51
|
Lei C, Guo T, Ding S, Liao L, Peng H, Tan Z, Luo H. Whole-exome sequencing identified a novel homozygous ASPH frameshift variant causing Traboulsi syndrome in a Chinese family. Mol Genet Genomic Med 2020; 9:e1553. [PMID: 33217155 PMCID: PMC7963421 DOI: 10.1002/mgg3.1553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/07/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
Background Traboulsi syndrome is a rare disorder characterized by ectopia lentis and facial dysmorphism (large beaked nose), which was only reported in 18 individuals to date. It is caused by homozygous/compound heterozygous variants in the aspartate/asparagine‐β‐hydroxylase (ASPH) gene, which hydroxylates the aspartic acid and asparagine in epidermal growth factor‐like domains of various proteins. Methods Whole‐exome and Sanger sequencing were used to identify the disease‐causing gene of the patient in a consanguineous Chinese family. Domain analysis was applied to predict the impact of the variant on ASPH protein. Results Through exome and Sanger sequencing, we identified a novel homozygous ASPH variant (NM_004318.4:c.1910del/NP_004309.2: p.(Asn637MetfsTer15)) in the patient, which may lead to blockage of the ASPH function through truncating the AspH oxygenase domain of the ASPH protein and/or nonsense‐mediated decay of the ASPH transcript. This is the first report of Traboulsi syndrome in a Chinese patient who was combined with ventricular septal defect, lung bullae, and recurrent spontaneous pneumothorax. Conclusion Our results revealed the clinical characteristics of the first Chinese patient with Traboulsi syndrome. Additionally, our study expands the mutational spectrum of Traboulsi syndrome and provides information for clinical genetic counseling to this family.
Collapse
Affiliation(s)
- Cheng Lei
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Ting Guo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Shuizi Ding
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Liyan Liao
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Hong Peng
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Zhiping Tan
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Respiratory Disease, Central South University, Changsha, China.,Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| |
Collapse
|
52
|
Li Y, Sun XX, Qian DZ, Dai MS. Molecular Crosstalk Between MYC and HIF in Cancer. Front Cell Dev Biol 2020; 8:590576. [PMID: 33251216 PMCID: PMC7676913 DOI: 10.3389/fcell.2020.590576] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
The transcription factor c-MYC (MYC thereafter) is a global regulator of gene expression. It is overexpressed or deregulated in human cancers of diverse origins and plays a key role in the development of cancers. Hypoxia-inducible factors (HIFs), a central regulator for cells to adapt to low cellular oxygen levels, is also often overexpressed and activated in many human cancers. HIF mediates the primary transcriptional response of a wide range of genes in response to hypoxia. Earlier studies focused on the inhibition of MYC by HIF during hypoxia, when MYC is expressed at physiological level, to help cells survive under low oxygen conditions. Emerging evidence suggests that MYC and HIF also cooperate to promote cancer cell growth and progression. This review will summarize the current understanding of the complex molecular interplay between MYC and HIF.
Collapse
Affiliation(s)
- Yanping Li
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States
| | - Xiao-Xin Sun
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States
| | - David Z Qian
- The OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| | - Mu-Shui Dai
- Department of Molecular and Medical Genetics, School of Medicine, Portland, OR, United States.,The OHSU Knight Cancer Institute, Oregon Health and Science University, Portland, OR, United States
| |
Collapse
|
53
|
Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression. Int J Mol Sci 2020; 21:ijms21218162. [PMID: 33142830 PMCID: PMC7663541 DOI: 10.3390/ijms21218162] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. The key molecules of the hypoxia/oxygen-sensing signaling include the transcriptional regulator hypoxia-inducible factor (HIF) which widely controls oxygen responsive genes, the central members of the 2-oxoglutarate (2-OG)-dependent dioxygenases, such as prolyl hydroxylase (PHD or EglN), and an E3 ubiquitin ligase component for HIF degeneration called von Hippel–Lindau (encoding protein pVHL). In this review, we summarize the current knowledge about the canonical hypoxia signaling, HIF transcription factors, and pVHL. In addition, the role of 2-OG-dependent enzymes, such as DNA/RNA-modifying enzymes, JmjC domain-containing enzymes, and prolyl hydroxylases, in gene regulation of cancer progression, is specifically reviewed. We also discuss the therapeutic advancement of targeting hypoxia and oxygen sensing pathways in cancer.
Collapse
|
54
|
Fletcher SC, Coleman ML. Human 2-oxoglutarate-dependent oxygenases: nutrient sensors, stress responders, and disease mediators. Biochem Soc Trans 2020; 48:1843-1858. [PMID: 32985654 PMCID: PMC7609023 DOI: 10.1042/bst20190333] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/30/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate (2OG)-dependent oxygenases are a conserved enzyme class that catalyse diverse oxidative reactions across nature. In humans, these enzymes hydroxylate a broad range of biological substrates including DNA, RNA, proteins and some metabolic intermediates. Correspondingly, members of the 2OG-dependent oxygenase superfamily have been linked to fundamental biological processes, and found dysregulated in numerous human diseases. Such findings have stimulated efforts to understand both the biochemical activities and cellular functions of these enzymes, as many have been poorly studied. In this review, we focus on human 2OG-dependent oxygenases catalysing the hydroxylation of protein and polynucleotide substrates. We discuss their modulation by changes in the cellular microenvironment, particularly with respect to oxygen, iron, 2OG and the effects of oncometabolites. We also describe emerging evidence that these enzymes are responsive to cellular stresses including hypoxia and DNA damage. Moreover, we examine how dysregulation of 2OG-dependent oxygenases is associated with human disease, and the apparent paradoxical role for some of these enzymes during cancer development. Finally, we discuss some of the challenges associated with assigning biochemical activities and cellular functions to 2OG-dependent oxygenases.
Collapse
Affiliation(s)
- Sally C. Fletcher
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| | - Mathew L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, U.K
| |
Collapse
|
55
|
Huang M, Yang L, Peng X, Wei S, Fan Q, Yang S, Li X, Li B, Jin H, Wu B, Liu J, Li H. Autonomous glucose metabolic reprogramming of tumour cells under hypoxia: opportunities for targeted therapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:185. [PMID: 32928258 PMCID: PMC7491117 DOI: 10.1186/s13046-020-01698-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022]
Abstract
Molecular oxygen (O2) is a universal electron acceptor that is eventually synthesized into ATP in the mitochondrial respiratory chain of all metazoans. Therefore, hypoxia biology has become an organizational principle of cell evolution, metabolism and pathology. Hypoxia-inducible factor (HIF) mediates tumour cells to produce a series of glucose metabolism adaptations including the regulation of glucose catabolism, glycogen metabolism and the biological oxidation of glucose to hypoxia. Since HIF can regulate the energy metabolism of cancer cells and promote the survival of cancer cells, targeting HIF or HIF mediated metabolic enzymes may become one of the potential treatment methods for cancer. In this review, we summarize the established and recently discovered autonomous molecular mechanisms that can induce cell reprogramming of hypoxic glucose metabolism in tumors and explore opportunities for targeted therapy.
Collapse
Affiliation(s)
- Mingyao Huang
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shibo Wei
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Qing Fan
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Bowen Li
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongyuan Jin
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Bo Wu
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jingang Liu
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hangyu Li
- Department of General Surgery, the Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
| |
Collapse
|
56
|
Zhao Y, Feng F, Guo QH, Wang YP, Zhao R. Role of succinate dehydrogenase deficiency and oncometabolites in gastrointestinal stromal tumors. World J Gastroenterol 2020; 26:5074-5089. [PMID: 32982110 PMCID: PMC7495036 DOI: 10.3748/wjg.v26.i34.5074] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/14/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. At the molecular level, GISTs can be categorized into two groups based on the causative oncogenic mutations. Approximately 85% of GISTs are caused by gain-of-function mutations in the tyrosine kinase receptor KIT or platelet-derived growth factor receptor alpha (PDGFRA). The remaining GISTs, referred to as wild-type (WT) GISTs, are often deficient in succinate dehydrogenase complex (SDH), a key metabolic enzyme complex in the tricarboxylic acid (TCA) cycle and electron transport chain. SDH deficiency leads to the accumulation of succinate, a metabolite produced by the TCA cycle. Succinate inhibits α-ketoglutarate-dependent dioxygenase family enzymes, which comprise approximately 60 members and regulate key aspects of tumorigenesis such as DNA and histone demethylation, hypoxia responses, and m6A mRNA modification. For this reason, succinate and metabolites with similar structures, such as D-2-hydroxyglutarate and fumarate, are considered oncometabolites. In this article, we review recent advances in the understanding of how metabolic enzyme mutations and oncometabolites drive human cancer with an emphasis on SDH mutations and succinate in WT GISTs.
