1
|
Shen M, Goforth JB, Eisenstein RS. Iron-dependent post transcriptional control of mitochondrial aconitase expression. Metallomics 2023; 15:mfac099. [PMID: 36702557 PMCID: PMC9902864 DOI: 10.1093/mtomcs/mfac099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/23/2022] [Indexed: 01/28/2023]
Abstract
Iron regulatory proteins (IRPs) control the translation of animal cell mRNAs encoding proteins with diverse roles. This includes the iron storage protein ferritin and the tricarboxylic cycle (TCA) enzyme mitochondrial aconitase (ACO2) through iron-dependent binding of IRP to the iron responsive element (IRE) in the 5' untranslated region (UTR). To further elucidate the mechanisms allowing IRPs to control translation of 5' IRE-containing mRNA differentially, we focused on Aco2 mRNA, which is weakly controlled versus the ferritins. Rat liver contains two classes of Aco2 mRNAs, with and without an IRE, due to alterations in the transcription start site. Structural analysis showed that the Aco2 IRE adopts the canonical IRE structure but lacks the dynamic internal loop/bulge five base pairs 5' of the CAGUG(U/C) terminal loop in the ferritin IREs. Unlike ferritin mRNAs, the Aco2 IRE lacks an extensive base-paired flanking region. Using a full-length Aco2 mRNA expression construct, iron controlled ACO2 expression in an IRE-dependent and IRE-independent manner, the latter of which was eliminated with the ACO23C3S mutant that cannot bind the FeS cluster. Iron regulation of ACO23C3S encoded by the full-length mRNA was completely IRE-dependent. Replacement of the Aco23C3S 5' UTR with the Fth1 IRE with base-paired flanking sequences substantially improved iron responsiveness, as did fusing of the Fth1 base-paired flanking sequences to the native IRE in the Aco3C3S construct. Our studies further define the mechanisms underlying the IRP-dependent translational regulatory hierarchy and reveal that Aco2 mRNA species lacking the IRE contribute to the expression of this TCA cycle enzyme.
Collapse
Affiliation(s)
- Macy Shen
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Department of Chemistry and Biochemistry, California State University-Fullerton, Fullerton, CA 92834-6866, USA
| | - Jeremy B Goforth
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
- Science Department, Lodi Middle School, 945 S. Ham Lane, Lodi, CA 95242, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin-Madison, 1415 Linden Drive, Madison, WI 53706, USA
| |
Collapse
|
2
|
Hin N, Newman M, Pederson S, Lardelli M. Iron Responsive Element-Mediated Responses to Iron Dyshomeostasis in Alzheimer's Disease. J Alzheimers Dis 2021; 84:1597-1630. [PMID: 34719489 DOI: 10.3233/jad-210200] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Iron trafficking and accumulation is associated with Alzheimer's disease (AD) pathogenesis. However, the role of iron dyshomeostasis in early disease stages is uncertain. Currently, gene expression changes indicative of iron dyshomeostasis are not well characterized, making it difficult to explore these in existing datasets. OBJECTIVE To identify sets of genes predicted to contain iron responsive elements (IREs) and use these to explore possible iron dyshomeostasis-associated gene expression responses in AD. METHODS Comprehensive sets of genes containing predicted IRE or IRE-like motifs in their 3' or 5' untranslated regions (UTRs) were identified in human, mouse, and zebrafish reference transcriptomes. Further analyses focusing on these genes were applied to a range of cultured cell, human, mouse, and zebrafish gene expression datasets. RESULTS IRE gene sets are sufficiently sensitive to distinguish not only between iron overload and deficiency in cultured cells, but also between AD and other pathological brain conditions. Notably, changes in IRE transcript abundance are among the earliest observable changes in zebrafish familial AD (fAD)-like brains, preceding other AD-typical pathologies such as inflammatory changes. Unexpectedly, while some IREs in the 3' untranslated regions of transcripts show significantly increased stability under iron deficiency in line with current assumptions, many such transcripts instead display decreased stability, indicating that this is not a generalizable paradigm. CONCLUSION Our results reveal IRE gene expression changes as early markers of the pathogenic process in fAD and are consistent with iron dyshomeostasis as an important driver of this disease. Our work demonstrates how differences in the stability of IRE-containing transcripts can be used to explore and compare iron dyshomeostasis-associated gene expression responses across different species, tissues, and conditions.
Collapse
Affiliation(s)
- Nhi Hin
- South Australian Genomics Centre, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, Australia.,Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Morgan Newman
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| | - Stephen Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, Faculty of Health & Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Michael Lardelli
- Alzheimer's Disease Genetics Laboratory, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA, Australia
| |
Collapse
|
3
|
Fiddler JL, Clarke SL. Evaluation of candidate reference genes for quantitative real-time PCR analysis in a male rat model of dietary iron deficiency. GENES & NUTRITION 2021; 16:17. [PMID: 34600467 PMCID: PMC8487497 DOI: 10.1186/s12263-021-00698-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/15/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Quantitative real-time polymerase chain reaction (qPCR) is a reliable and efficient method for quantitation of gene expression. Due to the increased use of qPCR in examining nutrient-gene interactions, it is important to examine, develop, and utilize standardized approaches for data analyses and interpretation. A common method used to normalize expression data involves the use of reference genes (RG) to determine relative mRNA abundance. When calculating the relative abundance, the selection of RG can influence experimental results and has the potential to skew data interpretation. Although common RG may be used for normalization, often little consideration is given to the suitability of RG selection for an experimental condition or between various tissue or cell types. In the current study, we examined the stability of gene expression using BestKeeper, comparative delta quantitation cycle, NormFinder, and RefFinder in a variety of tissues obtained from iron-deficient and pair-fed iron-replete rats to determine the optimal selection among ten candidate RG. RESULTS Our results suggest that several commonly used RG (e.g., Actb and Gapdh) exhibit less stability compared to other candidate RG (e.g., Rpl19 and Rps29) in both iron-deficient and iron-replete pair-fed conditions. For all evaluated RG, Tfrc expression significantly increased in iron-deficient animal livers compared to the iron-replete pair-fed controls; however, the relative induction varied nearly 4-fold between the most suitable (Rpl19) and least suitable (Gapdh) RG. CONCLUSION These results indicate the selection and use of RG should be empirically determined and RG selection may vary across experimental conditions and biological tissues.
Collapse
Affiliation(s)
- Joanna L Fiddler
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14850-6301, USA.
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, 74078, USA.
| | - Stephen L Clarke
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| |
Collapse
|
4
|
Conservation in the Iron Responsive Element Family. Genes (Basel) 2021; 12:genes12091365. [PMID: 34573347 PMCID: PMC8466369 DOI: 10.3390/genes12091365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Iron responsive elements (IREs) are mRNA stem-loop targets for translational control by the two iron regulatory proteins IRP1 and IRP2. They are found in the untranslated regions (UTRs) of genes that code for proteins involved in iron metabolism. There are ten “classic” IRE types that define the conserved secondary and tertiary structure elements necessary for proper IRP binding, and there are 83 published “IRE-like” sequences, most of which depart from the established IRE model. Here are structurally-guided discussions regarding the essential features of an IRE and what is important for IRE family membership.
Collapse
|
5
|
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
|
6
|
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
|
7
|
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
|
8
|
Iron-responsive-like elements and neurodegenerative ferroptosis. ACTA ACUST UNITED AC 2020; 27:395-413. [PMID: 32817306 PMCID: PMC7433652 DOI: 10.1101/lm.052282.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022]
Abstract
A set of common-acting iron-responsive 5′untranslated region (5′UTR) motifs can fold into RNA stem loops that appear significant to the biology of cognitive declines of Parkinson's disease dementia (PDD), Lewy body dementia (LDD), and Alzheimer's disease (AD). Neurodegenerative diseases exhibit perturbations of iron homeostasis in defined brain subregions over characteristic time intervals of progression. While misfolding of Aβ from the amyloid-precursor-protein (APP), alpha-synuclein, prion protein (PrP) each cause neuropathic protein inclusions in the brain subregions, iron-responsive-like element (IRE-like) RNA stem–loops reside in their transcripts. APP and αsyn have a role in iron transport while gene duplications elevate the expression of their products to cause rare familial cases of AD and PDD. Of note, IRE-like sequences are responsive to excesses of brain iron in a potential feedback loop to accelerate neuronal ferroptosis and cognitive declines as well as amyloidosis. This pathogenic feedback is consistent with the translational control of the iron storage protein ferritin. We discuss how the IRE-like RNA motifs in the 5′UTRs of APP, alpha-synuclein and PrP mRNAs represent uniquely folded drug targets for therapies to prevent perturbed iron homeostasis that accelerates AD, PD, PD dementia (PDD) and Lewy body dementia, thus preventing cognitive deficits. Inhibition of alpha-synuclein translation is an option to block manganese toxicity associated with early childhood cognitive problems and manganism while Pb toxicity is epigenetically associated with attention deficit and later-stage AD. Pathologies of heavy metal toxicity centered on an embargo of iron export may be treated with activators of APP and ferritin and inhibitors of alpha-synuclein translation.
