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Li S, Ye X, Wen X, Yang X, Wang L, Gao K, Xiao H, Jiang Z. Arginine and its metabolites stimulate proliferation, differentiation, and physiological function of porcine trophoblast cells through β-catenin and mTOR pathways. BMC Vet Res 2024; 20:167. [PMID: 38689278 PMCID: PMC11062007 DOI: 10.1186/s12917-024-04023-w] [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: 03/30/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Arginine, which is metabolized into ornithine, proline, and nitric oxide, plays an important role in embryonic development. The present study was conducted to investigate the molecular mechanism of arginine in proliferation, differentiation, and physiological function of porcine trophoblast cells (pTr2) through metabolic pathways. The results showed that arginine significantly increased cell viability (P < 0.05). The addition of arginine had a quadratic tendency to increase the content of progesterone (P = 0.06) and protein synthesis rate (P = 0.03), in which the maximum protein synthesis rate was observed at 0.4 mM arginine. Arginine quadratically increased (P < 0.05) the intracellular contents of spermine, spermidine and putrescine, as well as linearly increased (P < 0.05) the intracellular content of NO in a dose-dependent manner. Arginine showed a quadratic tendency to increase the content of putrescine (P = 0.07) and a linear tendency to increase NO content (P = 0.09) in cell supernatant. Moreover, increasing arginine activated (P < 0.05) the mRNA expressions for ARG, ODC, iNOS and PCNA. Furthermore, inhibitors of arginine metabolism (L-NMMA and DFMO) both inhibited cell proliferation, while addition of its metabolites (NO and putrescine) promoted the cell proliferation and cell cycle, the mRNA expressions of PCNA, EGF and IGF-1, and increased (P < 0.05) cellular protein synthesis rate, as well as estradiol and hCG secretion (P < 0.05). In conclusion, our results suggested that arginine could promote cell proliferation and physiological function by regulating the metabolic pathway. Further studies showed that arginine and its metabolites modulate cell function mainly through β-catenin and mTOR pathways.
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Affiliation(s)
- Shuai Li
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiangyang Ye
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaolu Wen
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xuefen Yang
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Li Wang
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Kaiguo Gao
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Hao Xiao
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
| | - Zongyong Jiang
- Institute of Animal Science, State Key Laboratory of Swine and Poultry Breeding Industry, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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2
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Li Z, Wu Y, Yang W, Wang W, Li J, Huang X, Yang Y, Zhang X, Ye X. Characterization of polyamine metabolism predicts prognosis, immune profile, and therapeutic efficacy in lung adenocarcinoma patients. Front Cell Dev Biol 2024; 12:1331759. [PMID: 38650895 PMCID: PMC11033315 DOI: 10.3389/fcell.2024.1331759] [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: 11/01/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Background Polyamine modification patterns in lung adenocarcinoma (LUAD) and their impact on prognosis, immune infiltration, and anti-tumor efficacy have not been systematically explored. Methods Patients from The Cancer Genome Atlas (TCGA) were classified into subtypes according to polyamine metabolism-related genes using the consensus clustering method, and the survival outcomes and immune profile were compared. Meanwhile, the geneCluster was constructed according to the differentially expressed genes (DEGs) of the subtypes. Subsequently, the polyamine metabolism-related score (PMRS) system was established using the least absolute shrinkage and selection operator (LASSO) multivariate regression analysis in the TCGA training cohort (n = 245), which can be applied to characterize the prognosis. To verify the predictive performance of the PMRS, the internal cohort (n = 245) and the external cohort (n = 244) were recruited. The relationship between the PMRS and immune infiltration and antitumor responses was investigated. Results Two distinct patterns (C1 and C2) were identified, in which the C1 subtype presented an adverse prognosis, high CD8+ T cell infiltration, tumor mutational burden (TMB), immune checkpoint, and low tumor immune dysfunction and exclusion (TIDE). Furthermore, two geneClusters were established, and similar findings were observed. The PMRS, including three genes (SMS, SMOX, and PSMC6), was then constructed to characterize the polyamine metabolic patterns, and the patients were divided into high- and low-PMRS groups. As confirmed by the validation cohort, the high-PMRS group possessed a poor prognosis. Moreover, external samples and immunohistochemistry confirmed that the three genes were highly expressed in tumor samples. Finally, immunotherapy and chemotherapy may be beneficial to the high-PMRS group based on the immunotherapy cohorts and low half-maximal inhibitory concentration (IC50) values. Conclusion We identified distinct polyamine modification patterns and established a PMRS to provide new insights into the mechanism of polyamine action and improve the current anti-tumor strategy of LUAD.