Collapse
Affiliation(s)
- Yue Zhao
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Fei Feng
- Department of Ultrasound, the First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Qing-Hong Guo
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Yu-Ping Wang
- Department of Gastroenterology, the First Hospital of Lanzhou University, Key Laboratory for Gastrointestinal Disease of Gansu Province, Lanzhou 730000, Gansu Province, China
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, the University of Alabama at Birmingham, Birmingham, AL 35294, United States
| |
Collapse
|
57
|
Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the JmjC histone demethylase KDM4A integrates substrate dynamics, correlated motions and molecular orbital control. Chem Sci 2020; 11:9950-9961. [PMID: 34094257 PMCID: PMC8162366 DOI: 10.1039/d0sc03713c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Nε-methyl lysine status of histones is important in the regulation of eukaryotic transcription. The Fe(ii) and 2-oxoglutarate (2OG) -dependent JmjC domain enzymes are the largest family of histone Nε-methyl lysine demethylases (KDMs). The human KDM4 subfamily of JmjC KDMs is linked with multiple cancers and some of its members are medicinal chemistry targets. We describe the use of combined molecular dynamics (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) methods to study the mechanism of KDM4A, which catalyzes demethylation of both tri- and di-methylated forms of histone H3 at K9 and K36. The results show that the oxygen activation at the active site of KDM4A is optimized towards the generation of the reactive Fe(iv)-oxo intermediate. Factors including the substrate binding mode, correlated motions of the protein and histone substrates, and molecular orbital control synergistically contribute to the reactivity of the Fe(iv)-oxo intermediate. In silico substitutions were performed to investigate the roles of residues (Lys241, Tyr177, and Asn290) in substrate orientation. The Lys241Ala substitution abolishes activity due to altered substrate orientation consistent with reported experimental studies. Calculations with a macrocyclic peptide substrate analogue reveal that induced conformational changes/correlated motions in KDM4A are sequence-specific in a manner that influences substrate binding affinity. Second sphere residues, such as Ser288 and Thr289, may contribute to KDM4A catalysis by correlated motions with active site residues. Residues that stabilize key intermediates, and which are predicted to be involved in correlated motions with other residues in the second sphere and beyond, are shown to be different in KDM4A compared to those in another JmjC KDM (PHF8), which acts on H3K9 di- and mono-methylated forms, suggesting that allosteric type inhibition is of interest from the perspective of developing selective JmjC KDM inhibitors. The second sphere residues and regions of the protein in histone demethylase enzymes that makes correlated motion with the active site contribute to efficient catalysis.![]()
Collapse
Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan Ann Arbor MI 48019 USA
| | | | | | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| |
Collapse
|
58
|
Sturm S, Dowle A, Audsley N, Isaac RE. The structure of the Drosophila melanogaster sex peptide: Identification of hydroxylated isoleucine and a strain variation in the pattern of amino acid hydroxylation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 124:103414. [PMID: 32589920 DOI: 10.1016/j.ibmb.2020.103414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/05/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
In Drosophila melanogaster mating triggers profound changes in the behaviour and reproductive physiology of the female. Many of these post-mating effects are elicited by sex peptide (SP), a 36-mer pheromone made in the male accessory gland and passed to the female in the seminal fluid. The peptide comprises several structurally and functionally distinct domains, one of which consists of five 4-hydroxyprolines and induces a female immune response. The SP gene predicts an isoleucine (Ile14) sandwiched between two of the hydroxyprolines of the mature secreted peptide, but the identity of this residue was not established by peptide sequencing and amino acid analysis, presumably because of modification of the side chain. Here we have used matrix-assisted laser desorption ionisation mass spectrometry together with Fourier-transform ion cyclotron resonance mass spectrometry to show that Ile14 is modified by oxidation of the side chain - a very unusual post-translational modification. Mass spectrometric analysis of glands from different geographical populations of male D. melanogaster show that SP with six hydroxylated side chains is the most common form of the peptide, but that a sub-strain of Canton-S flies held at Leeds only has two or three hydroxylated prolines and an unmodified Ile14. The D. melanogaster genome has remarkably 17 putative hydroxylase genes that are strongly and almost exclusively expressed in the male accessory gland, suggesting that the gland is a powerhouse of protein oxidation. Strain variation in the pattern of sex peptide hydroxylation might be explained by differences in the expression of individual hydroxylase genes.
Collapse
Affiliation(s)
- Sebastian Sturm
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Adam Dowle
- Bioscience Technology Facility, Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Neil Audsley
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon-Tyne, NE1 7RU, UK
| | - R Elwyn Isaac
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
59
|
Matthews KA, Senagbe KM, Nötzel C, Gonzales CA, Tong X, Rijo-Ferreira F, Bhanu NV, Miguel-Blanco C, Lafuente-Monasterio MJ, Garcia BA, Kafsack BFC, Martinez ED. Disruption of the Plasmodium falciparum Life Cycle through Transcriptional Reprogramming by Inhibitors of Jumonji Demethylases. ACS Infect Dis 2020; 6:1058-1075. [PMID: 32272012 PMCID: PMC7748244 DOI: 10.1021/acsinfecdis.9b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Little
is known about the role of the three Jumonji C (JmjC) enzymes
in Plasmodium falciparum (Pf). Here,
we show that JIB-04 and other established inhibitors of mammalian
JmjC histone demethylases kill asexual blood stage parasites and are
even more potent at blocking gametocyte development and gamete formation.
In late stage parasites, JIB-04 increased levels of trimethylated
lysine residues on histones, suggesting the inhibition of P. falciparum Jumonji demethylase activity. These epigenetic
defects coincide with deregulation of invasion, cell motor, and sexual
development gene programs, including gene targets coregulated by the
PfAP2-I transcription factor and chromatin-binding factor, PfBDP1.
Mechanistically, we demonstrate that PfJmj3 converts 2-oxoglutarate
to succinate in an iron-dependent manner consistent with mammalian
Jumonji enzymes, and this catalytic activity is inhibited by JIB-04
and other Jumonji inhibitors. Our pharmacological studies of Jumonji
activity in the malaria parasite provide evidence that inhibition
of these enzymatic activities is detrimental to the parasite.
Collapse
Affiliation(s)
- Krista A. Matthews
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Kossi M. Senagbe
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Christopher Nötzel
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
- Biochemistry, Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Christopher A. Gonzales
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Xinran Tong
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| | - Natarajan V. Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, Pennsylvania 19104, United States
| | - Celia Miguel-Blanco
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, P.T.M. Severo Ochoa, Tres Cantos, Madrid 28760, Spain
| | | | - Benjamin A. Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Bldg. 421, Philadelphia, Pennsylvania 19104, United States
| | - Björn F. C. Kafsack
- Department of Microbiology & Immunology, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
- Biochemistry, Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, 1300 York Avenue, W-705, New York, New York 10065, United States
| | - Elisabeth D. Martinez
- Department of Pharmacology, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, Texas 75390, United States
| |
Collapse
|
60
|
Turning the Oxygen Dial: Balancing the Highs and Lows. Trends Cell Biol 2020; 30:516-536. [PMID: 32386878 DOI: 10.1016/j.tcb.2020.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/02/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Abstract
Oxygen is both vital and toxic to life. Molecular oxygen is the most used substrate in the human body and is required for several hundred diverse biochemical reactions. The discovery of the PHD-HIF-pVHL system revolutionized our fundamental understanding of oxygen sensing and cellular adaptations to hypoxia. It deepened our knowledge of the biochemical underpinnings of numerous diseases, ranging from anemia to cancer. Cellular dysfunction and tissue pathology can result from a mismatch of oxygen supply and demand. Recent work has shown that mitochondrial disease models display tissue hyperoxia and that disease pathology can be reversed by normalization of excess oxygen, suggesting that certain disease states can potentially be treated by modulating oxygen levels. In this review, we describe cellular and organismal mechanisms of oxygen sensing and adaptation. We provide a revitalized framework for understanding pathologies of too little or too much oxygen.
Collapse
|
61
|
Lee P, Chandel NS, Simon MC. Cellular adaptation to hypoxia through hypoxia inducible factors and beyond. Nat Rev Mol Cell Biol 2020; 21:268-283. [PMID: 32144406 PMCID: PMC7222024 DOI: 10.1038/s41580-020-0227-y] [Citation(s) in RCA: 566] [Impact Index Per Article: 141.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
Molecular oxygen (O2) sustains intracellular bioenergetics and is consumed by numerous biochemical reactions, making it essential for most species on Earth. Accordingly, decreased oxygen concentration (hypoxia) is a major stressor that generally subverts life of aerobic species and is a prominent feature of pathological states encountered in bacterial infection, inflammation, wounds, cardiovascular defects and cancer. Therefore, key adaptive mechanisms to cope with hypoxia have evolved in mammals. Systemically, these adaptations include increased ventilation, cardiac output, blood vessel growth and circulating red blood cell numbers. On a cellular level, ATP-consuming reactions are suppressed, and metabolism is altered until oxygen homeostasis is restored. A critical question is how mammalian cells sense oxygen levels to coordinate diverse biological outputs during hypoxia. The best-studied mechanism of response to hypoxia involves hypoxia inducible factors (HIFs), which are stabilized by low oxygen availability and control the expression of a multitude of genes, including those involved in cell survival, angiogenesis, glycolysis and invasion/metastasis. Importantly, changes in oxygen can also be sensed via other stress pathways as well as changes in metabolite levels and the generation of reactive oxygen species by mitochondria. Collectively, this leads to cellular adaptations of protein synthesis, energy metabolism, mitochondrial respiration, lipid and carbon metabolism as well as nutrient acquisition. These mechanisms are integral inputs into fine-tuning the responses to hypoxic stress.