Collapse
|
9
|
Pulos-Holmes MC, Srole DN, Juarez MG, Lee ASY, McSwiggen DT, Ingolia NT, Cate JH. Repression of ferritin light chain translation by human eIF3. eLife 2019; 8:48193. [PMID: 31414986 PMCID: PMC6721798 DOI: 10.7554/elife.48193] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
A central problem in human biology remains the discovery of causal molecular links between mutations identified in genome-wide association studies (GWAS) and their corresponding disease traits. This challenge is magnified for variants residing in non-coding regions of the genome. Single-nucleotide polymorphisms (SNPs) in the 5ʹ untranslated region (5ʹ-UTR) of the ferritin light chain (FTL) gene that cause hyperferritinemia are reported to disrupt translation repression by altering iron regulatory protein (IRP) interactions with the FTL mRNA 5ʹ-UTR. Here, we show that human eukaryotic translation initiation factor 3 (eIF3) acts as a distinct repressor of FTL mRNA translation, and eIF3-mediated FTL repression is disrupted by a subset of SNPs in FTL that cause hyperferritinemia. These results identify a direct role for eIF3-mediated translational control in a specific human disease.
Collapse
Affiliation(s)
- Mia C Pulos-Holmes
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Daniel N Srole
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Maria G Juarez
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Amy S-Y Lee
- Biology Department, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, United States
| | - David T McSwiggen
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nicholas T Ingolia
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States
| | - Jamie H Cate
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, United States.,Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
10
|
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]
|
11
|
Phosphoinositide-3-kinase inhibition elevates ferritin level resulting depletion of labile iron pool and blocking of glioma cell proliferation. Biochim Biophys Acta Gen Subj 2019; 1863:547-564. [DOI: 10.1016/j.bbagen.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 11/23/2022]
|
12
|
Targeting the Iron-Response Elements of the mRNAs for the Alzheimer's Amyloid Precursor Protein and Ferritin to Treat Acute Lead and Manganese Neurotoxicity. Int J Mol Sci 2019; 20:ijms20040994. [PMID: 30823541 PMCID: PMC6412244 DOI: 10.3390/ijms20040994] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 12/29/2022] Open
Abstract
The therapeutic value of inhibiting translation of the amyloid precursor protein (APP) offers the possibility to reduce neurotoxic amyloid formation, particularly in cases of familial Alzheimer’s disease (AD) caused by APP gene duplications (Dup–APP) and in aging Down syndrome individuals. APP mRNA translation inhibitors such as the anticholinesterase phenserine, and high throughput screened molecules, selectively inhibited the uniquely folded iron-response element (IRE) sequences in the 5’untranslated region (5’UTR) of APP mRNA and this class of drug continues to be tested in a clinical trial as an anti-amyloid treatment for AD. By contrast, in younger age groups, APP expression is not associated with amyloidosis, instead it acts solely as a neuroprotectant while facilitating cellular ferroportin-dependent iron efflux. We have reported that the environmental metallotoxins Lead (Pb) and manganese (Mn) cause neuronal death by interfering with IRE dependent translation of APP and ferritin. The loss of these iron homeostatic neuroprotectants thereby caused an embargo of iron (Fe) export from neurons as associated with excess unstored intracellular iron and the formation of toxic reactive oxidative species (ROS). We propose that APP 5’UTR directed translation activators can be employed therapeutically to protect neurons exposed to high acute Pb and/or Mn exposure. Certainly, high potency APP translation activators, exemplified by the Food and Drug Administration (FDA) pre-approved M1 muscarinic agonist AF102B and high throughput-screened APP 5’UTR translation activators, are available for drug development to treat acute toxicity caused by Pb/Mn exposure to neurons. We conclude that APP translation activators can be predicted to prevent acute metal toxicity to neurons by a mechanism related to the 5’UTR specific yohimbine which binds and targets the canonical IRE RNA stem loop as an H-ferritin translation activator.
Collapse
|
13
|
Venkataramani V, Doeppner TR, Willkommen D, Cahill CM, Xin Y, Ye G, Liu Y, Southon A, Aron A, Au-Yeung HY, Huang X, Lahiri DK, Wang F, Bush AI, Wulf GG, Ströbel P, Michalke B, Rogers JT. Manganese causes neurotoxic iron accumulation via translational repression of amyloid precursor protein and H-Ferritin. J Neurochem 2018; 147:831-848. [PMID: 30152072 PMCID: PMC6310653 DOI: 10.1111/jnc.14580] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 12/24/2022]
Abstract
For more than 150 years, it is known that occupational overexposure of manganese (Mn) causes movement disorders resembling Parkinson's disease (PD) and PD-like syndromes. However, the mechanisms of Mn toxicity are still poorly understood. Here, we demonstrate that Mn dose- and time-dependently blocks the protein translation of amyloid precursor protein (APP) and heavy-chain Ferritin (H-Ferritin), both iron homeostatic proteins with neuroprotective features. APP and H-Ferritin are post-transcriptionally regulated by iron responsive proteins, which bind to homologous iron responsive elements (IREs) located in the 5'-untranslated regions (5'-UTRs) within their mRNA transcripts. Using reporter assays, we demonstrate that Mn exposure repressed the 5'-UTR-activity of APP and H-Ferritin, presumably via increased iron responsive proteins-iron responsive elements binding, ultimately blocking their protein translation. Using two specific Fe2+ -specific probes (RhoNox-1 and IP-1) and ion chromatography inductively coupled plasma mass spectrometry (IC-ICP-MS), we show that loss of the protective axis of APP and H-Ferritin resulted in unchecked accumulation of redox-active ferrous iron (Fe2+ ) fueling neurotoxic oxidative stress. Enforced APP expression partially attenuated Mn-induced generation of cellular and lipid reactive oxygen species and neurotoxicity. Lastly, we could validate the Mn-mediated suppression of APP and H-Ferritin in two rodent in vivo models (C57BL6/N mice and RjHan:SD rats) mimicking acute and chronic Mn exposure. Together, these results suggest that Mn-induced neurotoxicity is partly attributable to the translational inhibition of APP and H-Ferritin resulting in impaired iron metabolism and exacerbated neurotoxic oxidative stress. OPEN SCIENCE BADGES: This article has received a badge for *Open Materials* because it provided all relevant information to reproduce the study in the manuscript. The complete Open Science Disclosure form for this article can be found at the end of the article. More information about the Open Practices badges can be found at https://cos.io/our-services/open-science-badges/.
Collapse
Affiliation(s)
- Vivek Venkataramani
- Department of Hematology and Medical Oncology, University Medical Center Göttingen (UMG), Robert-Koch-Str. 40, 37075 Göttingen, Germany
- Institute of Pathology, University Medical Center Göttingen (UMG), Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Thorsten R. Doeppner
- Department of Neurology, University Medical Center Göttingen (UMG), Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Desiree Willkommen
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit Analytical BioGeoChemistry, Ingolstädter Landstr. 1, 85764 Neuherberg
| | - Catherine M. Cahill
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Yongjuan Xin
- Department of Nutrition, Precision Nutrition Innovation Center, School of Public Health, Zhengzhou University, Zhengzhou 450001
- Department of Nutrition, Nutrition Discovery Innovation Center, Institute of Nutrition and Food Safety, School of Public Health, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guilin Ye
- Department of Nutrition, Precision Nutrition Innovation Center, School of Public Health, Zhengzhou University, Zhengzhou 450001
- Department of Nutrition, Nutrition Discovery Innovation Center, Institute of Nutrition and Food Safety, School of Public Health, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yanyan Liu
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Adam Southon
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, University of Melbourne, 30 Royal Parade, Parkville Vic, Australia 3052
| | - Allegra Aron
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Ho Yu Au-Yeung
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Xudong Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| | - Debomoy K. Lahiri
- Department of Psychiatry, Indiana Alzheimer Disease Center, Stark Neurosciences Research Institute, Indiana University School of Medicine
| | - Fudi Wang
- Department of Nutrition, Precision Nutrition Innovation Center, School of Public Health, Zhengzhou University, Zhengzhou 450001
- Department of Nutrition, Nutrition Discovery Innovation Center, Institute of Nutrition and Food Safety, School of Public Health, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ashley I. Bush
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, University of Melbourne, 30 Royal Parade, Parkville Vic, Australia 3052
| | - Gerald G. Wulf
- Department of Hematology and Medical Oncology, University Medical Center Göttingen (UMG), Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Philipp Ströbel
- Institute of Pathology, University Medical Center Göttingen (UMG), Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Bernhard Michalke
- Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Research Unit Analytical BioGeoChemistry, Ingolstädter Landstr. 1, 85764 Neuherberg
| | - Jack T. Rogers
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA
| |
Collapse
|
14
|
El-Maleky NF, Ebrahim RH. Effects of exposure to electromagnetic field from mobile phone on serum hepcidin and iron status in male albino rats. Electromagn Biol Med 2018; 38:66-73. [DOI: 10.1080/15368378.2018.1531423] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nanees F. El-Maleky
- Faculty of Medicine, Physiology Department, Zagazig University, Zagazig, Egypt
| | - Reham H. Ebrahim
- Faculty of Medicine, Physiology Department, Zagazig University, Zagazig, Egypt
| |
Collapse
|
15
|
Pourcelot E, Lénon M, Charbonnier P, Louis F, Mossuz P, Moulis JM. The iron regulatory proteins are defective in repressing translation via exogenous 5' iron responsive elements despite their relative abundance in leukemic cellular models. Metallomics 2018; 10:639-649. [PMID: 29652073 DOI: 10.1039/c8mt00006a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In animal cells the specific translational control of proteins contributing to iron homeostasis is mediated by the interaction between the Iron Regulatory Proteins (IRP1 and IRP2) and the Iron Responsive Elements (IRE) located in the untranslated regions (UTR) of regulated messengers, such as those encoding ferritin or the transferrin receptor. The absolute concentrations of the components of this regulatory system in hematopoietic cells and the ability of the endogenous IRP to regulate exogenous IRE have been measured. The IRP concentration is in the low μM (10-6 M) range, whereas the most abundant IRE-containing messenger RNA (mRNA), i.e. those of the ferritin subunits, do not exceed 100 nM (10-7 M). Most other IRP mRNA targets are around or below 1 nM. The distribution of the mRNA belonging to the cellular iron network is similar in human leukemic cell lines and in normal cord blood progenitors, with differences among the cellular models only associated with their different propensities to synthesize hemoglobin. Thus, the IRP regulator is in large excess over its presently identified regulated mRNA targets. Yet, despite this excess, endogenous IRP poorly represses translation of transfected luciferase cDNA engineered with a series of IRE sequences in the 5' UTR. The cellular concentrations of the central hubs of the mammalian translational iron network will have to be included in the description of the proliferative phenotype of leukemic cells and in assessing any therapeutic action targeting iron provision.
