1
|
Yao Z, Jiao Q, Du X, Jia F, Chen X, Yan C, Jiang H. Ferroptosis in Parkinson's disease -- The iron-related degenerative disease. Ageing Res Rev 2024; 101:102477. [PMID: 39218077 DOI: 10.1016/j.arr.2024.102477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/16/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Parkinson's disease (PD) is a prevalent and advancing age-related neurodegenerative disorder, distinguished by the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Iron regional deposit in SNpc is a significant pathological characteristic of PD. Brain iron homeostasis is precisely regulated by iron metabolism related proteins, whereas disorder of these proteins can damage neurons and glial cells in the brain. Additionally, growing studies have reported iron metabolism related proteins are involved in the ferroptosis progression in PD. However, the effect of these proteins in the ferroptosis of PD has not been systematically summarized. This review focuses on the roles of iron metabolism related proteins in the ferroptosis of PD. Finally, we put forward the iron early diagnosis according to the observation of iron deposits in the brain and showed the recent advances in iron chelation therapy in PD.
Collapse
Affiliation(s)
- Zhengyang Yao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Qian Jiao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Xixun Du
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Fengju Jia
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Xi Chen
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Chunling Yan
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines: Physiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Hong Jiang
- Qingdao Key Laboratory of Neurorehabilitation, University of Health and Rehabilitation Sciences, Qingdao, 266113, China.
| |
Collapse
|
2
|
Babić Leko M, Langer Horvat L, Španić Popovački E, Zubčić K, Hof PR, Šimić G. Metals in Alzheimer's Disease. Biomedicines 2023; 11:1161. [PMID: 37189779 PMCID: PMC10136077 DOI: 10.3390/biomedicines11041161] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
The role of metals in the pathogenesis of Alzheimer's disease (AD) is still debated. Although previous research has linked changes in essential metal homeostasis and exposure to environmental heavy metals to the pathogenesis of AD, more research is needed to determine the relationship between metals and AD. In this review, we included human studies that (1) compared the metal concentrations between AD patients and healthy controls, (2) correlated concentrations of AD cerebrospinal fluid (CSF) biomarkers with metal concentrations, and (3) used Mendelian randomization (MR) to assess the potential metal contributions to AD risk. Although many studies have examined various metals in dementia patients, understanding the dynamics of metals in these patients remains difficult due to considerable inconsistencies among the results of individual studies. The most consistent findings were for Zn and Cu, with most studies observing a decrease in Zn levels and an increase in Cu levels in AD patients. However, several studies found no such relation. Because few studies have compared metal levels with biomarker levels in the CSF of AD patients, more research of this type is required. Given that MR is revolutionizing epidemiologic research, additional MR studies that include participants from diverse ethnic backgrounds to assess the causal relationship between metals and AD risk are critical.
Collapse
Affiliation(s)
- Mirjana Babić Leko
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Lea Langer Horvat
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Ena Španić Popovački
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Klara Zubčić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Patrick R. Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute and Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| |
Collapse
|
3
|
Khan MA, Mohammad T, Malik A, Hassan MI, Domashevskiy AV. Iron response elements (IREs)-mRNA of Alzheimer's amyloid precursor protein binding to iron regulatory protein (IRP1): a combined molecular docking and spectroscopic approach. Sci Rep 2023; 13:5073. [PMID: 36977734 PMCID: PMC10050399 DOI: 10.1038/s41598-023-32073-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP IRE mRNA∙IRP1 reveals that 11 residues are involved in hydrogen bonding as the main driving force for the interaction. Fluorescence binding results revealed a strong interaction between APP IRE mRNA and IRP1 with a binding affinity and an average binding sites of 31.3 × 106 M-1 and 1.0, respectively. Addition of Fe2+(anaerobic) showed a decreased (3.3-fold) binding affinity of APP mRNA∙IRP1. Further, thermodynamic parameters of APP mRNA∙IRP1 interactions were an enthalpy-driven and entropy-favored event, with a large negative ΔH (-25.7 ± 2.5 kJ/mol) and a positive ΔS (65.0 ± 3.7 J/mol·K). A negative ΔH value for the complex formation suggested the contribution of hydrogen bonds and van der Waals forces. The addition of iron increased the enthalpic contribution by 38% and decreased the entropic influence by 97%. Furthermore, the stopped-flow kinetics of APP IRE mRNA∙IRP1 also confirmed the complex formation, having the rate of association (kon) and the rate of dissociation (koff) as 341 μM-1 s-1, and 11 s-1, respectively. The addition of Fe2+ has decreased the rate of association (kon) by ~ three-fold, whereas the rate of dissociation (koff) has increased by ~ two-fold. The activation energy for APP mRNA∙IRP1 complex was 52.5 ± 2.1 kJ/mol. The addition of Fe2+ changed appreciably the activation energy for the binding of APP mRNA with IRP1. Moreover, circular dichroism spectroscopy has confirmed further the APP mRNA∙IRP1 complex formation and IRP1 secondary structure change with the addition of APP mRNA. In the interaction between APP mRNA and IRP1, iron promotes structural changes in the APP IRE mRNA∙IRP1 complexes by changing the number of hydrogen bonds and promoting a conformational change in the IRP1 structure when it is bound to the APP IRE mRNA. It further illustrates how IRE stem-loop structure influences selectively the thermodynamics and kinetics of these protein-RNA interactions.
Collapse
Affiliation(s)
- Mateen A Khan
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia.
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Ajamaluddin Malik
- Department of Biochemistry, Protein Research Laboratory, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Artem V Domashevskiy
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York, NY, 10019, USA
| |
Collapse
|
4
|
QU L, HE X, TANG Q, FAN X, LIU J, LIN A. Iron metabolism, ferroptosis, and lncRNA in cancer: knowns and unknowns. J Zhejiang Univ Sci B 2022; 23:844-862. [PMID: 36226538 PMCID: PMC9561407 DOI: 10.1631/jzus.b2200194] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cancer cells undergo substantial metabolic alterations to sustain increased energy supply and uncontrolled proliferation. As an essential trace element, iron is vital for many biological processes. Evidence has revealed that cancer cells deploy various mechanisms to elevate the cellular iron concentration to accelerate proliferation. Ferroptosis, a form of cell death caused by iron-catalyzed excessive peroxidation of polyunsaturated fatty acids (PUFAs), is a promising therapeutic target for therapy-resistant cancers. Previous studies have reported that long noncoding RNA (lncRNA) is a group of critical regulators involved in modulating cell metabolism, proliferation, apoptosis, and ferroptosis. In this review, we summarize the associations among iron metabolism, ferroptosis, and ferroptosis-related lncRNA in tumorigenesis. This information will help deepen understanding of the role of lncRNA in iron metabolism and raise the possibility of targeting lncRNA and ferroptosis in cancer combination therapy.
Collapse
Affiliation(s)
- Lei QU
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Xinyu HE
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Qian TANG
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining314400, China,Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou310006, China,College of Medicine and Veterinary Medicine, the University of Edinburgh, EdinburghEH16 4SB, UK,Biomedical and Health Translational Research Center of Zhejiang Province, Haining314400, China
| | - Xiao FAN
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Jian LIU
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining314400, China,Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou310006, China,College of Medicine and Veterinary Medicine, the University of Edinburgh, EdinburghEH16 4SB, UK,Biomedical and Health Translational Research Center of Zhejiang Province, Haining314400, China,Jian LIU,
| | - Aifu LIN
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China,Breast Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310003, China,International School of Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu322000, China,ZJU-QILU Joint Research Institute, Hangzhou310058, China,Aifu LIN,
| |
Collapse
|
5
|
Xu J, Cotruvo JA. Reconsidering the czcD (NiCo) Riboswitch as an Iron Riboswitch. ACS BIO & MED CHEM AU 2022; 2:376-385. [PMID: 35996475 PMCID: PMC9389577 DOI: 10.1021/acsbiomedchemau.1c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
Recent work has proposed
a new mechanism of bacterial iron regulation:
riboswitches that undergo a conformational change in response to FeII. The czcD (NiCo) riboswitch was initially
proposed to be specific for NiII and CoII, but
we recently showed via a czcD-based fluorescent sensor
that FeII is also a plausible physiological ligand for
this riboswitch class. Here, we provide direct evidence that this
riboswitch class responds to FeII. Isothermal titration
calorimetry studies of the native czcD riboswitches
from three organisms show no response to MnII, a weak response
to ZnII, and similar dissociation constants (∼1
μM) and conformational responses for FeII, CoII, and NiII. Only the iron response is in the physiological
concentration regime; the riboswitches’ responses to CoII, NiII, and ZnII require 103-, 105-, and 106-fold higher “free”
metal ion concentrations, respectively, than the typical availability
of those metal ions in cells. By contrast, the “Sensei”
RNA, recently claimed to be an iron-specific riboswitch, exhibits
no response to FeII. Our results demonstrate that iron
responsiveness is a conserved property of czcD riboswitches
and clarify that this is the only family of iron-responsive riboswitch
identified to date, setting the stage for characterization of their
physiological function.