Collapse
Affiliation(s)
- Pearl Lee
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Navdeep S Chandel
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| |
Collapse
|
62
|
Ueki Y, Saito K, Iioka H, Sakamoto I, Kanda Y, Sakaguchi M, Horii A, Kondo E. PLOD2 Is Essential to Functional Activation of Integrin β1 for Invasion/Metastasis in Head and Neck Squamous Cell Carcinomas. iScience 2020; 23:100850. [PMID: 32058962 PMCID: PMC6997870 DOI: 10.1016/j.isci.2020.100850] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 09/20/2019] [Accepted: 01/14/2020] [Indexed: 10/26/2022] Open
Abstract
Identifying the specific functional regulator of integrin family molecules in cancer cells is critical because they are directly involved in tumor invasion and metastasis. Here we report high expression of PLOD2 in oropharyngeal squamous cell carcinomas (SCCs) and its critical role as a stabilizer of integrin β1, enabling integrin β1 to initiate tumor invasion/metastasis. Integrin β1 stabilized by PLOD2-mediated hydroxylation was recruited to the plasma membrane, its functional site, and accelerated tumor cell motility, leading to tumor metastasis in vivo, whereas loss of PLOD2 expression abrogated it. In accordance with molecular analysis, examination of oropharyngeal SCC tissues from patients corroborated PLOD2 expression associated with integrin β1 at the invasive front of tumor nests. PLOD2 is thus implicated as the key regulator of integrin β1 that prominently regulates tumor invasion and metastasis, and it provides important clues engendering novel therapeutics for these intractable cancers.
Collapse
Affiliation(s)
- Yushi Ueki
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan; Department of Otolaryngology, Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan
| | - Ken Saito
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan.
| | - Hidekazu Iioka
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan
| | | | - Yasuhiro Kanda
- Department of Immunology, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan
| | - Masakiyo Sakaguchi
- Department of Cell Biology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Shikata-cho, Kita-ku, Okayama, Japan
| | - Arata Horii
- Department of Otolaryngology, Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan
| | - Eisaku Kondo
- Division of Molecular and Cellular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Asahimachi-dori, Chuo-ku, Niigata, Japan.
| |
Collapse
|
63
|
Abstract
AbstractFormaldehyde is a biological electrophile produced via processes including enzymatic demethylation. Despite its apparent simplicity, the reactions of formaldehyde with even basic biological components are incompletely defined. Here we report NMR-based studies on the reactions of formaldehyde with common proteinogenic and other nucleophilic amino acids. The results reveal formaldehyde reacts at different rates, forming hydroxymethylated, cyclised, cross-linked, or disproportionated products of varying stabilities. Of the tested common amino acids, cysteine reacts most efficiently, forming a stable thiazolidine. The reaction with lysine is less efficient; low levels of an Nε-methylated product are observed, raising the possibility of non-enzymatic lysine methylation by formaldehyde. Reactions with formaldehyde are faster than reactions with other tested biological carbonyl compounds, and the adducts are also more stable. The results reveal reactions of formaldehyde with amino acids, and by extension peptides and proteins, have potential roles in healthy and diseased biology, as well as in evolution.
Collapse
|
64
|
Reduced Iron in Diabetic Wounds: An Oxidative Stress-Dependent Role for STEAP3 in Extracellular Matrix Deposition and Remodeling. J Invest Dermatol 2019; 139:2368-2377.e7. [DOI: 10.1016/j.jid.2019.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/16/2019] [Accepted: 05/23/2019] [Indexed: 12/18/2022]
|
65
|
Mennerich D, Kubaichuk K, Kietzmann T. DUBs, Hypoxia, and Cancer. Trends Cancer 2019; 5:632-653. [PMID: 31706510 DOI: 10.1016/j.trecan.2019.08.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/24/2019] [Accepted: 08/27/2019] [Indexed: 02/08/2023]
Abstract
Alterations in protein ubiquitylation and hypoxia are commonly associated with cancer. Ubiquitylation is carried out by three sequentially acting ubiquitylating enzymes and can be opposed by deubiquitinases (DUBs), which have emerged as promising drug targets. Apart from protein localization and activity, ubiquitylation regulates degradation of proteins, among them hypoxia-inducible factors (HIFs). Thereby, various E3 ubiquitin ligases and DUBs regulate HIF abundance. Conversely, several E3s and DUBs are regulated by hypoxia. While hypoxia is a powerful HIF regulator, less is known about hypoxia-regulated DUBs and their impact on HIFs. Here, we review current knowledge about the relationship of E3s, DUBs, and hypoxia signaling. We also discuss the reciprocal regulation of DUBs by hypoxia and use of DUB-specific drugs in cancer.
Collapse
Affiliation(s)
- Daniela Mennerich
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland
| | - Kateryna Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, 90570, Finland; Biocenter Oulu, University of Oulu, Oulu, 90570, Finland.
| |
Collapse
|
66
|
Lin HY, Ko CY, Kao TJ, Yang WB, Tsai YT, Chuang JY, Hu SL, Yang PY, Lo WL, Hsu TI. CYP17A1 Maintains the Survival of Glioblastomas by Regulating SAR1-Mediated Endoplasmic Reticulum Health and Redox Homeostasis. Cancers (Basel) 2019; 11:cancers11091378. [PMID: 31527549 PMCID: PMC6770831 DOI: 10.3390/cancers11091378] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/30/2022] Open
Abstract
Cytochrome P450 (CYP) 17A1 is an important steroidogenic enzyme harboring 17α-hydroxylase and performing 17,20 lyase activities in multiple steps of steroid hormone synthesis, including dehydroepiandrosterone (DHEA) biosynthesis. Previously, we showed that CYP17A1-mediated DHEA production clearly protects glioblastomas from temozolomide-induced apoptosis, leading to drug resistance. Herein, we attempt to clarify whether the inhibition of CYP17A1 has a tumor-suppressive effect, and to determine the steroidogenesis-independent functions of CYP17A1 in glioblastomas. Abiraterone, an inhibitor of CYP17A1, significantly inhibits the proliferation of A172, T98G, and PT#3 (the primary glioblastoma cells) by inducing apoptosis. In parallel, abiraterone potently suppresses tumor growth in mouse models through transplantation of PT#3 cells to the back or to the brain. Based on evidence that abiraterone induces endoplasmic reticulum (ER) stress, followed by the accumulation of reactive oxygen species (ROS), CYP17A1 is important for ER health and redox homeostasis. To confirm our hypothesis, we showed that CYP17A1 overexpression prevents the initiation of ER stress and attenuates ROS production by regulating SAR1a/b expression. Abiraterone dissociates SAR1a/b from ER-localized CYP17A1, and induces SAR1a/b ubiquitination, leading to degradation. Furthermore, SAR1 overexpression rescues abiraterone-induced apoptosis and impairs redox homeostasis. In addition to steroid hormone synthesis, CYP17A1 associates with SAR1a/b to regulate protein processing and maintain ER health in glioblastomas.
Collapse
Affiliation(s)
- Hong-Yi Lin
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
| | - Chiung-Yuan Ko
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Tzu-Jen Kao
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
| | - Wen-Bin Yang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Yu-Ting Tsai
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Jian-Ying Chuang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Siou-Lian Hu
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
| | - Pei-Yu Yang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
| | - Wei-Lun Lo
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- Division of Neurosurgery, Taipei Medical University-Shuang-Ho Hospital, New Taipei City 23561, Taiwan.
| | - Tsung-I Hsu
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, 11031 Taipei, Taiwan.
- Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University and National Health Research Institutes, Taipei 11031, Taiwan.
- TMU Research Center of Neuroscience, Taipei Medical University, Taipei, Taiwan.
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| |
Collapse
|
67
|
Reed DR, Elsarrag RZ, Morris AL, Keng MK. Enasidenib in acute myeloid leukemia: clinical development and perspectives on treatment. Cancer Manag Res 2019; 11:8073-8080. [PMID: 31564968 PMCID: PMC6724422 DOI: 10.2147/cmar.s162784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Recently there has been a significant progression in the understanding of molecular mutations driving biochemical and cellular signaling changes leading to survival and proliferation of leukemia cells in patients with acute myeloid leukemia (AML). Preclinical studies have demonstrated a mutated enzyme in the citric acid cycle, isocitrate dehydrogenase (IDH), leads to the production of an oncogenic metabolite R-2-hydroxy-glutarate (R-2-HG). This causes the arrest in the differentiation of hematopoietic stem cells leading to the promotion of leukemia. Inhibitors of the IDH enzyme have been shown in preclinical studies to reduce the production of R-2-HG, resulting in terminal differentiation of leukemia blast cells. In recent phase I and II trials, the IDH2 inhibitor enasidenib has shown clinical activity in patients with relapsed and refractory (R/R) AML. This review will describe the preclinical and clinical developments of enasidenib and its Food and Drug Administration approval in R/R AML, treatment recommendations and management will be outlined.
Collapse
Affiliation(s)
- Daniel R Reed
- Division of Hematology/Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Ramey Z Elsarrag
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Amy L Morris
- Department of Pharmacy Services, University of Virginia, Charlottesville, VA, USA
| | - Michael K Keng
- Division of Hematology/Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
68
|
Wende K, von Woedtke T, Weltmann KD, Bekeschus S. Chemistry and biochemistry of cold physical plasma derived reactive species in liquids. Biol Chem 2019; 400:19-38. [PMID: 30403650 DOI: 10.1515/hsz-2018-0242] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/29/2018] [Indexed: 02/01/2023]
Abstract
Reactive oxygen and nitrogen species deposited by cold physical plasma are proposed as predominant effectors in the interaction between discharge and biomedical application. Most reactive species found in plasma sources are known in biology for inter- and intracellular communication (redox signaling) and mammalian cells are equipped to interpret the plasma derived redox signal. As such, considerable effort has been put into the investigation of potential clinical applications and the underlying mechanism, with a special emphasis on conditions orchestrated significantly via redox signaling. Among these, immune system control in wound healing and cancer control stands out with promising in vitro and in vivo effects. From the fundamental point of view, further insight in the interaction of the plasma-derived species with biological systems is desired to (a) optimize treatment conditions, (b) identify new fields of application, (c) to improve plasma source design, and (d) to identify the trajectories of reactive species. Knowledge on the biochemical reactivity of non-thermal plasmas is compiled and discussed. While there is considerable knowledge on proteins, lipids and carbohydrates have not received the attention deserved. Nucleic acids have been profoundly investigated yet focusing on molecule functionality rather than chemistry. The data collected underline the efforts taken to understand the fundamentals of plasma medicine but also indicate 'no man's lands' waiting to be discovered.
