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Dixon SJ, Olzmann JA. The cell biology of ferroptosis. Nat Rev Mol Cell Biol 2024; 25:424-442. [PMID: 38366038 DOI: 10.1038/s41580-024-00703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2024] [Indexed: 02/18/2024]
Abstract
Ferroptosis is a non-apoptotic cell death mechanism characterized by iron-dependent membrane lipid peroxidation. Here, we review what is known about the cellular mechanisms mediating the execution and regulation of ferroptosis. We first consider how the accumulation of membrane lipid peroxides leads to the execution of ferroptosis by altering ion transport across the plasma membrane. We then discuss how metabolites and enzymes that are distributed in different compartments and organelles throughout the cell can regulate sensitivity to ferroptosis by impinging upon iron, lipid and redox metabolism. Indeed, metabolic pathways that reside in the mitochondria, endoplasmic reticulum, lipid droplets, peroxisomes and other organelles all contribute to the regulation of ferroptosis sensitivity. We note how the regulation of ferroptosis sensitivity by these different organelles and pathways seems to vary between different cells and death-inducing conditions. We also highlight transcriptional master regulators that integrate the functions of different pathways and organelles to modulate ferroptosis sensitivity globally. Throughout this Review, we highlight open questions and areas in which progress is needed to better understand the cell biology of ferroptosis.
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Affiliation(s)
- Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - James A Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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2
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Shetty SP, He D, Copeland PR. Selenoprotein synthesis is not induced by hepatotoxic drugs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.12.540527. [PMID: 38826422 PMCID: PMC11142112 DOI: 10.1101/2023.05.12.540527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background and Aims Many of the proteins that contain the amino acid selenocysteine are required for optimal defense against cellular stress. As such, one might expect selenoprotein synthesis to persist or be induced upon cellular insult. Because selenocysteine is incorporated by a complex post-transcriptional mechanism, monitoring the transcription of selenoprotein genes is not adequate to understand the regulation of selenoprotein synthesis. We aimed to determine whether selenoprotein synthesis is regulated by the induction of hepatotoxic stress. Methods We used hepatotropic clinically relevant drugs to evaluate the regulation of selenoprotein synthesis in human hepatocarcinoma cells. Results We found that two drugs, benzbromarone and sorafenib, caused significant inhibition of selenoprotein synthesis. However, the loss of selenoprotein expression was not specific as total protein synthesis was similarly down-regulated only by benzbromarone and sorafenib. Conclusions These results allow us to conclude that these hepatotoxins do not induce or preserve selenoprotein synthesis as a protective mechanism. Highlights The treatment of liver cells with hepatotoxic and hepatotropic compounds does not result in increased synthesis of selenoproteins.Compounds that induced the canonical oxidative stress response that features NRF2 activation eliminated selenoprotein synthesis.The downregulation of selenoproteins was accompanied by general inhibition of protein synthesis.
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3
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Dos Santos AF, Fazeli G, Xavier da Silva TN, Friedmann Angeli JP. Ferroptosis: mechanisms and implications for cancer development and therapy response. Trends Cell Biol 2023; 33:1062-1076. [PMID: 37230924 DOI: 10.1016/j.tcb.2023.04.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/13/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
As cancer cells develop resistance to apoptosis, non-apoptotic cell death modalities, such as ferroptosis, have emerged as promising strategies to combat therapy-resistant cancers. Cells that develop resistance to conventional therapies or metastatic cancer cells have been shown to have increased sensitivity to ferroptosis. Therefore, targeting the regulatory elements of ferroptosis in cancer could offer novel therapeutic opportunities. In this review, we first provide an overview of the known ferroptosis regulatory networks and discuss recent findings on how they contribute to cancer plasticity. We then expand into the critical role of selenium metabolism in regulating ferroptosis. Finally, we highlight specific cases where induction of ferroptosis could be used to sensitize cancer cells to this form of cell death.
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Affiliation(s)
- Ancély Ferreira Dos Santos
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - Gholamreza Fazeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - Thamara Nishida Xavier da Silva
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany
| | - José Pedro Friedmann Angeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, Würzburg, Germany.
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4
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Bera S, Kadkol S, Hong LK, Ali W, Brockman JD, Sverdlov M, Brister E, Macais V, Kajdacsy-Balla A, Valyi-Nagy K, Xu Z, Kastrati I, Liu L, Diamond AM. Regulation of SELENOF translation by eIF4a3: Possible role in prostate cancer progression. Mol Carcinog 2023; 62:1803-1816. [PMID: 37555760 DOI: 10.1002/mc.23616] [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: 06/01/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
The levels of the SELENOF selenoprotein are dramatically reduced in prostate cancer compared to adjacent benign tissue and reducing SELENOF in prostate epithelial cells results in the acquisition of features of the transformed phenotype. It was hypothesized that the aberrant increase in the eiF4a3 translation factor, which has an established role in RNA splicing and the regulation of selenoprotein translation, contributes to the lower levels of SELENOF. Using the available databases, eIF4a3 messenger RNA (mRNA) levels are elevated in prostate cancer compared to normal tissue as is the hypomethylation of the corresponding gene. Using a prostate cancer tissue microarray, we established that eiF4a3 levels are higher in prostate cancer tissue. Ectopic expression of eIF4a3 in prostate cancer cells reduced SELENOF levels and attenuated the readthrough of the UGA codon using a specialized reporter construct designed to examine UGA decoding, with the opposite effects observed using eIF4a3 knock-down constructs. Direct binding of eIF4a3 to the regulatory regions of SELENOF mRNA was established with pull-down experiments. Lastly, we show that an eIF4a3 inhibitor, eIF4a3-IN-2, increases SELENOF levels, UGA readthrough, and reduces binding of eIF4a3 to the SELENOF mRNA 3'-UTR in exposed cells. These data establish eIF4a3 as a likely prostate cancer oncogene and a regulator of SELENOF translation.
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Affiliation(s)
- Soumen Bera
- Department of Pathology, Chicago, Illinois, USA
- School of Life Sciences, B.S.Abdur Rahman Crescent Institute of Science and Technology, Chennai, Tamil Nadu, India
| | | | | | - Waleed Ali
- Albert Einstein College of Medicine, Bronx, New York, USA
| | - John D Brockman
- Department of Chemistry, University of Missouri Research Reactor, Columbia, Missouri, USA
| | - Maria Sverdlov
- Department of Pathology, Chicago, Illinois, USA
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | | | | | | | - Ziqiao Xu
- Department of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Irida Kastrati
- Departments of Cancer Biology and Pathology & Laboratory Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, Chicago, Illinois, USA
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5
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Dogaru CB, Muscurel C, Duță C, Stoian I. "Alphabet" Selenoproteins: Their Characteristics and Physiological Roles. Int J Mol Sci 2023; 24:15992. [PMID: 37958974 PMCID: PMC10650576 DOI: 10.3390/ijms242115992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/29/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023] Open
Abstract
Selenium (Se) is a metalloid that is recognized as one of the vital trace elements in our body and plays multiple biological roles, largely mediated by proteins containing selenium-selenoproteins. Selenoproteins mainly have oxidoreductase functions but are also involved in many different molecular signaling pathways, physiological roles, and complex pathogenic processes (including, for example, teratogenesis, neurodegenerative, immuno-inflammatory, and obesity development). All of the selenoproteins contain one selenocysteine (Sec) residue, with only one notable exception, the selenoprotein P (SELENOP), which has 10 Sec residues. Although these mechanisms have been studied intensely and in detail, the characteristics and functions of many selenoproteins remain unknown. This review is dedicated to the recent data describing the identity and the functions of several selenoproteins that are less known than glutathione peroxidases (Gpxs), iodothyronine deiodinases (DIO), thioredoxin reductases (TRxRs), and methionine sulfoxide reductases (Msrs) and which are named after alphabetical letters (i.e., F, H, I, K, M, N, O, P, R, S, T, V, W). These "alphabet" selenoproteins are involved in a wide range of physiological and pathogenetic processes such as antioxidant defense, anti-inflammation, anti-apoptosis, regulation of immune response, regulation of oxidative stress, endoplasmic reticulum (ER) stress, immune and inflammatory response, and toxin antagonism. In selenium deficiency, the "alphabet" selenoproteins are affected hierarchically, both with respect to the particular selenoprotein and the tissue of expression, as the brain or endocrine glands are hardly affected by Se deficiency due to their equipment with LRP2 or LRP8.
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Affiliation(s)
| | | | - Carmen Duță
- Department of Biochemistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania (I.S.)
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6
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Dogaru CB, Duță C, Muscurel C, Stoian I. "Alphabet" Selenoproteins: Implications in Pathology. Int J Mol Sci 2023; 24:15344. [PMID: 37895024 PMCID: PMC10607139 DOI: 10.3390/ijms242015344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Selenoproteins are a group of proteins containing selenium in the form of selenocysteine (Sec, U) as the 21st amino acid coded in the genetic code. Their synthesis depends on dietary selenium uptake and a common set of cofactors. Selenoproteins accomplish diverse roles in the body and cell processes by acting, for example, as antioxidants, modulators of the immune function, and detoxification agents for heavy metals, other xenobiotics, and key compounds in thyroid hormone metabolism. Although the functions of all this protein family are still unknown, several disorders in their structure, activity, or expression have been described by researchers. They concluded that selenium or cofactors deficiency, on the one hand, or the polymorphism in selenoproteins genes and synthesis, on the other hand, are involved in a large variety of pathological conditions, including type 2 diabetes, cardiovascular, muscular, oncological, hepatic, endocrine, immuno-inflammatory, and neurodegenerative diseases. This review focuses on the specific roles of selenoproteins named after letters of the alphabet in medicine, which are less known than the rest, regarding their implications in the pathological processes of several prevalent diseases and disease prevention.
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Affiliation(s)
| | | | - Corina Muscurel
- Department of Biochemistry, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania (I.S.)
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7
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Kabin E, Dong Y, Roy S, Smirnova J, Smith JW, Ralle M, Summers K, Yang H, Dev S, Wang Y, Devenney B, Cole RN, Palumaa P, Lutsenko S. α-lipoic acid ameliorates consequences of copper overload by up-regulating selenoproteins and decreasing redox misbalance. Proc Natl Acad Sci U S A 2023; 120:e2305961120. [PMID: 37751556 PMCID: PMC10556618 DOI: 10.1073/pnas.2305961120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/18/2023] [Indexed: 09/28/2023] Open
Abstract
α-lipoic acid (LA) is an essential cofactor for mitochondrial dehydrogenases and is required for cell growth, metabolic fuel production, and antioxidant defense. In vitro, LA binds copper (Cu) with high affinity and as an endogenous membrane permeable metabolite could be advantageous in mitigating the consequences of Cu overload in human diseases. We tested this hypothesis in 3T3-L1 preadipocytes with inactivated Cu transporter Atp7a; these cells accumulate Cu and show morphologic changes and mitochondria impairment. Treatment with LA corrected the morphology of Atp7a-/- cells similar to the Cu chelator bathocuproinedisulfonate (BCS) and improved mitochondria function; however, the mechanisms of LA and BCS action were different. Unlike BCS, LA did not decrease intracellular Cu but instead increased selenium levels that were low in Atp7a-/- cells. Proteome analysis confirmed distinct cell responses to these compounds and identified upregulation of selenoproteins as the major effect of LA on preadipocytes. Upregulation of selenoproteins was associated with an improved GSH:GSSG ratio in cellular compartments, which was lowered by elevated Cu, and reversal of protein oxidation. Thus, LA diminishes toxic effects of elevated Cu by improving cellular redox environment. We also show that selenium levels are decreased in tissues of a Wilson disease animal model, especially in the liver, making LA an attractive candidate for supplemental treatment of this disease.
