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Caldovic L, Ahn JJ, Andricovic J, Balick VM, Brayer M, Chansky PA, Dawson T, Edwards AC, Felsen SE, Ismat K, Jagannathan SV, Mann BT, Medina JA, Morizono T, Morizono M, Salameh S, Vashist N, Williams EC, Zhou Z, Morizono H. Datamining approaches for examining the low prevalence of N-acetylglutamate synthase deficiency and understanding transcriptional regulation of urea cycle genes. J Inherit Metab Dis 2023. [PMID: 37847851 DOI: 10.1002/jimd.12687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Ammonia, which is toxic to the brain, is converted into non-toxic urea, through a pathway of six enzymatically catalyzed steps known as the urea cycle. In this pathway, N-acetylglutamate synthase (NAGS, EC 2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetyl coenzyme A. NAGS deficiency (NAGSD) is the rarest of the urea cycle disorders, yet is unique in that ureagenesis can be restored with the drug N-carbamylglutamate (NCG). We investigated whether the rarity of NAGSD could be due to low sequence variation in the NAGS genomic region, high NAGS tolerance for amino acid replacements, and alternative sources of NAG and NCG in the body. We also evaluated whether the small genomic footprint of the NAGS catalytic domain might play a role. The small number of patients diagnosed with NAGSD could result from the absence of specific disease biomarkers and/or short NAGS catalytic domain. We screened for sequence variants in NAGS regulatory regions in patients suspected of having NAGSD and found a novel NAGS regulatory element in the first intron of the NAGS gene. We applied the same datamining approach to identify regulatory elements in the remaining urea cycle genes. In addition to the known promoters and enhancers of each gene, we identified several novel regulatory elements in their upstream regions and first introns. The identification of cis-regulatory elements of urea cycle genes and their associated transcription factors holds promise for uncovering shared mechanisms governing urea cycle gene expression and potentially leading to new treatments for urea cycle disorders.
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Affiliation(s)
- Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Julie J Ahn
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jacklyn Andricovic
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Veronica M Balick
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mallory Brayer
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Pamela A Chansky
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Tyson Dawson
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- AMPEL BioSolutions LLC, Charlottesville, Virginia, USA
| | - Alex C Edwards
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
| | - Sara E Felsen
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
| | - Karim Ismat
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Sveta V Jagannathan
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Brendan T Mann
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jacob A Medina
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Toshio Morizono
- College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michio Morizono
- College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Shatha Salameh
- Department of Pharmacology & Physiology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Hospital, Washington, DC, USA
| | - Neerja Vashist
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Emily C Williams
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- The George Washington University Cancer Center, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Zhe Zhou
- Department of Civil and Environmental Engineering, The George Washington University, Washington, DC, USA
| | - Hiroki Morizono
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
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Yang Z, Stemmer PM, Petriello MC. Proteomics-Based Identification of Interaction Partners of the Xenobiotic Detoxification Enzyme FMO3 Reveals Involvement in Urea Cycle. TOXICS 2022; 10:60. [PMID: 35202247 PMCID: PMC8877285 DOI: 10.3390/toxics10020060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/18/2022] [Accepted: 01/25/2022] [Indexed: 02/06/2023]
Abstract
The hepatic xenobiotic metabolizing enzyme flavin-containing monooxygenase 3 (FMO3) has been implicated in the development of cardiometabolic disease primarily due to its enzymatic product trimethylamine-N oxide (TMAO), which has recently been shown to be associated with multiple chronic diseases, including kidney and coronary artery diseases. Although TMAO may have causative roles as a pro-inflammatory mediator, the possibility for roles in metabolic disease for FMO3, irrespective of TMAO formation, does exist. We hypothesized that FMO3 may interact with other proteins known to be involved in cardiometabolic diseases and that modulating the expression of FMO3 may impact on these interaction partners. Here, we combine a co-immunoprecipitation strategy coupled to unbiased proteomic workflow to report a novel protein:protein interaction network for FMO3. We identified 51 FMO3 protein interaction partners, and through gene ontology analysis, have identified urea cycle as an enriched pathway. Using mice deficient in FMO3 on two separate backgrounds, we validated and further investigated expressional and functional associations between FMO3 and the identified urea cycle genes. FMO3-deficient mice showed hepatic overexpression of carbamoylphosphate synthetase (CPS1), the rate-limiting gene of urea cycle, and increased hepatic urea levels, especially in mice of FVB (Friend leukemia virus B strain) background. Finally, overexpression of FMO3 in murine AML12 hepatocytes led to downregulation of CPS1. Although there is past literature linking TMAO to urea cycle, this is the first published work showing that FMO3 and CPS1 may directly interact, implicating a role for FMO3 in chronic kidney disease irrespective of TMAO formation.