Collapse
Affiliation(s)
- Kristian Wende
- ZIK Plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany.,Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
| | - Thomas von Woedtke
- Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany.,Greifswald University Medicine, Fleischmannstr. 8, D-17475 Greifswald, Germany
| | - Klaus-Dieter Weltmann
- Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
| | - Sander Bekeschus
- ZIK Plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany.,Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, D-17489 Greifswald, Germany
| |
Collapse
|
69
|
Islam MS, McDonough MA, Chowdhury R, Gault J, Khan A, Pires E, Schofield CJ. Biochemical and structural investigations clarify the substrate selectivity of the 2-oxoglutarate oxygenase JMJD6. J Biol Chem 2019; 294:11637-11652. [PMID: 31147442 PMCID: PMC6663879 DOI: 10.1074/jbc.ra119.008693] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
JmjC domain-containing protein 6 (JMJD6) is a 2-oxoglutarate (2OG)-dependent oxygenase linked to various cellular processes, including splicing regulation, histone modification, transcriptional pause release, hypoxia sensing, and cancer. JMJD6 is reported to catalyze hydroxylation of lysine residue(s) of histones, the tumor-suppressor protein p53, and splicing regulatory proteins, including u2 small nuclear ribonucleoprotein auxiliary factor 65-kDa subunit (U2AF65). JMJD6 is also reported to catalyze N-demethylation of N-methylated (both mono- and di-methylated) arginine residues of histones and other proteins, including HSP70 (heat-shock protein 70), estrogen receptor α, and RNA helicase A. Here, we report MS- and NMR-based kinetic assays employing purified JMJD6 and multiple substrate fragment sequences, the results of which support the assignment of purified JMJD6 as a lysyl hydroxylase. By contrast, we did not observe N-methyl arginyl N-demethylation with purified JMJD6. Biophysical analyses, including crystallographic analyses of JMJD6Δ344-403 in complex with iron and 2OG, supported its assignment as a lysyl hydroxylase rather than an N-methyl arginyl-demethylase. The screening results supported some, but not all, of the assigned JMJD6 substrates and identified other potential JMJD6 substrates. We envision these results will be useful in cellular and biological work on the substrates and functions of JMJD6 and in the development of selective inhibitors of human 2OG oxygenases.
Collapse
Affiliation(s)
- Md Saiful Islam
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rasheduzzaman Chowdhury
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph Gault
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Amjad Khan
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| |
Collapse
|
70
|
Llurba Olive E, Xiao E, Natale DR, Fisher SA. Oxygen and lack of oxygen in fetal and placental development, feto-placental coupling, and congenital heart defects. Birth Defects Res 2019; 110:1517-1530. [PMID: 30576091 DOI: 10.1002/bdr2.1430] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022]
Abstract
Low oxygen concentration (hypoxia) is part of normal embryonic development, yet the situation is complex. Oxygen (O2 ) is a janus gas with low levels signaling through hypoxia-inducible transcription factor (HIF) that are required for development of fetal and placental vasculature and fetal red blood cells. This results in coupling of fetus and mother around midgestation as a functional feto-placental unit (FPU) for O2 transport, which is required for continued growth and development of the fetus. Defects in these processes may leave the developing fetus vulnerable to O2 deprivation or other stressors during this critical midgestational transition when common septal and conotruncal heart defects (CHDs) are likely to arise. Recent human epidemiological and case-control studies support an association between placental dysfunction, manifest as early onset pre-eclampsia (PE) and increased serum bio-markers, and CHD. Animal studies support this association, in particular those using gene inactivation in the mouse. Sophisticated methods for gene inactivation, cell fate mapping, and a quantitative bio-reporter of O2 concentration support the premise that hypoxic stress at critical stages of development leads to CHD. The secondary heart field contributing to the cardiac outlet is a key target, with activation of the un-folded protein response and abrogation of FGF signaling or precocious activation of a cardiomyocyte transcriptional program for differentiation, suggested as mechanisms. These studies provide a strong foundation for further study of feto-placental coupling and hypoxic stress in the genesis of human CHD.
Collapse
Affiliation(s)
- Elisa Llurba Olive
- Director of the Obstetrics and Gynecology Department, Sant Pau University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain.,Maternal and Child Health and Development Network II (SAMID II) RD16/0022, Institute of Health Carlos III, Madrid, Spain
| | - Emily Xiao
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - David R Natale
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of California San Diego, San Diego, California
| | - Steven A Fisher
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland.,Department of Physiology and Biophysics, University of Maryland School of Medicine, Baltimore, Maryland
| |
Collapse
|
71
|
Metabolic Plasticity and Epithelial-Mesenchymal Transition. J Clin Med 2019; 8:jcm8070967. [PMID: 31277295 PMCID: PMC6678349 DOI: 10.3390/jcm8070967] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/13/2023] Open
Abstract
A major transcriptional and phenotypic reprogramming event during development is the establishment of the mesodermal layer from the ectoderm through epithelial-mesenchymal transition (EMT). EMT is employed in subsequent developmental events, and also in many physiological and pathological processes, such as the dissemination of cancer cells through metastasis, as a reversible transition between epithelial and mesenchymal states. The remarkable phenotypic remodeling accompanying these transitions is driven by characteristic transcription factors whose activities and/or activation depend upon signaling cues and co-factors, including intermediary metabolites. In this review, we summarize salient metabolic features that enable or instigate these transitions, as well as adaptations undergone by cells to meet the metabolic requirements of their new states, with an emphasis on the roles played by the metabolic regulation of epigenetic modifications, notably methylation and acetylation.
Collapse
|
72
|
The multifaceted contribution of α-ketoglutarate to tumor progression: An opportunity to exploit? Semin Cell Dev Biol 2019; 98:26-33. [PMID: 31175937 DOI: 10.1016/j.semcdb.2019.05.031] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/29/2019] [Accepted: 05/31/2019] [Indexed: 01/25/2023]
Abstract
The thriving field that constitutes cancer metabolism has unveiled some groundbreaking facts over the past two decades, at the heart of which is the TCA cycle and its intermediates. As such and besides its metabolic role, α-ketoglutarate was shown to withstand a wide range of physiological reactions from protection against oxidative stress, collagen and bone maintenance to development and immunity. Most importantly, it constitutes the rate-limiting substrate of 2-oxoglutarate-dependent dioxygenases family enzymes, which are involved in hypoxia sensing and in the shaping of cellular epigenetic landscape, two major drivers of oncogenic transformation. Based on literature reports, we hereby review the benefits of this metabolite as a possible novel adjuvant therapeutic opportunity to target tumor progression. This article is part of the special issue "Mitochondrial metabolic alterations in cancer cells and related therapeutic targets".
Collapse
|
73
|
Jing X, Wang X, Zhang W, An J, Luo P, Nie Y, Xu Y. Highly Regioselective and Stereoselective Hydroxylation of Free Amino Acids by a 2-Oxoglutarate-Dependent Dioxygenase from Kutzneria albida. ACS OMEGA 2019; 4:8350-8358. [PMID: 31459923 PMCID: PMC6648376 DOI: 10.1021/acsomega.9b00983] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 04/30/2019] [Indexed: 05/13/2023]
Abstract
Hydroxyl amino acids have tremendous potential applications in food and pharmaceutical industries. However, available dioxygenases are limited for selective and efficient hydroxylation of free amino acids. Here, we identified a 2-oxoglutarate-dependent dioxygenase from Kutzneria albida by gene mining and characterized the encoded protein (KaPH1). KaPH1 was estimated to have a molecular weight of 29 kDa. The optimal pH and temperature for its l-proline hydroxylation activity were 6.5 and 30 °C, respectively. The K m and k cat values of KaPH1 were 1.07 mM and 0.54 s-1, respectively, for this reaction by which 120 mM l-proline was converted to trans-4-hydroxy-l-proline with 92.8% yield (3.93 g·L-1·h-1). EDTA, [1,10-phenanthroline], Cu2+, Zn2+, Co2+, and Ni2+ inhibited this reaction. KaPH1 was also active toward l-isoleucine for 4-hydroxyisoleucine synthesis. Additionally, the unique biophysical features of KaPH1 were predicted by molecular modeling whereby this study also contributes to our understanding of the catalytic mechanisms of 2-oxoglutarate-dependent dioxygenases.