Collapse
Affiliation(s)
- Jiansong Xu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Joseph A. Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
6
|
Rethinking IRPs/IRE system in neurodegenerative disorders: Looking beyond iron metabolism. Ageing Res Rev 2022; 73:101511. [PMID: 34767973 DOI: 10.1016/j.arr.2021.101511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022]
Abstract
Iron regulatory proteins (IRPs) and iron regulatory element (IRE) systems are well known in the progression of neurodegenerative disorders by regulating iron related proteins. IRPs are also regulated by iron homeostasis. However, an increasing number of studies have suggested a close relationship between the IRPs/IRE system and non-iron-related neurodegenerative disorders. In this paper, we reviewed that the IRPs/IRE system is not only controlled by iron ions, but also regulated by such factors as post-translational modification, oxygen, nitric oxide (NO), heme, interleukin-1 (IL-1), and metal ions. In addition, by regulating the transcription of non-iron related proteins, the IRPs/IRE system functioned in oxidative metabolism, cell cycle regulation, abnormal proteins aggregation, and neuroinflammation. Finally, by emphasizing the multiple regulations of IRPs/IRE system and its potential relationship with non-iron metabolic neurodegenerative disorders, we provided new strategies for disease treatment targeting IRPs/IRE system.
Collapse
|
7
|
Manglass LM, Wintenberg M, Vogel C, Blenner M, Martinez NE. Accumulation of radio-iron and plutonium, alone and in combination, in Pseudomonas putidagrown in liquid cultures. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2021; 41:1199-1212. [PMID: 34644681 DOI: 10.1088/1361-6498/ac2f86] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
The impact of low doses of ionising radiation on biological and environmental systems have been historically difficult to study. Modern biological tools have provided new methods for studying these mechanisms but applying these tools to a dose-response relationship may require refinement of dosimetric techniques that incorporate a detailed understand of radionuclide accumulation in biological cells, particularly when assessing the impact of low doses of ionising radiation. In this workPseudomonas putida (KT2440) grown in liquid culture was exposed to low dose rates (10-20 mGy d-1) of239Pu and55Fe, both alone and in combination, for a period of 20 days, and the accumulation of239Pu and55Fe in cell pellets was analysed via liquid scintillation counting. The study also considered of cells grown with239Pu and stable Fe (primarily56Fe). In addition to the analysis of cell pellet and media samples, this work includes analysis of the radiological content of ribonucleic acid extraction samples to examine uptake of radionuclides. Results indicate that239Pu inhibited the uptake of55Fe, and that the presence of stable and radioactive isotopes of Fe in cultures may promote pathways for Fe accumulation that are used by239Pu. The work herein provides foundational insight into future dosimetric models for our work with environmental bacteria.
Collapse
Affiliation(s)
- Lisa M Manglass
- Department of Environmental Engineering and Earth Science, Clemson University, Clemson, SC, United States of America
- Department of Physics and Engineering, Francis Marion University, Florence, SC, United States of America
| | - Molly Wintenberg
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
| | - Charlotte Vogel
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, United States of America
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States of America
| | - Nicole E Martinez
- Department of Environmental Engineering and Earth Science, Clemson University, Clemson, SC, United States of America
| |
Collapse
|
8
|
Chan D, Feng C, England WE, Wyman D, Flynn R, Wang X, Shi Y, Mortazavi A, Spitale R. Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res 2021; 49:11868-11882. [PMID: 34634799 PMCID: PMC8599799 DOI: 10.1093/nar/gkab885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
RNA molecules can fold into complex structures and interact with trans-acting factors to control their biology. Recent methods have been focused on developing novel tools to measure RNA structure transcriptome-wide, but their utility to study and predict RNA-protein interactions or RNA processing has been limited thus far. Here, we extend these studies with the first transcriptome-wide mapping method for cataloging RNA solvent accessibility, icLASER. By combining solvent accessibility (icLASER) with RNA flexibility (icSHAPE) data, we efficiently predict RNA-protein interactions transcriptome-wide and catalog RNA polyadenylation sites by RNA structure alone. These studies showcase the power of designing novel chemical approaches to studying RNA biology. Further, our study exemplifies merging complementary methods to measure RNA structure inside cells and its utility for predicting transcriptome-wide interactions that are critical for control of and regulation by RNA structure. We envision such approaches can be applied to studying different cell types or cells under varying conditions, using RNA structure and footprinting to characterize cellular interactions and processing involving RNA.
Collapse
Affiliation(s)
- Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Chao Feng
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
| | - Dana Wyman
- Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA 92697, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children’s Hospital, Boston, MA, USA and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Xiuye Wang
- Department Microbiology and Molecular Genetics, University of California, Irvine. Irvine, CA 92697, USA
| | - Yongsheng Shi
- Department Microbiology and Molecular Genetics, University of California, Irvine. Irvine, CA 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine. Irvine, CA 92697, USA
| |
Collapse
|
9
|
Abstract
Significance: Iron is an essential element required for growth and proper functioning of the body. However, an excess of labile ferrous iron increases the risk of oxidative stress-induced injury due to the high reactivity of the unpaired reactive electrons of both ferrous iron and oxygen. This high reactivity can be exemplified in the outside world by one of its consequences, rust formation. In cells, this redox-active iron is involved in the formation of lipid radicals. Recent Advances: Defect or insufficient membrane-protective mechanisms can result in iron-catalyzed excessive lipid peroxidation and subsequent cell death, now conceptualized as ferroptosis. Growing reports propose the detrimental role of iron and ferroptosis in many experimental disease models such as ischemia-reperfusion, acute and chronic organ injuries. Critical Issues: This review first provides a snapshot of iron metabolism, followed by a brief introduction of the molecular mechanisms of ferroptosis, as an iron-dependent lipid peroxidation-driven mode of cell death. Upon describing how iron dysbiosis affects ferroptosis induction, we elaborate on the detrimental role of the iron-ferroptosis axis in several diseases. Future Directions: Despite compelling findings suggesting a role of ferroptosis in experimental animal models, the exact contribution of ferroptosis in human contexts still needs further investigation. Development of reliable ferroptosis biomarkers will be an important step in characterizing ferroptosis in human disease. This can provide therapeutic opportunities aiming at targeting ferroptosis in human diseases. Antioxid. Redox Signal. 35, 487-509.
Collapse
Affiliation(s)
- Behrouz Hassannia
- VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Samya Van Coillie
- VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Tom Vanden Berghe
- VIB-UGent Center for Inflammation Research (IRC), Ghent, Belgium.,Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
10
|
Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
Collapse
Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| |
Collapse
|
11
|
Wang B, Thompson MS, Adkins KM. Characteristics of the Iron-responsive Element (IRE) Stems in the Untranslated Regions of Animal mRNAs. Open Biochem J 2021. [DOI: 10.2174/1874091x02115010026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Iron-responsive Elements (IREs) are hairpin structures located in the 5’ or 3’ untranslated region of some animal mRNAs. IREs have a highly conserved terminal loop and a UGC/C or C bulge five bases upstream of the terminal loop, which divides the hairpin stem into an upper stem and a lower stem.
Objective:
The objective of this study was to investigate the base-pair composition of the upper and lower stems of IREs to determine whether they are highly conserved among mRNAs from different genes.
Methods:
The mRNA sequences of six 5’IREs and five 3’IREs from several animal species were retrieved from the National Center for Biotechnology Information. The folding free energy of each IRE mRNA sequence was predicted using the RNAfold WebServer.
Results:
We found that the upper and lower stems of IREs are not highly conserved among the mRNAs of different genes. There are no statistically significant differences in the IRE structures or folding free energies between mammalian and non-mammalian species relative to either the ferritin heavy chain 5’IRE or ferroportin 5’IRE. There are no overall significant differences in the folding free energies between UGC/C-containing 5’IREs and C-bulge-containing 5’IREs, or between 5’IREs and 3’IREs.
Conclusion:
Further studies are needed to investigate whether the variations in IRE stem composition are responsible for fine-tuning the IRE/Iron-Regulatory Protein interactions among different mRNAs to maintain the balance of cellular iron metabolism, and to identify whether evolutionary processes drive the base-pair composition of the upper and lower stems of IREs toward any particular configuration.
Collapse
|
12
|
Khan MA, Domashevskiy AV. Iron enhances the binding rates and translational efficiency of iron responsive elements (IREs) mRNA with initiation factor eIF4F. PLoS One 2021; 16:e0250374. [PMID: 33882101 PMCID: PMC8059860 DOI: 10.1371/journal.pone.0250374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/26/2021] [Indexed: 12/14/2022] Open
Abstract
Interaction of iron responsive elements (IRE) mRNA with the translational machinery is an early step critical in the initiation of protein synthesis. To investigate the binding specificity of IRE mRNA for eIF4F, kinetic rates for the eIF4F·IRE RNA interactions were determined and correlated with the translational efficiency. The observed rate of eIF4F·FRT IRE RNA interactions was 2-fold greater as compared to eIF4F·ACO2 IRE RNA binding. Addition of iron enhanced the association rates and lowered the dissociation rates for the eIF4F binding to both IRE RNAs, with having higher preferential binding to the FRT IRE RNA. The binding rates of both eIF4F·IRE RNA complexes correlated with the enhancement of protein synthesis in vitro. Presence of iron and eIF4F in the depleted WGE significantly enhanced translation for both IRE RNAs. This suggests that iron promotes translation by enhancing the binding rates of the eIF4F∙IRE RNA complex. eIF4F·IRE RNA binding is temperature-dependent; raising the temperature from 5 to 25°C, enhanced the binding rates of eIF4F·FRT IRE (4-fold) and eIF4F·ACO2 IRE (5-fold). Presence of Fe2+ caused reduction in the activation energy for the binding of FRT IRE and ACO2 IRE to eIF4F, suggesting a more stable platform for initiating protein synthesis. In the presence of iron, lowered energy barrier has leads to the faster association rate and slower rate of dissociation for the protein-RNA complex, thus favoring efficient protein synthesis. Our results correlate well with the observed translational efficiency of IRE RNA, thereby suggesting that the presence of iron leads to a rapid, favorable, and stable complex formation that directs regulatory system to respond efficiently to cellular iron levels.