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Affiliation(s)
- Zhao Yang
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmaceutical Sciences, College of Pharmacy, Wayne State University, Detroit, MI 48202, USA
| | - Michael C. Petriello
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48202, USA; (Z.Y.); (P.M.S.)
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI 48202, USA
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Li M, Quan C, Chen S, Wang HY. The 14-3-3 protein is an essential component of cyclic AMP signaling for regulation of chemotaxis and development in Dictyostelium. Cell Signal 2020; 75:109739. [PMID: 32818671 DOI: 10.1016/j.cellsig.2020.109739] [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: 03/11/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 10/23/2022]
Abstract
The evolutionarily-conserved 14-3-3 proteins regulate many cellular processes through binding to various phosphorylated targets in eukaryotes. It first appears in Dictyostelium, however its role in this organism is poorly understood. Here we show that down-regulation of the 14-3-3 impairs chemotaxis and causes multiple-tip formation in Dictyostelium. Mechanistically, the 14-3-3 is a critical component of cyclic AMP (cAMP) signaling and binds to nearly a hundred of proteins in Dictyostelium, including a number of evolutionarily-conserved proteins. 14-3-3 - interaction with its targets is up-regulated in response to developmental cues/regulators including starvation, osmotic stress and cAMP. cAMP stimulates 14-3-3 - binding to phospho-Ser431 on a guanine nucleotide exchange factor Gef-Q. Interestingly, overexpression of Gef-QSer431Ala mutant but not wild-type Gef-Q protein causes a multiple-tip phenotype in Dictyostelium, which partially resembles phenotypes of the 14-3-3 - deficient mutant. Collectively, these data demonstrate that the 14-3-3 plays an important role in Dictyostelium and may help to deepen our understanding of the evolution of 14-3-3 - interactomes in eukaryotes.
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Affiliation(s)
- Min Li
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Pukou District, Nanjing 210061, China
| | - Chao Quan
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Pukou District, Nanjing 210061, China
| | - Shuai Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Pukou District, Nanjing 210061, China; Nanjing Biomedical Research Institute, Nanjing University, Nanjing 210061, China.
| | - Hong Yu Wang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Pukou District, Nanjing 210061, China.
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Stanulovic VS, Cauchy P, Assi SA, Hoogenkamp M. LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage. Nucleic Acids Res 2017; 45:9874-9888. [PMID: 28973433 PMCID: PMC5622341 DOI: 10.1093/nar/gkx573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 06/27/2017] [Indexed: 02/06/2023] Open
Abstract
LMO2 is a bridging factor within a DNA binding complex and is required for definitive haematopoiesis to occur. The developmental stage of the block in haematopoietic specification is not known. We show that Lmo2−/− mouse embryonic stem cells differentiated to Flk-1+ haemangioblasts, but less efficiently to haemogenic endothelium, which only produced primitive haematopoietic progenitors. Genome-wide approaches indicated that LMO2 is required at the haemangioblast stage to position the TAL1/LMO2/LDB1 complex to regulatory elements that are important for the establishment of the haematopoietic developmental program. In the absence of LMO2, the target site recognition of TAL1 is impaired. The lack of LMO2 resulted in altered gene expression levels already at the haemangioblast stage, with transcription factor genes accounting for ∼15% of affected genes. Comparison of Lmo2−/− with Tal1−/− Flk-1+ cells further showed that TAL1 was required to initiate or sustain Lmo2 expression.