Collapse
Affiliation(s)
- Xiaoran Jing
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Xinye Wang
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Wenli Zhang
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Jianhong An
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Pengjie Luo
- China
National Center for Food Safety Risk Assessment, NHC Key Laboratory of Food Safety Risk Assessment, 37 Guangqu Road, Beijing 100022, China
- E-mail: (P.L.)
| | - Yao Nie
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
- E-mail: (Y.N.)
| | - Yan Xu
- Key
Laboratory of Industrial Biotechnology of Ministry of Education
and School of Biotechnology and State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| |
Collapse
|
74
|
Stoehr A, Kennedy L, Yang Y, Patel S, Lin Y, Linask KL, Fergusson M, Zhu J, Gucek M, Zou J, Murphy E. The ribosomal prolyl-hydroxylase OGFOD1 decreases during cardiac differentiation and modulates translation and splicing. JCI Insight 2019; 5:128496. [PMID: 31112528 DOI: 10.1172/jci.insight.128496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The mechanisms regulating translation and splicing are not well understood. We provide insight into a new regulator of translation, OGFOD1 (2-oxoglutarate and iron dependent oxygenase domain-containing protein 1), which is a prolyl-hydroxylase that catalyzes the posttranslational hydroxylation of Pro-62 in the small ribosomal protein S23. We show that deletion of OGFOD1 in an in vitro model of human cardiomyocytes decreases translation of specific proteins (e.g., RNA-binding proteins) and alters splicing. RNA sequencing showed poor correlation between changes in mRNA and protein synthesis, suggesting that posttranscriptional regulation was the primary cause for the observed differences. We found that loss of OGFOD1 and the resultant alterations in protein translation modulates the cardiac proteome, shifting it towards higher protein amounts of sarcomeric proteins such as cardiac troponins, titin and cardiac myosin binding protein C. Furthermore, we found a decrease of OGFOD1 during cardiomyocyte differentiation. These results suggest that loss of OGFOD1 modulates protein translation and splicing, thereby leading to alterations in the cardiac proteome and highlight the role of altered translation and splicing in regulating the proteome..
Collapse
Affiliation(s)
| | | | | | | | - Yongshun Lin
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Kaari L Linask
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | | | - Jun Zhu
- DNA Sequencing and Genomics Core
| | | | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | | |
Collapse
|
75
|
Tommasini-Ghelfi S, Murnan K, Kouri FM, Mahajan AS, May JL, Stegh AH. Cancer-associated mutation and beyond: The emerging biology of isocitrate dehydrogenases in human disease. SCIENCE ADVANCES 2019; 5:eaaw4543. [PMID: 31131326 PMCID: PMC6530995 DOI: 10.1126/sciadv.aaw4543] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/16/2019] [Indexed: 05/12/2023]
Abstract
Isocitrate dehydrogenases (IDHs) are critical metabolic enzymes that catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate (αKG), NAD(P)H, and CO2. IDHs epigenetically control gene expression through effects on αKG-dependent dioxygenases, maintain redox balance and promote anaplerosis by providing cells with NADPH and precursor substrates for macromolecular synthesis, and regulate respiration and energy production through generation of NADH. Cancer-associated mutations in IDH1 and IDH2 represent one of the most comprehensively studied mechanisms of IDH pathogenic effect. Mutant enzymes produce (R)-2-hydroxyglutarate, which in turn inhibits αKG-dependent dioxygenase function, resulting in a global hypermethylation phenotype, increased tumor cell multipotency, and malignancy. Recent studies identified wild-type IDHs as critical regulators of normal organ physiology and, when transcriptionally induced or down-regulated, as contributing to cancer and neurodegeneration, respectively. We describe how mutant and wild-type enzymes contribute on molecular levels to disease pathogenesis, and discuss efforts to pharmacologically target IDH-controlled metabolic rewiring.
Collapse
Affiliation(s)
- Serena Tommasini-Ghelfi
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Kevin Murnan
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Fotini M. Kouri
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Akanksha S. Mahajan
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Jasmine L. May
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Alexander H. Stegh
- Ken and Ruth Davee Department of Neurology, The Northwestern Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 303 East Superior, Chicago, IL 60611, USA
- International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Corresponding author.
| |
Collapse
|
76
|
Oh S, Shin S, Janknecht R. The small members of the JMJD protein family: Enzymatic jewels or jinxes? Biochim Biophys Acta Rev Cancer 2019; 1871:406-418. [PMID: 31034925 DOI: 10.1016/j.bbcan.2019.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
Jumonji C domain-containing (JMJD) proteins are mostly epigenetic regulators that demethylate histones. However, a hitherto neglected subfamily of JMJD proteins, evolutionarily distant and characterized by their relatively small molecular weight, exerts different functions by hydroxylating proteins and RNA. Recently, unsuspected proteolytic and tyrosine kinase activities were also ascribed to some of these small JMJD proteins, further increasing their enzymatic versatility. Here, we discuss the ten human small JMJD proteins (HIF1AN, HSPBAP1, JMJD4, JMJD5, JMJD6, JMJD7, JMJD8, RIOX1, RIOX2, TYW5) and their diverse physiological functions. In particular, we focus on the roles of these small JMJD proteins in cancer and other maladies and how they are modulated in diseased cells by an altered metabolic milieu, including hypoxia, reactive oxygen species and oncometabolites. Because small JMJD proteins are enzymes, they are amenable to inhibition by small molecules and may represent novel targets in the therapy of cancer and other diseases.
Collapse
Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| |
Collapse
|
77
|
Wild-Type IDH Enzymes as Actionable Targets for Cancer Therapy. Cancers (Basel) 2019; 11:cancers11040563. [PMID: 31010244 PMCID: PMC6520797 DOI: 10.3390/cancers11040563] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/11/2022] Open
Abstract
Isocitrate dehydrogenases (IDHs) are enzymes that catalyze the oxidative decarboxylation of isocitrate, producing α-ketoglutarate (αKG) and CO2. The discovery of IDH1 and IDH2 mutations in several malignancies has brought to the approval of drugs targeting IDH1/2 mutants in cancers. Here, we summarized findings addressing the impact of IDH mutants in rare pathologies and focused on the relevance of non-mutated IDH enzymes in tumors. Several pieces of evidence suggest that the enzymatic inhibition of IDHs may have therapeutic potentials also in wild-type IDH cancers. Moreover, IDHs inhibition could enhance the efficacy of canonical cancer therapies, such as chemotherapy, target therapy, and radiotherapy. However, further studies are required to elucidate whether IDH proteins are diagnostic/prognostic markers, instrumental for tumor initiation and maintenance, and could be exploited as targets for anticancer therapy. The development of wild-type IDH inhibitors is expected to improve our understanding of a potential non-oncogenic addition to IDH1/2 activities and to fully address their applicability in combination with other therapies.
Collapse
|
78
|
Zhang J, Jing L, Li M, He L, Guo Z. Regulation of histone arginine methylation/demethylation by methylase and demethylase (Review). Mol Med Rep 2019; 19:3963-3971. [PMID: 30942418 PMCID: PMC6471501 DOI: 10.3892/mmr.2019.10111] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
Histone arginine methylation is a universal post-translational modification that has been implicated in multiple cellular and sub-cellular processes, including pre-mRNA splicing, DNA damage signaling, mRNA translation, cell signaling and cell death. Despite these important roles, the understanding of its regulation with respect to certain other modifications, such as phosphorylation and acetylation, is very poor. Thus far, few histone arginine demethylases have been identified in mammalian cells, compared with nine protein arginine methyltransferases (PRMTs) that have been reported. Studies have reported that aberrant histone arginine methylation is strongly associated with carcinogenesis and metastasis. This increases the requirement for understanding the regulation of histone arginine demethylation. The present review summarizes the published studies and provides further insights into histone arginine methylases and demethylases.
Collapse
Affiliation(s)
- Jing Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210097, P.R. China
| | - Li Jing
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210097, P.R. China
| | - Menghan Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210097, P.R. China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210097, P.R. China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210097, P.R. China
| |
Collapse
|
79
|
Gaffney-Stomberg E. The Impact of Trace Minerals on Bone Metabolism. Biol Trace Elem Res 2019; 188:26-34. [PMID: 30467628 DOI: 10.1007/s12011-018-1583-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
Bone is a metabolically active tissue that responds to alterations in dietary intake and nutritional status. It is ~ 35% protein, mostly collagen which provides an organic scaffolding for bone mineral. The mineral is the remaining ~ 65% of bone tissue and composed mostly of calcium and phosphate in a form that is structurally similar to mineral within the apatite group. The skeletal tissue is constantly undergoing turnover through resorption by osteoclasts coupled with formation by osteoblasts. In this regard, the overall bone balance is determined by the relative contribution of each of these processes. In addition to macro minerals such as calcium, phosphorus, and magnesium which have well-known roles in bone health, trace elements such as boron, iron, zinc, copper, and selenium also impact bone metabolism. Effects of trace elements on skeletal metabolism and tissue properties may be indirect through regulation of macro mineral metabolism, or direct by affecting osteoblast or osteoclast proliferation or activity, or finally through incorporation into the bone mineral matrix. This review focuses on the skeletal impact of the following trace elements: boron, iron, zinc, copper, and selenium, and overviews the state of the evidence for each of these minerals.
Collapse
Affiliation(s)
- Erin Gaffney-Stomberg
- Military Performance Division of the US Army Research Institute of Environmental Medicine, Natick, MA, 01760, USA.
| |
Collapse
|
80
|
Hydroxylation of protein constituents of the human translation system: structural aspects and functional assignments. Future Med Chem 2019; 11:357-369. [PMID: 30802140 DOI: 10.4155/fmc-2018-0317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
During the current decade, data on the post-translational hydroxylation of specific amino acid residues of some ribosomal proteins and translation factors in both eukaryotes and eubacteria have accumulated. The reaction is catalyzed by dedicated oxygenases (so-called ribosomal oxygenases), whose action is impaired under hypoxia conditions. The modification occurs at amino acid residues directly involved in the formation of the main functional sites of ribosomes and factors. This review summarizes currently available data on the specific hydroxylation of protein constituents of eukaryotic and eubacterial translation systems with a special emphasis on the human system, as well as on the links between hypoxia impacts on the operation of ribosomal oxygenases, the functioning of the translational apparatus and human health problems.
