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Shangguan S, Zhang X, Ge Y, Han Y, Xiao L, Zhang Y, Xie H, Chen X, Wang X. Confirming the enzymatic activity and neurodevelopmental trajectory of PYCR1 mutation in one child with autosomal-recessive cutis laxa type 2. Mol Genet Genomics 2024; 299:81. [PMID: 39172257 PMCID: PMC11341742 DOI: 10.1007/s00438-024-02173-y] [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: 02/09/2024] [Accepted: 07/30/2024] [Indexed: 08/23/2024]
Abstract
Autosomal-recessive cutis laxa type 2 (ARCL2) is a rare genetic disorder caused by pyrroline-5-carboxylate reductase 1 (PYCR1) mutations and characterized by loose and sagging skin, typical facial features, intrauterine growth retardation, and developmental delay. To study the effect of PYCR1 mutations on protein function and clinical features, we identified a homozygous missense mutation c.559G > A (p.Ala187Thr) in PYCR1 in a Chinese child with typical clinical features, especially severe developmental delays. The three-dimensional (3D) model showed the modification of the hydrogen bonds produce a misfolding in the mutant PYCR1 protein. Mutagenesis and enzyme assay study revealed decreased activity of the mutant protein in vitro, indicating that this mutation impairs PYCR1 function. Our findings confirmed abnormal enzymatic activity and neurodevelopmental trajectory of this PYCR1 mutation.
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Affiliation(s)
- Shaofang Shangguan
- Department of Medical Genetics, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Xueyuan Zhang
- Department of Children's Nutrition Research Center, Affiliated Children's Hospital of Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Yangyang Ge
- Department of Medical Genetics, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Ye Han
- Department of Neurology, Affiliated Children's hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ling Xiao
- Department of Children's Nutrition Research Center, Affiliated Children's Hospital of Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Yu Zhang
- Department of Laboratory Center, Capital Institute of Pediatrics, Beijing, China
| | - Hua Xie
- Department of Medical Genetics, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Xiaoli Chen
- Department of Medical Genetics, Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Xiaoyan Wang
- Department of Children's Nutrition Research Center, Affiliated Children's Hospital of Capital Institute of Pediatrics, Yabao Road, Chaoyang District, Beijing, 100020, China.
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Disease variants of human Δ 1-pyrroline-5-carboxylate reductase 2 (PYCR2). Arch Biochem Biophys 2021; 703:108852. [PMID: 33771508 DOI: 10.1016/j.abb.2021.108852] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Pyrroline-5-carboxylate reductase (PYCR in humans) catalyzes the final step of l-proline biosynthesis by catalyzing the reduction of L-Δ1-pyrroline-5-carboxylate (L-P5C) to l-proline using NAD(P)H as the hydride donor. In humans, three isoforms PYCR1, PYCR2, and PYCR3 are known. Recent genome-wide association and clinical studies have revealed that homozygous mutations in human PYCR2 lead to postnatal microcephaly and hypomyelination, including hypomyelinating leukodystrophy type 10. To uncover biochemical and structural insights into human PYCR2, we characterized the steady-state kinetics of the wild-type enzyme along with two protein variants, Arg119Cys and Arg251Cys, that were previously identified in patients with microcephaly and hypomyelination. Kinetic measurements with PYCR2 suggest a sequential binding mechanism with L-P5C binding before NAD(P)H and NAD(P)+ releasing before L-Pro. Both disease-related variants are catalytically impaired. Depending on whether NADPH or NADH was used, the catalytic efficiency of the R119C protein variant was 40 or 366 times lower than that of the wild-type enzyme, while the catalytic efficiency of the R251C protein variant was 7 or 26 times lower than that of the wild-type enzyme. In addition, thermostability and circular dichroism measurements suggest that the R251C protein variant has a pronounced folding defect. These results are consistent with the involvement of Arg119Cys and Arg251Cys in disease pathology.
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Chen S, Yang X, Yu M, Wang Z, Liu B, Liu M, Liu L, Ren M, Qi H, Zou J, Vucenik I, Zhu WG, Luo J. SIRT3 regulates cancer cell proliferation through deacetylation of PYCR1 in proline metabolism. Neoplasia 2019; 21:665-675. [PMID: 31108370 PMCID: PMC6526305 DOI: 10.1016/j.neo.2019.04.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022]
Abstract
SIRT3 is a major mitochondrial deacetylase, which regulates various metabolic pathways by deacetylation; however, the effect of SIRT3 on proline metabolism is not reported. Pyrroline-5-carboxylate reductase 1 (PYCR1) participates in proline synthesis process by catalyzing the reduction of P5C to proline with concomitant generation of NAD+ and NADP+. PYCR1 is highly expressed in various cancers, and it can promote the growth of tumor cells. Here, through immunoprecipitation and mass spectrometry, we found that PYCR1 is in SIRT3's interacting network. PYCR1 directly binds to SIRT3 both in vivo and in vitro. CBP is the acetyltransferase for PYCR1, whereas SIRT3 deacetylates PYCR1. We further identified that K228 is the major acetylation site for PYCR1. Acetylation of PYCR1 at K228 reduced its enzymatic activity by impairing the formation of the decamer of PYCR1. As a result, acetylation of PYCR1 at K228 inhibits cell proliferation, while deacetylation of PYCR1 mediated by SIRT3 increases PYCR1's activity. Our findings on the regulation of PYCR1 linked proline metabolism with SIRT3, CBP and cell growth, thus providing a potential approach for cancer therapy.