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Affiliation(s)
- Ekaterina Kabin
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12618, Estonia
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Yixuan Dong
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Shubhrajit Roy
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Julia Smirnova
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12618, Estonia
| | - Joshua W. Smith
- Mass Spectrometry and Proteomics Core, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR97201
| | - Kelly Summers
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Haojun Yang
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Som Dev
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Yu Wang
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Benjamin Devenney
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Core, Johns Hopkins Medical Institutes, Baltimore, MD21205
| | - Peep Palumaa
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn12618, Estonia
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins Medical Institutes, Baltimore, MD21205
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8
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Lyu T, Li X, Song Y. Ferroptosis in acute leukemia. Chin Med J (Engl) 2023; 136:886-898. [PMID: 37010259 PMCID: PMC10278762 DOI: 10.1097/cm9.0000000000002642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Indexed: 04/04/2023] Open
Abstract
ABSTRACT Ferroptosis is an iron-dependent cell death pathway that is different from apoptosis, pyroptosis, and necrosis. The main characteristics of ferroptosis are the Fenton reaction mediated by intracellular free divalent iron ions, lipid peroxidation of cell membrane lipids, and inhibition of the anti-lipid peroxidation activity of intracellular glutathione peroxidase 4 (GPX4). Recent studies have shown that ferroptosis can be involved in the pathological processes of many disorders, such as ischemia-reperfusion injury, nervous system diseases, and blood diseases. However, the specific mechanisms by which ferroptosis participates in the occurrence and development of acute leukemia still need to be more fully and deeply studied. This article reviews the characteristics of ferroptosis and the regulatory mechanisms promoting or inhibiting ferroptosis. More importantly, it further discusses the role of ferroptosis in acute leukemia and predicts a change in treatment strategy brought about by increased knowledge of the role of ferroptosis in acute leukemia.
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Affiliation(s)
- Tianxin Lyu
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
| | - Xudong Li
- Department of Hematology, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, Henan 450008, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yongping Song
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
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9
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Effects of Selenium Yeast on Egg Quality, Plasma Antioxidants, Selenium Deposition and Eggshell Formation in Aged Laying Hens. Animals (Basel) 2023; 13:ani13050902. [PMID: 36899759 PMCID: PMC10000209 DOI: 10.3390/ani13050902] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 03/06/2023] Open
Abstract
Internal egg and eggshell quality are often deteriorated in aging laying hens, which causes huge economic losses in the poultry industry. Selenium yeast (SY), as an organic food additive, is utilized to enhance laying performance and egg quality. To extend the egg production cycle, effects of selenium yeast supplementation on egg quality, plasma antioxidants and selenium deposition in aged laying hens were evaluated. In this study, five hundred and twenty-five 76-week-old Jing Hong laying hens were fed a selenium-deficient (SD) diet for 6 weeks. After Se depletion, the hens were randomly divided into seven treatments, which included an SD diet, and dietary supplementation of SY and sodium selenite (SS) at 0.15, 0.30, and 0.45 mg/kg to investigate the effect on egg quality, plasma antioxidant capacity, and selenium content in reproductive organs. After 12 weeks of feeding, dietary SY supplementation resulted in higher eggshell strength (SY0.45) (p < 0.05) and lower shell translucence. Moreover, organs Se levels and plasma antioxidant capacity (T-AOC, T-SOD, and GSH-Px activity) were significantly higher with Se supplementation (p < 0.05). Transcriptomic analysis identified some key candidate genes including cell migration inducing hyaluronidase 1 (CEMIP), ovalbumin (OVAL), solute carrier family 6 member 17 (SLC6A17), proopiomelanocortin (POMC), and proenkephalin (PENK), and potential molecular processes (eggshell mineralization, ion transport, and eggshell formation) involved in selenium yeast's effects on eggshell formation. In conclusion, SY has beneficial functions for eggshell and we recommend the supplementation of 0.45 mg/kg SY to alleviate the decrease in eggshell quality in aged laying hens.
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10
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Li Q, Chen KC, Bridges PJ, Matthews JC. Pituitary and liver selenoprotein transcriptome profiles of grazing steers and their sensitivity to the form of selenium in vitamin-mineral mixes. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.911094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many supplemental Se-dependent metabolic effects are mediated through the function of selenoproteins. The full complement and relative abundance of selenoproteins expressed by highly metabolic cattle tissues have not been characterized in cattle. The complement and number of selenoprotein mRNA transcripts expressed by the pituitary and liver of healthy growing beef steers (n = 7 to 8) was characterized using NanoString methodology (Study 1). Of the 25 known bovine selenoproteins, 24 (all but SELENOH) were expressed by the pituitary and 23 (all but SELENOH and SELENOV) by the liver. Transcript abundance ranged (P ≤ 0.05) over 5 orders of magnitude in the pituitary (> 10,000 for GPX3, < 10 for DIO1 and GPX2) and liver (> 35,000 for SELENOP, < 10 for DIO2). Also unknown is the sensitivity of the selenoprotein transcriptome to the form of supplemental Se. The effect of form of supplemental Se on the relative content of selenoprotein mRNA species in the pituitary and liver of steers grazing a Se-deficient (0.07 ppm Se) tall fescue pasture and consuming 85 g/d of a basal vitamin-mineral mix that contained 35 ppm Se as either ISe (n = 6), organically-bound Se (SELPLEX; OSe, n = 7 to 8), or a 1:1 blend of ISe and OSe (MIX, n = 7 to 8) was determined by RT-PCR after sequence-validating the 25 bovine selenoprotein cDNA products (Study 2). In the pituitary, Se form affected (P < 0.05) the relative content of 9 selenoprotein mRNAs and 2 selenoprotein P receptor mRNAs in a manner consistent with a greater capacity to manage against oxidative damage, maintain cellular redox balance, and have a better control of protein-folding in the pituitaries of OSe and MIX versus ISe steers. In the liver, expression of 5 selenoprotein mRNA was affected (P ≤ 0.05) in a manner consistent with MIX steers having greater redox signaling capacity and capacity to manage oxidative damage than ISe steers. We conclude that inclusion of 3 mg Se/d as OSe or MIX versus ISe, forms of supplemental Se in vitamin-mineral mixes alters the selenoprotein transcriptome in a beneficial manner in both the pituitary and liver of growing steers consuming toxic endophyte-infected tall fescue.
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11
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Selenocysteine Machinery Primarily Supports TXNRD1 and GPX4 Functions and Together They Are Functionally Linked with SCD and PRDX6. Biomolecules 2022; 12:biom12081049. [PMID: 36008942 PMCID: PMC9405853 DOI: 10.3390/biom12081049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 01/23/2023] Open
Abstract
The human genome has 25 genes coding for selenocysteine (Sec)-containing proteins, whose synthesis is supported by specialized Sec machinery proteins. Here, we carried out an analysis of the co-essentiality network to identify functional partners of selenoproteins and Sec machinery. One outstanding cluster included all seven known Sec machinery proteins and two critical selenoproteins, GPX4 and TXNRD1. Additionally, these nine genes were further positively associated with PRDX6 and negatively with SCD, linking the latter two genes to the essential role of selenium. We analyzed the essentiality scores of gene knockouts in this cluster across one thousand cancer cell lines and found that Sec metabolism genes are strongly selective for a subset of primary tissues, suggesting that certain cancer cell lineages are particularly dependent on selenium. A separate outstanding cluster included selenophosphate synthetase SEPHS1, which was linked to a group of transcription factors, whereas the remaining selenoproteins were linked neither to these clusters nor among themselves. The data suggest that key components of Sec machinery have already been identified and that their primary role is to support the functions of GPX4 and TXNRD1, with further functional links to PRDX6 and SCD.
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Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability. Nat Chem Biol 2022; 18:751-761. [PMID: 35637349 PMCID: PMC9469796 DOI: 10.1038/s41589-022-01033-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/06/2022] [Indexed: 01/23/2023]
Abstract
The selenoprotein glutathione peroxidase 4 (GPX4) prevents ferroptosis by converting lipid peroxides into nontoxic lipid alcohols. GPX4 has emerged as a promising therapeutic target for cancer treatment, but some cancer cells are resistant to ferroptosis triggered by GPX4 inhibition. Using a chemical-genetic screen, we identify LRP8 (also known as ApoER2) as a ferroptosis resistance factor that is upregulated in cancer. Loss of LRP8 decreases cellular selenium levels and the expression of a subset of selenoproteins. Counter to the canonical hierarchical selenoprotein regulatory program, GPX4 levels are strongly reduced due to impaired translation. Mechanistically, low selenium levels result in ribosome stalling at the inefficiently decoded GPX4 selenocysteine UGA codon, leading to ribosome collisions, early translation termination and proteasomal clearance of the N-terminal GPX4 fragment. These findings reveal rewiring of the selenoprotein hierarchy in cancer cells and identify ribosome stalling and collisions during GPX4 translation as ferroptosis vulnerabilities in cancer.
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Kieliszek M, Bano I, Zare H. A Comprehensive Review on Selenium and Its Effects on Human Health and Distribution in Middle Eastern Countries. Biol Trace Elem Res 2022; 200:971-987. [PMID: 33884538 PMCID: PMC8761138 DOI: 10.1007/s12011-021-02716-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/08/2021] [Indexed: 12/16/2022]
Abstract
Selenium (Se) is an important microelement with numerous positive effects on human health and diseases. It is important to specify that the status and consumption of Se are for a specific community as the levels of Se are extremely unpredictable between different populations and regions. Our existing paper was based on the impacts of Se on human health and disease along with data on the Se levels in Middle Eastern countries. Overall, the findings of this comprehensive review show that the consumption and levels of Se are inadequate in Middle Eastern nations. Such findings, together with the growing awareness of the importance of Se to general health, require further work primarily on creating an acceptable range of blood Se concentration or other measures to determine optimal Se consumption and, consequently, to guarantee adequate Se supplementation in populations at high risk of low Se intake.