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Affiliation(s)
- Zhouhua Li
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yue Wu
- Health Team, Jiangsu Marine Police Bureau, Nanjing, China
| | - Weichang Yang
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Wenjun Wang
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jinbo Li
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaotian Huang
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yanqiang Yang
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xinyi Zhang
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaoqun Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
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3
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Zeng J, Ye Z, Shi S, Liang Y, Meng Q, Zhang Q, Le AD. Targeted inhibition of eIF5A hpu suppresses tumor growth and polarization of M2-like tumor-associated macrophages in oral cancer. Cell Death Dis 2023; 14:579. [PMID: 37653021 PMCID: PMC10471704 DOI: 10.1038/s41419-023-06109-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023]
Abstract
Eukaryotic initiation factor 5A2 (eIF5A2) is overexpressed in many types of cancer, and spermidine-mediated eIF5A hypusination (eIF5Ahpu) appears to be essential to most of eIF5A's biological functions, including its important role in regulating cancer cell proliferation, epithelial-mesenchymal transition (EMT), and cancer stem cell (CSC) properties as well as immune cell functions. Here we investigated the role of eIF5Ahpu in the growth of oral squamous cell carcinoma cells (OSCCs) and OSCC-induced polarization of M2-like tumor-associated macrophages (TAMs). TCGA dataset analysis revealed an overall upregulation in the mRNA expression of eIF5A2 and several key enzymes involved in polyamine (PA) metabolism in HNSCC, which was confirmed by Western blot and IHC studies. Blocking eIF5Ahpu by GC-7 but not the upstream key enzyme activities of PA metabolism, remarkably inhibited cell proliferation and the expression of EMT- and CSC-related genes in OSCC cells. In addition, blocking eIF5Ahpu robustly inhibited OSCC-induced M2-like TAM polarization in vitro. More Importantly, blocking eIF5Ahpu dramatically retarded tumor growth and infiltration/polarization of M2-like TAM in a syngeneic orthotopic murine tongue SCC model. Thus, eIF5Ahpu plays dual functions in regulating tumor cell growth and polarization of M2-TAMs in OSCC.
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Affiliation(s)
- Jincheng Zeng
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, 523808, Dongguan, China
| | - Ziyu Ye
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
- Dongguan Key Laboratory of Medical Bioactive Molecular Developmental and Translational Research, Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Guangdong Medical University, 523808, Dongguan, China
| | - Shihong Shi
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Yanfang Liang
- Department of Pathology, Dongguan Hospital Affiliated to Jinan University, Bin-haiwan Central Hospital of Dongguan, 523905, Dongguan, China
| | - Qingyu Meng
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA
| | - Qunzhou Zhang
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA.
| | - Anh D Le
- Department of Oral and Maxillofacial Surgery and Pharmacology, University of Pennsylvania School of Dental Medicine, Philadelphia, PA, USA.
- Department of Oral & Maxillofacial Surgery, Penn Medicine Hospital of the University of Pennsylvania, Perelman Center for Advanced Medicine, Philadelphia, PA, USA.
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Identification and Characterization of Novel Small-Molecule SMOX Inhibitors. Med Sci (Basel) 2022; 10:medsci10030047. [PMID: 36135832 PMCID: PMC9504029 DOI: 10.3390/medsci10030047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 11/29/2022] Open
Abstract
The major intracellular polyamines spermine and spermidine are abundant and ubiquitous compounds that are essential for cellular growth and development. Spermine catabolism is mediated by spermine oxidase (SMOX), a highly inducible flavin-dependent amine oxidase that is upregulated during excitotoxic, ischemic, and inflammatory states. In addition to the loss of radical scavenging capabilities associated with spermine depletion, the catabolism of spermine by SMOX results in the production of toxic byproducts, including H2O2 and acrolein, a highly toxic aldehyde with the ability to form adducts with DNA and inactivate vital cellular proteins. Despite extensive evidence implicating SMOX as a key enzyme contributing to secondary injury associated with multiple pathologic states, the lack of potent and selective inhibitors has significantly impeded the investigation of SMOX as a therapeutic target. In this study, we used a virtual and physical screening approach to identify and characterize a series of hit compounds with inhibitory activity against SMOX. We now report the discovery of potent and highly selective SMOX inhibitors 6 (IC50 0.54 μM, Ki 1.60 μM) and 7 (IC50 0.23 μM, Ki 0.46 μM), which are the most potent SMOX inhibitors reported to date. We hypothesize that these selective SMOX inhibitors will be useful as chemical probes to further elucidate the impact of polyamine catabolism on mechanisms of cellular injury.