Collapse
Affiliation(s)
- Emmanuel Pourcelot
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR BEeSy, 38000 Grenoble, France
| | | | | | | | | | | |
Collapse
|
16
|
Mattila RM, Sainio A, Järveläinen M, Pursiheimo J, Järveläinen H. A novel double nucleotide variant in the ferritin-L iron-responsive element in a Finnish patient with hereditary hyperferritinaemia-cataract syndrome. Acta Ophthalmol 2018. [PMID: 28636169 DOI: 10.1111/aos.13492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE To present a novel Finnish double nucleotide variant in the iron-responsive element (IRE) of the ferritin L-chain gene (FTL) leading to hyperferritinaemia-cataract syndrome (HHCS). METHODS Genomic DNA extracted from peripheral blood leucocytes and synthetized with three different primers flanking the IRE in the FTL 5'-untranslated region of the FTL was used in polymerase chain reaction (PCR). Thereafter, Sanger sequencing was performed on the 487-bp and 602-bp PCR amplification products with specific primers to reveal FTL IRE mutations. RESULTS A 58-year-old female patient with elevated serum ferritin level (1339 μg/l) was diagnosed with HHCS after extensive workup. Genetic testing identified a novel double point mutation g.48965355G>C (chr19, hg19) and g.48965356G>T (chr19, hg19) in the lower stem region of the IRE canonical structure of the FTL. CONCLUSION After excluding other causes, elevated serum ferritin level in a person with early onset cataract is indicative for HHCS, a genetic disorder caused by mutation in the IRE of the FTL.
Collapse
Affiliation(s)
| | - Annele Sainio
- Department of Medical Biochemistry and Genetics; University of Turku; Turku Finland
| | | | - Juha Pursiheimo
- Department of Medical Biochemistry and Genetics; University of Turku; Turku Finland
| | - Hannu Järveläinen
- Department of Medical Biochemistry and Genetics; University of Turku; Turku Finland
- Department of Internal Medicine; Satakunta Central Hospital; Pori Finland
| |
Collapse
|
17
|
Johnson NB, Deck KM, Nizzi CP, Eisenstein RS. A synergistic role of IRP1 and FBXL5 proteins in coordinating iron metabolism during cell proliferation. J Biol Chem 2017; 292:15976-15989. [PMID: 28768766 DOI: 10.1074/jbc.m117.785741] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/25/2017] [Indexed: 12/31/2022] Open
Abstract
Iron-regulatory protein 1 (IRP1) belongs to a family of RNA-binding proteins that modulate metazoan iron metabolism. Multiple mechanisms are employed to control the action of IRP1 in dictating changes in the uptake and metabolic fate of iron. Inactivation of IRP1 RNA binding by iron primarily involves insertion of a [4Fe-4S] cluster by the cytosolic iron-sulfur cluster assembly (CIA) system, converting it into cytosolic aconitase (c-acon), but can also involve iron-mediated degradation of IRP1 by the E3 ligase FBXL5 that also targets IRP2. How CIA and FBXL5 collaborate to maintain cellular iron homeostasis through IRP1 and other pathways is poorly understood. Because impaired Fe-S cluster biogenesis associates with human disease, we determined the importance of FBXL5 for regulating IRP1 when CIA is impaired. Suppression of FBXL5 expression coupled with induction of an IRP1 mutant (IRP13C>3S) that cannot insert the Fe-S cluster, or along with knockdown of the CIA factors NUBP2 or FAM96A, reduced cell viability. Iron supplementation reversed this growth defect and was associated with FBXL5-dependent polyubiquitination of IRP1. Phosphorylation of IRP1 at Ser-138 increased when CIA was inhibited and was required for iron rescue. Impaired CIA activity, as noted by reduced c-acon activity, was associated with enhanced FBXL5 expression and a concomitant reduction in IRP1 and IRP2 protein level and RNA-binding activity. Conversely, expression of either IRP induced FBXL5 protein level, demonstrating a negative feedback loop limiting excessive accumulation of iron-response element RNA-binding activity, whose disruption reduces cell growth. We conclude that a regulatory circuit involving FBXL5 and CIA acts through both IRPs to control iron metabolism and promote optimal cell growth.
Collapse
Affiliation(s)
- Nathan B Johnson
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Kathryn M Deck
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Christopher P Nizzi
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Richard S Eisenstein
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| |
Collapse
|
18
|
Rogers JT, Venkataramani V, Washburn C, Liu Y, Tummala V, Jiang H, Smith A, Cahill CM. A role for amyloid precursor protein translation to restore iron homeostasis and ameliorate lead (Pb) neurotoxicity. J Neurochem 2016; 138:479-94. [PMID: 27206843 DOI: 10.1111/jnc.13671] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 03/31/2016] [Accepted: 04/08/2016] [Indexed: 12/30/2022]
Abstract
Iron supplementation ameliorates the neurotoxicity of the environmental contaminant lead (Pb); however, the mechanism remains undefined. Iron is an essential nutrient but high levels are toxic due to the catalytic generation of destructive hydroxyl radicals. Using human neuroblastoma SH-SY5Y cells to model human neurons, we investigated the effect of Pb on proteins of iron homeostasis: the Alzheimer's amyloid precursor protein (APP), which stabilizes the iron exporter ferroportin 1; and, the heavy subunit of the iron-storage protein, ferritin (FTH). Lead (Pb(II) and Pb(IV) inhibited APP translation and raised cytosolic iron(II). Lead also increased iron regulatory protein-1 binding to the cognate 5'untranslated region-specific iron-responsive element (IRE) of APP and FTH mRNAs. Concurrent iron treatment rescued cells from Pb toxicity by specifically restoring APP synthesis, i.e. levels of the APP-related protein, APLP-2, were unchanged. Significantly, iron/IRE-independent over-expression of APP695 protected SH-SY5Y cells from Pb toxicity, demonstrating that APP plays a key role in maintaining safe levels of intracellular iron. Overall, our data support a model of neurotoxicity where Pb enhances iron regulatory protein/IRE-mediated repression of APP and FTH translation. We propose novel treatment options for Pb poisoning to include chelators and the use of small molecules to maintain APP and FTH translation. We propose the following cascade for Lead (Pb) toxicity to neurons; by targeting the interaction between Iron regulatory protein-1 and Iron-responsive elements, Pb caused translational repression of proteins that control intracellular iron homeostasis, including the Alzheimer's amyloid precursor protein (APP) that stabilizes the iron exporter ferroportin, and the ferroxidase heavy subunit of the iron-storage protein, ferritin. When unregulated, IRE-independent over-expression of APP695 protected SH-SY5Y neurons from Pb toxicity. There is a novel and key role for APP in maintaining safe levels of intracellular iron pertinent to lead toxicity.