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Affiliation(s)
- Marek Kieliszek
- Department of Food Biotechnology and Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159C, 02-776 Warsaw, Poland
| | - Iqra Bano
- Department of Veterinary Physiology and Biochemistry, Shaheed Benazir Bhutto University of Veterinary & Animal Sciences Sakrand, Sindh, 67210 Pakistan
| | - Hamed Zare
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
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14
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Guillin OM, Vindry C, Ohlmann T, Chavatte L. Interplay between Selenium, Selenoproteins and HIV-1 Replication in Human CD4 T-Lymphocytes. Int J Mol Sci 2022; 23:ijms23031394. [PMID: 35163318 PMCID: PMC8835795 DOI: 10.3390/ijms23031394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/12/2022] Open
Abstract
The infection of CD4 T-lymphocytes with human immunodeficiency virus (HIV), the etiological agent of acquired immunodeficiency syndrome (AIDS), disrupts cellular homeostasis, increases oxidative stress and interferes with micronutrient metabolism. Viral replication simultaneously increases the demand for micronutrients and causes their loss, as for selenium (Se). In HIV-infected patients, selenium deficiency was associated with a lower CD4 T-cell count and a shorter life expectancy. Selenium has an important role in antioxidant defense, redox signaling and redox homeostasis, and most of these biological activities are mediated by its incorporation in an essential family of redox enzymes, namely the selenoproteins. Here, we have investigated how selenium and selenoproteins interplay with HIV infection in different cellular models of human CD4 T lymphocytes derived from established cell lines (Jurkat and SupT1) and isolated primary CD4 T cells. First, we characterized the expression of the selenoproteome in various human T-cell models and found it tightly regulated by the selenium level of the culture media, which was in agreement with reports from non-immune cells. Then, we showed that selenium had no significant effect on HIV-1 protein production nor on infectivity, but slightly reduced the percentage of infected cells in a Jurkat cell line and isolated primary CD4 T cells. Finally, in response to HIV-1 infection, the selenoproteome was slightly altered.
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Affiliation(s)
- Olivia M. Guillin
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
| | - Caroline Vindry
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
| | - Théophile Ohlmann
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
- Correspondence: (T.O.); (L.C.); Tel.: +33-4-72-72-89-53 (T.O.); +33-4-72-72-86-24 (L.C.)
| | - Laurent Chavatte
- Centre International de Recherche en Infectiologie (CIRI), 69007 Lyon, France; (O.M.G.); (C.V.)
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon (ENS), 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 5308 (UMR5308), 69007 Lyon, France
- Correspondence: (T.O.); (L.C.); Tel.: +33-4-72-72-89-53 (T.O.); +33-4-72-72-86-24 (L.C.)
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15
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Markley RL, Restori KH, Katkere B, Sumner SE, Nicol MJ, Tyryshkina A, Nettleford SK, Williamson DR, Place DE, Dewan KK, Shay AE, Carlson BA, Girirajan S, Prabhu KS, Kirimanjeswara GS. Macrophage Selenoproteins Restrict Intracellular Replication of Francisella tularensis and Are Essential for Host Immunity. Front Immunol 2021; 12:701341. [PMID: 34777335 PMCID: PMC8586653 DOI: 10.3389/fimmu.2021.701341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
The essential micronutrient Selenium (Se) is co-translationally incorporated as selenocysteine into proteins. Selenoproteins contain one or more selenocysteines and are vital for optimum immunity. Interestingly, many pathogenic bacteria utilize Se for various biological processes suggesting that Se may play a role in bacterial pathogenesis. A previous study had speculated that Francisella tularensis, a facultative intracellular bacterium and the causative agent of tularemia, sequesters Se by upregulating Se-metabolism genes in type II alveolar epithelial cells. Therefore, we investigated the contribution of host vs. pathogen-associated selenoproteins in bacterial disease using F. tularensis as a model organism. We found that F. tularensis was devoid of any Se utilization traits, neither incorporated elemental Se, nor exhibited Se-dependent growth. However, 100% of Se-deficient mice (0.01 ppm Se), which express low levels of selenoproteins, succumbed to F. tularensis-live vaccine strain pulmonary challenge, whereas 50% of mice on Se-supplemented (0.4 ppm Se) and 25% of mice on Se-adequate (0.1 ppm Se) diet succumbed to infection. Median survival time for Se-deficient mice was 8 days post-infection while Se-supplemented and -adequate mice was 11.5 and >14 days post-infection, respectively. Se-deficient macrophages permitted significantly higher intracellular bacterial replication than Se-supplemented macrophages ex vivo, corroborating in vivo observations. Since Francisella replicates in alveolar macrophages during the acute phase of pneumonic infection, we hypothesized that macrophage-specific host selenoproteins may restrict replication and systemic spread of bacteria. F. tularensis infection led to an increased expression of several macrophage selenoproteins, suggesting their key role in limiting bacterial replication. Upon challenge with F. tularensis, mice lacking selenoproteins in macrophages (TrspM) displayed lower survival and increased bacterial burden in the lung and systemic tissues in comparison to WT littermate controls. Furthermore, macrophages from TrspM mice were unable to restrict bacterial replication ex vivo in comparison to macrophages from littermate controls. We herein describe a novel function of host macrophage-specific selenoproteins in restriction of intracellular bacterial replication. These data suggest that host selenoproteins may be considered as novel targets for modulating immune response to control a bacterial infection.
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Affiliation(s)
- Rachel L. Markley
- Pathobiology Graduate Program, The Pennsylvania State University, University Park, PA, United States,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Katherine H. Restori
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Bhuvana Katkere
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Sarah E. Sumner
- Pathobiology Graduate Program, The Pennsylvania State University, University Park, PA, United States,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - McKayla J. Nicol
- Pathobiology Graduate Program, The Pennsylvania State University, University Park, PA, United States,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Anastasia Tyryshkina
- Neuroscience Graduate Program, Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA, United States,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Shaneice K. Nettleford
- Pathobiology Graduate Program, The Pennsylvania State University, University Park, PA, United States,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - David R. Williamson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
| | - David E. Place
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Kalyan K. Dewan
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Department of Infectious Diseases, The University of Georgia, Athens, GA, United States
| | - Ashley E. Shay
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Bradley A. Carlson
- Office of Research Support, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - K. Sandeep Prabhu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Center for Molecular Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, United States
| | - Girish S. Kirimanjeswara
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States,Center for Molecular Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, United States,*Correspondence: Girish S. Kirimanjeswara,
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16
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Fradejas-Villar N, Bohleber S, Zhao W, Reuter U, Kotter A, Helm M, Knoll R, McFarland R, Taylor RW, Mo Y, Miyauchi K, Sakaguchi Y, Suzuki T, Schweizer U. The Effect of tRNA [Ser]Sec Isopentenylation on Selenoprotein Expression. Int J Mol Sci 2021; 22:ijms222111454. [PMID: 34768885 PMCID: PMC8583801 DOI: 10.3390/ijms222111454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/22/2022] Open
Abstract
Transfer RNA[Ser]Sec carries multiple post-transcriptional modifications. The A37G mutation in tRNA[Ser]Sec abrogates isopentenylation of base 37 and has a profound effect on selenoprotein expression in mice. Patients with a homozygous pathogenic p.R323Q variant in tRNA-isopentenyl-transferase (TRIT1) show a severe neurological disorder, and hence we wondered whether selenoprotein expression was impaired. Patient fibroblasts with the homozygous p.R323Q variant did not show a general decrease in selenoprotein expression. However, recombinant human TRIT1R323Q had significantly diminished activities towards several tRNA substrates in vitro. We thus engineered mice conditionally deficient in Trit1 in hepatocytes and neurons. Mass-spectrometry revealed that hypermodification of U34 to mcm5Um occurs independently of isopentenylation of A37 in tRNA[Ser]Sec. Western blotting and 75Se metabolic labeling showed only moderate effects on selenoprotein levels and 75Se incorporation. A detailed analysis of Trit1-deficient liver using ribosomal profiling demonstrated that UGA/Sec re-coding was moderately affected in Selenop, Txnrd1, and Sephs2, but not in Gpx1. 2′O-methylation of U34 in tRNA[Ser]Sec depends on FTSJ1, but does not affect UGA/Sec re-coding in selenoprotein translation. Taken together, our results show that a lack of isopentenylation of tRNA[Ser]Sec affects UGA/Sec read-through but differs from a A37G mutation.
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Affiliation(s)
- Noelia Fradejas-Villar
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Simon Bohleber
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Wenchao Zhao
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Uschi Reuter
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Annika Kotter
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany; (A.K.); (M.H.)
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Staudingerweg 5, D-55128 Mainz, Germany; (A.K.); (M.H.)
| | - Rainer Knoll
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (R.M.); (R.W.T.)
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (R.M.); (R.W.T.)
| | - Yufeng Mo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan; (Y.M.); (K.M.); (Y.S.); (T.S.)
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, D-53115 Bonn, Germany; (N.F.-V.); (S.B.); (W.Z.); (U.R.); (R.K.)
- Correspondence:
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17
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Lozoya OA, Xu F, Grenet D, Wang T, Stevanovic KD, Cushman JD, Hagler TB, Gruzdev A, Jensen P, Hernandez B, Riadi G, Moy SS, Santos JH, Woychik RP. A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice. Life Sci Alliance 2021; 4:4/12/e202101122. [PMID: 34649938 PMCID: PMC8548212 DOI: 10.26508/lsa.202101122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/24/2022] Open
Abstract
This study shows that loss of a brain-specific fusion isoform of PGC1a leads to up-regulation of genes and motor impairments in mice, suggesting functional differences between PGC1 isoforms in the brain. PGC1α is a transcriptional coactivator in peripheral tissues, but its function in the brain remains poorly understood. Various brain-specific Pgc1α isoforms have been reported in mice and humans, including two fusion transcripts (FTs) with non-coding repetitive sequences, but their function is unknown. The FTs initiate at a simple sequence repeat locus ∼570 Kb upstream from the reference promoter; one also includes a portion of a short interspersed nuclear element (SINE). Using publicly available genomics data, here we show that the SINE FT is the predominant form of Pgc1α in neurons. Furthermore, mutation of the SINE in mice leads to altered behavioural phenotypes and significant up-regulation of genes in the female, but not male, cerebellum. Surprisingly, these genes are largely involved in neurotransmission, having poor association with the classical mitochondrial or antioxidant programs. These data expand our knowledge on the role of Pgc1α in neuronal physiology and suggest that different isoforms may have distinct functions. They also highlight the need for further studies before modulating levels of Pgc1α in the brain for therapeutic purposes.