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5
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Application of gold nanoparticles to determine spermine in the presence of other polyamines. UKRAINIAN BIOCHEMICAL JOURNAL 2022. [DOI: 10.15407/ubj94.02.066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The development of methods for the detection of polyamines in biological fluids is essential to improve early diagnosis and treatment of patients with prostate cancer. One of the promising areas is the use of noble metal nanoparticles. According to the literature data, there is no methodological approach have been developed to reliably distinguish spermine from other polyamines, in particular, from their acetylated forms and related compounds present in biological fluids. The paper presents the results of spectrophotometric determination of spermine both alone and in the presence of putrescine, spermidine or urea in the urine using gold nanoparticles. The results of the experiments proved that the developed method is suitable for the selective determination of spermine. It was shown that the presence of spermidine, putrescine, acetylated forms of polyamines or carbamide does not affect the results of the analysis.
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6
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Bernstein HG, Keilhoff G, Laube G, Dobrowolny H, Steiner J. Polyamines and polyamine-metabolizing enzymes in schizophrenia: Current knowledge and concepts of therapy. World J Psychiatry 2021; 11:1177-1190. [PMID: 35070769 PMCID: PMC8717027 DOI: 10.5498/wjp.v11.i12.1177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/30/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
Polyamines play preeminent roles in a variety of cellular functions in the central nervous system and other organs. A large body of evidence suggests that the polyamine pathway is prominently involved in the etiology and pathology of schizophrenia. Alterations in the expression and activity of polyamine metabolizing enzymes, as well as changes in the levels of the individual polyamines, their precursors and derivatives, have been measured in schizophrenia and animal models of the disease. Additionally, neuroleptic treatment has been shown to influence polyamine concentrations in brain and blood of individuals with schizophrenia. Thus, the polyamine system may appear to be a promising target for neuropharmacological treatment of schizophrenia. However, for a number of practical reasons there is currently only limited hope for a polyamine-based schizophrenia therapy.
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Affiliation(s)
- Hans-Gert Bernstein
- Department of Psychiatry, University of Magdeburg, Magdeburg D-39116, Saxony-Anhalt, Germany
| | - Gerburg Keilhoff
- Institute of Biochemistry and Cell Biology, University of Magdeburg, Magdeburg D-39116, Saxony-Anhalt, Germany
| | - Gregor Laube
- Department of Anatomy, Charite, Berlin D-10117, Germany
| | - Henrik Dobrowolny
- Department of Psychiatry, University of Magdeburg, Magdeburg D-39116, Saxony-Anhalt, Germany
| | - Johann Steiner
- Department of Psychiatry, University of Magdeburg, Magdeburg D-39116, Saxony-Anhalt, Germany
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7
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Li QZ, Zuo ZW, Zhou ZR, Ji Y. Polyamine homeostasis-based strategies for cancer: The role of combination regimens. Eur J Pharmacol 2021; 910:174456. [PMID: 34464603 DOI: 10.1016/j.ejphar.2021.174456] [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: 06/04/2021] [Revised: 08/14/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023]
Abstract
Spermine, spermidine and putrescine polyamines are naturally occurring ubiquitous positively charged amines and are essential metabolites for biological functions in our life. These compounds play a crucial role in many cell processes, including cellular proliferation, growth, and differentiation. Intracellular levels of polyamines depend on their biosynthesis, transport and degradation. Polyamine levels are high in cancer cells, which leads to the promotion of tumor growth, invasion and metastasis. Targeting polyamine metabolism as an anticancer strategy is considerably rational. Due to compensatory mechanisms, a single strategy does not achieve satisfactory clinical effects when using a single agent. Combination regimens are more clinically promising for cancer chemoprevention because they work synergistically with causing little or no adverse effects due to each individual agent being used at lower doses. Moreover, bioactive substances have advantages over single chemical agents because they can affect multiple targets. In this review, we discuss anticancer strategies targeting polyamine metabolism and describe how combination treatments and effective natural active ingredients are promising therapies. The existing research suggests that polyamine metabolic enzymes are important therapeutic targets and that combination therapies can be more effective than monotherapies based on polyamine depletion.