Collapse
Affiliation(s)
- Jack T Rogers
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital (East), Harvard Medical School, Charlestown, Massachusetts, USA
| | - Vivek Venkataramani
- Department of Hematology and Medical Oncology, University Medical Center, Goettingen, Germany
| | - Cecilia Washburn
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital (East), Harvard Medical School, Charlestown, Massachusetts, USA
| | - Yanyan Liu
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital (East), Harvard Medical School, Charlestown, Massachusetts, USA
| | - Vinusha Tummala
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital (East), Harvard Medical School, Charlestown, Massachusetts, USA
| | - Hong Jiang
- State Key Disciplines: Physiology, Medical College of Qingdao University, Qingdao, China
| | - Ann Smith
- School of Biological Sciences, University of Missouri-K.C., Kansas City, Missouri, USA
| | - Catherine M Cahill
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital (East), Harvard Medical School, Charlestown, Massachusetts, USA
| |
Collapse
|
19
|
Abstract
Virulence gene expression serves two main functions, growth in/on the host, and the acquisition of nutrients. Therefore, it is obvious that nutrient availability is important to control expression of virulence genes. In any cell, enzymes are the components that are best informed about the availability of their respective substrates and products. It is thus not surprising that bacteria have evolved a variety of strategies to employ this information in the control of gene expression. Enzymes that have a second (so-called moonlighting) function in the regulation of gene expression are collectively referred to as trigger enzymes. Trigger enzymes may have a second activity as a direct regulatory protein that can bind specific DNA or RNA targets under particular conditions or they may affect the activity of transcription factors by covalent modification or direct protein-protein interaction. In this chapter, we provide an overview on these mechanisms and discuss the relevance of trigger enzymes for virulence gene expression in bacterial pathogens.
Collapse
|
20
|
Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, Chen ZH, Goldklang MP, Yuan GC, Moore SC, Demeo DL, Rouault TA, D’Armiento JM, Schon EA, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AM. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med 2016; 22:163-74. [PMID: 26752519 PMCID: PMC4742374 DOI: 10.1038/nm.4021] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is linked to both cigarette smoking and genetic determinants. We have previously identified iron-responsive element-binding protein 2 (IRP2) as an important COPD susceptibility gene and have shown that IRP2 protein is increased in the lungs of individuals with COPD. Here we demonstrate that mice deficient in Irp2 were protected from cigarette smoke (CS)-induced experimental COPD. By integrating RNA immunoprecipitation followed by sequencing (RIP-seq), RNA sequencing (RNA-seq), and gene expression and functional enrichment clustering analysis, we identified Irp2 as a regulator of mitochondrial function in the lungs of mice. Irp2 increased mitochondrial iron loading and levels of cytochrome c oxidase (COX), which led to mitochondrial dysfunction and subsequent experimental COPD. Frataxin-deficient mice, which had higher mitochondrial iron loading, showed impaired airway mucociliary clearance (MCC) and higher pulmonary inflammation at baseline, whereas mice deficient in the synthesis of cytochrome c oxidase, which have reduced COX, were protected from CS-induced pulmonary inflammation and impairment of MCC. Mice treated with a mitochondrial iron chelator or mice fed a low-iron diet were protected from CS-induced COPD. Mitochondrial iron chelation also alleviated CS-induced impairment of MCC, CS-induced pulmonary inflammation and CS-associated lung injury in mice with established COPD, suggesting a critical functional role and potential therapeutic intervention for the mitochondrial-iron axis in COPD.
Collapse
MESH Headings
- Aged
- Aged, 80 and over
- Airway Remodeling
- Animals
- Bronchitis/etiology
- Bronchitis/genetics
- Disease Models, Animal
- Electron Transport Complex IV/metabolism
- Electrophoretic Mobility Shift Assay
- Enzyme-Linked Immunosorbent Assay
- Flow Cytometry
- Gene Expression Profiling
- Humans
- Immunoblotting
- Immunohistochemistry
- Immunoprecipitation
- Iron/metabolism
- Iron Chelating Agents/pharmacology
- Iron Regulatory Protein 2/genetics
- Iron Regulatory Protein 2/metabolism
- Iron, Dietary
- Iron-Binding Proteins/genetics
- Lung/drug effects
- Lung/metabolism
- Lung Injury/etiology
- Lung Injury/genetics
- Membrane Potential, Mitochondrial
- Mice
- Mice, Knockout
- Microscopy, Confocal
- Microscopy, Electron, Transmission
- Microscopy, Fluorescence
- Mitochondria/drug effects
- Mitochondria/metabolism
- Mucociliary Clearance/genetics
- Pneumonia/etiology
- Pneumonia/genetics
- Pulmonary Disease, Chronic Obstructive/etiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Emphysema/etiology
- Pulmonary Emphysema/genetics
- Real-Time Polymerase Chain Reaction
- Smoke/adverse effects
- Smoking/adverse effects
- Nicotiana
- Frataxin
Collapse
Affiliation(s)
- Suzanne M. Cloonan
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria E. Laucho-Contreras
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Abhiram R. Bhashyam
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Morgan Cervo
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria A. Pabón
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Csaba Konrad
- Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research institute, Albuquerque, NM, USA
- Pulmonary Department, University of Parma, Parma, Italy
| | - Ilias I. Siempos
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- First Department of Critical Care Medicine and Pulmonary Services, Evangelismos Hospital, University of Athens, Medical School, Athens, Greece
| | - Elizabeth Perez
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Kenji Mizumura
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Manik C. Ghosh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
| | | | - Niamh C. Williams
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Kristen T. Rooney
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Zhi-Hua Chen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Respiratory and Critical Care Medicine, Second Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Monica P. Goldklang
- Department of Anesthesiology, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephen C. Moore
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. Demeo
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tracey A. Rouault
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
| | - Jeanine M. D’Armiento
- Department of Anesthesiology, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- Department of Physiology & Cellular Biophysics, Columbia University, New York, NY, USA
| | - Eric A. Schon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Giovanni Manfredi
- Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashfaq Mahmood
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline A. Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research institute, Albuquerque, NM, USA
| | - Augustine M.K. Choi
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
21
|
Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:61-88. [PMID: 27256382 DOI: 10.1007/978-3-319-29073-7_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dynamic regulation of RNA molecules is critical to the survival and development of cells. Messenger RNAs are transcribed in the nucleus as intron-containing pre-mRNAs and bound by RNA-binding proteins, which control their fate by regulating RNA stability, splicing, polyadenylation, translation, and cellular localization. Most RBPs have distinct mRNA-binding and functional domains; thus, the function of an RBP can be studied independently of RNA-binding by artificially recruiting the RBP to a reporter RNA and then measuring the effect of RBP recruitment on reporter splicing, stability, translational efficiency, or intracellular trafficking. These tethered function assays therefore do not require prior knowledge of the RBP's endogenous RNA targets or its binding sites within these RNAs. Here, we provide an overview of the experimental strategy and the strengths and limitations of common tethering systems. We illustrate specific examples of the application of the assay in elucidating the function of various classes of RBPs. We also discuss how classic tethering assay approaches and insights gained from them have been empowered by more recent technological advances, including efficient genome editing and high-throughput RNA-sequencing.
Collapse
|
22
|
Figueroa-Angulo EE, Calla-Choque JS, Mancilla-Olea MI, Arroyo R. RNA-Binding Proteins in Trichomonas vaginalis: Atypical Multifunctional Proteins. Biomolecules 2015; 5:3354-95. [PMID: 26703754 PMCID: PMC4693282 DOI: 10.3390/biom5043354] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/07/2015] [Accepted: 11/12/2015] [Indexed: 01/08/2023] Open
Abstract
Iron homeostasis is highly regulated in vertebrates through a regulatory system mediated by RNA-protein interactions between the iron regulatory proteins (IRPs) that interact with an iron responsive element (IRE) located in certain mRNAs, dubbed the IRE-IRP regulatory system. Trichomonas vaginalis, the causal agent of trichomoniasis, presents high iron dependency to regulate its growth, metabolism, and virulence properties. Although T. vaginalis lacks IRPs or proteins with aconitase activity, possesses gene expression mechanisms of iron regulation at the transcriptional and posttranscriptional levels. However, only one gene with iron regulation at the transcriptional level has been described. Recently, our research group described an iron posttranscriptional regulatory mechanism in the T. vaginalis tvcp4 and tvcp12 cysteine proteinase mRNAs. The tvcp4 and tvcp12 mRNAs have a stem-loop structure in the 5'-coding region or in the 3'-UTR, respectively that interacts with T. vaginalis multifunctional proteins HSP70, α-Actinin, and Actin under iron starvation condition, causing translation inhibition or mRNA stabilization similar to the previously characterized IRE-IRP system in eukaryotes. Herein, we summarize recent progress and shed some light on atypical RNA-binding proteins that may participate in the iron posttranscriptional regulation in T. vaginalis.
Collapse
Affiliation(s)
- Elisa E Figueroa-Angulo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
| | - Jaeson S Calla-Choque
- Laboratorio de Inmunopatología en Neurocisticercosis, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Urb. Ingeniería, S.M.P., Lima 15102, Peru.
| | - Maria Inocente Mancilla-Olea
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Av. IPN # 2508, Col. San Pedro Zacatenco, CP 07360 México, D.F., Mexico.
| |
Collapse
|
23
|
Abstract
Cellular iron homeostasis is regulated by post-transcriptional feedback mechanisms, which control the expression of proteins involved in iron uptake, release and storage. Two cytoplasmic proteins with mRNA-binding properties, iron regulatory proteins 1 and 2 (IRP1 and IRP2) play a central role in this regulation. Foremost, IRPs regulate ferritin H and ferritin L translation and thus iron storage, as well as transferrin receptor 1 (TfR1) mRNA stability, thereby adjusting receptor expression and iron uptake via receptor-mediated endocytosis of iron-loaded transferrin. In addition splice variants of iron transporters for import and export at the plasma-membrane, divalent metal transporter 1 (DMT1) and ferroportin are regulated by IRPs. These mechanisms have probably evolved to maintain the cytoplasmic labile iron pool (LIP) at an appropriate level. In certain tissues, the regulation exerted by IRPs influences iron homeostasis and utilization of the entire organism. In intestine, the control of ferritin expression limits intestinal iron absorption and, thus, whole body iron levels. In bone marrow, erythroid heme biosynthesis is coordinated with iron availability through IRP-mediated translational control of erythroid 5-aminolevulinate synthase mRNA. Moreover, the translational control of HIF2α mRNA in kidney by IRP1 coordinates erythropoietin synthesis with iron and oxygen supply. Besides IRPs, body iron absorption is negatively regulated by hepcidin. This peptide hormone, synthesized and secreted by the liver in response to high serum iron, downregulates ferroportin at the protein level and thereby limits iron absorption from the diet. Hepcidin will not be discussed in further detail here.