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Affiliation(s)
- Oswaldo A Lozoya
- Genomic Integrity and Structural Biology Laboratory, National Institutes of Health, Durham, NC, USA
| | - Fuhua Xu
- Genomic Integrity and Structural Biology Laboratory, National Institutes of Health, Durham, NC, USA
| | - Dagoberto Grenet
- Genomic Integrity and Structural Biology Laboratory, National Institutes of Health, Durham, NC, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Branch, National Institutes of Health, Durham, NC, USA
| | - Korey D Stevanovic
- Neurobehavioral Core Laboratory, National Institutes of Health, Durham, NC, USA
| | - Jesse D Cushman
- Neurobehavioral Core Laboratory, National Institutes of Health, Durham, NC, USA
| | - Thomas B Hagler
- Knockout Mouse Core Facility, National Institutes of Health, Durham, NC, USA
| | - Artiom Gruzdev
- Knockout Mouse Core Facility, National Institutes of Health, Durham, NC, USA
| | - Patricia Jensen
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - Bairon Hernandez
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Gonzalo Riadi
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile
| | - Sheryl S Moy
- Department of Psychiatry, Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Janine H Santos
- Genomic Integrity and Structural Biology Laboratory, National Institutes of Health, Durham, NC, USA
| | - Richard P Woychik
- Genomic Integrity and Structural Biology Laboratory, National Institutes of Health, Durham, NC, USA
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18
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Yan HF, Zou T, Tuo QZ, Xu S, Li H, Belaidi AA, Lei P. Ferroptosis: mechanisms and links with diseases. Signal Transduct Target Ther 2021; 6:49. [PMID: 33536413 PMCID: PMC7858612 DOI: 10.1038/s41392-020-00428-9] [Citation(s) in RCA: 499] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/03/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Ferroptosis is an iron-dependent cell death, which is different from apoptosis, necrosis, autophagy, and other forms of cell death. The process of ferroptotic cell death is defined by the accumulation of lethal lipid species derived from the peroxidation of lipids, which can be prevented by iron chelators (e.g., deferiprone, deferoxamine) and small lipophilic antioxidants (e.g., ferrostatin, liproxstatin). This review summarizes current knowledge about the regulatory mechanism of ferroptosis and its association with several pathways, including iron, lipid, and cysteine metabolism. We have further discussed the contribution of ferroptosis to the pathogenesis of several diseases such as cancer, ischemia/reperfusion, and various neurodegenerative diseases (e.g., Alzheimer's disease and Parkinson's disease), and evaluated the therapeutic applications of ferroptosis inhibitors in clinics.
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Affiliation(s)
- Hong-Fa Yan
- Department of Neurology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Center for Biotherapy, 610041, Chengdu, China
| | - Ting Zou
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, 610041, Chengdu, China
| | - Qing-Zhang Tuo
- Department of Neurology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Center for Biotherapy, 610041, Chengdu, China
| | - Shuo Xu
- Department of Neurology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Center for Biotherapy, 610041, Chengdu, China
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, 610041, Chengdu, China
| | - Hua Li
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, 610041, Chengdu, China
| | - Abdel Ali Belaidi
- Melbourne Dementia Research Centre and the Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Peng Lei
- Department of Neurology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Center for Biotherapy, 610041, Chengdu, China.
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19
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Takahashi N, Cho P, Selfors LM, Kuiken HJ, Kaul R, Fujiwara T, Harris IS, Zhang T, Gygi SP, Brugge JS. 3D Culture Models with CRISPR Screens Reveal Hyperactive NRF2 as a Prerequisite for Spheroid Formation via Regulation of Proliferation and Ferroptosis. Mol Cell 2020; 80:828-844.e6. [PMID: 33128871 PMCID: PMC7718371 DOI: 10.1016/j.molcel.2020.10.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/03/2020] [Accepted: 10/04/2020] [Indexed: 01/09/2023]
Abstract
Cancer-associated mutations that stabilize NRF2, an oxidant defense transcription factor, are predicted to promote tumor development. Here, utilizing 3D cancer spheroid models coupled with CRISPR-Cas9 screens, we investigate the molecular pathogenesis mediated by NRF2 hyperactivation. NRF2 hyperactivation was necessary for proliferation and survival in lung tumor spheroids. Antioxidant treatment rescued survival but not proliferation, suggesting the presence of distinct mechanisms. CRISPR screens revealed that spheroids are differentially dependent on the mammalian target of rapamycin (mTOR) for proliferation and the lipid peroxidase GPX4 for protection from ferroptosis of inner, matrix-deprived cells. Ferroptosis inhibitors blocked death from NRF2 downregulation, demonstrating a critical role of NRF2 in protecting matrix-deprived cells from ferroptosis. Interestingly, proteomics analyses show global enrichment of selenoproteins, including GPX4, by NRF2 downregulation, and targeting NRF2 and GPX4 killed spheroids overall. These results illustrate the value of spheroid culture in revealing environmental or spatial differential dependencies on NRF2 and reveal exploitable vulnerabilities of NRF2-hyperactivated tumors.
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Affiliation(s)
- Nobuaki Takahashi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA.
| | - Patricia Cho
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA
| | - Laura M Selfors
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA
| | - Hendrik J Kuiken
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA
| | - Roma Kaul
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA
| | - Takuro Fujiwara
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Kyoto 615-8510, Japan
| | - Isaac S Harris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA
| | - Tian Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joan S Brugge
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Ludwig Cancer Center, Boston, MA 02115, USA.
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20
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Abstract
The emergence of genome-wide analyses to interrogate cellular DNA, RNA, and protein content has revolutionized the study of control networks that mediate cellular homeostasis. mRNA translation represents the last step of genetic flow and primarily defines the proteome. Translational regulation is thus critical for gene expression, in particular under nutrient excess or deficiency. Until recently, it was unclear how the global effects of translational control are orchestrated by nutrient signaling pathways. An emerging concept of translational reprogramming addresses how to maintain the expression of specific proteins during nutrient stress by translation of selective mRNAs. In this review, we describe recent advances in our understanding of translational control principles; nutrient-sensing mechanisms; and their dysregulation in human diseases such as diabetes, cancer, and aging. The mechanistic understanding of translational regulation in response to different nutrient conditions may help identify potential dietary and therapeutic targets to improve human health.
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Affiliation(s)
- Xin Erica Shu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Robert V. Swanda
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York 14853, USA
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21
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Santesmasses D, Mariotti M, Gladyshev VN. Bioinformatics of Selenoproteins. Antioxid Redox Signal 2020; 33:525-536. [PMID: 32031018 PMCID: PMC7409585 DOI: 10.1089/ars.2020.8044] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Significance: Bioinformatics has brought important insights into the field of selenium research. The progress made in the development of computational tools in the last two decades, coordinated with growing genome resources, provided new opportunities to study selenoproteins. The present review discusses existing tools for selenoprotein gene finding and other bioinformatic approaches to study the biology of selenium. Recent Advances: The availability of complete selenoproteomes allowed assessing a global distribution of the use of selenocysteine (Sec) across the tree of life, as well as studying the evolution of selenoproteins and their biosynthetic pathway. Beyond gene identification and characterization, human genetic variants in selenoprotein genes were used to examine adaptations to selenium levels in diverse human populations and to estimate selective constraints against gene loss. Critical Issues: The synthesis of selenoproteins is essential for development in mice. In humans, several mutations in selenoprotein genes have been linked to rare congenital disorders. And yet, the mechanism of Sec insertion and the regulation of selenoprotein synthesis in mammalian cells are not completely understood. Future Directions: Omics technologies offer new possibilities to study selenoproteins and mechanisms of Sec incorporation in cells, tissues, and organisms.
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Affiliation(s)
- Didac Santesmasses
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
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22
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Arpat AB, Liechti A, De Matos M, Dreos R, Janich P, Gatfield D. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res 2020; 30:985-999. [PMID: 32703885 PMCID: PMC7397865 DOI: 10.1101/gr.257741.119] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 06/29/2020] [Indexed: 01/28/2023]
Abstract
Translation initiation is the major regulatory step defining the rate of protein production from an mRNA. Meanwhile, the impact of nonuniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing signals. Pause site association with specific amino acids, peptide motifs, and nascent polypeptide structure is suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites indicates functional relevance of translational pausing. Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.
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Affiliation(s)
- Alaaddin Bulak Arpat
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mara De Matos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Peggy Janich
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
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23
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Gobet C, Weger BD, Marquis J, Martin E, Neelagandan N, Gachon F, Naef F. Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver. Proc Natl Acad Sci U S A 2020; 117:9630-9641. [PMID: 32295881 PMCID: PMC7196831 DOI: 10.1073/pnas.1918145117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) profiling to investigate the relations between translation elongation rates, (aminoacyl-) tRNA levels, and codon usage in mammals. We modeled codon-specific ribosome dwell times from ribosome profiling, considering codon pair interactions between ribosome sites. In mouse liver, the model revealed site- and codon-specific dwell times that differed from those in yeast, as well as pairs of adjacent codons in the P and A site that markedly slow down or speed up elongation. While translation efficiencies vary across diurnal time and feeding regimen, codon dwell times were highly stable and conserved in human. Measured tRNA levels correlated with codon usage and several tRNAs showed reduced aminoacylation, which was conserved in fasted mice. Finally, we uncovered that the longest codon dwell times could be explained by aminoacylation levels or high codon usage relative to tRNA abundance.
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Affiliation(s)
- Cédric Gobet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Benjamin Dieter Weger
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | | | - Eva Martin
- Nestlé Research, CH-1015 Lausanne, Switzerland
| | - Nagammal Neelagandan
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | | | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland;
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Hofstee P, Cuffe JS, Perkins AV. Analysis of Selenoprotein Expression in Response to Dietary Selenium Deficiency During Pregnancy Indicates Tissue Specific Differential Expression in Mothers and Sex Specific Changes in the Fetus and Offspring. Int J Mol Sci 2020; 21:ijms21062210. [PMID: 32210049 PMCID: PMC7139809 DOI: 10.3390/ijms21062210] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
The human selenoproteome is comprised of ~25 genes, which incorporate selenium, in the form of selenocysteine, into their structure. Since it is well known that selenium is important to maternal health and foetal development during pregnancy, this study aimed at defining the impact of selenium deficiency on maternal, placental, foetal and offspring selenoprotein gene expression. Female C57BL/6 mice were randomly allocated to control (>190 μg/kg) or low selenium (<50 μg/kg) diets four weeks prior to mating and throughout gestation. At embryonic day (E)18.5, pregnant mice were sacrificed followed by collection of maternal and foetal tissues. A subset of mice littered down, and offspring were monitored from postnatal day (PN) 8, weaned at PN24 and sacrificed at PN180, followed by tissue collection. Following RNA extraction, the expression of 14 selenoproteins was assessed with qPCR in liver, kidneys, muscle and placenta. Selenium deficiency downregulated expression (Ptrt < 0.05) of many selenoproteins in maternal tissues and the placenta. However, foetal selenoprotein expression was upregulated (Ptrt < 0.05) in all tissues, especially the kidneys. This was not reflected at PN180; however, a sexually dimorphic relationship in selenoprotein expression was observed in offspring. This study demonstrates the selenoproteome is sensitive to dietary selenium levels, which may be exacerbated by pregnancy. We concluded that transcriptional regulation of selenoproteins is complex and multifaceted, with expression exhibiting tissue-, age- and sex-specificities.
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Affiliation(s)
- Pierre Hofstee
- School of Medical Science, Menzies Health Institute Queensland, Griffith University Gold, Coast Campus, Southport, QLD 4215, Australia;
| | - James S.M. Cuffe
- The School of Biomedical Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
- Correspondence: (J.S.M.C.); (A.V.P.); Tel.: +61-755529774 (A.V.P.)
| | - Anthony V. Perkins
- School of Medical Science, Menzies Health Institute Queensland, Griffith University Gold, Coast Campus, Southport, QLD 4215, Australia;
- Correspondence: (J.S.M.C.); (A.V.P.); Tel.: +61-755529774 (A.V.P.)
