1
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Mullegama SV, Kiernan KA, Torti E, Pavlovsky E, Tilton N, Sekula A, Gao H, Alaimo JT, Engleman K, Rush ET, Blocker K, Dipple KM, Fettig VM, Hare H, Glass I, Grange DK, Griffin M, Phornphutkul C, Massingham L, Mehta L, Miller DE, Thies J, Merritt JL, Muller E, Osmond M, Sawyer SL, Slaugh R, Hickey RE, Wolf B, Choudhary S, Simonović M, Zhang Y, Palculict TB, Telegrafi A, Carere DA, Wentzensen IM, Morrow MM, Monaghan KG, Yang J, Juusola J. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features. Am J Hum Genet 2024; 111:778-790. [PMID: 38531365 PMCID: PMC11023921 DOI: 10.1016/j.ajhg.2024.02.016] [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: 04/04/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/28/2024] Open
Abstract
Selenophosphate synthetase (SEPHS) plays an essential role in selenium metabolism. Two mammalian SEPHS paralogues, SEPHS1 and SEPHS2, share high sequence identity and structural homology with SEPHS. Here, we report nine individuals from eight families with developmental delay, growth and feeding problems, hypotonia, and dysmorphic features, all with heterozygous missense variants in SEPHS1. Eight of these individuals had a recurrent variant at amino acid position 371 of SEPHS1 (p.Arg371Trp, p.Arg371Gln, and p.Arg371Gly); seven of these variants were known to be de novo. Structural modeling and biochemical assays were used to understand the effect of these variants on SEPHS1 function. We found that a variant at residue Trp352 results in local structural changes of the C-terminal region of SEPHS1 that decrease the overall thermal stability of the enzyme. In contrast, variants of a solvent-exposed residue Arg371 do not impact enzyme stability and folding but could modulate direct protein-protein interactions of SEPSH1 with cellular factors in promoting cell proliferation and development. In neuronal SH-SY5Y cells, we assessed the impact of SEPHS1 variants on cell proliferation and ROS production and investigated the mRNA expression levels of genes encoding stress-related selenoproteins. Our findings provided evidence that the identified SEPHS1 variants enhance cell proliferation by modulating ROS homeostasis. Our study supports the hypothesis that SEPHS1 plays a critical role during human development and provides a basis for further investigation into the molecular mechanisms employed by SEPHS1. Furthermore, our data suggest that variants in SEPHS1 are associated with a neurodevelopmental disorder.
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Affiliation(s)
- Sureni V Mullegama
- GeneDx, Gaithersburg, MD 20877, USA; Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA.
| | - Kaitlyn A Kiernan
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - Ethan Pavlovsky
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Nicholas Tilton
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Austin Sekula
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Hua Gao
- GeneDx, Gaithersburg, MD 20877, USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, USA; Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA
| | - Eric T Rush
- Department of Pediatrics, University of Missouri Kansas City, School of Medicine, Kansas City, MO, USA; Division of Clinical Genetics, Children's Mercy Hospital, Kansas City, MO, USA; Department of Internal Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Karli Blocker
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Veronica M Fettig
- Center for Inherited Cardiovascular Disease, Cardiovascular Genetics Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Heather Hare
- Northeastern Ontario Medical Genetics Program, Health Sciences, North Sudbury, ON, Canada
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Dorothy K Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael Griffin
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Chanika Phornphutkul
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lauren Massingham
- Division of Genetics, Department of Pediatrics, Alpert School of Medicine at Brown University, Providence, RI, USA
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jenny Thies
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA, USA
| | - J Lawrence Merritt
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Eric Muller
- Division of Clinical Genetics, Stanford Children's Health, San Francisco, CA, USA
| | - Matthew Osmond
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah L Sawyer
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Hickey
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Barry Wolf
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Anne & Robert H. Lurie Children's Hospital, Chicago, IL, USA
| | - Sanjeev Choudhary
- Department of Molecular and Cellular Biology, College of Osteopathic Medicine, Sam Houston State University, Conroe, TX 77304, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Yueqing Zhang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | | | | | | | | | | | | | - Jun Yang
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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2
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Kim Y, Cho S, Kim JC, Park HS. tRNA engineering strategies for genetic code expansion. Front Genet 2024; 15:1373250. [PMID: 38516376 PMCID: PMC10954879 DOI: 10.3389/fgene.2024.1373250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The advancement of genetic code expansion (GCE) technology is attributed to the establishment of specific aminoacyl-tRNA synthetase/tRNA pairs. While earlier improvements mainly focused on aminoacyl-tRNA synthetases, recent studies have highlighted the importance of optimizing tRNA sequences to enhance both unnatural amino acid incorporation efficiency and orthogonality. Given the crucial role of tRNAs in the translation process and their substantial impact on overall GCE efficiency, ongoing efforts are dedicated to the development of tRNA engineering techniques. This review explores diverse tRNA engineering approaches and provides illustrative examples in the context of GCE, offering insights into the user-friendly implementation of GCE technology.