Collapse
Affiliation(s)
- Lukas C Kühn
- Ecole Polytechnique Fédérale de Lausanne (EPFL), ISREC - Swiss Institute for Experimental Cancer Research, EPFL_SV_ISREC, Room SV2516, Station 19, CH-1015 Lausanne, Switzerland.
| |
Collapse
|
24
|
Fillebeen C, Wilkinson N, Pantopoulos K. Electrophoretic mobility shift assay (EMSA) for the study of RNA-protein interactions: the IRE/IRP example. J Vis Exp 2014:52230. [PMID: 25548934 PMCID: PMC4396942 DOI: 10.3791/52230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
RNA/protein interactions are critical for post-transcriptional regulatory pathways. Among the best-characterized cytosolic RNA-binding proteins are iron regulatory proteins, IRP1 and IRP2. They bind to iron responsive elements (IREs) within the untranslated regions (UTRs) of several target mRNAs, thereby controlling the mRNAs translation or stability. IRE/IRP interactions have been widely studied by EMSA. Here, we describe the EMSA protocol for analyzing the IRE-binding activity of IRP1 and IRP2, which can be generalized to assess the activity of other RNA-binding proteins as well. A crude protein lysate containing an RNA-binding protein, or a purified preparation of this protein, is incubated with an excess of(32) P-labeled RNA probe, allowing for complex formation. Heparin is added to preclude non-specific protein to probe binding. Subsequently, the mixture is analyzed by non-denaturing electrophoresis on a polyacrylamide gel. The free probe migrates fast, while the RNA/protein complex exhibits retarded mobility; hence, the procedure is also called "gel retardation" or "bandshift" assay. After completion of the electrophoresis, the gel is dried and RNA/protein complexes, as well as free probe, are detected by autoradiography. The overall goal of the protocol is to detect and quantify IRE/IRP and other RNA/protein interactions. Moreover, EMSA can also be used to determine specificity, binding affinity, and stoichiometry of the RNA/protein interaction under investigation.
Collapse
Affiliation(s)
- Carine Fillebeen
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University
| | - Nicole Wilkinson
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Jewish General Hospital; Department of Medicine, McGill University;
| |
Collapse
|
25
|
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
|
26
|
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
|
27
|
Bandyopadhyay S, Cahill C, Balleidier A, Huang C, Lahiri DK, Huang X, Rogers JT. Novel 5' untranslated region directed blockers of iron-regulatory protein-1 dependent amyloid precursor protein translation: implications for down syndrome and Alzheimer's disease. PLoS One 2013; 8:e65978. [PMID: 23935819 PMCID: PMC3729844 DOI: 10.1371/journal.pone.0065978] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 04/30/2013] [Indexed: 11/19/2022] Open
Abstract
We reported that iron influx drives the translational expression of the neuronal amyloid precursor protein (APP), which has a role in iron efflux. This is via a classic release of repressor interaction of APP mRNA with iron-regulatory protein-1 (IRP1) whereas IRP2 controls the mRNAs encoding the L- and H-subunits of the iron storage protein, ferritin. Here, we identified thirteen potent APP translation blockers that acted selectively towards the uniquely configured iron-responsive element (IRE) RNA stem loop in the 5' untranslated region (UTR) of APP mRNA. These agents were 10-fold less inhibitory of 5'UTR sequences of the related prion protein (PrP) mRNA. Western blotting confirmed that the 'ninth' small molecule in the series selectively reduced neural APP production in SH-SY5Y cells at picomolar concentrations without affecting viability or the expression of α-synuclein and ferritin. APP blocker-9 (JTR-009), a benzimidazole, reduced the production of toxic Aβ in SH-SY5Y neuronal cells to a greater extent than other well tolerated APP 5'UTR-directed translation blockers, including posiphen, that were shown to limit amyloid burden in mouse models of Alzheimer's disease (AD). RNA binding assays demonstrated that JTR-009 operated by preventing IRP1 from binding to the IRE in APP mRNA, while maintaining IRP1 interaction with the H-ferritin IRE RNA stem loop. Thus, JTR-009 constitutively repressed translation driven by APP 5'UTR sequences. Calcein staining showed that JTR-009 did not indirectly change iron uptake in neuronal cells suggesting a direct interaction with the APP 5'UTR. These studies provide key data to develop small molecules that selectively reduce neural APP and Aβ production at 10-fold lower concentrations than related previously characterized translation blockers. Our data evidenced a novel therapeutic strategy of potential impact for people with trisomy of the APP gene on chromosome 21, which is a phenotype long associated with Down syndrome (DS) that can also cause familial Alzheimer's disease.
Collapse
Affiliation(s)
- Sanghamitra Bandyopadhyay
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Catherine Cahill
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
- Department of Pediatrics, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Amelie Balleidier
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Conan Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Debomoy K. Lahiri
- Laboratory of Molecular Neurogenetics, Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Xudong Huang
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
| | - Jack T. Rogers
- Neurochemistry Laboratory, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
28
|
Selezneva AI, Walden WE, Volz KW. Nucleotide-specific recognition of iron-responsive elements by iron regulatory protein 1. J Mol Biol 2013; 425:3301-10. [PMID: 23806658 DOI: 10.1016/j.jmb.2013.06.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 05/31/2013] [Accepted: 06/17/2013] [Indexed: 12/26/2022]
Abstract
IRP1 [iron regulatory protein (IRP) 1] is a bifunctional protein with mutually exclusive end-states. In one mode of operation, IRP1 binds iron-responsive element (IRE) stem-loops in messenger RNAs encoding proteins of iron metabolism to control their rate of translation. In its other mode, IRP1 serves as cytoplasmic aconitase to correlate iron availability with the energy and oxidative stress status of the cell. IRP1/IRE binding occurs through two separate interfaces, which together contribute about two-dozen hydrogen bonds. Five amino acids make base-specific contacts and are expected to contribute significantly to binding affinity and specificity of this protein:RNA interaction. In this mutagenesis study, each of the five base-specific amino acids was changed to alter binding at each site. Analysis of IRE binding affinity and translational repression activity of the resulting IRP1 mutants showed that four of the five contact points contribute uniquely to the overall binding affinity of the IRP1:IRE interaction, while one site was found to be unimportant. The stronger-than-expected effect on binding affinity of mutations at Lys379 and Ser681, residues that make contact with the conserved nucleotides G16 and C8, respectively, identified them as particularly critical for providing specificity and stability to IRP1:IRE complex formation. We also show that even though the base-specific RNA-binding residues are not part of the aconitase active site, their substitutions can affect the aconitase activity of holo-IRP1, positively or negatively.
Collapse
Affiliation(s)
- Anna I Selezneva
- Department of Microbiology and Immunology, University of Illinois at Chicago, IL 60612-7334, USA.
| | | | | |
Collapse
|
29
|
Anderson SA, Nizzi CP, Chang YI, Deck KM, Schmidt PJ, Galy B, Damnernsawad A, Broman AT, Kendziorski C, Hentze MW, Fleming MD, Zhang J, Eisenstein RS. The IRP1-HIF-2α axis coordinates iron and oxygen sensing with erythropoiesis and iron absorption. Cell Metab 2013; 17:282-90. [PMID: 23395174 PMCID: PMC3612289 DOI: 10.1016/j.cmet.2013.01.007] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 11/19/2012] [Accepted: 01/14/2013] [Indexed: 11/21/2022]
Abstract
Red blood cell production is a finely tuned process that requires coordinated oxygen- and iron-dependent regulation of cell differentiation and iron metabolism. Here, we show that translational regulation of hypoxia-inducible factor 2α (HIF-2α) synthesis by iron regulatory protein 1 (IRP1) is critical for controlling erythrocyte number. IRP1-null (Irp1(-/-)) mice display a marked transient polycythemia. HIF-2α messenger RNA (mRNA) is derepressed in kidneys of Irp1(-/-) mice but not in kidneys of Irp2(-/-) mice, leading to increased renal erythropoietin (Epo) mRNA and inappropriately elevated serum Epo levels. Expression of the iron transport genes DCytb, Dmt1, and ferroportin, as well as other HIF-2α targets, is enhanced in Irp1(-/-) duodenum. Analysis of mRNA translation state in the liver revealed IRP1-dependent dysregulation of HIF-2α mRNA translation, whereas IRP2 deficiency derepressed translation of all other known 5' iron response element (IRE)-containing mRNAs expressed in the liver. These results uncover separable physiological roles of each IRP and identify IRP1 as a therapeutic target for manipulating HIF-2α action in hematologic, oncologic, and other disorders.