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25
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Okumura F, Fujiki Y, Oki N, Osaki K, Nishikimi A, Fukui Y, Nakatsukasa K, Kamura T. Cul5-type Ubiquitin Ligase KLHDC1 Contributes to the Elimination of Truncated SELENOS Produced by Failed UGA/Sec Decoding. iScience 2020; 23:100970. [PMID: 32200094 PMCID: PMC7090344 DOI: 10.1016/j.isci.2020.100970] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/10/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023] Open
Abstract
The UGA codon signals protein translation termination, but it can also be translated into selenocysteine (Sec, U) to produce selenocysteine-containing proteins (selenoproteins) by dedicated machinery. As Sec incorporation can fail, Sec-containing longer and Sec-lacking shorter proteins co-exist. Cul2-type ubiquitin ligases were recently shown to destabilize such truncated proteins; however, which ubiquitin ligase targets truncated proteins for degradation remained unclear. We report that the Cul5-type ubiquitin ligase KLHDC1 targets truncated SELENOS, a selenoprotein, for proteasomal degradation. SELENOS is involved in endoplasmic reticulum (ER)-associated degradation, which is linked to reactive oxygen species (ROS) production, and the knockdown of KLHDC1 in U2OS cells decreased ER stress-induced cell death. Knockdown of SELENOS increased the cell population with lower ROS levels. Our findings reveal that, in addition to Cul2-type ubiquitin ligases, KLHDC1 is involved in the elimination of truncated oxidoreductase-inactive SELENOS, which would be crucial for maintaining ROS levels and preventing cancer development. KLHDC1 is a Cul5-type ubiquitin ligase KLHDC1 targets immature SELENOS for proteasomal degradation KLHDC1 knockdown in U2OS cells decreases ER stress-induced cell death
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Affiliation(s)
- Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka 813-8582, Japan.
| | - Yuha Fujiki
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka 813-8582, Japan
| | - Nodoka Oki
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka 813-8582, Japan
| | - Kana Osaki
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka 813-8582, Japan
| | - Akihiko Nishikimi
- Laboratory of Biosafety Research, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan
| | - Yoshinori Fukui
- Division of Immunogenetics, Department of Immunobiology and Neuroscience and Research Center for Advanced Immunology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kunio Nakatsukasa
- Graduate School of Natural Sciences, Nagoya City University, Aichi 467-8501, Japan
| | - Takumi Kamura
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi 464-8602, Japan.
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26
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Schomburg L. The other view: the trace element selenium as a micronutrient in thyroid disease, diabetes, and beyond. Hormones (Athens) 2020; 19:15-24. [PMID: 31823341 DOI: 10.1007/s42000-019-00150-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 02/08/2023]
Abstract
Antibiotics are provided for infections caused by bacteria, and statins help to control hypercholesterolemia. When hungry, you need to eat, and when you are deficient in a particular nutrient, the diet should be chosen wisely to provide what is missing. In the matter of providing the essential trace element selenium (Se), there are two different but partly overlapping views on its nature and requirements. Some consider it a medication that should be given to a subset of more or less well-defined (thyroid) patients only, in order to alleviate symptoms, to improve the course of the disease or even to provide a cure, alone or in an adjuvant mode. Such treatment attempts are conducted for a short time period, and potential medical benefits and side effects are evaluated thoroughly. One could also approach Se in medicine in a more holistic way and evaluate primarily the nutritional status of the patient before considering supplementation. The available evidence for positive health effects of supplemental Se can be interpreted as the consequence of correcting deficiency instead of speculating on a direct pharmaceutical action. This short review provides a novel view on Se in (thyroid) disease and beyond and offers an alternative explanation for its positive health effects, i.e., its provision of the substrate needed for allowing adequate endogenous expression of those selenoproteins that are required in certain conditions. In Se deficiency, the lack of the trace element constitutes the main limitation for the required adaptation of selenoprotein expression to counteract health risks and alleviate disease symptoms. Supplemental Se lifts this restriction and enables the full endogenous response of selenoprotein expression. However, since Se does not act as a pharmacological medication per se, it should not be viewed as a dangerous drug, and, importantly, current data show that supplemental Se does not cause diabetes.
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Affiliation(s)
- Lutz Schomburg
- Institute for Experimental Endocrinology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Freie Universität Berlin, Berlin, Germany.
- Humboldt-Universität zu Berlin, Berlin, Germany.
- Berlin Institute of Health, Berlin, Suedring 10, D-13353, Berlin, Germany.
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27
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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28
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Copeland PR. Gained in translation: The power of digging deep into disease models. J Biol Chem 2019; 294:14201-14202. [PMID: 31562227 DOI: 10.1074/jbc.h119.010864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations affecting the SECISBP2 protein necessary for selenocysteine incorporation are linked to human disease, but with a wide range of clinical outcomes. To gain insight into this diversity, Zhao et al. dissect the phenotypic and molecular consequences of two specific mutations in the Secisbp2 gene that partially disrupt selenoprotein synthesis. They observe surprising tissue-dependent effects, emphasizing the complexities of translational science.
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Affiliation(s)
- Paul R Copeland
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
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29
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Guillin OM, Vindry C, Ohlmann T, Chavatte L. Selenium, Selenoproteins and Viral Infection. Nutrients 2019; 11:nu11092101. [PMID: 31487871 PMCID: PMC6769590 DOI: 10.3390/nu11092101] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) are frequently produced during viral infections. Generation of these ROS can be both beneficial and detrimental for many cellular functions. When overwhelming the antioxidant defense system, the excess of ROS induces oxidative stress. Viral infections lead to diseases characterized by a broad spectrum of clinical symptoms, with oxidative stress being one of their hallmarks. In many cases, ROS can, in turn, enhance viral replication leading to an amplification loop. Another important parameter for viral replication and pathogenicity is the nutritional status of the host. Viral infection simultaneously increases the demand for micronutrients and causes their loss, which leads to a deficiency that can be compensated by micronutrient supplementation. Among the nutrients implicated in viral infection, selenium (Se) has an important role in antioxidant defense, redox signaling and redox homeostasis. Most of biological activities of selenium is performed through its incorporation as a rare amino acid selenocysteine in the essential family of selenoproteins. Selenium deficiency, which is the main regulator of selenoprotein expression, has been associated with the pathogenicity of several viruses. In addition, several selenoprotein members, including glutathione peroxidases (GPX), thioredoxin reductases (TXNRD) seemed important in different models of viral replication. Finally, the formal identification of viral selenoproteins in the genome of molluscum contagiosum and fowlpox viruses demonstrated the importance of selenoproteins in viral cycle.
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Affiliation(s)
- Olivia M Guillin
- CIRI, Centre International de Recherche en Infectiologie, CIRI, 69007 Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon, 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Unité Mixte de Recherche 5308 (UMR5308), Centre national de la recherche scientifique (CNRS), 69007 Lyon, France
| | - Caroline Vindry
- CIRI, Centre International de Recherche en Infectiologie, CIRI, 69007 Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon, 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Unité Mixte de Recherche 5308 (UMR5308), Centre national de la recherche scientifique (CNRS), 69007 Lyon, France
| | - Théophile Ohlmann
- CIRI, Centre International de Recherche en Infectiologie, CIRI, 69007 Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France
- Ecole Normale Supérieure de Lyon, 69007 Lyon, France
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France
- Unité Mixte de Recherche 5308 (UMR5308), Centre national de la recherche scientifique (CNRS), 69007 Lyon, France
| | - Laurent Chavatte
- CIRI, Centre International de Recherche en Infectiologie, CIRI, 69007 Lyon, France.
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité U1111, 69007 Lyon, France.
- Ecole Normale Supérieure de Lyon, 69007 Lyon, France.
- Université Claude Bernard Lyon 1 (UCBL1), 69622 Lyon, France.
- Unité Mixte de Recherche 5308 (UMR5308), Centre national de la recherche scientifique (CNRS), 69007 Lyon, France.
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30
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Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs. J Mol Biol 2019; 431:4381-4407. [PMID: 31442478 DOI: 10.1016/j.jmb.2019.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023]
Abstract
Selenoproteins typically contain a single selenocysteine, the 21st amino acid, encoded by a context-redefined UGA. However, human selenoprotein P (SelenoP) has a redox-functioning selenocysteine in its N-terminal domain and nine selenium transporter-functioning selenocysteines in its C-terminal domain. Here we show that diverse SelenoP genes are present across metazoa with highly variable numbers of Sec-UGAs, ranging from a single UGA in certain insects, to 9 in common spider, and up to 132 in bivalve molluscs. SelenoP genes were shaped by a dynamic evolutionary process linked to selenium usage. Gene evolution featured modular expansions of an ancestral multi-Sec domain, which led to particularly Sec-rich SelenoP proteins in many aquatic organisms. We focused on molluscs, and chose Pacific oyster Magallana gigas as experimental model. We show that oyster SelenoP mRNA with 46 UGAs is translated full-length in vivo. Ribosome profiling indicates that selenocysteine specification occurs with ∼5% efficiency at UGA1 and approaches 100% efficiency at distal 3' UGAs. We report genetic elements relevant to its expression, including a leader open reading frame and an RNA structure overlapping the initiation codon that modulates ribosome progression in a selenium-dependent manner. Unlike their mammalian counterparts, the two SECIS elements in oyster SelenoP (3'UTR recoding elements) do not show functional differentiation in vitro. Oysters can increase their tissue selenium level up to 50-fold upon supplementation, which also results in extensive changes in selenoprotein expression.
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31
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Rajput B, Pruitt KD, Murphy TD. RefSeq curation and annotation of stop codon recoding in vertebrates. Nucleic Acids Res 2019; 47:594-606. [PMID: 30535227 PMCID: PMC6344875 DOI: 10.1093/nar/gky1234] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
Recoding of stop codons as amino acid-specifying codons is a co-translational event that enables C-terminal extension of a protein. Synthesis of selenoproteins requires recoding of internal UGA stop codons to the 21st non-standard amino acid selenocysteine (Sec) and plays a vital role in human health and disease. Separately, canonical stop codons can be recoded to specify standard amino acids in a process known as stop codon readthrough (SCR), producing extended protein isoforms with potential novel functions. Conventional computational tools cannot distinguish between the dual functionality of stop codons as stop signals and sense codons, resulting in misannotation of selenoprotein gene products and failure to predict SCR. Manual curation is therefore required to correctly represent recoded gene products and their functions. Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR transcript and protein records to serve as annotation standards and to promote basic and biomedical research. Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93 genes exhibiting SCR encoding 94 SCR isoforms.