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Affiliation(s)
- Qi-Zhang Li
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Industrial Fermentation (Ministry of Education), Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei, 430068, PR China.
| | - Zan-Wen Zuo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Industrial Fermentation (Ministry of Education), Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei, 430068, PR China
| | - Ze-Rong Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Industrial Fermentation (Ministry of Education), Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei, 430068, PR China
| | - Yan Ji
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Industrial Fermentation (Ministry of Education), Institute of Biomedical and Pharmaceutical Sciences, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei, 430068, PR China
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8
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Dunston TT, Khomutov MA, Gabelli SB, Stewart TM, Foley JR, Kochetkov SN, Khomutov AR, Casero Jr. RA. Identification of a Novel Substrate-Derived Spermine Oxidase Inhibitor. Acta Naturae 2020; 12:140-144. [PMID: 33173604 PMCID: PMC7604895 DOI: 10.32607/actanaturae.10992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Homeostasis of the biogenic polyamines spermine (Spm) and spermidine (Spd),
present in μM-mM concentrations in all eukaryotic cells, is precisely
regulated by coordinated activities of the enzymes of polyamine synthesis,
degradation, and transport, in order to sustain normal cell growth and
viability. Spermine oxidase (SMOX) is the key and most recently discovered
enzyme of polyamine metabolism that plays an essential role in regulating
polyamine homeostasis by catalyzing the back-conversion of Spm to Spd. The
development of many types of epithelial cancer is associated with inflammation,
and disease-related inflammatory stimuli induce SMOX. MDL72527 is widely used
in vitro and in vivo as an irreversible
inhibitor of SMOX, but it is also potent towards
N1-acetylpolyamine oxidase. Although SMOX has high substrate
specificity, Spm analogues have not been systematically studied as enzyme
inhibitors. Here we demonstrate that
1,12-diamino-2,11-bis(methylidene)-4,9-diazadodecane (2,11-Met2-Spm) has, under
standard assay conditions, an IC50 value of 169 μM towards SMOX
and is an interesting instrument and lead compound for studying polyamine
catabolism.
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Affiliation(s)
- T. T. Dunston
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - M. A. Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - S. B. Gabelli
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - T. M. Stewart
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - J. R. Foley
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - S. N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A. R. Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - R. A. Casero Jr.
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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9
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Tararina MA, Allen KN. Bioinformatic Analysis of the Flavin-Dependent Amine Oxidase Superfamily: Adaptations for Substrate Specificity and Catalytic Diversity. J Mol Biol 2020; 432:3269-3288. [PMID: 32198115 DOI: 10.1016/j.jmb.2020.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 03/06/2020] [Indexed: 12/29/2022]
Abstract
The flavin-dependent amine oxidase (FAO) superfamily consists of over 9000 nonredundant sequences represented in all domains of life. Of the thousands of members identified, only 214 have been functionally annotated to date, and 40 unique structures are represented in the Protein Data Bank. The few functionally characterized members share a catalytic mechanism involving the oxidation of an amine substrate through transfer of a hydride to the FAD cofactor, with differences observed in substrate specificities. Previous studies have focused on comparing a subset of superfamily members. Here, we present a comprehensive analysis of the FAO superfamily based on reaction mechanism and substrate recognition. Using a dataset of 9192 sequences, a sequence similarity network, and subsequently, a genome neighborhood network were constructed, organizing the superfamily into eight subgroups that accord with substrate type. Likewise, through phylogenetic analysis, the evolutionary relationship of subgroups was determined, delineating the divergence between enzymes based on organism, substrate, and mechanism. In addition, using sequences and atomic coordinates of 22 structures from the Protein Data Bank to perform sequence and structural alignments, active-site elements were identified, showing divergence from the canonical aromatic-cage residues to accommodate large substrates. These specificity determinants are held in a structural framework comprising a core domain catalyzing the oxidation of amines with an auxiliary domain for substrate recognition. Overall, analysis of the FAO superfamily reveals a modular fold with cofactor and substrate-binding domains allowing for diversity of recognition via insertion/deletions. This flexibility allows facile evolution of new activities, as shown by reinvention of function between subfamilies.
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Affiliation(s)
- Margarita A Tararina
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Karen N Allen
- Program in Biomolecular Pharmacology, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA; Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA 02215, USA.
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