Collapse
Affiliation(s)
- Sheila A. Anderson
- Dept. of Nutritional Sciences, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christopher P. Nizzi
- Dept. of Nutritional Sciences, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuan-I Chang
- McCardle Laboratory for Cancer Research, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kathryn M. Deck
- Dept. of Nutritional Sciences, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Paul J. Schmidt
- Dept. of Pathology, Boston Children’s Hospital and Harvard Medical School, 320 Longwood Ave., Boston, MA 02115, USA
| | - Bruno Galy
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Alisa Damnernsawad
- McCardle Laboratory for Cancer Research, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Aimee T. Broman
- Biostatistics and Medical Informatics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christina Kendziorski
- Biostatistics and Medical Informatics, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthias W. Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mark D. Fleming
- Dept. of Pathology, Boston Children’s Hospital and Harvard Medical School, 320 Longwood Ave., Boston, MA 02115, USA
| | - Jing Zhang
- McCardle Laboratory for Cancer Research, Univ. of Wisconsin-Madison, Madison, WI 53706, USA
| | | |
Collapse
|
30
|
Mikkilineni S, Cantuti-Castelvetri I, Cahill CM, Balliedier A, Greig NH, Rogers JT. The anticholinesterase phenserine and its enantiomer posiphen as 5'untranslated-region-directed translation blockers of the Parkinson's alpha synuclein expression. PARKINSON'S DISEASE 2012; 2012:142372. [PMID: 22693681 PMCID: PMC3368596 DOI: 10.1155/2012/142372] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 02/29/2012] [Indexed: 12/15/2022]
Abstract
There is compelling support for limiting expression of alpha-synuclein (α-syn) in the brains of Parkinson's disease (PD) patients. An increase of SNCA gene copy number can genetically cause familial PD where increased dose of this pathogenic protein correlates with severity of symptoms (triplication of the SNCA gene causes dementia in PD patients). Gene promoter polymorphisms were shown to increase α-synuclein expression as a risk for PD. Cholinesterase inhibitors can clinically slow cognitive decline in the later stages of PD etiology similar to their widespread use in Alzheimer's disease (AD). Pertinent to this, we identified that the well-tolerated anticholinesterase, phenserine, blocked neural SNCA mRNA translation and tested for targeting via its 5'untranslated region (5'UTR) in a manner similar to its action to limit the expression of the AD-specific amyloid precursor protein (APP). Posiphen, its better-tolerated (+) enantiomer (devoid of anticholinesterase action), repressed neural α-synuclein translation. Primary metabolic analogs of posiphen were, likewise, characterized using primary fetal neurons grown ex vivo from the brains of Parkinson's transgenic mice expressing the human SNCA gene.
Collapse
Affiliation(s)
- Sohan Mikkilineni
- Neurochemistry Laboratory, Massachusetts General Hospital (East), CNY2, 149, 13th Street, Charlestown, MA 02129, USA
| | | | - Catherine M. Cahill
- Neurochemistry Laboratory, Massachusetts General Hospital (East), CNY2, 149, 13th Street, Charlestown, MA 02129, USA
| | - Amelie Balliedier
- Neurochemistry Laboratory, Massachusetts General Hospital (East), CNY2, 149, 13th Street, Charlestown, MA 02129, USA
| | - Nigel H. Greig
- Drug Design and Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, Baltimore, MD 21224, USA
| | - Jack T. Rogers
- Neurochemistry Laboratory, Massachusetts General Hospital (East), CNY2, 149, 13th Street, Charlestown, MA 02129, USA
| |
Collapse
|
31
|
Anderson CP, Shen M, Eisenstein RS, Leibold EA. Mammalian iron metabolism and its control by iron regulatory proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:1468-83. [PMID: 22610083 DOI: 10.1016/j.bbamcr.2012.05.010] [Citation(s) in RCA: 331] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/07/2012] [Accepted: 05/11/2012] [Indexed: 02/06/2023]
Abstract
Cellular iron homeostasis is maintained by iron regulatory proteins 1 and 2 (IRP1 and IRP2). IRPs bind to iron-responsive elements (IREs) located in the untranslated regions of mRNAs encoding protein involved in iron uptake, storage, utilization and export. Over the past decade, significant progress has been made in understanding how IRPs are regulated by iron-dependent and iron-independent mechanisms and the pathological consequences of IRP2 deficiency in mice. The identification of novel IREs involved in diverse cellular pathways has revealed that the IRP-IRE network extends to processes other than iron homeostasis. A mechanistic understanding of IRP regulation will likely yield important insights into the basis of disorders of iron metabolism. This article is part of a Special Issue entitled: Cell Biology of Metals.
Collapse
Affiliation(s)
- Cole P Anderson
- Department of Oncological Sciences, University of Utah, 15 N. 2030 E., Salt Lake City, UT 84112, USA
| | | | | | | |
Collapse
|
32
|
Fe2+ binds iron responsive element-RNA, selectively changing protein-binding affinities and regulating mRNA repression and activation. Proc Natl Acad Sci U S A 2012; 109:8417-22. [PMID: 22586079 DOI: 10.1073/pnas.1120045109] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Iron increases synthesis rates of proteins encoded in iron-responsive element (IRE)-mRNAs; metabolic iron ("free," "labile") is Fe(2+). The noncoding IRE-RNA structure, approximately 30 nt, folds into a stem loop to control synthesis of proteins in iron trafficking, cell cycling, and nervous system function. IRE-RNA riboregulators bind specifically to iron-regulatory proteins (IRP) proteins, inhibiting ribosome binding. Deletion of the IRE-RNA from an mRNA decreases both IRP binding and IRP-independent protein synthesis, indicating effects of other "factors." Current models of IRE-mRNA regulation, emphasizing iron-dependent degradation/modification of IRP, lack answers about how iron increases IRE-RNA/IRP protein dissociation or how IRE-RNA, after IRP dissociation, influences protein synthesis rates. However, we observed Fe(2+) (anaerobic) or Mn(2+) selectively increase the IRE-RNA/IRP K(D). Here we show: (i) Fe(2+) binds to the IRE-RNA, altering its conformation (by 2-aminopurine fluorescence and ethidium bromide displacement); (ii) metal ions increase translation of IRE-mRNA in vitro; (iii) eukaryotic initiation factor (eIF)4F binds specifically with high affinity to IRE-RNA; (iv) Fe(2+) increased eIF4F/IRE-RNA binding, which outcompetes IRP binding; (v) exogenous eIF4F rescued metal-dependent IRE-RNA translation in eIF4F-depeleted extracts. The regulation by metabolic iron binding to IRE-RNA to decrease inhibitor protein (IRP) binding and increase activator protein (eIF4F) binding identifies IRE-RNA as a riboregulator.
Collapse
|
33
|
Synowiec E, Pogorzelska M, Blasiak J, Szaflik J, Szaflik JP. Genetic polymorphism of the iron-regulatory protein-1 and -2 genes in age-related macular degeneration. Mol Biol Rep 2012; 39:7077-87. [PMID: 22331484 PMCID: PMC3334491 DOI: 10.1007/s11033-012-1539-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 01/24/2012] [Indexed: 12/24/2022]
Abstract
Iron can be involved in the pathogenesis of AMD through the oxidative stress because it may catalyze the Haber–Weiss and Fenton reactions converting hydrogen peroxide to free radicals, which can induce cellular damage. We hypothesized that genetic polymorphism in genes related to iron metabolism may predispose individuals to the development of AMD and therefore we checked for an association between the g.32373708 G>A polymorphism (rs867469) of the IRP1 gene and the g.49520870 G>A (rs17483548) polymorphism of the IRP2 gene and AMD risk as well as the modulation of this association by some environmental and life-style factors. Genotypes were determined in DNA from blood of 269 AMD patients and 116 controls by the allele-specific oligonucleotide-restriction fragment length polymorphism and the polymerase chain reaction-restriction fragment length polymorphism. An association between AMD, dry and wet forms of AMD and the G/G genotype of the g.32373708 G>A-IRP1 polymorphism was found (OR 3.40, 4.15, and 2.75). On the other hand, the G/A genotype reduced the risk of AMD as well as its dry or wet form (OR 0.23, 0.21, 0.26). Moreover, the G allele of the g.49520870 G>A-IRP2 polymorphism increased the risk of the dry form of the disease (OR 1.51) and the A/A genotype and the A allele decreased such risk (OR 0.43 and 0.66). Our data suggest that the g.32373708 G>A-IRP1 and g.49520870 G>A-IRP2 polymorphisms may be associated with increased risk for AMD.
