice treated with sAAVs survive long-term with markedly improved ammonia levels, diminished dysregulation of circulating amino acids, and increased hepatic CPS1 expression and activity. In response to acute ammonia challenging, sAAV-treated female mice rapidly incorporated nitrogen into urea. This study demonstrates the first proof-of-principle that sAAV-mediated therapy is a viable, potentially clinically translatable approach to CPS1 deficiency, a devastating urea cycle disorder.
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Affiliation(s)
- Matthew Nitzahn
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gabriella Allegri
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Suhail Khoja
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Brian Truong
- Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Georgios Makris
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital, Zurich, Switzerland
| | - Gerald S Lipshutz
- Molecular Biology Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Semel Institute for Neuroscience, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
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18
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Del Caño-Ochoa F, Moreno-Morcillo M, Ramón-Maiques S. CAD, A Multienzymatic Protein at the Head of de Novo Pyrimidine Biosynthesis. Subcell Biochem 2020; 93:505-538. [PMID: 31939163 DOI: 10.1007/978-3-030-28151-9_17] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CAD is a 1.5 MDa particle formed by hexameric association of a 250 kDa protein that carries the enzymatic activities for the first three steps in the de novo biosynthesis of pyrimidine nucleotides: glutamine-dependent Carbamoyl phosphate synthetase, Aspartate transcarbamoylase and Dihydroorotase. This metabolic pathway is essential for cell growth and proliferation and is conserved in all living organisms. However, the fusion of the first three enzymatic activities of the pathway into a single multienzymatic protein only occurs in animals. In prokaryotes, by contrast, these activities are encoded as distinct monofunctional enzymes that function independently or by forming more or less transient complexes. Whereas the structural information about these enzymes in bacteria is abundant, the large size and instability of CAD has only allowed a fragmented characterization of its structure. Here we retrace some of the most significant efforts to decipher the architecture of CAD and to understand its catalytic and regulatory mechanisms.
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Affiliation(s)
- Francisco Del Caño-Ochoa
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - María Moreno-Morcillo
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain
| | - Santiago Ramón-Maiques
- Department of Genome Dynamics and Function, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera 1, 28049, Madrid, Spain.
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19
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Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
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20
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Charlier D, Nguyen Le Minh P, Roovers M. Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis. Amino Acids 2018; 50:1647-1661. [PMID: 30238253 PMCID: PMC6245113 DOI: 10.1007/s00726-018-2654-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
In all organisms, carbamoylphosphate (CP) is a precursor common to the synthesis of arginine and pyrimidines. In Escherichia coli and most other Gram-negative bacteria, CP is produced by a single enzyme, carbamoylphosphate synthase (CPSase), encoded by the carAB operon. This particular situation poses a question of basic physiological interest: what are the metabolic controls coordinating the synthesis and distribution of this high-energy substance in view of the needs of both pathways? The study of the mechanisms has revealed unexpected moonlighting gene regulatory activities of enzymes and functional links between mechanisms as diverse as gene regulation and site-specific DNA recombination. At the level of enzyme production, various regulatory mechanisms were found to cooperate in a particularly intricate transcriptional control of a pair of tandem promoters. Transcription initiation is modulated by an interplay of several allosteric DNA-binding transcription factors using effector molecules from three different pathways (arginine, pyrimidines, purines), nucleoid-associated factors (NAPs), trigger enzymes (enzymes with a second unlinked gene regulatory function), DNA remodeling (bending and wrapping), UTP-dependent reiterative transcription initiation, and stringent control by the alarmone ppGpp. At the enzyme level, CPSase activity is tightly controlled by allosteric effectors originating from different pathways: an inhibitor (UMP) and two activators (ornithine and IMP) that antagonize the inhibitory effect of UMP. Furthermore, it is worth noticing that all reaction intermediates in the production of CP are extremely reactive and unstable, and protected by tunneling through a 96 Å long internal channel.
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Affiliation(s)
- Daniel Charlier
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Phu Nguyen Le Minh
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Martine Roovers
- LABIRIS Institut de Recherches, Av. Emile Gryson 1, 1070, Brussels, Belgium
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