Collapse
Affiliation(s)
- Mateen A. Khan
- Department of Life Science, College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia
- * E-mail:
| | - Artem V. Domashevskiy
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York, NY, United States of America
| |
Collapse
|
13
|
Garza KR, Clarke SL, Ho YH, Bruss MD, Vasanthakumar A, Anderson SA, Eisenstein RS. Differential translational control of 5' IRE-containing mRNA in response to dietary iron deficiency and acute iron overload. Metallomics 2020; 12:2186-2198. [PMID: 33325950 DOI: 10.1039/d0mt00192a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron regulatory proteins (IRPs) are iron-responsive RNA binding proteins that dictate changes in cellular iron metabolism in animal cells by controlling the fate of mRNAs containing iron responsive elements (IREs). IRPs have broader physiological roles as some targeted mRNAs encode proteins with functions beyond iron metabolism suggesting hierarchical regulation of IRP-targeted mRNAs. We observe that the translational regulation of IRP-targeted mRNAs encoding iron storage (L- and H-ferritins) and export (ferroportin) proteins have different set-points of iron responsiveness compared to that for the TCA cycle enzyme mitochondrial aconitase. The ferritins and ferroportin mRNA were largely translationally repressed in the liver of rats fed a normal diet whereas mitochondrial aconitase mRNA is primarily polysome bound. Consequently, acute iron overload increases polysome association of H- and L-ferritin and ferroportin mRNAs while mitochondrial aconitase mRNA showed little stimulation. Conversely, mitochondrial aconitase mRNA is most responsive in iron deficiency. These differences in regulation were associated with a faster off-rate of IRP1 for the IRE of mitochondrial aconitase in comparison to that of L-ferritin. Thus, hierarchical control of mRNA translation by IRPs involves selective control of cellular functions acting at different states of cellular iron status and that are critical for adaptations to iron deficiency or prevention of iron toxicity.
Collapse
Affiliation(s)
- Kerry R Garza
- University of Wisconsin-Madison, Department of Nutritional Sciences, 1415 Linden Drive, Madison, WI 53706, USA.
| | | | | | | | | | | | | |
Collapse
|
14
|
Khan MA, Malik A, Domashevskiy AV, San A, Khan JM. Interaction of ferritin iron responsive element (IRE) mRNA with translation initiation factor eIF4F. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 243:118776. [PMID: 32829157 DOI: 10.1016/j.saa.2020.118776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 07/26/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
The interaction of ferritin iron responsive element (IRE) mRNA with eIF4F was examined by fluorescence and circular dichroism spectroscopy. Fluorescence quenching data indicated that eIF4F contains one high affinity binding site for ferritin IRE RNA. The Scatchard analysis revealed strong binding affinity (Ka = 11.1 × 107 M-1) and binding capacity (n = 1.0) between IRE RNA and eIF4F. The binding affinity of IRE RNA for eIF4F decreased (~4-fold) as temperature increased (from 5 °C to 30 °C). The van't Hoff analysis revealed that IRE RNA binding to eIF4F is enthalpy-driven (ΔH = -47.1 ± 3.4 kJ/mol) and entropy-opposed (ΔS = -30.1 ± 1.5 J/mol/K). The addition of iron increased the enthalpic, while decreasing the entropic contribution towards the eIF4F•IRE RNA complex, resulting in favorable free energy (ΔG = -49.8 ± 2.8 kJ/mol). Thermodynamic values and ionic strength data suggest that the presence of iron increases hydrogen bonding and decreases hydrophobic interactions, leading to formation of a more stable complex. The interaction of IRE RNA with eIF4F at higher concentrations produced significant changes in the secondary structure of the protein, as revealed from the far-UV CD results, clearly illustrating the structural alterations resulted from formation of the eIF4F•IRE RNA complex. A Lineweaver-Burk plot showed an uncompetitive binding behavior between IRE RNA and m7G cap for the eIF4F, indicating that there are different binding sites on the eIF4F for the IRE RNA and the cap analog; molecular docking analysis further supports this notion. Our findings suggest that the eIF4F•IRE RNA complex formation is accompanied by an elevated hydrogen bonding and weakened hydrophobic interactions, leading to an overall conformational change, favored in terms of its free energy. The conformational change in the eIF4F structure, caused by the IRE RNA binding, provides a more stable platform for effective IRE translation in iron homeostasis.
Collapse
Affiliation(s)
- Mateen A Khan
- Department of Life Sciences, College of Science & General Studies, Alfaisal University, Riyadh, Saudi Arabia.
| | - Ajamaluddin Malik
- Department of Biochemistry, Protein Research Laboratory, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Artem V Domashevskiy
- Department of Sciences, John Jay College of Criminal Justice, The City University of New York, New York, NY 10019, USA
| | - Avdar San
- Department of Chemistry, Brooklyn College of the City University of New York, NY, New York, USA
| | - Javed M Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
15
|
Senoura T, Kobayashi T, An G, Nakanishi H, Nishizawa NK. Defects in the rice aconitase-encoding OsACO1 gene alter iron homeostasis. PLANT MOLECULAR BIOLOGY 2020; 104:629-645. [PMID: 32909184 DOI: 10.1007/s11103-020-01065-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/30/2020] [Indexed: 05/16/2023]
Abstract
Rice aconitase gene OsACO1 is involved in the iron deficiency-signaling pathway for the expression of iron deficiency-inducible genes, either thorough enzyme activity or possible specific RNA binding for post-transcriptional regulation. Iron (Fe) is an essential element for virtually all living organisms. When plants are deficient in Fe, Fe acquisition systems are activated to maintain Fe homeostasis, and this regulation is mainly executed at the gene transcription level. Many molecules responsible for Fe uptake, translocation, and storage in plants have been identified and characterized. However, how plants sense Fe status within cells and then induce a transcriptional response is still unclear. In the present study, we found that knockdown of the OsACO1 gene, which encodes an aconitase in rice, leads to the down-regulation of selected Fe deficiency-inducible genes involved in Fe uptake and translocation in roots, and a decrease in Fe concentration in leaves, even when grown under Fe-sufficient conditions. OsACO1 knockdown plants showed a delayed transcriptional response to Fe deficiency compared to wild-type plants. In contrast, overexpression of OsACO1 resulted in the opposite effects. These results suggest that OsACO1 is situated upstream of the Fe deficiency-signaling pathway. Furthermore, we found that the OsACO1 protein potentially has RNA-binding activity. In vitro screening of RNA interactions with OsACO1 revealed that RNA potentially forms a unique stem-loop structure that interacts with OsACO1 via a conserved GGUGG motif within the loop structure. These results suggest that OsACO1 regulate Fe deficiency response either thorough enzyme activity catalyzing isomerization of citrate, or specific RNA binding for post-transcriptional regulation.
Collapse
Affiliation(s)
- Takeshi Senoura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Takanori Kobayashi
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Gynheung An
- Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin, 17104, Korea
| | - Hiromi Nakanishi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| |
Collapse
|
16
|
Leitão MIPS, Gonzalez C, Francescato G, Filipiak Z, Petronilho A. On the reactivity of mRNA Cap0: C-H oxidative addition of 7-methylguanosine to Pt 0 and base pairing studies. Chem Commun (Camb) 2020; 56:13365-13368. [PMID: 33030477 DOI: 10.1039/d0cc06075e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
7-Methylguanosine, whose lability to form an ylide/NHC has been known for decades, reacts with [Pt(PPh3)4] via C-H oxidative addition to yield a hydrido-PtII carbene complex. 1H NMR studies on Watson-Crick base-pairs showed no significant effect of metallation.
Collapse
Affiliation(s)
- Maria Inês P S Leitão
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Carmen Gonzalez
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Giulia Francescato
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Zuzanna Filipiak
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| | - Ana Petronilho
- ITQB NOVA - Instituto de Tecnologia Química e Biológica António Xavier, Avd. Da República s/n, 2780-157 Oeiras, Portugal.
| |
Collapse
|
17
|
Mukherjee H, Blain JC, Vandivier LE, Chin DN, Friedman JE, Liu F, Maillet A, Fang C, Kaplan JB, Li J, Chenoweth DM, Christensen AB, Petersen LK, Hansen NJV, Barrera L, Kubica N, Kumaravel G, Petter JC. PEARL-seq: A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions. ACS Chem Biol 2020; 15:2374-2381. [PMID: 32804474 DOI: 10.1021/acschembio.0c00357] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
RNA is emerging as a valuable target for the development of novel therapeutic agents. The rational design of RNA-targeting small molecules, however, has been hampered by the relative lack of methods for the analysis of small molecule-RNA interactions. Here, we present our efforts to develop such a platform using photoaffinity labeling. This technique, termed Photoaffinity Evaluation of RNA Ligation-Sequencing (PEARL-seq), enables the rapid identification of small molecule binding locations within their RNA targets and can provide information on ligand selectivity across multiple different RNAs. These data, when supplemented with small molecule SAR data and RNA probing data enable the construction of a computational model of the RNA-ligand structure, thereby enabling the rational design of novel RNA-targeted ligands.