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Affiliation(s)
- Vesna S Stanulovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Maarten Hoogenkamp
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Chen YR, Sekine K, Nakamura K, Yanai H, Tanaka M, Miyajima A. Y-box binding protein-1 down-regulates expression of carbamoyl phosphate synthetase-I by suppressing CCAAT enhancer-binding protein-alpha function in mice. Gastroenterology 2009; 137:330-40. [PMID: 19272383 DOI: 10.1053/j.gastro.2009.02.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 02/09/2009] [Accepted: 02/17/2009] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Carbamoyl phosphate synthetase-I (CPS1) is a key enzyme in the urea cycle and patients with defects in the function or expression of CPS1 suffer from hyperammonemia. CPS1 is expressed in the liver at neonatal and adult stages in a CCAAT enhancer-binding protein-alpha (C/EBPalpha)-dependent manner. Despite expression of C/EBPalpha, CPS1 is not expressed in fetal liver, indicating an additional factor is involved in the regulation of CPS1 expression. The aim of this study was to elucidate the mechanism of CPS1 expression. METHODS Microarray was performed to find Y-box binding protein-1 (YB-1) that was expressed in mouse fetal liver. The role of YB-1 in CPS1 expression was investigated by overexpression of YB-1 in mouse fetal liver culture and luciferase reporter assays using the CPS1 promoter. Chromatin immunoprecipitation assay was used to examine recruitment of YB-1 to the CPS1 promoter in vivo. RESULTS Expression of YB-1 and CPS1 was inversely correlated in vivo, and YB-1 inhibited CPS1 expression and ammonia clearance in fetal liver culture. Although YB-1 was not expressed in adult liver, acute liver injury up-regulated YB-1 and down-regulated CPS1, accompanying an increase of the serum ammonia level. YB-1 inhibited C/EBPalpha-induced transcription from the CPS1 promoter via the Y-box near the C/EBPalpha-binding site. Chromatin immunoprecipitation assays demonstrated that YB-1 was recruited to the CPS1 promoter in fetal and injured adult liver, but not in normal adult liver. CONCLUSIONS YB-1 is a key regulator of ammonia detoxification by negatively regulating CPS1 expression via suppression of C/EBPalpha function.
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Affiliation(s)
- Yen-Rong Chen
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
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Hoogenkamp M, Gaemers IC, Schoneveld OJLM, Das AT, Grange T, Lamers WH. Hepatocyte-specific interplay of transcription factors at the far-upstream enhancer of the carbamoylphosphate synthetase gene upon glucocorticoid induction. FEBS J 2006; 274:37-45. [PMID: 17140418 DOI: 10.1111/j.1742-4658.2006.05561.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Carbamoylphosphate synthetase-I is the flux-determining enzyme of the ornithine cycle, and neutralizes toxic ammonia by converting it to urea. An 80 bp glucocorticoid response unit located 6.3 kb upstream of the transcription start site mediates hormone responsiveness and liver-specific expression of carbamoylphosphate synthetase-I. The glucocorticoid response unit consists of response elements for the glucocorticoid receptor, forkhead box A, CCAAT/enhancer-binding protein, and an unidentified protein. With only four transcription factor response elements, the carbamoylphosphate synthetase-I glucocorticoid response unit is a relatively simple unit. The relationship between carbamoylphosphate synthetase-I expression and in vivo occupancy of the response elements was examined by comparing a carbamoylphosphate synthetase-I-expressing hepatoma cell line with a carbamoylphosphate synthetase-I-negative fibroblast cell line. DNaseI hypersensitivity assays revealed an open chromatin configuration of the carbamoylphosphate synthetase-I enhancer in hepatoma cells only. In vivo footprinting assays showed that the accessory transcription factors of the glucocorticoid response unit bound to their response elements in carbamoylphosphate synthetase-I-positive cells, irrespective of whether carbamoylphosphate synthetase-I expression was induced with hormones. In contrast, the binding of glucocorticoid receptor to the carbamoylphosphate synthetase-I glucocorticoid response unit was dependent on treatment of the cells with glucocorticoids. Only forkhead box A was exclusively present in hepatoma cells, and therefore appears to be an important determinant of the observed tissue specificity of carbamoylphosphate synthetase-I expression. As the glucocorticoid receptor is the only DNA-binding protein specifically recruited to the glucocorticoid response unit upon stimulation by glucocorticoids, it is likely to be directly responsible for the transcriptional activation mediated by the glucocorticoid response unit.
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Affiliation(s)
- Maarten Hoogenkamp
- AMC Liver Center, Academic Medical Center, University of Amsterdam, the Netherlands
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