Collapse
|
81
|
Naffa R, Edwards PJB, Norris G. Isolation and characterization of collagen type I crosslink from skin: high-resolution NMR reveals diastereomers of hydroxylysinonorleucine crosslink. Amino Acids 2019; 51:705-715. [PMID: 30788600 DOI: 10.1007/s00726-019-02708-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 02/06/2019] [Indexed: 12/24/2022]
Abstract
Skin is made up of mainly collagen type I and its structure is stabilised by the formation of covalent immature and mature crosslinks. In this study, collagen immature crosslink hydroxylysinonorleucine (HLNL) was isolated from bovine skin in high purity using two sequential purification steps. These consisted of preparative fibrous cellulose and size exclusion chromatography. The purified crosslink was then analysed using tandem mass spectrometry and high-resolution nuclear magnetic resonance (NMR) spectroscopy. The mass of singly and doubly charged ions of HLNL was 292.1865 and 146.5970 m/z and their optimised fragmentation energy was 17 keV and 5 keV, respectively. The 13C NMR of HLNL showed a doubled-up peak at 67.84 and 67.91 ppm which corroborated a diastereomeric form of collagen immature crosslink HLNL and both are chiroptically indistinguishable. The chemical structure was fully resolved using 1H, 13C and DEPT-135 high-resolution NMR spectroscopy and compared with other previous studies. We also obtained for the first time the 2D NMR spectra COSY and HSQC of HLNL. We therefore suggested that collagen organization into specific fibrils' orientation may be affected by the different configuration of these diastereomers of HLNL.
Collapse
Affiliation(s)
- Rafea Naffa
- NZ Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand. .,Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
| | - Patrick J B Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Gillian Norris
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| |
Collapse
|
82
|
Noe JT, Mitchell RA. Tricarboxylic acid cycle metabolites in the control of macrophage activation and effector phenotypes. J Leukoc Biol 2019; 106:359-367. [DOI: 10.1002/jlb.3ru1218-496r] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Jordan T. Noe
- Department of Biochemistry and Molecular GeneticsUniversity of Louisville Louisville Kentucky USA
- J.G. Brown Cancer CenterUniversity of Louisville Louisville Kentucky USA
| | - Robert A. Mitchell
- Department of Biochemistry and Molecular GeneticsUniversity of Louisville Louisville Kentucky USA
- J.G. Brown Cancer CenterUniversity of Louisville Louisville Kentucky USA
- Department of Microbiology and ImmunologyUniversity of Louisville Louisville Kentucky USA
- Department of MedicineUniversity of Louisville Louisville Kentucky USA
| |
Collapse
|
83
|
Leon KE, Aird KM. Jumonji C Demethylases in Cellular Senescence. Genes (Basel) 2019; 10:genes10010033. [PMID: 30634491 PMCID: PMC6356615 DOI: 10.3390/genes10010033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
Abstract
Senescence is a stable cell cycle arrest that is either tumor suppressive or tumor promoting depending on context. Epigenetic changes such as histone methylation are known to affect both the induction and suppression of senescence by altering expression of genes that regulate the cell cycle and the senescence-associated secretory phenotype. A conserved group of proteins containing a Jumonji C (JmjC) domain alter chromatin state, and therefore gene expression, by demethylating histones. Here, we will discuss what is currently known about JmjC demethylases in the induction of senescence, and how these enzymes suppress senescence to contribute to tumorigenesis.
Collapse
Affiliation(s)
- Kelly E Leon
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| | - Katherine M Aird
- Department of Cellular & Molecular Physiology, Penn Stage College of Medicine, Hershey, PA 17033, USA.
| |
Collapse
|
84
|
Yonekura-Sakakibara K, Higashi Y, Nakabayashi R. The Origin and Evolution of Plant Flavonoid Metabolism. FRONTIERS IN PLANT SCIENCE 2019; 10:943. [PMID: 31428108 PMCID: PMC6688129 DOI: 10.3389/fpls.2019.00943] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/08/2019] [Indexed: 05/18/2023]
Abstract
During their evolution, plants have acquired the ability to produce a huge variety of compounds. Unlike the specialized metabolites that accumulate in limited numbers of species, flavonoids are widely distributed in the plant kingdom. Therefore, a detailed analysis of flavonoid metabolism in genomics and metabolomics is an ideal way to investigate how plants have developed their unique metabolic pathways during the process of evolution. More comprehensive and precise metabolite profiling integrated with genomic information are helpful to emerge unexpected gene functions and/or pathways. The distribution of flavonoids and their biosynthetic genes in the plant kingdom suggests that flavonoid biosynthetic pathways evolved through a series of steps. The enzymes that form the flavonoid scaffold structures probably first appeared by recruitment of enzymes from primary metabolic pathways, and later, enzymes that belong to superfamilies such as 2-oxoglutarate-dependent dioxygenase, cytochrome P450, and short-chain dehydrogenase/reductase modified and varied the structures. It is widely accepted that the first two enzymes in flavonoid biosynthesis, chalcone synthase, and chalcone isomerase, were derived from common ancestors with enzymes in lipid metabolism. Later enzymes acquired their function by gene duplication and the subsequent acquisition of new functions. In this review, we describe the recent progress in metabolomics technologies for flavonoids and the evolution of flavonoid skeleton biosynthetic enzymes to understand the complicate evolutionary traits of flavonoid metabolism in plant kingdom.
Collapse
|
85
|
Bundred JR, Hendrix E, Coleman ML. The emerging roles of ribosomal histidyl hydroxylases in cell biology, physiology and disease. Cell Mol Life Sci 2018; 75:4093-4105. [PMID: 30151692 PMCID: PMC6182338 DOI: 10.1007/s00018-018-2903-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 12/27/2022]
Abstract
Hydroxylation is a novel protein modification catalyzed by a family of oxygenases that depend on fundamental nutrients and metabolites for activity. Protein hydroxylases have been implicated in a variety of key cellular processes that play important roles in both normal homeostasis and pathogenesis. Here, in this review, we summarize the current literature on a highly conserved sub-family of oxygenases that catalyze protein histidyl hydroxylation. We discuss the evidence supporting the biochemical assignment of these emerging enzymes as ribosomal protein hydroxylases, and provide an overview of their role in immunology, bone development, and cancer.
Collapse
Affiliation(s)
- James R Bundred
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Eline Hendrix
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mathew L Coleman
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
86
|
Liu C, Zhao J, Liu J, Guo X, Rao D, Liu H, Zheng P, Sun J, Ma Y. Simultaneously improving the activity and thermostability of a new proline 4-hydroxylase by loop grafting and site-directed mutagenesis. Appl Microbiol Biotechnol 2018; 103:265-277. [DOI: 10.1007/s00253-018-9410-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023]
|
87
|
Biamonti G, Maita L, Montecucco A. The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism. Front Oncol 2018; 8:408. [PMID: 30319972 PMCID: PMC6168629 DOI: 10.3389/fonc.2018.00408] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing is a pervasive mechanism that molds the transcriptome to meet cell and organism needs. However, how this layer of gene expression regulation is coordinated with other aspects of the cell metabolism is still largely undefined. Glucose is the main energy and carbon source of the cell. Not surprisingly, its metabolism is finely tuned to satisfy growth requirements and in response to nutrient availability. A number of studies have begun to unveil the connections between glucose metabolism and splicing programs. Alternative splicing modulates the ratio between M1 and M2 isoforms of pyruvate kinase in this way determining the choice between aerobic glycolysis and complete glucose oxidation in the Krebs cycle. Reciprocally, intermediates in the Krebs cycle may impact splicing programs at different levels by modulating the activity of 2-oxoglutarate-dependent oxidases. In this review we discuss the molecular mechanisms that coordinate alternative splicing programs with glucose metabolism, two aspects with profound implications in human diseases.
Collapse
Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Lucia Maita
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | | |
Collapse
|
88
|
Kumar A, Davies TG, Itasaki N. Developmental abnormalities of the otic capsule and inner ear following application of prolyl-hydroxylase inhibitors in chick embryos. Birth Defects Res 2018; 110:1194-1204. [PMID: 30079508 DOI: 10.1002/bdr2.1375] [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: 03/15/2018] [Revised: 06/30/2018] [Accepted: 07/08/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND Naturally hypoxic conditions in amniote embryos play important roles in normal development. We previously showed that a hypoxic condition is required to produce a sufficient amount of neural crest cells (NCCs) during embryogenesis and that promoting a hypoxic response by prolyl-hydroxylase (PHD) inhibitors increases NCCs. Given that PHD inhibitors are considered as a potential treatment for anemia and ischemic diseases, we investigated the phenotypic effect of PHD inhibitors on embryonic development. METHODS Chick embryos were administered with PHD inhibitors prior to the induction of NCCs on day 1.5. Three main events relating to hypoxia, NCCs induction, vasculogenesis and chondrogenesis, were examined. RESULTS PHD inhibitors caused an increase of Sox10-positive NCCs in vivo. Vasculogenesis was promoted temporarily, although rapid vasculogenesis diminished the effect by day 5 in cephalic and pharyngeal regions. Studies on chondrogenesis at day 7 showed advanced development of the otic capsule, a cartilaginous structure encapsulating the inner ear. Analysis by X-ray micro-computed-tomography (μCT) revealed smaller otic capsule, suggesting premature differentiation. This in turn, deformed the developing semicircular canals within it. Other skeletal structures such as the palate and jaw were unaffected. The localized effect on the otic capsule was considered a result of the multiple effects from the hypoxic responses, increased NCCs and promoted chondrogenesis. CONCLUSION Given the wide range of clinical applications being considered for PHD inhibitors, this study provides crucial information to caution and guide use of PHD inhibitors when treating women of childbearing age.