Collapse
Affiliation(s)
- Herschel Mukherjee
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - J. Craig Blain
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Lee E. Vandivier
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Donovan N. Chin
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Jessica E. Friedman
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Fei Liu
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Ashley Maillet
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Chao Fang
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Jenifer B. Kaplan
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Jinxing Li
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania, United States
| | | | | | | | - Luis Barrera
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | - Neil Kubica
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| | | | - Jennifer C. Petter
- Arrakis Therapeutics, 830 Winter Street, Waltham, Massachusetts, United States
| |
Collapse
|
18
|
Haizel SA, Bhardwaj U, Gonzalez RL, Mitra S, Goss DJ. 5'-UTR recruitment of the translation initiation factor eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs. J Biol Chem 2020; 295:11693-11706. [PMID: 32571876 DOI: 10.1074/jbc.ra120.013678] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/16/2020] [Indexed: 01/04/2023] Open
Abstract
During unfavorable conditions (e.g. tumor hypoxia or viral infection), canonical, cap-dependent mRNA translation is suppressed in human cells. Nonetheless, a subset of physiologically important mRNAs (e.g. hypoxia-inducible factor 1α [HIF-1α], fibroblast growth factor 9 [FGF-9], and p53) is still translated by an unknown, cap-independent mechanism. Additionally, expression levels of eukaryotic translation initiation factor 4GI (eIF4GI) and of its homolog, death-associated protein 5 (DAP5), are elevated. By examining the 5' UTRs of HIF-1α, FGF-9, and p53 mRNAs and using fluorescence anisotropy binding studies, luciferase reporter-based in vitro translation assays, and mutational analyses, we demonstrate here that eIF4GI and DAP5 specifically bind to the 5' UTRs of these cap-independently translated mRNAs. Surprisingly, we found that the eIF4E-binding domain of eIF4GI increases not only the binding affinity but also the selectivity among these mRNAs. We further demonstrate that the affinities of eIF4GI and DAP5 binding to these 5' UTRs correlate with the efficiency with which these factors drive cap-independent translation of these mRNAs. Integrating the results of our binding and translation assays, we conclude that eIF4GI or DAP5 is critical for recruitment of a specific subset of mRNAs to the ribosome, providing mechanistic insight into their cap-independent translation.
Collapse
Affiliation(s)
- Solomon A Haizel
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA.,Department of Chemistry, Hunter College, New York, New York, USA
| | - Usha Bhardwaj
- Department of Chemistry, Hunter College, New York, New York, USA
| | - Ruben L Gonzalez
- Department of Chemistry, Columbia University, New York, New York, USA
| | - Somdeb Mitra
- Department of Chemistry, New York University, New York, New York, USA
| | - Dixie J Goss
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA .,Department of Chemistry, Hunter College, New York, New York, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York, USA
| |
Collapse
|
19
|
Brown RAM, Richardson KL, Kabir TD, Trinder D, Ganss R, Leedman PJ. Altered Iron Metabolism and Impact in Cancer Biology, Metastasis, and Immunology. Front Oncol 2020; 10:476. [PMID: 32328462 PMCID: PMC7160331 DOI: 10.3389/fonc.2020.00476] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 03/17/2020] [Indexed: 12/12/2022] Open
Abstract
Iron is an essential nutrient that plays a complex role in cancer biology. Iron metabolism must be tightly controlled within cells. Whilst fundamental to many cellular processes and required for cell survival, excess labile iron is toxic to cells. Increased iron metabolism is associated with malignant transformation, cancer progression, drug resistance and immune evasion. Depleting intracellular iron stores, either with the use of iron chelating agents or mimicking endogenous regulation mechanisms, such as microRNAs, present attractive therapeutic opportunities, some of which are currently under clinical investigation. Alternatively, iron overload can result in a form of regulated cell death, ferroptosis, which can be activated in cancer cells presenting an alternative anti-cancer strategy. This review focuses on alterations in iron metabolism that enable cancer cells to meet metabolic demands required during different stages of tumorigenesis in relation to metastasis and immune response. The strength of current evidence is considered, gaps in knowledge are highlighted and controversies relating to the role of iron and therapeutic targeting potential are discussed. The key question we address within this review is whether iron modulation represents a useful approach for treating metastatic disease and whether it could be employed in combination with existing targeted drugs and immune-based therapies to enhance their efficacy.
Collapse
Affiliation(s)
- Rikki A. M. Brown
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
- UWA Medical School, University of Western Australia, Perth, WA, Australia
| | - Kirsty L. Richardson
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Tasnuva D. Kabir
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Debbie Trinder
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
- UWA Medical School, University of Western Australia, Perth, WA, Australia
| | - Ruth Ganss
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
| | - Peter J. Leedman
- Queen Elizabeth II Medical Centre, Harry Perkins Institute of Medical Research, Perth, WA, Australia
- UWA Centre for Medical Research, University of Western Australia, Perth, WA, Australia
- UWA Medical School, University of Western Australia, Perth, WA, Australia
| |
Collapse
|
20
|
Relevance of the iron-responsive element (IRE) pseudotriloop structure for IRP1/2 binding and validation of IRE-like structures using the yeast three-hybrid system. Gene 2019; 710:399-405. [DOI: 10.1016/j.gene.2019.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/16/2019] [Accepted: 06/06/2019] [Indexed: 01/28/2023]
|
21
|
Vatikioti A, Karkoulia E, Ioannou M, Strouboulis J. Translational regulation and deregulation in erythropoiesis. Exp Hematol 2019; 75:11-20. [PMID: 31154069 DOI: 10.1016/j.exphem.2019.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/23/2019] [Accepted: 05/25/2019] [Indexed: 02/02/2023]
Abstract
Translational regulation plays a critical role in erythropoiesis, as it reflects the translational needs of enucleated mature erythroid cells in the absence of transcription and the large translational demands of balanced globin chain synthesis during erythroid maturation. In addition, red blood cells need to respond quickly to changes in their environment and the demands of the organism. Translational regulation occurs at several levels in erythroid cells, including the differential utilization of upstream open reading frames during differentiation and in response to signaling and the employment of RNA-binding proteins in an erythroid cell-specific fashion. Translation initiation is a critical juncture for translational regulation in response to environmental signals such as heme and iron availability, whereas regulatory mechanisms for ribosome recycling are consistent with recent observations highlighting the importance of maintaining adequate ribosome levels in differentiating erythroid cells. Translational deregulation in erythroid cells leads to disease associated with ineffective erythropoiesis, further highlighting the pivotal role translational regulation in erythropoiesis plays in human physiology and homeostasis. Overall, erythropoiesis has served as a unique model that has provided invaluable insight into translational regulation.
Collapse
Affiliation(s)
- Alexandra Vatikioti
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece; Graduate Program in Molecular Biology and Biomedicine, Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Elena Karkoulia
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - Marina Ioannou
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece
| | - John Strouboulis
- Laboratory of Molecular Hematopoiesis, Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Crete, Greece.
| |
Collapse
|
22
|
Zinskie JA, Ghosh A, Trainor BM, Shedlovskiy D, Pestov DG, Shcherbik N. Iron-dependent cleavage of ribosomal RNA during oxidative stress in the yeast Saccharomyces cerevisiae. J Biol Chem 2018; 293:14237-14248. [PMID: 30021840 DOI: 10.1074/jbc.ra118.004174] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Stress-induced strand breaks in rRNA have been observed in many organisms, but the mechanisms by which they originate are not well-understood. Here we show that a chemical rather than an enzymatic mechanism initiates rRNA cleavages during oxidative stress in yeast (Saccharomyces cerevisiae). We used cells lacking the mitochondrial glutaredoxin Grx5 to demonstrate that oxidant-induced cleavage formation in 25S rRNA correlates with intracellular iron levels. Sequestering free iron by chemical or genetic means decreased the extent of rRNA degradation and relieved the hypersensitivity of grx5Δ cells to the oxidants. Importantly, subjecting purified ribosomes to an in vitro iron/ascorbate reaction precisely recapitulated the 25S rRNA cleavage pattern observed in cells, indicating that redox activity of the ribosome-bound iron is responsible for the strand breaks in the rRNA. In summary, our findings provide evidence that oxidative stress-associated rRNA cleavages can occur through rRNA strand scission by redox-active, ribosome-bound iron that potentially promotes Fenton reaction-induced hydroxyl radical production, implicating intracellular iron as a key determinant of the effects of oxidative stress on ribosomes. We propose that iron binding to specific ribosome elements primes rRNA for cleavages that may play a role in redox-sensitive tuning of the ribosome function in stressed cells.