Collapse
Affiliation(s)
- Ewelina Synowiec
- Department of Molecular Genetics, University of Lodz, Lodz, Poland
| | | | | | | | | |
Collapse
|
34
|
Goss DJ, Theil EC. Iron responsive mRNAs: a family of Fe2+ sensitive riboregulators. Acc Chem Res 2011; 44:1320-8. [PMID: 22026512 DOI: 10.1021/ar2001149] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Messenger RNAs (mRNAs) are emerging as prime targets for small-molecule drugs. They afford an opportunity to assert control over an enormous range of biological processes: mRNAs regulate protein synthesis rates, have specific 3-D regulatory structures, and, in nucleated cells, are separated from DNA in space and time. All of the many steps between DNA copying (transcription) and ribosome binding (translation) represent potential control points. Messenger RNAs can fold into complex, 3-D shapes, such as tRNAs and rRNAs, providing an added dimension to the 2-D RNA structure (base pairing) targeted in many mRNA interference approaches. In this Account, we describe the structural and functional properties of the IRE (iron-responsive element) family, one of the few 3-D mRNA regulatory elements with known 3-D structure. This family of related base sequences regulates the mRNAs that encode proteins for iron metabolism. We begin by considering the IRE-RNA structure, which consists of a short (~30-nucleotide) RNA helix. Nature tuned the structure by combining a conserved AGU pseudotriloop, a closing C-G base pair, and a bulge C with various RNA helix base pairs. The result is a set of IRE-mRNAs with individual iron responses. The physiological iron signal is hexahydrated ferrous ion; in vivo iron responses vary over 10-fold depending on the individual IRE-RNA structure. We then discuss the interaction between the IRE-RNA structure and the proteins associated with it. IRE-RNA structures, which are usually noncoding, tightly bind specific proteins called IRPs. These repressor proteins are bound to IRE-RNA through C-bulge and AGU contacts that flip out a loop AG and a bulge C, bending the RNA helix. After binding, the exposed RNA surface then invites further interactions, such as with iron and other proteins. Binding of the IRE-RNA and the IRP also changes the IRP conformation. IRP binding stabilities vary 10-fold within the IRE family, reflecting individual IRE-RNA paired and unpaired bases. This variation contributes to the graded (hierarchical) iron responses in vivo. We also consider the mechanisms of IRE-mRNA control. The binding of Fe(2+) to IRE-RNA facilitates IRP release and the binding of eukaryotic initiation factors (eIFs), which are proteins that assemble mRNA, ribosomes, and tRNA for translation. IRE-RNAs are riboregulators for the inorganic metabolic signal, Fe(2+); they control protein synthesis rates by changing the distribution of the iron metabolic mRNAs between complexes with enhancing eIFs and inhibitory IRPs. The regulation of mRNA in the cytoplasm of eukaryotic cells is a burgeoning frontier in biomedicine. The evolutionarily refined IRE-RNAs, although absent in plants and bacteria, constitute a model system for 3-D mRNAs in all organisms. IRE-mRNAs have yielded "proof of principle" data for small-molecule targeting of mRNA structures, demonstrating tremendous potential for chemical manipulation of mRNA and protein synthesis in living systems.
Collapse
Affiliation(s)
- Dixie J. Goss
- Department of Chemistry, Hunter College CUNY, 695 Park Avenue, New York, New York 10065, United States
| | - Elizabeth C. Theil
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King, Jr. Way, Oakland, California 94609, United States
| |
Collapse
|
35
|
Walden WE, Selezneva A, Volz K. Accommodating variety in iron-responsive elements: Crystal structure of transferrin receptor 1 B IRE bound to iron regulatory protein 1. FEBS Lett 2011; 586:32-5. [PMID: 22119729 DOI: 10.1016/j.febslet.2011.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 12/27/2022]
Abstract
Iron responsive elements (IREs) are short stem-loop structures found in several mRNAs encoding proteins involved in cellular iron metabolism. Iron regulatory proteins (IRPs) control iron homeostasis through differential binding to the IREs, accommodating any sequence or structural variations that the IREs may present. Here we report the structure of IRP1 in complex with transferrin receptor 1 B (TfR B) IRE, and compare it to the complex with ferritin H (Ftn H) IRE. The two IREs are bound to IRP1 through nearly identical protein-RNA contacts, although their stem conformations are significantly different. These results support the view that binding of different IREs with IRP1 depends both on protein and RNA conformational plasticity, adapting to RNA variation while retaining conserved protein-RNA contacts.
Collapse
Affiliation(s)
- William E Walden
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
| | | | | |
Collapse
|
36
|
Iron regulatory protein-1 and -2: transcriptome-wide definition of binding mRNAs and shaping of the cellular proteome by iron regulatory proteins. Blood 2011; 118:e168-79. [PMID: 21940823 DOI: 10.1182/blood-2011-04-343541] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Iron regulatory proteins (IRPs) 1 and 2 are RNA-binding proteins that control cellular iron metabolism by binding to conserved RNA motifs called iron-responsive elements (IREs). The currently known IRP-binding mRNAs encode proteins involved in iron uptake, storage, and release as well as heme synthesis. To systematically define the IRE/IRP regulatory network on a transcriptome-wide scale, IRP1/IRE and IRP2/IRE messenger ribonucleoprotein complexes were immunoselected, and the mRNA composition was determined using microarrays. We identify 35 novel mRNAs that bind both IRP1 and IRP2, and we also report for the first time cellular mRNAs with exclusive specificity for IRP1 or IRP2. To further explore cellular iron metabolism at a system-wide level, we undertook proteomic analysis by pulsed stable isotope labeling by amino acids in cell culture in an iron-modulated mouse hepatic cell line and in bone marrow-derived macrophages from IRP1- and IRP2-deficient mice. This work investigates cellular iron metabolism in unprecedented depth and defines a wide network of mRNAs and proteins with iron-dependent regulation, IRP-dependent regulation, or both.
Collapse
|
37
|
Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. Understanding the transcriptome through RNA structure. Nat Rev Genet 2011; 12:641-55. [PMID: 21850044 DOI: 10.1038/nrg3049] [Citation(s) in RCA: 325] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by high-throughput sequencing has enabled genome-wide measurements of RNA structure and has provided the first picture of the structural organization of a eukaryotic transcriptome - the 'RNA structurome'. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes and thereby increase understanding of RNA function.
Collapse
Affiliation(s)
- Yue Wan
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|
38
|
Abstract
Nonheme food ferritin (FTN) iron minerals, nonheme iron complexes, and heme iron contribute to the balance between food iron absorption and body iron homeostasis. Iron absorption depends on membrane transporter proteins DMT1, PCP/HCP1, ferroportin (FPN), TRF2, and matriptase 2. Mutations in DMT1 and matriptase-2 cause iron deficiency; mutations in FPN, HFE, and TRF2 cause iron excess. Intracellular iron homeostasis depends on coordinated regulation of iron trafficking and storage proteins encoded in iron responsive element (IRE)-mRNA. The noncoding IRE-mRNA structures bind protein repressors, IRP1 or 2, during iron deficiency. Integration of the IRE-RNA in translation regulators (near the cap) or turnover elements (after the coding region) increases iron uptake (DMT1/TRF1) or decreases iron storage/efflux (FTN/FPN) when IRP binds. An antioxidant response element in FTN DNA binds Bach1, a heme-sensitive transcription factor that coordinates expression among antioxidant response proteins like FTN, thioredoxin reductase, and quinone reductase. FTN, an antioxidant because Fe(2+) and O(2) (reactive oxygen species generators) are consumed to make iron mineral, is also a nutritional iron concentrate that is an efficiently absorbed, nonheme source of iron from whole legumes. FTN protein cages contain thousands of mineralized iron atoms and enter cells by receptor-mediated endocytosis, an absorption mechanism distinct from transport of nonheme iron salts (ferrous sulfate), iron chelators (ferric-EDTA), or heme. Recognition of 2 nutritional nonheme iron sources, small and large (FTN), will aid the solution of iron deficiency, a major public health problem, and the development of new policies on iron nutrition.
Collapse
|
39
|
Rogers JT, Mikkilineni S, Cantuti-Castelvetri I, Smith DH, Huang X, Bandyopadhyay S, Cahill CM, Maccecchini ML, Lahiri DK, Greig NH. The alpha-synuclein 5'untranslated region targeted translation blockers: anti-alpha synuclein efficacy of cardiac glycosides and Posiphen. J Neural Transm (Vienna) 2011; 118:493-507. [PMID: 21221670 PMCID: PMC6625511 DOI: 10.1007/s00702-010-0513-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/15/2010] [Indexed: 12/24/2022]
Abstract
Increased brain α-synuclein (SNCA) protein expression resulting from gene duplication and triplication can cause a familial form of Parkinson's disease (PD). Dopaminergic neurons exhibit elevated iron levels that can accelerate toxic SNCA fibril formation. Examinations of human post mortem brain have shown that while mRNA levels for SNCA in PD have been shown to be either unchanged or decreased with respect to healthy controls, higher levels of insoluble protein occurs during PD progression. We show evidence that SNCA can be regulated via the 5'untranslated region (5'UTR) of its transcript, which we modeled to fold into a unique RNA stem loop with a CAGUGN apical loop similar to that encoded in the canonical iron-responsive element (IRE) of L- and H-ferritin mRNAs. The SNCA IRE-like stem loop spans the two exons that encode its 5'UTR, whereas, by contrast, the H-ferritin 5'UTR is encoded by a single first exon. We screened a library of 720 natural products (NPs) for their capacity to inhibit SNCA 5'UTR driven luciferase expression. This screen identified several classes of NPs, including the plant cardiac glycosides, mycophenolic acid (an immunosuppressant and Fe chelator), and, additionally, posiphen was identified to repress SNCA 5'UTR conferred translation. Western blotting confirmed that Posiphen and the cardiac glycoside, strophanthidine, selectively blocked SNCA expression (~1 μM IC(50)) in neural cells. For Posiphen this inhibition was accelerated in the presence of iron, thus providing a known APP-directed lead with potential for use as a SNCA blocker for PD therapy. These are candidate drugs with the potential to limit toxic SNCA expression in the brains of PD patients and animal models in vivo.