Collapse
Affiliation(s)
- Akshay Kumar
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Thomas G Davies
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Nobue Itasaki
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
89
|
Recalcati S, Gammella E, Buratti P, Doni A, Anselmo A, Locati M, Cairo G. Macrophage ferroportin is essential for stromal cell proliferation in wound healing. Haematologica 2018; 104:47-58. [PMID: 30115660 PMCID: PMC6312033 DOI: 10.3324/haematol.2018.197517] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/14/2018] [Indexed: 01/01/2023] Open
Abstract
Iron recycling by macrophages is essential for erythropoiesis, but may also be relevant for iron redistribution to neighboring cells at the local tissue level. Using mice with iron retention in macrophages due to targeted inactivation of the iron exporter ferroportin, we investigated the role of macrophage iron release in hair follicle cycling and wound healing, a complex process leading to major clinical problems, if impaired. Genetic deletion of ferroportin in macrophages resulted in iron deficiency and decreased proliferation in epithelial cells, which consequently impaired hair follicle growth and caused transient alopecia. Hair loss was not related to systemic iron deficiency or anemia, thus indicating the necessity of local iron release from macrophages. Inactivation of macrophage ferroportin also led to delayed skin wound healing with defective granulation tissue formation and diminished fibroplasia. Iron retention in macrophages had no impact on the inflammatory processes accompanying wound healing, but affected stromal cell proliferation, blood and lymphatic vessel formation, and fibrogenesis. Our findings reveal that iron/ferroportin plays a largely underestimated role in macrophage trophic function in skin homeostasis and repair.
Collapse
Affiliation(s)
| | - Elena Gammella
- Department of Biomedical Sciences for Health, University of Milan
| | - Paolo Buratti
- Department of Biomedical Sciences for Health, University of Milan
| | - Andrea Doni
- Humanitas Clinical and Research Center, Rozzano
| | | | - Massimo Locati
- Humanitas Clinical and Research Center, Rozzano .,Department of Medical Biotechnologies and Translational Medicine, University of Milan, Italy
| | - Gaetano Cairo
- Department of Biomedical Sciences for Health, University of Milan
| |
Collapse
|
90
|
Ge J, Cui H, Xie N, Banerjee S, Guo S, Dubey S, Barnes S, Liu G. Glutaminolysis Promotes Collagen Translation and Stability via α-Ketoglutarate-mediated mTOR Activation and Proline Hydroxylation. Am J Respir Cell Mol Biol 2018; 58:378-390. [PMID: 29019707 DOI: 10.1165/rcmb.2017-0238oc] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Glutaminolysis is the metabolic process of glutamine, aberration of which has been implicated in several pathogeneses. Although we and others recently found a diversity of metabolic dysregulation in organ fibrosis, it is unknown if glutaminolysis regulates the profibrotic activities of myofibroblasts, the primary effector in this pathology. In this study, we found that lung myofibroblasts demonstrated significantly augmented glutaminolysis that was mediated by elevated glutaminase 1 (Gls1). Inhibition of glutaminolysis by specific Gls1 inhibitors CB-839 and BPTES as well as Gls1 siRNA blunted the expression of collagens but not that of fibronectin, elastin, or myofibroblastic marker smooth muscle actin-α. We found that glutaminolysis enhanced collagen translation and stability, which were mediated by glutaminolysis-dependent mTOR complex 1 activation and collagen proline hydroxylation, respectively. Furthermore, we found that the amount of the glutaminolytic end product α-ketoglutarate (α-KG) was increased in myofibroblasts. Similar to glutaminolysis, α-KG activated mTOR complex 1 and promoted the expression of collagens but not of fibronectin, elastin, or smooth muscle actin-α. α-KG also remarkably inhibited collagen degradation in fibroblasts. Taken together, our studies identified a previously unrecognized mechanism by which a major metabolic program regulates the exuberant production of collagens in myofibroblasts and suggest that glutaminolysis is a novel therapeutic target for treating organ fibrosis, including idiopathic pulmonary fibrosis.
Collapse
Affiliation(s)
- Jing Ge
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,2 Department of Geriatrics and Institute of Geriatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; and
| | - Huachun Cui
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Na Xie
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Sami Banerjee
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Sijia Guo
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,3 Department of Pulmonary, Allergy, and Critical Care Medicine, The Second Affiliated Hospital, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shubham Dubey
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Stephen Barnes
- 4 Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Gang Liu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| |
Collapse
|
91
|
Markolovic S, Zhuang Q, Wilkins SE, Eaton CD, Abboud MI, Katz MJ, McNeil HE, Leśniak RK, Hall C, Struwe WB, Konietzny R, Davis S, Yang M, Ge W, Benesch JLP, Kessler BM, Ratcliffe PJ, Cockman ME, Fischer R, Wappner P, Chowdhury R, Coleman ML, Schofield CJ. The Jumonji-C oxygenase JMJD7 catalyzes (3S)-lysyl hydroxylation of TRAFAC GTPases. Nat Chem Biol 2018; 14:688-695. [PMID: 29915238 PMCID: PMC6027965 DOI: 10.1038/s41589-018-0071-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/03/2018] [Indexed: 11/14/2022]
Abstract
Biochemical, structural and cellular studies reveal Jumonji-C (JmjC) domain-containing 7 (JMJD7) to be a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes (3S)-lysyl hydroxylation. Crystallographic analyses reveal JMJD7 to be more closely related to the JmjC hydroxylases than to the JmjC demethylases. Biophysical and mutation studies show that JMJD7 has a unique dimerization mode, with interactions between monomers involving both N- and C-terminal regions and disulfide bond formation. A proteomic approach identifies two related members of the translation factor (TRAFAC) family of GTPases, developmentally regulated GTP-binding proteins 1 and 2 (DRG1/2), as activity-dependent JMJD7 interactors. Mass spectrometric analyses demonstrate that JMJD7 catalyzes Fe(II)- and 2OG-dependent hydroxylation of a highly conserved lysine residue in DRG1/2; amino-acid analyses reveal that JMJD7 catalyzes (3S)-lysyl hydroxylation. The functional assignment of JMJD7 will enable future studies to define the role of DRG hydroxylation in cell growth and disease.
Collapse
Affiliation(s)
- Suzana Markolovic
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Qinqin Zhuang
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sarah E Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte D Eaton
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Helen E McNeil
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Robert K Leśniak
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Charlotte Hall
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Weston B Struwe
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Simon Davis
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Ming Yang
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Peter J Ratcliffe
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Matthew E Cockman
- Target Discovery Institute, University of Oxford, Oxford, UK
- The Francis Crick Institute, London, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | | | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Clark Center, Stanford, CA, USA.
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | | |
Collapse
|
92
|
Niu X, Ah-Fong AMV, Lopez LA, Judelson HS. Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development. PLoS One 2018; 13:e0198186. [PMID: 29897992 PMCID: PMC5999078 DOI: 10.1371/journal.pone.0198186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/14/2018] [Indexed: 11/19/2022] Open
Abstract
Sexual reproduction remains an understudied feature of oomycete biology. To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.
Collapse
Affiliation(s)
- Xiaofan Niu
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Audrey M. V. Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Lilianna A. Lopez
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America
| |
Collapse
|
93
|
Bonnici J, Tumber A, Kawamura A, Schofield CJ. Inhibitors of both the N-methyl lysyl- and arginyl-demethylase activities of the JmjC oxygenases. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170071. [PMID: 29685975 PMCID: PMC5915715 DOI: 10.1098/rstb.2017.0071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
The Jumonji C (JmjC) family of 2-oxoglutarate (2OG)-dependent oxygenases have established roles in the regulation of transcription via the catalysis of demethylation of Nε-methylated lysine residues in histone tails, especially the N-terminal tail of histone H3. Most human JmjC Nɛ -methyl lysine demethylases (KDMs) are complex enzymes, with 'reader domains' in addition to their catalytic domains. Recent biochemical evidence has shown that some, but not all, JmjC KDMs also have Nω-methyl arginyl demethylase (RDM) activity. JmjC KDM activity has been linked to multiple cancers and some JmjC proteins are therapeutic targets. It is, therefore, important to test not only whether compounds in development inhibit the KDM activity of targeted JmjC demethylases, but also whether they inhibit other activities of these proteins. Here we report biochemical studies on the potential dual inhibition of JmjC KDM and RDM activities using a model JmjC demethylase, KDM4E (JMJD2E). The results reveal that all of the tested compounds inhibit both the KDM and RDM activities, raising questions about the in vivo effects of the inhibitors.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
Collapse
Affiliation(s)
- Joanna Bonnici
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Anthony Tumber
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| |
Collapse
|
94
|
Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain – A fragment based approach. Bioorg Med Chem Lett 2018; 28:1708-1713. [DOI: 10.1016/j.bmcl.2018.04.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
|
95
|
Herr CQ, Hausinger RP. Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases. Trends Biochem Sci 2018; 43:517-532. [PMID: 29709390 DOI: 10.1016/j.tibs.2018.04.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/21/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
Since their discovery in the 1960s, the family of Fe(II)/2-oxoglutarate-dependent oxygenases has undergone a tremendous expansion to include enzymes catalyzing a vast diversity of biologically important reactions. Recent examples highlight roles in controlling chromatin modification, transcription, mRNA demethylation, and mRNA splicing. Others generate modifications in tRNA, translation factors, ribosomes, and other proteins. Thus, oxygenases affect all components of molecular biology's central dogma, in which information flows from DNA to RNA to proteins. These enzymes also function in biosynthesis and catabolism of cellular metabolites, including antibiotics and signaling molecules. Due to their critical importance, ongoing efforts have targeted family members for the development of specific therapeutics. This review provides a general overview of recently characterized oxygenase reactions and their key biological roles.