Collapse
Affiliation(s)
| | - Arnab Ghosh
- From the Department of Cell Biology and Neuroscience and
| | - Brandon M Trainor
- From the Department of Cell Biology and Neuroscience and.,Graduate School for Biomedical Sciences, Rowan University, Stratford, New Jersey 08084
| | | | | | | |
Collapse
|
23
|
Lackey L, Coria A, Woods C, McArthur E, Laederach A. Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure. RNA (NEW YORK, N.Y.) 2018; 24:513-528. [PMID: 29317542 PMCID: PMC5855952 DOI: 10.1261/rna.064469.117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 05/22/2023]
Abstract
The impact of inherited and somatic mutations on messenger RNA (mRNA) structure remains poorly understood. Recent technological advances that leverage next-generation sequencing to obtain experimental structure data, such as SHAPE-MaP, can reveal structural effects of mutations, especially when these data are incorporated into structure modeling. Here, we analyze the ability of SHAPE-MaP to detect the relatively subtle structural changes caused by single-nucleotide mutations. We find that allele-specific sorting greatly improved our detection ability. Thus, we used SHAPE-MaP with a novel combination of clone-free robotic mutagenesis and allele-specific sorting to perform a rapid, comprehensive survey of noncoding somatic and inherited riboSNitches in two cancer-associated mRNAs, TPT1 and LCP1 Using rigorous thermodynamic modeling of the Boltzmann suboptimal ensemble, we identified a subset of mutations that change TPT1 and LCP1 RNA structure, with approximately 14% of all variants identified as riboSNitches. To confirm that these in vitro structures were biologically relevant, we tested how dependent TPT1 and LCP1 mRNA structures were on their environments. We performed SHAPE-MaP on TPT1 and LCP1 mRNAs in the presence or absence of cellular proteins and found that both mRNAs have similar overall folds in all conditions. RiboSNitches identified within these mRNAs in vitro likely exist under biological conditions. Overall, these data reveal a robust mRNA structural landscape where differences in environmental conditions and most sequence variants do not significantly alter RNA structural ensembles. Finally, predicting riboSNitches in mRNAs from sequence alone remains particularly challenging; these data will provide the community with benchmarks for further algorithmic development.
Collapse
Affiliation(s)
- Lela Lackey
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Aaztli Coria
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Chanin Woods
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Evonne McArthur
- School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| |
Collapse
|
24
|
Holmes-Hampton GP, Ghosh MC, Rouault TA. Methods for Studying Iron Regulatory Protein 1: An Important Protein in Human Iron Metabolism. Methods Enzymol 2017; 599:139-155. [PMID: 29746238 DOI: 10.1016/bs.mie.2017.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Iron regulatory proteins 1 and 2 (IRP1 and IRP2) are two cytosolic proteins that maintain cellular iron homeostasis by regulating the expression of genes involved in iron metabolism. IRPs respond to cellular iron deficiency by binding to iron-responsive elements (IREs) found in the mRNAs of iron metabolism transcripts, enhancing iron import, and reducing iron storage, utilization, and export. IRP1, a bifunctional protein, exists in equilibrium between a [Fe4S4] cluster containing cytosolic aconitase, and an apoprotein that binds to IREs. At high cellular iron levels, this equilibrium is shifted more toward iron-sulfur cluster containing aconitase, whereas IRP2 undergoes proteasomal degradation by an E3 ubiquitin ligase complex that contains an F-box protein, FBXL5. Irp1-/- mice develop polycythemia and pulmonary hypertension, whereas Irp2-/- mice develop microcytic anemia and progressive neurodegeneration, indicating that Irp1 has important functions in the erythropoietic and pulmonary systems, and Irp2 has essential roles in supporting erythropoiesis and nervous system functions. Mice lacking both Irp1 and Irp2 die during embryogenesis, suggesting that functions of Irp1 and Irp2 are redundant. In this review, we will focus on the methods for studying IRP1 activities and function in cells and animals.
Collapse
Affiliation(s)
- Gregory P Holmes-Hampton
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Manik C Ghosh
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, United States.
| |
Collapse
|
25
|
Zhou ZD, Tan EK. Iron regulatory protein (IRP)-iron responsive element (IRE) signaling pathway in human neurodegenerative diseases. Mol Neurodegener 2017; 12:75. [PMID: 29061112 PMCID: PMC5654065 DOI: 10.1186/s13024-017-0218-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022] Open
Abstract
The homeostasis of iron is vital to human health, and iron dyshomeostasis can lead to various disorders. Iron homeostasis is maintained by iron regulatory proteins (IRP1 and IRP2) and the iron-responsive element (IRE) signaling pathway. IRPs can bind to RNA stem-loops containing an IRE in the untranslated region (UTR) to manipulate translation of target mRNA. However, iron can bind to IRPs, leading to the dissociation of IRPs from the IRE and altered translation of target transcripts. Recently an IRE is found in the 5′-UTR of amyloid precursor protein (APP) and α-synuclein (α-Syn) transcripts. The levels of α-Syn, APP and amyloid β-peptide (Aβ) as well as protein aggregation can be down-regulated by IRPs but are up-regulated in the presence of iron accumulation. Therefore, inhibition of the IRE-modulated expression of APP and α-Syn or chelation of iron in patient’s brains has therapeutic significance to human neurodegenerative diseases. Currently, new pre-drug IRE inhibitors with therapeutic effects have been identified and are at different stages of clinical trials for human neurodegenerative diseases. Although some promising drug candidates of chemical IRE inhibitors and iron-chelating agents have been identified and are being validated in clinical trials for neurodegenerative diseases, future studies are expected to further establish the clinical efficacy and safety of IRE inhibitors and iron-chelating agents in patients with neurodegenerative diseases.
Collapse
Affiliation(s)
- Zhi Dong Zhou
- National Neuroscience Institute of Singapore, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore. .,Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School Singapore, 8 College Road, Singapore, 169857, Singapore.
| | - Eng-King Tan
- National Neuroscience Institute of Singapore, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore.,Department of Neurology, Singapore General Hospital, Outram Road, Singapore, 169608, Singapore.,Signature Research Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School Singapore, 8 College Road, Singapore, 169857, Singapore
| |
Collapse
|
26
|
Bian K, Chen F, Humulock ZT, Tang Q, Li D. Copper Inhibits the AlkB Family DNA Repair Enzymes under Wilson's Disease Condition. Chem Res Toxicol 2017; 30:1794-1796. [PMID: 28926697 DOI: 10.1021/acs.chemrestox.7b00230] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Disturbed metabolism of copper ions can cause diseases such as Wilson's disease (WD). In this work, we investigated the inhibitory effect of Cu(II) ion in vitro on the AlkB family DNA repair enzymes, which are members of the Fe(II)/alpha-ketoglutarate-dependent dioxygenase and include human ALKBH2, ALKBH3, and E. coli AlkB proteins. None of the three proteins was significantly inhibited under normal cellular copper concentrations. However, under WD related condition, we observed that the activities of all three enzymes were strongly suppressed (from 95.2 to 100.0%). We also noted the repair efficiency under ds-DNA condition was less susceptible than ss-DNA to the inhibition.
Collapse
Affiliation(s)
- Ke Bian
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Fangyi Chen
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Zachary T Humulock
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Qi Tang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island , Kingston, Rhode Island 02881, United States
| |
Collapse
|
27
|
Balaban CL, Banchio C, Ceccarelli EA. TAT-mediated transduction of bacterial redox proteins generates a cytoprotective effect on neuronal cells. PLoS One 2017; 12:e0184617. [PMID: 28886198 PMCID: PMC5591030 DOI: 10.1371/journal.pone.0184617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/28/2017] [Indexed: 12/23/2022] Open
Abstract
Cell penetrating peptides, also known as protein transduction domains, have the capacity to ubiquitously cross cellular membranes carrying many different cargos with negligible cytotoxicity. As a result, they have emerged as a powerful tool for macromolecular delivery-based therapies. In this study, catalytically active bacterial Ferredoxin-NADP+ reductase (LepFNR) and Heme oxygenase (LepHO) fused to the HIV TAT-derived protein transduction peptide (TAT) were efficiently transduced to neuroblastoma SHSY-5Y cells. Proteins entered the cells through an endocytic pathway showing a time/concentration dependent mechanism that was clearly modulated by the nature of the cargo protein. Since ferredoxin-NADP+ reductases and heme oxygenases have been implicated in mechanisms of oxidative stress defense, neuroblastoma cells simultaneously transduced with TAT-LepFNR and TAT-LepHO were challenged by H2O2 incubations to judge the cytoprotective power of these bacterial enzymes. Accumulation of reactive oxygen species was significantly reduced in these transduced neuronal cells. Moreover, measurements of metabolic viability, membrane integrity, and cell survival indicated that these cells showed a better tolerance to oxidative stress. Our results open the possibility for the application of transducible active redox proteins to overcome the damage elicited by oxidative stress in cells and tissues.