Collapse
Affiliation(s)
- Jack T Rogers
- Neurochemistry Laboratory, Psychiatry-Neuroscience, Massachusetts General Hospital, Charlestown, MA 02129, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Ahmed F, Benedito VA, Zhao PX. Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. FRONTIERS IN PLANT SCIENCE 2011; 2:84. [PMID: 22639614 PMCID: PMC3355573 DOI: 10.3389/fpls.2011.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/03/2011] [Indexed: 05/03/2023]
Abstract
Eukaryotic messenger RNA (mRNA) contains not only protein-coding regions but also a plethora of functional cis-elements that influence or coordinate a number of regulatory aspects of gene expression, such as mRNA stability, splicing forms, and translation rates. Understanding the rules that apply to each of these element types (e.g., whether the element is defined by primary or higher-order structure) allows for the discovery of novel mechanisms of gene expression as well as the design of transcripts with controlled expression. Bioinformatics plays a major role in creating databases and finding non-evident patterns governing each type of eukaryotic functional element. Much of what we currently know about mRNA regulatory elements in eukaryotes is derived from microorganism and animal systems, with the particularities of plant systems lagging behind. In this review, we provide a general introduction to the most well-known eukaryotic mRNA regulatory motifs (splicing regulatory elements, internal ribosome entry sites, iron-responsive elements, AU-rich elements, zipcodes, and polyadenylation signals) and describe available bioinformatics resources (databases and analysis tools) to analyze eukaryotic transcripts in search of functional elements, focusing on recent trends in bioinformatics methods and tool development. We also discuss future directions in the development of better computational tools based upon current knowledge of these functional elements. Improved computational tools would advance our understanding of the processes underlying gene regulations. We encourage plant bioinformaticians to turn their attention to this subject to help identify novel mechanisms of gene expression regulation using RNA motifs that have potentially evolved or diverged in plant species.
Collapse
Affiliation(s)
- Firoz Ahmed
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Vagner A. Benedito
- Genetics and Developmental Biology, Plant and Soil Sciences Division, West Virginia UniversityMorgantown, WV, USA
| | - Patrick Xuechun Zhao
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
- *Correspondence: Patrick Xuechun Zhao, Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA e-mail:
| |
Collapse
|
41
|
Recalcati S, Minotti G, Cairo G. Iron regulatory proteins: from molecular mechanisms to drug development. Antioxid Redox Signal 2010; 13:1593-616. [PMID: 20214491 DOI: 10.1089/ars.2009.2983] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Eukaryotic cells require iron for survival but, as an excess of poorly liganded iron can lead to the catalytic production of toxic radicals that can damage cell structures, regulatory mechanisms have been developed to maintain appropriate cell and body iron levels. The interactions of iron responsive elements (IREs) with iron regulatory proteins (IRPs) coordinately regulate the expression of the genes involved in iron uptake, use, storage, and export at the post-transcriptional level, and represent the main regulatory network controlling cell iron homeostasis. IRP1 and IRP2 are similar (but not identical) proteins with partially overlapping and complementary functions, and control cell iron metabolism by binding to IREs (i.e., conserved RNA stem-loops located in the untranslated regions of a dozen mRNAs directly or indirectly related to iron metabolism). The discovery of the presence of IREs in a number of other mRNAs has extended our knowledge of the influence of the IRE/IRP regulatory network to new metabolic pathways, and it has been recently learned that an increasing number of agents and physiopathological conditions impinge on the IRE/IRP system. This review focuses on recent findings concerning the IRP-mediated regulation of iron homeostasis, its alterations in disease, and new research directions to be explored in the near future.
Collapse
Affiliation(s)
- Stefania Recalcati
- Department of Human Morphology and Biomedical Sciences Città Studi, University of Milan, Milano, Italy
| | | | | |
Collapse
|
42
|
Hentze MW, Muckenthaler MU, Galy B, Camaschella C. Two to tango: regulation of Mammalian iron metabolism. Cell 2010; 142:24-38. [PMID: 20603012 DOI: 10.1016/j.cell.2010.06.028] [Citation(s) in RCA: 1408] [Impact Index Per Article: 100.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 06/14/2010] [Accepted: 06/21/2010] [Indexed: 02/06/2023]
Abstract
Disruptions in iron homeostasis from both iron deficiency and overload account for some of the most common human diseases. Iron metabolism is balanced by two regulatory systems, one that functions systemically and relies on the hormone hepcidin and the iron exporter ferroportin, and another that predominantly controls cellular iron metabolism through iron-regulatory proteins that bind iron-responsive elements in regulated messenger RNAs. We describe how the two distinct systems function and how they "tango" together in a coordinated manner. We also highlight some of the current questions in mammalian iron metabolism and discuss therapeutic opportunities arising from a better understanding of the underlying biological principles.
Collapse
Affiliation(s)
- Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | | | | | | |
Collapse
|
43
|
Cho HH, Cahill CM, Vanderburg CR, Scherzer CR, Wang B, Huang X, Rogers JT. Selective translational control of the Alzheimer amyloid precursor protein transcript by iron regulatory protein-1. J Biol Chem 2010; 285:31217-32. [PMID: 20558735 DOI: 10.1074/jbc.m110.149161] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Iron influx increases the translation of the Alzheimer amyloid precursor protein (APP) via an iron-responsive element (IRE) RNA stem loop in its 5'-untranslated region. Equal modulated interaction of the iron regulatory proteins (IRP1 and IRP2) with canonical IREs controls iron-dependent translation of the ferritin subunits. However, our immunoprecipitation RT-PCR and RNA binding experiments demonstrated that IRP1, but not IRP2, selectively bound the APP IRE in human neural cells. This selective IRP1 interaction pattern was evident in human brain and blood tissue from normal and Alzheimer disease patients. We computer-predicted an optimal novel RNA stem loop structure for the human, rhesus monkey, and mouse APP IREs with reference to the canonical ferritin IREs but also the IREs encoded by erythroid heme biosynthetic aminolevulinate synthase and Hif-2α mRNAs, which preferentially bind IRP1. Selective 2'-hydroxyl acylation analyzed by primer extension analysis was consistent with a 13-base single-stranded terminal loop and a conserved GC-rich stem. Biotinylated RNA probes deleted of the conserved CAGA motif in the terminal loop did not bind to IRP1 relative to wild type probes and could no longer base pair to form a predicted AGA triloop. An AGU pseudo-triloop is key for IRP1 binding to the canonical ferritin IREs. RNA probes encoding the APP IRE stem loop exhibited the same high affinity binding to rhIRP1 as occurs for the H-ferritin IRE (35 pm). Intracellular iron chelation increased binding of IRP1 to the APP IRE, decreasing intracellular APP expression in SH-SY5Y cells. Functionally, shRNA knockdown of IRP1 caused increased expression of neural APP consistent with IRP1-APP IRE-driven translation.
Collapse
Affiliation(s)
- Hyun-Hee Cho
- Neurochemistry Laboratory, Department of Psychiatry-Neuroscience, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
| | | | | | | | | | | | | |
Collapse
|
44
|
Campillos M, Cases I, Hentze MW, Sanchez M. SIREs: searching for iron-responsive elements. Nucleic Acids Res 2010; 38:W360-7. [PMID: 20460462 PMCID: PMC2896125 DOI: 10.1093/nar/gkq371] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The iron regulatory protein/iron-responsive element regulatory system plays a crucial role in the post-transcriptional regulation of gene expression and its disruption results in human disease. IREs are cis-acting regulatory motifs present in mRNAs that encode proteins involved in iron metabolism. They function as binding sites for two related trans-acting factors, namely the IRP-1 and -2. Among cis-acting RNA regulatory elements, the IRE is one of the best characterized. It is defined by a combination of RNA sequence and structure. However, currently available programs to predict IREs do not show a satisfactory level of sensitivity and fail to detect some of the functional IREs. Here, we report an improved software for the prediction of IREs implemented as a user-friendly web server tool. The SIREs web server uses a simple data input interface and provides structure analysis, predicted RNA folds, folding energy data and an overall quality flag based on properties of well characterized IREs. Results are reported in a tabular format and as a schematic visual representation that highlights important features of the IRE. The SIREs (Search for iron-responsive elements) web server is freely available on the web at http://ccbg.imppc.org/sires/index.html
Collapse
Affiliation(s)
- Monica Campillos
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | |
Collapse
|