Collapse
Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
96
|
Chicco AJ, Le CH, Gnaiger E, Dreyer HC, Muyskens JB, D'Alessandro A, Nemkov T, Hocker AD, Prenni JE, Wolfe LM, Sindt NM, Lovering AT, Subudhi AW, Roach RC. Adaptive remodeling of skeletal muscle energy metabolism in high-altitude hypoxia: Lessons from AltitudeOmics. J Biol Chem 2018. [PMID: 29540485 DOI: 10.1074/jbc.ra117.000470] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Metabolic responses to hypoxia play important roles in cell survival strategies and disease pathogenesis in humans. However, the homeostatic adjustments that balance changes in energy supply and demand to maintain organismal function under chronic low oxygen conditions remain incompletely understood, making it difficult to distinguish adaptive from maladaptive responses in hypoxia-related pathologies. We integrated metabolomic and proteomic profiling with mitochondrial respirometry and blood gas analyses to comprehensively define the physiological responses of skeletal muscle energy metabolism to 16 days of high-altitude hypoxia (5260 m) in healthy volunteers from the AltitudeOmics project. In contrast to the view that hypoxia down-regulates aerobic metabolism, results show that mitochondria play a central role in muscle hypoxia adaptation by supporting higher resting phosphorylation potential and enhancing the efficiency of long-chain acylcarnitine oxidation. This directs increases in muscle glucose toward pentose phosphate and one-carbon metabolism pathways that support cytosolic redox balance and help mitigate the effects of increased protein and purine nucleotide catabolism in hypoxia. Muscle accumulation of free amino acids favor these adjustments by coordinating cytosolic and mitochondrial pathways to rid the cell of excess nitrogen, but might ultimately limit muscle oxidative capacity in vivo Collectively, these studies illustrate how an integration of aerobic and anaerobic metabolism is required for physiological hypoxia adaptation in skeletal muscle, and highlight protein catabolism and allosteric regulation as unexpected orchestrators of metabolic remodeling in this context. These findings have important implications for the management of hypoxia-related diseases and other conditions associated with chronic catabolic stress.
Collapse
Affiliation(s)
- Adam J Chicco
- From the Departments of Biomedical Sciences, .,Cell and Molecular Biology, and
| | | | - Erich Gnaiger
- the Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Hans C Dreyer
- the Department of Human Physiology, University of Oregon, Eugene, Oregon 97403-1240, and
| | - Jonathan B Muyskens
- the Department of Human Physiology, University of Oregon, Eugene, Oregon 97403-1240, and
| | | | - Travis Nemkov
- the Department of Biochemistry and Molecular Genetics and
| | - Austin D Hocker
- the Department of Human Physiology, University of Oregon, Eugene, Oregon 97403-1240, and
| | - Jessica E Prenni
- Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Lisa M Wolfe
- Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Nathan M Sindt
- Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Andrew T Lovering
- the Department of Human Physiology, University of Oregon, Eugene, Oregon 97403-1240, and
| | - Andrew W Subudhi
- the Department of Biology, University of Colorado, Colorado Springs, Colorado 80918
| | - Robert C Roach
- Altitude Research Center, University of Colorado-Anschutz Medical Campus, Aurora 80045, Colorado 80045
| |
Collapse
|
97
|
Jia B, Tang K, Chun BH, Jeon CO. Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa. Biochim Biophys Acta Gen Subj 2017; 1861:2922-2933. [DOI: 10.1016/j.bbagen.2017.08.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/22/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022]
|
98
|
Schnicker NJ, Razzaghi M, Guha Thakurta S, Chakravarthy S, Dey M. Bacillus anthracis Prolyl 4-Hydroxylase Interacts with and Modifies Elongation Factor Tu. Biochemistry 2017; 56:5771-5785. [PMID: 28981257 DOI: 10.1021/acs.biochem.7b00601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl hydroxylation is a very common post-translational modification and plays many roles in eukaryotes such as collagen stabilization, hypoxia sensing, and controlling protein transcription and translation. There is a growing body of evidence that suggests that prokaryotes contain prolyl 4-hydroxylases (P4Hs) homologous to the hypoxia-inducible factor (HIF) prolyl hydroxylase domain (PHD) enzymes that act on elongation factor Tu (EFTu) and are likely involved in the regulation of bacterial translation. Recent biochemical and structural studies with a PHD from Pseudomonas putida (PPHD) determined that it forms a complex with EFTu and hydroxylates a prolyl residue of EFTu. Moreover, while animal, plant, and viral P4Hs act on peptidyl proline, most prokaryotic P4Hs have been known to target free l-proline; the exceptions include PPHD and a P4H from Bacillus anthracis (BaP4H) that modifies collagen-like proline-rich peptides. Here we use biophysical and mass spectrometric methods to demonstrate that BaP4H recognizes full-length BaEFTu and a BaEFTu 9-mer peptide for site-specific proline hydroxylation. Using size-exclusion chromatography coupled small-angle X-ray scattering (SEC-SAXS) and binding studies, we determined that BaP4H forms a 1:1 heterodimeric complex with BaEFTu. The SEC-SAXS studies reveal dissociation of BaP4H dimeric subunits upon interaction with BaEFTu. While BaP4H is unusual within bacteria in that it is structurally and functionally similar to the animal PHDs and collagen P4Hs, respectively, this work provides further evidence of its promiscuous substrate recognition. It is possible that the enzyme might have evolved to hydroxylate a universally conserved protein in prokaryotes, similar to the PHDs, and implies a functional role in B. anthracis.
Collapse
Affiliation(s)
- Nicholas J Schnicker
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mortezaali Razzaghi
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Sanjukta Guha Thakurta
- Department of Cell Biology, Harvard Medical School , 240 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| |
Collapse
|
99
|
Abstract
The EGLN (also called PHD) prolyl hydroxylase enzymes and their canonical targets, the HIFα subunits, represent the core of an ancient oxygen-monitoring machinery used by metazoans. In this review, we highlight recent progress in understanding the overlapping versus specific roles of EGLN enzymes and HIF isoforms and discuss how feedback loops based on recently identified noncoding RNAs introduce additional layers of complexity to the hypoxic response. Based on novel interactions identified upstream and downstream of EGLNs, an integrated network connecting oxygen-sensing functions to metabolic and signaling pathways is gradually emerging with broad therapeutic implications.
Collapse
Affiliation(s)
- Mircea Ivan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - William G Kaelin
- Howard Hughes Medical Institute, Boston, MA 02215, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| |
Collapse
|
100
|
Yao R, Zhao Y, Liu T, Huang C, Xu S, Sui Z, Luo J, Kong L. Identification and functional characterization of a p-coumaroyl CoA 2'-hydroxylase involved in the biosynthesis of coumarin skeleton from Peucedanum praeruptorum Dunn. PLANT MOLECULAR BIOLOGY 2017; 95:199-213. [PMID: 28822035 DOI: 10.1007/s11103-017-0650-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/09/2017] [Indexed: 06/07/2023]
Abstract
A p-coumaroyl CoA 2'-hydroxylase responsible for the formation of coumarin lactone ring was identified from Peucedanum praeruptorum Dunn and functionally characterized in vitro. Coumarins are important plant secondary metabolites with a variety of biological activities. Ortho-hydroxylation of cinnamates leads to the formation of coumarin lactone ring and is generally thought to be a key step in coumarin biosynthesis. However, ortho-hydroxylases, especially p-coumaroyl CoA 2'-hydroxylase (C2'H) responsible for the biosynthesis of the most common coumarin skeleton, have received insufficient attention. Here, a putative ortho-hydroxylase PpC2'H was isolated from P. praeruptorum Dunn, a traditional Chinese medicinal herb rich in coumarins. Expression profile indicated that PpC2'H exhibited the highest transcript level in roots and could be up-regulated by MeJA elicitation. Subcellular localization of PpC2'H was demonstrated to be cytosol in planta. In order to functionally characterize PpC2'H, the purified recombinant protein was incubated with various potential substrates. HPLC-ESI-MS analysis indicated that PpC2'H catalyzed the conversion of p-coumaroyl CoA into hydroxylated intermediate, which then underwent spontaneous lactonization to generate umbelliferone. Our data also showed that light would promote the spontaneous process. In addition, based on homology modeling and site-directed mutagenesis, amino acid residues Phe-130, Lys-141, Asn-207, His-224, Asp-226, His-282 and Phe-298 were verified essential for enzymatic activity. These findings provide insight into structure-function relationship of this pivotal ortho-hydroxylase and also contribute to elucidating the biosynthetic mechanism of coumarin skeleton.
Collapse
MESH Headings
- Amino Acid Sequence
- Apiaceae/enzymology
- Biosynthetic Pathways/genetics
- Chromatography, High Pressure Liquid
- Coumarins/chemistry
- Coumarins/metabolism
- DNA, Complementary/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/radiation effects
- Kinetics
- Light
- Mixed Function Oxygenases/chemistry
- Mixed Function Oxygenases/metabolism
- Models, Molecular
- Mutagenesis, Site-Directed
- Organ Specificity/genetics
- Organ Specificity/radiation effects
- Phylogeny
- Plant Proteins/chemistry
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Protoplasts/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Spectrometry, Mass, Electrospray Ionization
- Structural Homology, Protein
- Subcellular Fractions/enzymology
- Transcriptome/genetics
- Transcriptome/radiation effects
Collapse
Affiliation(s)
- Ruolan Yao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Yucheng Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Tingting Liu
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Chuanlong Huang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, People's Republic of China
| | - Ziwei Sui
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China
| | - Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China.
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, People's Republic of China.
| |
Collapse
|