Collapse
Affiliation(s)
- Cecilia L. Balaban
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Claudia Banchio
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
| | - Eduardo A. Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda, Rosario, Argentina
- * E-mail:
| |
Collapse
|
28
|
Zhao H, Li H, Hao S, Chen J, Wu J, Song C, Zhang M, Qiao T, Li K. Peptide SS-31 upregulates frataxin expression and improves the quality of mitochondria: implications in the treatment of Friedreich ataxia. Sci Rep 2017; 7:9840. [PMID: 28852135 PMCID: PMC5575096 DOI: 10.1038/s41598-017-10320-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/01/2017] [Indexed: 12/11/2022] Open
Abstract
Friedreich ataxia is a progressive neurodegenerative disease caused by the expansion of GAA trinucleotide repeats within the first intron of the FXN gene, which encodes frataxin. The pathophysiology of the disease is thought to be derived from the decrease of Fe-S cluster biogenesis due to frataxin deficiency. There is currently no effective treatment for the disease. In our study, we demonstrated that treatment with the mitochondrion-targeted peptide SS-31 reduced frataxin deficiency-induced oxidative stress in lymphoblasts and fibroblasts derived from patients. Interestingly, SS-31 treatment translationally upregulated the protein level of frataxin in a dose-dependent manner. Furthermore, SS-31 treatment increased the enzymatic activities of the iron-sulphur enzymes, including aconitase and complex II and III of the respiratory chain. Further evaluation of the quality of mitochondria showed that mitochondrial membrane potential, ATP content, NAD+/NADH, and the morphology of mitochondria all improved. Our results suggest that SS-31 might potentially be a new drug for the early treatment of Friedreich ataxia.
Collapse
Affiliation(s)
- Hongting Zhao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
| | - Huihui Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
| | - Shuangying Hao
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
- Medical School of Henan Polytechnic University, 454000, Jiaozuo, P. R. China
| | - Jiping Chen
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
| | - Jing Wu
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
| | - Chuanhui Song
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China
| | - Meng Zhang
- Department of Vascular Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, P. R. China
| | - Tong Qiao
- Department of Vascular Surgery, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, P. R. China
| | - Kuanyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, 210093, Nanjing, P. R. China.
| |
Collapse
|
29
|
Thermodynamic and Kinetic Analyses of Iron Response Element (IRE)-mRNA Binding to Iron Regulatory Protein, IRP1. Sci Rep 2017; 7:8532. [PMID: 28819260 PMCID: PMC5561112 DOI: 10.1038/s41598-017-09093-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 07/21/2017] [Indexed: 11/08/2022] Open
Abstract
Comparison of kinetic and thermodynamic properties of IRP1 (iron regulatory protein1) binding to FRT (ferritin) and ACO2 (aconitase2) IRE-RNAs, with or without Mn2+, revealed differences specific to each IRE-RNA. Conserved among animal mRNAs, IRE-RNA structures are noncoding and bind Fe2+ to regulate biosynthesis rates of the encoded, iron homeostatic proteins. IRP1 protein binds IRE-RNA, inhibiting mRNA activity; Fe2+ decreases IRE-mRNA/IRP1 binding, increasing encoded protein synthesis. Here, we observed heat, 5 °C to 30 °C, increased IRP1 binding to IRE-RNA 4-fold (FRT IRE-RNA) or 3-fold (ACO2 IRE-RNA), which was enthalpy driven and entropy favorable. Mn2+ (50 µM, 25 °C) increased IRE-RNA/IRP1 binding (Kd) 12-fold (FRT IRE-RNA) or 6-fold (ACO2 IRE-RNA); enthalpic contributions decreased ~61% (FRT) or ~32% (ACO2), and entropic contributions increased ~39% (FRT) or ~68% (ACO2). IRE-RNA/IRP1 binding changed activation energies: FRT IRE-RNA 47.0 ± 2.5 kJ/mol, ACO2 IRE-RNA 35.0 ± 2.0 kJ/mol. Mn2+ (50 µM) decreased the activation energy of RNA-IRP1 binding for both IRE-RNAs. The observations suggest decreased RNA hydrogen bonding and changed RNA conformation upon IRP1 binding and illustrate how small, conserved, sequence differences among IRE-mRNAs selectively influence thermodynamic and kinetic selectivity of the protein/RNA interactions.
Collapse
|
30
|
Rupani DN, Connell GJ. Transferrin receptor mRNA interactions contributing to iron homeostasis. RNA (NEW YORK, N.Y.) 2016; 22:1271-82. [PMID: 27307498 PMCID: PMC4931119 DOI: 10.1261/rna.056184.116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/07/2016] [Indexed: 05/03/2023]
Abstract
The transferrin receptor is the primary means of iron importation for most mammalian cells and understanding its regulatory mechanisms is relevant to hematologic, oncologic, and other disorders in which iron homeostasis is perturbed. The 3' UTR of the transferrin receptor mRNA contains an instability element that is protected from degradation during iron depletion through interactions of iron regulatory proteins (IRPs) with five iron-responsive elements (IREs). The structural features required for degradation and the site of IRP binding required for in situ protection remain unclear. An RNA-CLIP strategy is described here that identifies the predominant site of IRP-1 interaction within a nontransformed primary cell line. This approach avoided complications associated with the use of elevated concentrations of protein and/or mRNA and detected interactions within the native environment of the mRNA. A compensatory mutagenesis strategy indicates that the instability element at minimum consists of three non-IRE stem-loops that can function additively, suggesting that they are not forming one highly interdependent structure. Although the IREs are not essential for instability, they enhance instability when IRP interactions are inhibited. These results are supportive of a mechanism for a graded response to the intracellular iron resulting from a progressive loss of IRP protection.
Collapse
Affiliation(s)
- Dhwani N Rupani
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Gregory J Connell
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| |
Collapse
|
31
|
Theil EC, Tosha T, Behera RK. Solving Biology's Iron Chemistry Problem with Ferritin Protein Nanocages. Acc Chem Res 2016; 49:784-91. [PMID: 27136423 DOI: 10.1021/ar500469e] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ferritins reversibly synthesize iron-oxy(ferrihydrite) biominerals inside large, hollow protein nanocages (10-12 nm, ∼480 000 g/mol); the iron biominerals are metabolic iron concentrates for iron protein biosyntheses. Protein cages of 12- or 24-folded ferritin subunits (4-α-helix polypeptide bundles) self-assemble, experimentally. Ferritin biomineral structures differ among animals and plants or bacteria. The basic ferritin mineral structure is ferrihydrite (Fe2O3·H2O) with either low phosphate in the highly ordered animal ferritin biominerals, Fe/PO4 ∼ 8:1, or Fe/PO4 ∼ 1:1 in the more amorphous ferritin biominerals of plants and bacteria. While different ferritin environments, plant bacterial-like plastid organelles and animal cytoplasm, might explain ferritin biomineral differences, investigation is required. Currently, the physiological significance of plant-specific and animal-specific ferritin iron minerals is unknown. The iron content of ferritin in living tissues ranges from zero in "apoferritin" to as high as ∼4500 iron atoms. Ferritin biomineralization begins with the reaction of Fe(2+) with O2 at ferritin enzyme (Fe(2+)/O oxidoreductase) sites. The product of ferritin enzyme activity, diferric oxy complexes, is also the precursor of ferritin biomineral. Concentrations of Fe(3+) equivalent to 2.0 × 10(-1) M are maintained in ferritin solutions, contrasting with the Fe(3+) Ks ∼ 10(-18) M. Iron ions move into, through, and out of ferritin protein cages in structural subdomains containing conserved amino acids. Cage subdomains include (1) ion channels for Fe(2+) entry/exit, (2) enzyme (oxidoreductase) site for coupling Fe(2+) and O yielding diferric oxy biomineral precursors, and (3) ferric oxy nucleation channels, where diferric oxy products from up to three enzyme sites interact while moving toward the central, biomineral growth cavity (12 nm diameter) where ferric oxy species, now 48-mers, grow in ferric oxy biomineral. High ferritin protein cage symmetry (3-fold and 4-fold axes) and amino acid conservation coincide with function, shown by amino acid substitution effects. 3-Fold symmetry axes control Fe(2+) entry (enzyme catalysis of Fe(2+)/O2 oxidoreduction) and Fe(2+) exit (reductive ferritin mineral dissolution); 3-fold symmetry axes influence Fe(2+)exit from dissolved mineral; bacterial ferritins diverge slightly in Fe/O2 reaction mechanisms and intracage paths of iron-oxy complexes. Biosynthesis rates of ferritin protein change with Fe(2+) and O2 concentrations, dependent on DNA-binding, and heme binding protein, Bach 1. Increased cellular O2 indirectly stabilizes ferritin DNA/Bach 1 interactions. Heme, Fe-protoporphyrin IX, decreases ferritin DNA-Bach 1 binding, causing increased ferritin mRNA biosynthesis (transcription). Direct Fe(2+) binding to ferritin mRNA decreases binding of an inhibitory protein, IRP, causing increased ferritin mRNA translation (protein biosynthesis). Newly synthesized ferritin protein consumes Fe(2+) in biomineral, decreasing Fe(2)(+) and creating a regulatory feedback loop. Ferritin without iron is "apoferritin". Iron removal from ferritin, experimentally, uses biological reductants, for example, NADH + FMN, or chemical reductants, for example, thioglycolic acid, with Fe(2+) chelators; physiological mechanism(s) are murky. Clear, however, is the necessity of ferritin for terrestrial life by conferring oxidant protection (plants, animals, and bacteria), virulence (bacteria), and embryonic survival (mammals). Future studies of ferritin structure/function and Fe(2+)/O2 chemistry will lead to new ferritin uses in medicine, nutrition, and nanochemistry.