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Affiliation(s)
- Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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32
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Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov PV. GWIPS-viz: 2018 update. Nucleic Acids Res 2019; 46:D823-D830. [PMID: 28977460 PMCID: PMC5753223 DOI: 10.1093/nar/gkx790] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 08/29/2017] [Indexed: 12/15/2022] Open
Abstract
The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been automated thereby increasing the number of available tracks to 1792, a 10-fold increase in the last three years. The increase is particularly substantial for data derived from human sources. Following user requests, we added the functionality to download these tracks in bigWig format. We also incorporated new types of data (e.g. TCP-seq) as well as auxiliary tracks from other sources that help with the interpretation of Ribo-seq data. Improvements in the visualization of the data have been carried out particularly for bacterial genomes where the Ribo-seq data are now shown in a strand specific manner. For higher eukaryotic datasets, we provide characteristics of individual datasets using the RUST program which includes the triplet periodicity, sequencing biases and relative inferred A-site dwell times. This information can be used for assessing the quality of Ribo-seq datasets. To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.
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Affiliation(s)
- Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | | | - James P Mullan
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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33
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Juniper DT, Rymer C, Briens M. Bioefficacy of hydroxy-selenomethionine as a selenium supplement in pregnant dairy heifers and on the selenium status of their calves. J Dairy Sci 2019; 102:7000-7010. [PMID: 31155245 DOI: 10.3168/jds.2018-16065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
This study aimed to determine the effects of supplementing pregnant heifers with the organic selenium (Se) source 2-hydroxy-4-methylselenobutanoic acid (HMSeBA) during the last 8 wk of pregnancy on dam and calf Se status. A total of 42 in-calf heifers were recruited to the study and randomly allocated to 1 of 3 treatments; a negative control (Con), sodium selenite (NaSe), or HMSeBA. Animals were blocked by body weight, body condition score, and expected calving date before treatment allocation. Following enrollment, all animals underwent a 7-wk wash-out period, after which they received their respective supplements, top-dressed daily onto a basal diet for the last 8 wk of pregnancy. Heifer blood samples were taken at weekly intervals from enrollment until 2 wk before expected calving date and as soon as possible after calving for determination of whole-blood glutathione peroxidase activity (GSH-Px) and plasma Se and malondialdehyde (MDA) concentrations. Selenized AA were determined in plasma samples taken at 3 wk precalving. A colostrum sample was taken as close to parturition as possible for determination of colostrum total Se, selenized AA, and IgG concentration. Calves were blood sampled as close to birth as possible for determination of whole-blood GSH-Px activity and plasma Se and MDA concentrations. Differences in whole-blood GSH-Px activity did not become apparent until calving; GSH-Px activity was lowest in Con heifers but similar between NaSe and HMSeBA heifers. Plasma Se was lowest in unsupplemented heifers and greatest in those supplemented with HMSeBA; this was attributable to greater selenomethionine concentrations in the plasma of HMSeBA heifers. Colostrum Se was lowest in Con heifers and greatest in HMSeBA heifers. The greater Se concentration of HMSeBA heifers was attributable to a greater proportion of total Se comprising selenocysteine; the reason for this is not known. There was no effect of supplementation on colostrum IgG concentration. Plasma Se was lowest in calves born to Con heifers and greatest in those born to HMSeBA heifers. There were no effects of treatment on calf whole-blood GSH-Px activity or plasma MDA concentration. The enhanced Se status associated with HMSeBA supplementation is likely a consequence of selenomethionine supply and may confer benefits to both the dam and her calf postpartum.
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Affiliation(s)
- D T Juniper
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, United Kingdom.
| | - C Rymer
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR, United Kingdom
| | - M Briens
- Adisseo France S.A.S., Centre of Excellence and Research in Nutrition, 6 Route Noire, 03600 Commentry, France
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34
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Forcina GC, Dixon SJ. GPX4 at the Crossroads of Lipid Homeostasis and Ferroptosis. Proteomics 2019; 19:e1800311. [PMID: 30888116 DOI: 10.1002/pmic.201800311] [Citation(s) in RCA: 460] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/27/2019] [Indexed: 12/16/2022]
Abstract
Oxygen is necessary for aerobic metabolism but can cause the harmful oxidation of lipids and other macromolecules. Oxidation of cholesterol and phospholipids containing polyunsaturated fatty acyl chains can lead to lipid peroxidation, membrane damage, and cell death. Lipid hydroperoxides are key intermediates in the process of lipid peroxidation. The lipid hydroperoxidase glutathione peroxidase 4 (GPX4) converts lipid hydroperoxides to lipid alcohols, and this process prevents the iron (Fe2+ )-dependent formation of toxic lipid reactive oxygen species (ROS). Inhibition of GPX4 function leads to lipid peroxidation and can result in the induction of ferroptosis, an iron-dependent, non-apoptotic form of cell death. This review describes the formation of reactive lipid species, the function of GPX4 in preventing oxidative lipid damage, and the link between GPX4 dysfunction, lipid oxidation, and the induction of ferroptosis.
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Affiliation(s)
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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35
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Short SP, Pilat JM, Williams CS. Roles for selenium and selenoprotein P in the development, progression, and prevention of intestinal disease. Free Radic Biol Med 2018; 127:26-35. [PMID: 29778465 PMCID: PMC6168360 DOI: 10.1016/j.freeradbiomed.2018.05.066] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/09/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023]
Abstract
Selenium (Se) is a micronutrient essential to human health, the function of which is mediated in part by incorporation into a class of proteins known as selenoproteins (SePs). As many SePs serve antioxidant functions, Se has long been postulated to protect against inflammation and cancer development in the gut by attenuating oxidative stress. Indeed, numerous studies over the years have correlated Se levels with incidence and severity of intestinal diseases such as inflammatory bowel disease (IBD) and colorectal cancer (CRC). Similar results have been obtained with the Se transport protein, selenoprotein P (SELENOP), which is decreased in the plasma of both IBD and CRC patients. While animal models further suggest that decreases in Se or SELENOP augment colitis and intestinal tumorigenesis, large-scale clinical trials have yet to show a protective effect in patient populations. In this review, we discuss the function of Se and SELENOP in intestinal diseases and how research into these mechanisms may impact patient treatment.
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Affiliation(s)
- Sarah P Short
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA; Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Jennifer M Pilat
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Christopher S Williams
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA; Program in Cancer Biology, Vanderbilt University, Nashville, TN, USA; Vanderbilt University School of Medicine, Vanderbilt University, Nashville, TN, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs Tennessee Valley HealthCare System, Nashville, TN, USA.
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Serrão VHB, Silva IR, da Silva MTA, Scortecci JF, de Freitas Fernandes A, Thiemann OH. The unique tRNASec and its role in selenocysteine biosynthesis. Amino Acids 2018; 50:1145-1167. [DOI: 10.1007/s00726-018-2595-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/26/2018] [Indexed: 12/26/2022]
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Translation regulation of mammalian selenoproteins. Biochim Biophys Acta Gen Subj 2018; 1862:2480-2492. [PMID: 29751099 DOI: 10.1016/j.bbagen.2018.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/28/2018] [Accepted: 05/04/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Interest in selenium research has considerably grown over the last decades owing to the association of selenium deficiencies with an increased risk of several human diseases, including cancers, cardiovascular disorders and infectious diseases. The discovery of a genetically encoded 21st amino acid, selenocysteine, is a fascinating breakthrough in molecular biology as it is the first addition to the genetic code deciphered in the 1960s. Selenocysteine is a structural and functional analog of cysteine, where selenium replaces sulfur, and its presence is critical for the catalytic activity of selenoproteins. SCOPE OF REVIEW The insertion of selenocysteine is a non-canonical translational event, based on the recoding of a UGA codon in selenoprotein mRNAs, normally used as a stop codon in other cellular mRNAs. Two RNA molecules and associated partners are crucial components of the selenocysteine insertion machinery, the Sec-tRNA[Ser]Sec devoted to UGA codon recognition and the SECIS elements located in the 3'UTR of selenoprotein mRNAs. MAJOR CONCLUSIONS The translational UGA recoding event is a limiting stage of selenoprotein expression and its efficiency is regulated by several factors. GENERAL SIGNIFICANCE The control of selenoproteome expression is crucial for redox homeostasis and antioxidant defense of mammalian organisms. In this review, we summarize current knowledge on the co-translational insertion of selenocysteine into selenoproteins, and its layers of regulation.
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Touat-Hamici Z, Bulteau AL, Bianga J, Jean-Jacques H, Szpunar J, Lobinski R, Chavatte L. Selenium-regulated hierarchy of human selenoproteome in cancerous and immortalized cells lines. Biochim Biophys Acta Gen Subj 2018; 1862:2493-2505. [PMID: 29660373 DOI: 10.1016/j.bbagen.2018.04.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/21/2018] [Accepted: 04/11/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Selenoproteins (25 genes in human) co-translationally incorporate selenocysteine using a UGA codon, normally used as a stop signal. The human selenoproteome is primarily regulated by selenium bioavailability with a tissue-specific hierarchy. METHODS We investigated the hierarchy of selenoprotein expression in response to selenium concentration variation in four cell lines originating from kidney (HEK293, immortalized), prostate (LNCaP, cancer), skin (HaCaT, immortalized) and liver (HepG2, cancer), using complementary analytical methods. We performed (i) enzymatic activity, (ii) RT-qPCR, (iii) immuno-detection, (iv) selenium-specific mass spectrometric detection after non-radioactive 76Se labeling of selenoproteins, and (v) luciferase-based reporter constructs in various cell extracts. RESULTS We characterized cell-line specific alterations of the selenoproteome in response to selenium variation that, in most of the cases, resulted from a translational control of gene expression. We established that UGA-selenocysteine recoding efficiency, which depends on the nature of the SECIS element, dictates the response to selenium variation. CONCLUSIONS We characterized that selenoprotein hierarchy is cell-line specific with conserved features. This analysis should be done prior to any experiments in a novel cell line. GENERAL SIGNIFICANCE We reported a strategy based on complementary methods to evaluate selenoproteome regulation in human cells in culture.
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Affiliation(s)
- Zahia Touat-Hamici
- From the Centre de Génétique Moléculaire, CGM, CNRS, UPR3404, Gif-sur-Yvette 91198, France
| | - Anne-Laure Bulteau
- Institut de Génomique Fonctionnelle de Lyon, IGFL, CNRS/ENS UMR5242, 69007 Lyon, France
| | - Juliusz Bianga
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux, IPREM-UMR5254, 64000 Pau, France
| | - Hélène Jean-Jacques
- Institut de Biologie Intégrative de la Cellule, I2BC, 91198 Gif-sur-Yvette, France
| | - Joanna Szpunar
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux, IPREM-UMR5254, 64000 Pau, France
| | - Ryszard Lobinski
- CNRS/Univ Pau & Pays Adour, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux, IPREM-UMR5254, 64000 Pau, France
| | - Laurent Chavatte
- Centre International de Recherche en Infectiologie, CIRI, 69007 Lyon, France; INSERM U1111, 69007 Lyon, France; CNRS/ENS/UCBL1 UMR5308, 69007 Lyon, France.