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Affiliation(s)
- Shuaiyi Chen
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Xin Yang
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Miao Yu
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Zhe Wang
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Boya Liu
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Minghui Liu
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Lu Liu
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Mengmeng Ren
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Hao Qi
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Junhua Zou
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China
| | - Ivana Vucenik
- Department of Medical and Research Technology, University of Maryland, Baltimore, MD 21201, USA
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518060, China
| | - Jianyuan Luo
- Department of Medical Genetics, Peking University Health Science Center, Beijing, 100191, China; Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Biophysics, Peking University Health Science Center, Beijing 100191, China.
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Guo L, Cui C, Zhang K, Wang J, Wang Y, Lu Y, Chen K, Yuan J, Xiao G, Tang B, Sun Y, Wu C. Kindlin-2 links mechano-environment to proline synthesis and tumor growth. Nat Commun 2019; 10:845. [PMID: 30783087 PMCID: PMC6381112 DOI: 10.1038/s41467-019-08772-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 01/24/2019] [Indexed: 12/16/2022] Open
Abstract
Cell metabolism is strongly influenced by mechano-environment. We show here that a fraction of kindlin-2 localizes to mitochondria and interacts with pyrroline-5-carboxylate reductase 1 (PYCR1), a key enzyme for proline synthesis. Extracellular matrix (ECM) stiffening promotes kindlin-2 translocation into mitochondria and its interaction with PYCR1, resulting in elevation of PYCR1 level and consequent increase of proline synthesis and cell proliferation. Depletion of kindlin-2 reduces PYCR1 level, increases reactive oxygen species (ROS) production and apoptosis, and abolishes ECM stiffening-induced increase of proline synthesis and cell proliferation. In vivo, both kindlin-2 and PYCR1 levels are markedly increased in lung adenocarcinoma. Ablation of kindlin-2 in lung adenocarcinoma substantially reduces PYCR1 and proline levels, and diminishes fibrosis in vivo, resulting in marked inhibition of tumor growth and reduction of mortality rate. Our findings reveal a mechanoresponsive kindlin-2-PYCR1 complex that links mechano-environment to proline metabolism and signaling, and suggest a strategy to inhibit tumor growth.
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Affiliation(s)
- Ling Guo
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Chunhong Cui
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Kuo Zhang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jiaxin Wang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yilin Wang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yixuan Lu
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ka Chen
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15261, USA
| | - Jifan Yuan
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Guozhi Xiao
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Bin Tang
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ying Sun
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Department of Biology and Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Chuanyue Wu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15261, USA.
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Homology Model and Docking-Based Virtual Screening for Ligands of Human Dyskerin as New Inhibitors of Telomerase for Cancer Treatment. Int J Mol Sci 2018; 19:ijms19103216. [PMID: 30340325 PMCID: PMC6214037 DOI: 10.3390/ijms19103216] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/06/2018] [Accepted: 10/08/2018] [Indexed: 01/31/2023] Open
Abstract
Immortality is one of the main features of cancer cells. Tumor cells have an unlimited replicative potential, principally due to the holoenzyme telomerase. Telomerase is composed mainly by dyskerin (DKC1), a catalytic retrotranscriptase (hTERT) and an RNA template (hTR). The aim of this work is to develop new inhibitors of telomerase, selecting the interaction between hTR⁻DKC1 as a target. We designed two models of the human protein DKC1: homology and ab initio. These models were evaluated by different procedures, revealing that the homology model parameters were the most accurate. We selected two hydrophobic pockets contained in the PUA (pseudouridine synthase and archaeosine transglycosylase) domain, using structural and stability analysis. We carried out a docking-based virtual screen on these pockets, using the reported mutation K314 as the center of the docking. The hDKC1 model was tested against a library of 450,000 drug-like molecules. We selected the first 10 molecules that showed the highest affinity values to test their inhibitory activity on the cell line MDA MB 231 (Monroe Dunaway Anderson Metastasis Breast cancer 231), obtaining three compounds that showed inhibitory effect. These results allowed us to validate our design and set the basis to continue with the study of telomerase inhibitors for cancer treatment.
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