Collapse
Affiliation(s)
- Elizabeth C. Theil
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, United States
- Department of Structural
and Molecular Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7313, United States
| | - Takehiko Tosha
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, United States
- Department of Structural
and Molecular Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7313, United States
| | - Rabindra K. Behera
- Children’s Hospital Oakland Research Institute, Oakland, California 94609, United States
- Department of Structural
and Molecular Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-7313, United States
| |
Collapse
|
32
|
Xie LH, Zhang XH, Hu XD, Min XY, Zhou QF, Zhang HQ. Mechanisms of an increased level of serum iron in gamma-irradiated mice. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2016; 55:81-88. [PMID: 26511140 DOI: 10.1007/s00411-015-0623-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 10/15/2015] [Indexed: 06/05/2023]
Abstract
The potential mechanisms underlying the increase in serum iron concentration in gamma-irradiated mice were studied. The gamma irradiation dose used was 4 Gy, and cobalt-60 ((60)Co) source was used for the irradiation. The dose rate was 0.25 Gy/min. In the serum of irradiated mice, the concentration of ferrous ions decreased, whereas the serum iron concentration increased. The concentration of ferrous ions in irradiated mice returned to normal at 21 day post-exposure. The concentration of reactive oxygen species in irradiated mice increased immediately following irradiation but returned to normal at 7 day post-exposure. Serum iron concentration in gamma-irradiated mice that were pretreated with reduced glutathione was significant lower (p < 0.01) than that in mice exposed to gamma radiation only. However, the serum iron concentration was still higher than that in normal mice (p < 0.01). This change was biphasic, characterized by a maximal decrease phase occurring immediately after gamma irradiation (relative to the irradiated mice) and a recovery plateau observed during the 7th and 21st day post-irradiation, but serum iron recovery was still less than that in the gamma-irradiated mice (4 Gy). In gamma-irradiated mice, ceruloplasmin activity increased and serum copper concentration decreased immediately after irradiation, and both of them were constant during the 7th and 21st day post-irradiation. It was concluded that ferrous ions in irradiated mice were oxidized to ferric ions by ionizing radiation. Free radicals induced by gamma radiation and ceruloplasmin mutually participated in this oxidation process. The ferroxidase effect of ceruloplasmin was achieved by transfer of electrons from ferrous ions to cupric ions.
Collapse
Affiliation(s)
- Li-hua Xie
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China
| | - Xiao-hong Zhang
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China
| | - Xiao-dan Hu
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China
| | - Xuan-yu Min
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China
| | - Qi-fu Zhou
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China
- Nuclear and Radiation Safety Center, Beijing, People's Republic of China
| | - Hai-qian Zhang
- Department of Nuclear Science and Engineering, Nanjing University of Aeronautics and Astronautics, 29 Yudao Street, Nanjing, 210016, People's Republic of China.
- Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing, Jiangsu, People's Republic of China.
| |
Collapse
|
33
|
Bogdan AR, Miyazawa M, Hashimoto K, Tsuji Y. Regulators of Iron Homeostasis: New Players in Metabolism, Cell Death, and Disease. Trends Biochem Sci 2015; 41:274-286. [PMID: 26725301 DOI: 10.1016/j.tibs.2015.11.012] [Citation(s) in RCA: 586] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/16/2015] [Accepted: 11/24/2015] [Indexed: 02/07/2023]
Abstract
Iron is necessary for life, but can also cause cell death. Accordingly, cells evolved a robust, tightly regulated suite of genes for maintaining iron homeostasis. Previous mechanistic studies on iron homeostasis have granted insight into the role of iron in human health and disease. We highlight new regulators of iron metabolism, including iron-trafficking proteins [solute carrier family 39, SLC39, also known as ZRT/IRT-like protein, ZIP; and poly-(rC)-binding protein, PCBP] and a cargo receptor (NCOA4) that is crucial for release of ferritin-bound iron. We also discuss emerging roles of iron in apoptosis and a novel iron-dependent cell death pathway termed 'ferroptosis', the dysregulation of iron metabolism in human pathologies, and the use of iron chelators in cancer therapy.
Collapse
Affiliation(s)
- Alexander R Bogdan
- Department of Biological Sciences, North Carolina State University, Campus Box 7633, Raleigh, NC 27695-7633, USA
| | - Masaki Miyazawa
- Department of Biological Sciences, North Carolina State University, Campus Box 7633, Raleigh, NC 27695-7633, USA
| | - Kazunori Hashimoto
- Department of Biological Sciences, North Carolina State University, Campus Box 7633, Raleigh, NC 27695-7633, USA
| | - Yoshiaki Tsuji
- Department of Biological Sciences, North Carolina State University, Campus Box 7633, Raleigh, NC 27695-7633, USA.
| |
Collapse
|
34
|
Sander SA, Van Hall AK, Morrow JR. Zn2+-Selective Switch of Duplex to Hairpin DNA. Inorg Chem 2015; 54:3084-6. [DOI: 10.1021/ic503074p] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Stephanie A. Sander
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
| | - Alexandra K. Van Hall
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
| | - Janet R. Morrow
- Department of Chemistry, University at Buffalo, the State University of New York, Amherst, New York 14260, United States
| |
Collapse
|
35
|
Fraser CS. Quantitative studies of mRNA recruitment to the eukaryotic ribosome. Biochimie 2015; 114:58-71. [PMID: 25742741 DOI: 10.1016/j.biochi.2015.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 12/20/2022]
Abstract
The process of peptide bond synthesis by ribosomes is conserved between species, but the initiation step differs greatly between the three kingdoms of life. This is illustrated by the evolution of roughly an order of magnitude more initiation factor mass found in humans compared with bacteria. Eukaryotic initiation of translation is comprised of a number of sub-steps: (i) recruitment of an mRNA and initiator methionyl-tRNA to the 40S ribosomal subunit; (ii) migration of the 40S subunit along the 5' UTR to locate the initiation codon; and (iii) recruitment of the 60S subunit to form the 80S initiation complex. Although the mechanism and regulation of initiation has been studied for decades, many aspects of the pathway remain unclear. In this review, I will focus discussion on what is known about the mechanism of mRNA selection and its recruitment to the 40S subunit. I will summarize how the 43S preinitiation complex (PIC) is formed and stabilized by interactions between its components. I will discuss what is known about the mechanism of mRNA selection by the eukaryotic initiation factor 4F (eIF4F) complex and how the selected mRNA is recruited to the 43S PIC. The regulation of this process by secondary structure located in the 5' UTR of an mRNA will also be discussed. Finally, I present a possible kinetic model with which to explain the process of mRNA selection and recruitment to the eukaryotic ribosome.
Collapse
Affiliation(s)
- Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
| |
Collapse
|
36
|
De novo secondary structure motif discovery using RNAProfile. Methods Mol Biol 2015. [PMID: 25577372 DOI: 10.1007/978-1-4939-2291-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
RNA secondary structure plays critical roles in several biological processes. For example, many trans-acting noncoding RNA genes and cis-acting RNA regulatory elements present functional motifs, conserved both in structure and sequence, that can be hardly detected by primary sequence analysis alone. We describe here how conserved secondary structure motifs shared by functionally related RNA sequences can be detected through the software tool RNAProfile. RNAProfile takes as input a set of unaligned RNA sequences expected to share a common motif, and outputs the regions that are most conserved throughout the sequences, according to a similarity measure that takes into account both the sequence of the regions and the secondary structure they can form according to base-pairing and thermodynamic rules. The method is split into two parts. First, it identifies candidate regions within the input sequences, and associates with each region a locally optimal secondary structure. Then, it compares candidate regions to one another, both at sequence and structure level, and builds motifs exploring the search space through a greedy heuristic. We provide a detailed guide to the different parameters that can be employed, and usage examples showing the different software capabilities.
Collapse
|
37
|
Theil EC. IRE mRNA riboregulators use metabolic iron (Fe(2+)) to control mRNA activity and iron chemistry in animals. Metallomics 2014; 7:15-24. [PMID: 25209685 DOI: 10.1039/c4mt00136b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A family of noncoding RNAs bind Fe(2+) to increase protein synthesis. The structures occur in messenger RNAs encoding animal proteins for iron metabolism. Each mRNA regulatory sequence, ∼30 ribonucleotides long, is called an IRE (Iron Responsive Element), and folds into a bent, A-RNA helix with a terminal loop. Riboregulatory RNAs, like t-RNAs, r-RNAs micro-RNAs, etc. contrast with DNA, since single-stranded RNA can fold into a variety of complex, three-dimensional structures. IRE-RNAs bind two types of proteins: (1) IRPs which are protein repressors, sequence-related to mitochondrial aconitases. (2) eIF-4F, which bind ribosomes and enhances general protein biosynthesis. The competition between IRP and eIF-4F binding to IRE-RNA is controlled by Fe(2+)-induced changes in the IRE-RNA conformation. Mn(2+), which also binds to IRE-RNA in solution, is a convenient experimental proxy for air-sensitive Fe(2+) studies of in vitro protein biosynthesis and protein binding. However, only Fe(2+) has physiological effects on protein biosynthesis directed by IRE-mRNAs. The structures of the IRE-RNA riboregulators is known indirectly from effects of base substitutions on function, from solution NMR of the free RNA, and of X-ray crystallography of the IRE-RNA-IRP repressor complex. However, the inability to date, to crystallize the free IRE-RNA, and the dissociation of the IRE-RNA-IRP complex when metal binds, have hampered direct identification and characterization of the RNA-metal binding sites. The high conservation of the primary sequence in IRE-mRNA control elements has facilitated their identification and analysis of metal-assisted riboregulator function. Expansion of RNA search analyses beyond primary will likely reveal other, metal-dependent families of mRNA riboregulators.