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On elongation factor eEFSec, its role and mechanism during selenium incorporation into nascent selenoproteins. Biochim Biophys Acta Gen Subj 2018; 1862:2463-2472. [PMID: 29555379 DOI: 10.1016/j.bbagen.2018.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/28/2018] [Accepted: 03/12/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND Selenium, an essential dietary micronutrient, is incorporated into proteins as the amino acid selenocysteine (Sec) in response to in-frame UGA codons. Complex machinery ensures accurate recoding of Sec codons in higher organisms. A specialized elongation factor eEFSec is central to the process. SCOPE OF REVIEW Selenoprotein synthesis relies on selenocysteinyl-tRNASec (Sec-tRNASec), selenocysteine inserting sequence (SECIS) and other selenoprotein mRNA elements, an in-trans SECIS binding protein 2 (SBP2) protein factor, and eEFSec. The exact mechanisms of discrete steps of the Sec UGA recoding are not well understood. However, recent studies on mammalian model systems have revealed the first insights into these mechanisms. Herein, we summarize the current knowledge about the structure and role of mammalian eEFSec. MAJOR CONCLUSIONS eEFSec folds into a chalice-like structure resembling that of the archaeal and bacterial orthologues SelB and the initiation protein factor IF2/eIF5B. The three N-terminal domains harbor major functional sites and adopt an EF-Tu-like fold. The C-terminal domain 4 binds to Sec-tRNASec and SBP2, senses distinct binding domains, and modulates the GTPase activity. Remarkably, GTP hydrolysis does not induce a canonical conformational change in eEFSec, but instead promotes a slight ratchet of domains 1 and 2 and a lever-like movement of domain 4, which may be critical for the release of Sec-tRNASec on the ribosome. GENERAL SIGNIFICANCE Based on current findings, a non-canonical mechanism for elongation of selenoprotein synthesis at the Sec UGA codon is proposed. Although incomplete, our understanding of this fundamental biological process is significantly improved, and it is being harnessed for biomedical and synthetic biology initiatives. This article is part of a Special Issue entitled "Selenium research" in celebration of 200 years of selenium discovery, edited by Dr. Elias Arnér and Dr. Regina Brigelius-Flohe.
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Dalgaard TS, Briens M, Engberg RM, Lauridsen C. The influence of selenium and selenoproteins on immune responses of poultry and pigs. Anim Feed Sci Technol 2018; 238:73-83. [PMID: 32336871 PMCID: PMC7173062 DOI: 10.1016/j.anifeedsci.2018.01.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022]
Abstract
Selenium is an essential nutrient for poultry and pigs, and is important for a number of physiological processes including regulation and function of the immune system. Through its incorporation into selenoproteins, Se is involved in the regulation of oxidative stress, redox mechanisms, and other crucial cellular processes involved in innate and adaptive immune response. This review provides current knowledge on the mechanisms by which selenium can modulate the resilience to infectious diseases, and how this micronutrient can influence the capacity of the bird or the pig to maintain its productivity during an infectious challenge. In relation to the most frequent and economically important infectious diseases in poultry and pig production, the present paper considers the influence of different selenium sources (organic vs. inorganic Se) as well as dietary concentrations on the immune responses of poultry and pigs with major emphasis on the potential beneficial impact on animal resilience to common infectious diseases.
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Affiliation(s)
- Tina S Dalgaard
- Dept. of Animal Science, Aarhus University, Blichers allé 20, 8830 Tjele, Denmark
| | - Mickaël Briens
- Adisseo France, CERN, 6 Route Noire, 03600 Commentry, France
| | - Ricarda M Engberg
- Dept. of Animal Science, Aarhus University, Blichers allé 20, 8830 Tjele, Denmark
| | - Charlotte Lauridsen
- Dept. of Animal Science, Aarhus University, Blichers allé 20, 8830 Tjele, Denmark
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41
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Dalley BK, Baird L, Howard MT. Studying Selenoprotein mRNA Translation Using RNA-Seq and Ribosome Profiling. Methods Mol Biol 2018; 1661:103-123. [PMID: 28917040 DOI: 10.1007/978-1-4939-7258-6_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Deep sequencing of ribosome protected mRNA footprints, also called ribosome profiling or Ribo-Seq, is a relatively new methodology well suited to address questions regarding the mechanisms and efficiency of protein expression. Specifically, the ability of this technique to quantify ribosome abundance with codon resolution enables experiments aimed at studying many aspects of translation, including gene-specific translational efficiency, translation of regulatory upstream short open reading frames, sites of ribosome pausing, and most importantly for selenoproteins, the efficiency by which UGA codons are redefined to encode selenocysteine. Here, we describe a streamlined protocol that was developed in our lab to process mammalian tissue to produce the requisite matched ribosome profiling and RNA-Seq libraries for deep sequencing.
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Affiliation(s)
- Brian K Dalley
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112, USA
| | - Lisa Baird
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA
| | - Michael T Howard
- Department of Human Genetics, University of Utah, Salt Lake City, UT, 84112, USA.
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42
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Beaupere C, Chen RB, Pelosi W, Labunskyy VM. Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling. JOURNAL OF VISUALIZED EXPERIMENTS : JOVE 2017:56820. [PMID: 29286414 PMCID: PMC5755679 DOI: 10.3791/56820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription reflect changes in protein synthesis, but many exceptions have been observed. Recently, a technique called ribosome profiling (or Ribo-Seq) has emerged as a powerful method that allows identification, with high accuracy, which regions of mRNA are translated into proteins and quantification of translation at the genome-wide level. Here, we present a generalized protocol for genome-wide quantification of translation using Ribo-Seq in budding yeast. In addition, combining Ribo-Seq data with mRNA abundance measurements allows us to simultaneously quantify translation efficiency of thousands of mRNA transcripts in the same sample and compare changes in these parameters in response to experimental manipulations or in different physiological states. We describe a detailed protocol for generation of ribosome footprints using nuclease digestion, isolation of intact ribosome-footprint complexes via sucrose gradient fractionation, and preparation of DNA libraries for deep sequencing along with appropriate quality controls necessary to ensure accurate analysis of in vivo translation.
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Affiliation(s)
- Carine Beaupere
- Department of Dermatology, Boston University School of Medicine
| | - Rosalyn B. Chen
- Department of Dermatology, Boston University School of Medicine
| | - William Pelosi
- Department of Dermatology, Boston University School of Medicine
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43
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Wu S, Mariotti M, Santesmasses D, Hill KE, Baclaocos J, Aparicio-Prat E, Li S, Mackrill J, Wu Y, Howard MT, Capecchi M, Guigó R, Burk RF, Atkins JF. Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements. Open Biol 2017; 6:rsob.160241. [PMID: 27881738 PMCID: PMC5133445 DOI: 10.1098/rsob.160241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 01/04/2023] Open
Abstract
Dynamic redefinition of the 10 UGAs in human and mouse selenoprotein P (Sepp1) mRNAs to specify selenocysteine instead of termination involves two 3' UTR structural elements (SECIS) and is regulated by selenium availability. In addition to the previously known human Sepp1 mRNA poly(A) addition site just 3' of SECIS 2, two further sites were identified with one resulting in 10-25% of the mRNA lacking SECIS 2. To address function, mutant mice were generated with either SECIS 1 or SECIS 2 deleted or with the first UGA substituted with a serine codon. They were fed on either high or selenium-deficient diets. The mutants had very different effects on the proportions of shorter and longer product Sepp1 protein isoforms isolated from plasma, and on viability. Spatially and functionally distinctive effects of the two SECIS elements on UGA decoding were inferred. We also bioinformatically identify two selenoprotein S mRNAs with different 5' sequences predicted to yield products with different N-termini. These results provide insights into SECIS function and mRNA processing in selenoprotein isoform diversity.
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Affiliation(s)
- Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, People's Republic of China
| | - Marco Mariotti
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Didac Santesmasses
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Kristina E Hill
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Janinah Baclaocos
- Department of Biochemistry, University College Cork, Cork, Republic of Ireland
| | - Estel Aparicio-Prat
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Shuping Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, People's Republic of China
| | - John Mackrill
- Department of Physiology, University College Cork, Cork, Republic of Ireland
| | - Yuanyuan Wu
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Michael T Howard
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Mario Capecchi
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Roderic Guigó
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Raymond F Burk
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John F Atkins
- Department of Biochemistry, University College Cork, Cork, Republic of Ireland .,Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
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Fradejas-Villar N, Seeher S, Anderson CB, Doengi M, Carlson BA, Hatfield DL, Schweizer U, Howard MT. The RNA-binding protein Secisbp2 differentially modulates UGA codon reassignment and RNA decay. Nucleic Acids Res 2017; 45:4094-4107. [PMID: 27956496 PMCID: PMC5397149 DOI: 10.1093/nar/gkw1255] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
Dual-assignment of codons as termination and elongation codons is used to expand the genetic code. In mammals, UGA can be reassigned to selenocysteine during translation of selenoproteins by a mechanism involving a 3΄ untranslated region (UTR) selenocysteine insertion sequence (SECIS) and the SECIS-binding protein Secisbp2. Here, we present data from ribosome profiling, RNA-Seq and mRNA half-life measurements that support distinct roles for Secisbp2 in UGA-redefinition and mRNA stability. Conditional deletions of the Secisbp2 and Trsp (tRNASec) genes in mouse liver were compared to determine if the effects of Secisbp2 loss on selenoprotein synthesis could be attributed entirely to the inability to incorporate Sec. As expected, tRNASec depletion resulted in loss of ribosome density downstream of all UGA-Sec codons. In contrast, the absence of Secisbp2 resulted in variable effects on ribosome density downstream of UGA-Sec codons that demonstrate gene-specific differences in Sec incorporation. For several selenoproteins in which loss of Secisbp2 resulted in greatly diminished mRNA levels, translational activity and Sec incorporation efficiency were shown to be unaffected on the remaining RNA. Collectively, these results demonstrate that Secisbp2 is not strictly required for Sec incorporation and has a distinct role in stabilizing mRNAs that can be separated from its effects on UGA-redefinition.
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Affiliation(s)
- Noelia Fradejas-Villar
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Sandra Seeher
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Michael Doengi
- Institut für Physiologie II, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dolph L Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Michael T Howard
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
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tRNA Modification Detection Using Graphene Nanopores: A Simulation Study. Biomolecules 2017; 7:biom7030065. [PMID: 32962315 PMCID: PMC5618246 DOI: 10.3390/biom7030065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/15/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
There are over 100 enzyme-catalyzed modifications on transfer RNA (tRNA) molecules. The levels and identity of wobble uridine (U) modifications are affected by environmental conditions and diseased states, making wobble U detection a potential biomarker for exposures and pathological conditions. The current detection of RNA modifications requires working with nucleosides in bulk samples. Nanopore detection technology uses a single-molecule approach that has the potential to detect tRNA modifications. To evaluate the feasibility of this approach, we have performed all-atom molecular dynamics (MD) simulation studies of a five-layered graphene nanopore by localizing canonical and modified uridine nucleosides. We found that in a 1 M KCl solution with applied positive and negative biases not exceeding 2 V, nanopores can distinguish U from 5-carbonylmethyluridine (cm5U), 5-methoxycarbonylmethyluridine (mcm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), and 5-methoxycarbonylmethyl-2′-O-methyluridine (mcm5Um) based on changes in the resistance of the nanopore. Specifically, we observed that in nanopores with dimensions less than 3 nm diameter, a localized mcm5Um and mcm5U modifications could be clearly distinguished from the canonical uridine, while the other modifications showed a modest yet detectable decrease in their respective nanopore conductance. We have compared the results between nanopores of various sizes to aid in the design, optimization, and fabrication of graphene nanopores devices for tRNA modification detection.