Collapse
Affiliation(s)
- Elizabeth C Theil
- The Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| |
Collapse
|
38
|
Iron-rich ferritin in the hypoxia-tolerant rodent Spalax ehrenbergi: a naturally-occurring biomarker confirms the internalization and pathways of intracellular macromolecules. J Struct Biol 2014; 187:254-265. [PMID: 25050761 DOI: 10.1016/j.jsb.2014.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/20/2014] [Accepted: 07/11/2014] [Indexed: 02/08/2023]
Abstract
The discovery of pits/caveolae in the plasmalemma advanced the study of macromolecule internalization. "Transcytosis" describes the transport of macromolecular cargo from one front of a polarized cell to the other within membrane-bounded carrier(s), via endocytosis, intracellular trafficking and exocytosis. Clathrin-mediated transcytosis is used extensively by epithelial cells, while caveolae-mediated transcytosis mostly occurs in endothelial cells. The internalization pathways were monitored by various markers, including radioisotopes, nanoparticles, enzymes, immunostains, and fluorophores. We describe an internalization pathway identified using a naturally-occurring biomarker, in vivo assembled ferritin, containing electron-dense iron cores. Iron, an essential trace metal for most living species and iron homeostasis, is crucial for cellular life. Ferritin is a ubiquitous and highly conserved archeoprotein whose main function is to store a reserve iron supply inside the cytoplasm in a non-toxic form. Ferritin is present in all organisms which have a metabolic requirement for iron and in even in organisms whose taxonomic rank is very low. The newborns of the blind mole, Spalax ehrenbergi, are born and live in a hypoxic environment and have significant iron overload in their liver and heart, but their iron metabolism has not been previously studied. These newborns, which are evolutionarily adapted to fluctuations in the environmental oxygen, have a unique ability to sequester transplacental iron and store it in ferritin without any signs of iron toxicity. Using the ferrihydrite cores of ferritin, we were able to monitor the ferritin internalization from portals of its entry into the cytosol of hepatocytes and cardiomyocytes and into the lysosomes.
Collapse
|
39
|
Kobayashi T, Nishizawa NK. Iron sensors and signals in response to iron deficiency. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:36-43. [PMID: 24908504 DOI: 10.1016/j.plantsci.2014.04.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/03/2014] [Accepted: 04/03/2014] [Indexed: 05/03/2023]
Abstract
The transcription of genes involved in iron acquisition in plants is induced under iron deficiency, but our understanding of iron sensors and signals remains limited. Iron Deficiency-responsive Element-binding Factor 1 (IDEF1) and Hemerythrin motif-containing Really Interesting New Gene- and Zinc-finger proteins (HRZs)/BRUTUS (BTS) have recently emerged as candidate iron sensors because of their functions as potent regulators of iron deficiency responses and their iron-binding properties. IDEF1 is a central transcriptional regulator of graminaceous genes involved in iron uptake and utilization, predominantly during the early stages of iron deficiency. HRZs/BTS are E3 ubiquitin ligases and negative regulators of iron deficiency responses in both graminaceous and non-graminaceous plants. Rice OsHRZ1 and OsHRZ2 are also potent regulators of iron accumulation. Characterizing these putative iron sensors also provides clues to understanding the nature of iron signals, which may involve ionized iron itself, other metals, oxygen, redox status, heme and iron-sulfur clusters, in addition to metabolites affected by iron deficiency. Systemic iron responses may also be regulated by phloem-mobile iron and its chelators such as nicotianamine. Iron sensors and signals will be identified by demonstration of signal transmission by IDEF1, HRZs/BTS, or unknown factors.
Collapse
Affiliation(s)
- Takanori Kobayashi
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
| | - Naoko K Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi, Ishikawa 921-8836, Japan.
| |
Collapse
|
40
|
Ward WL, Plakos K, DeRose VJ. Nucleic acid catalysis: metals, nucleobases, and other cofactors. Chem Rev 2014; 114:4318-42. [PMID: 24730975 PMCID: PMC4002065 DOI: 10.1021/cr400476k] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/17/2022]
Affiliation(s)
- W. Luke Ward
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Kory Plakos
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Victoria J. DeRose
- Department of Chemistry and Biochemistry and Institute of
Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| |
Collapse
|
41
|
Khan MA, Ma J, Walden WE, Merrick WC, Theil EC, Goss DJ. Rapid kinetics of iron responsive element (IRE) RNA/iron regulatory protein 1 and IRE-RNA/eIF4F complexes respond differently to metal ions. Nucleic Acids Res 2014; 42:6567-77. [PMID: 24728987 PMCID: PMC4041422 DOI: 10.1093/nar/gku248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Metal ion binding was previously shown to destabilize IRE-RNA/IRP1 equilibria and enhanced IRE-RNA/eIF4F equilibria. In order to understand the relative importance of kinetics and stability, we now report rapid rates of protein/RNA complex assembly and dissociation for two IRE-RNAs with IRP1, and quantitatively different metal ion response kinetics that coincide with the different iron responses in vivo. kon, for FRT IRE-RNA binding to IRP1 was eight times faster than ACO2 IRE-RNA. Mn2+ decreased kon and increased koff for IRP1 binding to both FRT and ACO2 IRE-RNA, with a larger effect for FRT IRE-RNA. In order to further understand IRE-mRNA regulation in terms of kinetics and stability, eIF4F kinetics with FRT IRE-RNA were determined. kon for eIF4F binding to FRT IRE-RNA in the absence of metal ions was 5-times slower than the IRP1 binding to FRT IRE-RNA. Mn2+ increased the association rate for eIF4F binding to FRT IRE-RNA, so that at 50 µM Mn2+ eIF4F bound more than 3-times faster than IRP1. IRP1/IRE-RNA complex has a much shorter life-time than the eIF4F/IRE-RNA complex, which suggests that both rate of assembly and stability of the complexes are important, and that allows this regulatory system to respond rapidly to change in cellular iron.
Collapse
Affiliation(s)
- Mateen A Khan
- Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - Jia Ma
- Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, NY 10065, USA
| | - William E Walden
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612-7334, USA
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Elizabeth C Theil
- Childeren's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Dixie J Goss
- Department of Chemistry and Biochemistry, Hunter College, City University of New York, New York, NY 10065, USA
| |
Collapse
|
42
|
Tzou WS, Chu Y, Lin TY, Hu CH, Pai TW, Liu HF, Lin HJ, Cases I, Rojas A, Sanchez M, You ZY, Hsu MW. Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PLoS One 2014; 9:e86718. [PMID: 24489775 PMCID: PMC3904948 DOI: 10.1371/journal.pone.0086718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/12/2013] [Indexed: 01/23/2023] Open
Abstract
Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5′ untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.
Collapse
Affiliation(s)
- Wen-Shyong Tzou
- Department of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
- * E-mail:
| | - Ying Chu
- Department of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzung-Yi Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chin-Hwa Hu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Hsin-Fu Liu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Han-Jia Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ildeofonso Cases
- Computational Cell Biology Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Ana Rojas
- Computational Cell Biology Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Mayka Sanchez
- Cancer and Iron Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Zong-Ye You
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ming-Wei Hsu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| |
Collapse
|
43
|
Abstract
At the center of iron and oxidant metabolism is the ferritin superfamily: protein cages with Fe(2+) ion channels and two catalytic Fe/O redox centers that initiate the formation of caged Fe2O3·H2O. Ferritin nanominerals, initiated within the protein cage, grow inside the cage cavity (5 or 8 nm in diameter). Ferritins contribute to normal iron flow, maintenance of iron concentrates for iron cofactor syntheses, sequestration of iron from invading pathogens, oxidant protection, oxidative stress recovery, and, in diseases where iron accumulates excessively, iron chelation strategies. In eukaryotic ferritins, biomineral order/crystallinity is influenced by nucleation channels between active sites and the mineral growth cavity. Animal ferritin cages contain, uniquely, mixtures of catalytically active (H) and inactive (L) polypeptide subunits with varied rates of Fe(2+)/O2 catalysis and mineral crystallinity. The relatively low mineral order in liver ferritin, for example, coincides with a high percentage of L subunits and, thus, a low percentage of catalytic sites and nucleation channels. Low mineral order facilitates rapid iron turnover and the physiological role of liver ferritin as a general iron source for other tissues. Here, current concepts of ferritin structure/function/genetic regulation are discussed and related to possible therapeutic targets such as mini-ferritin/Dps protein active sites (selective pathogen inhibition in infection), nanocage pores (iron chelation in therapeutic hypertransfusion), mRNA noncoding, IRE riboregulator (normalizing the ferritin iron content after therapeutic hypertransfusion), and protein nanovessels to deliver medicinal or sensor cargo.
Collapse
Affiliation(s)
- Elizabeth C Theil
- Children's Hospital Oakland Research Institute (CHORI) , 5700 Martin Luther King Jr. Way, Oakland, California 94609, United States , and Department of Molecular and Structural Biochemistry, North Carolina State University , Raleigh, North Carolina 2765-7622, United States
| |
Collapse
|
44
|
RNA with iron(II) as a cofactor catalyses electron transfer. Nat Chem 2013; 5:525-8. [DOI: 10.1038/nchem.1649] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 03/29/2013] [Indexed: 01/03/2023]
|