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46
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Aminoglycoside-driven biosynthesis of selenium-deficient Selenoprotein P. Sci Rep 2017; 7:4391. [PMID: 28663583 PMCID: PMC5491492 DOI: 10.1038/s41598-017-04586-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/17/2017] [Indexed: 12/17/2022] Open
Abstract
Selenoprotein biosynthesis relies on the co-translational insertion of selenocysteine in response to UGA codons. Aminoglycoside antibiotics interfere with ribosomal function and may cause codon misreading. We hypothesized that biosynthesis of the selenium (Se) transporter selenoprotein P (SELENOP) is particularly sensitive to antibiotics due to its ten in frame UGA codons. As liver regulates Se metabolism, we tested the aminoglycosides G418 and gentamicin in hepatoma cell lines (HepG2, Hep3B and Hepa1-6) and in experimental mice. In vitro, SELENOP levels increased strongly in response to G418, whereas expression of the glutathione peroxidases GPX1 and GPX2 was marginally affected. Se content of G418-induced SELENOP was dependent on Se availability, and was completely suppressed by G418 under Se-poor conditions. Selenocysteine residues were replaced mainly by cysteine, tryptophan and arginine in a codon-specific manner. Interestingly, in young healthy mice, antibiotic treatment failed to affect Selenop biosynthesis to a detectable degree. These findings suggest that the interfering activity of aminoglycosides on selenoprotein biosynthesis can be severe, but depend on the Se status, and other parameters likely including age and general health. Focused analyses with aminoglycoside-treated patients are needed next to evaluate a possible interference of selenoprotein biosynthesis by the antibiotics and elucidate potential side effects.
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47
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Elgendy R, Giantin M, Castellani F, Grotta L, Palazzo F, Dacasto M, Martino G. Transcriptomic signature of high dietary organic selenium supplementation in sheep: A nutrigenomic insight using a custom microarray platform and gene set enrichment analysis. J Anim Sci 2017; 94:3169-3184. [PMID: 27695782 DOI: 10.2527/jas.2016-0363] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The objective of this study was to investigate the effect of a high dietary Se supplementation on the whole transcriptome of sheep. A custom sheep whole-transcriptome microarray, with more than 23,000 unique transcripts, was designed and then used to profile the global gene expression of sheep after feeding a high dietary supplementation of organic Se. Lactating crossbred ewes ( = 10; 3 to 4 yr of age and 55 to 65 kg BW) at late lactation (100 ± 8 d in milk) were acclimated to indoor individual pen feeding of a basal control diet (0.40 mg Se/d, sodium selenite) for 4 wk. Sheep were then kept on a diet with an extra (high) supplementation of organic Se (1.45 mg Se/d as Sel-Plex; Alltech Biotechnology Pty Ltd, Dandenong, Victoria, Australia) for 40 d. Whole blood was collected at 2 time points (last day of the acclimatization period [T0] and after 40 d of the organic Se supplementation [T40]), and then total RNA was isolated and labeled for the subsequent microarray analysis. Significance Analysis of Microarrays, using the -statistic, of the microarray data (T40 versus T0) evidenced the up- and downregulation of 942 and 244 transcripts (false discovery rate < 0.05), respectively. Seven genes showed the same trend of expression (up- or downregulation) when tested by quantitative real-time PCR (qPCR) in a cross-validation step. The microarray showed significant upregulation of the following selenoproteins at T40: selenium binding protein 1 (SELENBP1), selenoprotein W1 (SEPW1), glutathione peroxidase 3 (GPX3), and septin 8 (SEPT8). And the expression trends for SEPW1 and SEPT8 were validated using qPCR. Functional annotation of the differentially expressed genes showed the enrichment of several immune system-related biological processes (lymphocyte activation, cytokine binding, leukocyte activation, T cell differentiation, and B cell activation) and pathways (cytokine and interleukin signaling). Moreover, Gene Set Enrichment Analysis evidenced the enrichment of B and T cell receptors signaling pathways, with an enrichment score of 0.63 and 0.59, respectively. Overall, from a global gene expression (whole-transcriptome) point of view, short-term supplementation of a high dietary organic Se to Se-nondeficient sheep results in a transcriptomic signature that mainly reflects an induced immune system and a modulation of transcription effect. Also, the present study provides a custom whole-transcriptome microarray platform that can be used in further global gene expression studies in the ovine species.
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48
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Carlson BA, Gupta N, Pinkerton MH, Hatfield DL, Copeland PR. The utilization of selenocysteine-tRNA [Ser]Sec isoforms is regulated in part at the level of translation in vitro. ACTA ACUST UNITED AC 2017; 5:e1314240. [PMID: 28702279 DOI: 10.1080/21690731.2017.1314240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 10/19/2022]
Abstract
The tRNA for the 21st proteinogenic amino acid, selenocysteine, exists in mammalian cells as 2 isoforms differing by a single 2'-O-methylribosyl moiety at position 34 (Um34). These isoforms contain either 5-methoxycarbonylmethyluridine (mcm5U) or 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) at position 34. The accumulation of the mcm5Um isoform is tightly correlated with the expression of nonessential "stress response" selenoproteins such as glutathione peroxidase 1 (GPX1). The expression of essential selenoproteins, such as thioredoxin reductase 1 (TXNRD1), is not affected by changes in Sec-tRNA[Ser]Sec isoform accumulation. In this work we used purified mcm5U and mcm5Um Sec-tRNA[Ser]Sec isoforms to analyze possible differences in binding to the selenocysteine-specific elongation factor, EEFSEC, and the translation of GPX1 and TXNRD1in vitro. Our results indicate that no major distinction between mcm5U and mcm5Um isoforms is made by the translation machinery, but a small consistent increase in GPX1 translation is associated with the mcm5Um isoform. These results implicate fundamental differences in translation efficiency in playing a role in regulating selenoprotein expression as a function of isoform accumulation.
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Affiliation(s)
- Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nirupama Gupta
- Department of Biochemistry and Molecular Biology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Mark H Pinkerton
- Department of Biochemistry and Molecular Biology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Dolph L Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul R Copeland
- Department of Biochemistry and Molecular Biology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
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Schweizer U, Bohleber S, Fradejas-Villar N. The modified base isopentenyladenosine and its derivatives in tRNA. RNA Biol 2017; 14:1197-1208. [PMID: 28277934 PMCID: PMC5699536 DOI: 10.1080/15476286.2017.1294309] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Base 37 in tRNA, 3′-adjacent to the anticodon, is occupied by a purine base that is thought to stabilize codon recognition by stacking interactions on the first Watson-Crick base pair. If the first codon position forms an A.U or U.A base pair, the purine is likely further modified in all domains of life. One of the first base modifications found in tRNA is N6-isopentenyl adenosine (i6A) present in a fraction of tRNAs in bacteria and eukaryotes, which can be further modified to 2-methyl-thio-N6-isopentenyladenosine (ms2i6A) in a subset of tRNAs. Homologous tRNA isopentenyl transferase enzymes have been identified in bacteria (MiaA), yeast (Mod5, Tit1), roundworm (GRO-1), and mammals (TRIT1). In eukaryotes, isopentenylation of cytoplasmic and mitochondrial tRNAs is mediated by products of the same gene. Accordingly, a patient with homozygous mutations in TRIT1 has mitochondrial disease. The role of i6A in a subset of tRNAs in gene expression has been linked with translational fidelity, speed of translation, skewed gene expression, and non-sense suppression. This review will not cover the action of i6A as a cytokinin in plants or the potential function of Mod5 as a prion in yeast.
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Affiliation(s)
- Ulrich Schweizer
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Simon Bohleber
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
| | - Noelia Fradejas-Villar
- a Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn , Bonn , Germany
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Chen YF, Lin HC, Chuang KN, Lin CH, Yen HCS, Yeang CH. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons. PLoS Comput Biol 2017; 13:e1005367. [PMID: 28178267 PMCID: PMC5323020 DOI: 10.1371/journal.pcbi.1005367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/23/2017] [Accepted: 01/18/2017] [Indexed: 12/20/2022] Open
Abstract
Ambiguity in genetic codes exists in cases where certain stop codons are alternatively used to encode non-canonical amino acids. In selenoprotein transcripts, the UGA codon may either represent a translation termination signal or a selenocysteine (Sec) codon. Translating UGA to Sec requires selenium and specialized Sec incorporation machinery such as the interaction between the SECIS element and SBP2 protein, but how these factors quantitatively affect alternative assignments of UGA has not been fully investigated. We developed a model simulating the UGA decoding process. Our model is based on the following assumptions: (1) charged Sec-specific tRNAs (Sec-tRNASec) and release factors compete for a UGA site, (2) Sec-tRNASec abundance is limited by the concentrations of selenium and Sec-specific tRNA (tRNASec) precursors, and (3) all synthesis reactions follow first-order kinetics. We demonstrated that this model captured two prominent characteristics observed from experimental data. First, UGA to Sec decoding increases with elevated selenium availability, but saturates under high selenium supply. Second, the efficiency of Sec incorporation is reduced with increasing selenoprotein synthesis. We measured the expressions of four selenoprotein constructs and estimated their model parameters. Their inferred Sec incorporation efficiencies did not correlate well with their SECIS-SBP2 binding affinities, suggesting the existence of additional factors determining the hierarchy of selenoprotein synthesis under selenium deficiency. This model provides a framework to systematically study the interplay of factors affecting the dual definitions of a genetic codon. The “code book” of protein translation maps 43 = 64 triplets of RNA sequences (codons) into 20 canonical amino acids and the stop signal. This code book is universal in almost all organisms on earth. Selenoproteins consist of selenium-containing amino acids–selenocysteines (Sec)–that are not among the 20 canonical amino acids. The cells “borrow” a stop codon UGA to translate selenocysteines. Since UGA maps to two possible outcomes, the translation machinery can synthesize both full-length selenoproteins (when UGA encodes selenocysteine) and truncated peptide chains (when UGA encodes translational termination). Despite extensive study about selenoprotein synthesis mechanisms, a quantitative model for how cells allocate resources to synthesize each species is yet to appear. We propose a quantitative model that can explain the dependency of experimental observables such as protein stability and Sec incorporation efficiency by various factors such as selenium concentration and mRNA levels. Saturation of those quantities implies the existence of limiting factors such as mRNA transcripts and Sec-specific tRNAs. The match between model simulations and experimental data suggests that the cellular decision making of synthesizing the two species of proteins may follow simple first-order kinetics.
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Affiliation(s)
- Yen-Fu Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsiu-Chuan Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Kai-Neng Chuang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Chih-Hsu Lin
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Hsueh-Chi S. Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
| | - Chen-Hsiang Yeang
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- * E-mail: (HCSY); (CHY)
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