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Affiliation(s)
| | | | | | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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3
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Wright DE, O’Donoghue P. Biosynthesis, Engineering, and Delivery of Selenoproteins. Int J Mol Sci 2023; 25:223. [PMID: 38203392 PMCID: PMC10778597 DOI: 10.3390/ijms25010223] [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: 11/15/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Selenocysteine (Sec) was discovered as the 21st genetically encoded amino acid. In nature, site-directed incorporation of Sec into proteins requires specialized biosynthesis and recoding machinery that evolved distinctly in bacteria compared to archaea and eukaryotes. Many organisms, including higher plants and most fungi, lack the Sec-decoding trait. We review the discovery of Sec and its role in redox enzymes that are essential to human health and important targets in disease. We highlight recent genetic code expansion efforts to engineer site-directed incorporation of Sec in bacteria and yeast. We also review methods to produce selenoproteins with 21 or more amino acids and approaches to delivering recombinant selenoproteins to mammalian cells as new applications for selenoproteins in synthetic biology.
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Affiliation(s)
- David E. Wright
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
| | - Patrick O’Donoghue
- Department of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada;
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
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4
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Zhao R, Zhang L, Lu H. Analysis of the Clinical Features and Imaging Findings of Pontocerebellar Hypoplasia Type 2D Caused by Mutations in SEPSECS Gene. CEREBELLUM (LONDON, ENGLAND) 2023; 22:938-946. [PMID: 36085396 DOI: 10.1007/s12311-022-01470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
Pontocerebellar hypoplasia type 2D (PCH2D) caused by SEPSECS gene mutations is very rare and only described in a few case reports. In this study, we analyzed the clinical features and imaging findings of these individuals, so as to provide references for the clinic. We reported a case of PCH2D caused by a new complex heterozygote mutation in SEPSECS gene, and reviewed the literatures to summarize the clinical features and imaging findings and compare the differences between early-onset patients (EOPs) and late-onset patients (LOPs). Of 23 PCH2D patients, 19 cases were early-onset and 4 cases were late-onset, with average ages of 4.1 ± 4.0 years and 21.8 ± 9.4 years, females were more prevalent (14/19). EOPs mainly distributed in Arab countries (10/14) and Finland (4/14), while LOPs in East Asia (3/3). EOPs develop severe initial symptoms at the average age of 4.1 ± 7.8 months or shortly after birth, while LOPs experienced mild developmental delay in infancy. Microcephaly (10/11), intellectual disability (10/11), decreased motor function (10/11), and spastic or dystonic quadriplegia (8/10) were the common clinical features of EOPs and LOPs. EOPs also presented with visual impairment (5/7), seizures (4/7), neonatal irritability/opisthotonus (3/7), tremors/myoclonus (3/7), dysmorphic features (3/7), and other symptoms. EOPs were characterized by cerebellar symptoms (4/4). Magnetic resonance imaging (MRI) revealed progressive cerebellar atrophy followed by less pronounced cerebral atrophy, and there was no pons atrophy in LOPs. Most patients of PCH2D were severe early-onset, and a few were late-onset with milder symptoms. EOPs and LOPs shared some common clinical features and MRI findings, but also had their own characteristics.
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Affiliation(s)
- Ran Zhao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Limin Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hong Lu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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5
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Xie Y, Kang R, Klionsky DJ, Tang D. GPX4 in cell death, autophagy, and disease. Autophagy 2023; 19:2621-2638. [PMID: 37272058 PMCID: PMC10472888 DOI: 10.1080/15548627.2023.2218764] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
Selenoprotein GPX4 (glutathione peroxidase 4), originally known as PHGPX (phospholipid hydroperoxide glutathione peroxidase), is the main oxidoreductase in the use of glutathione as a reducing agent in scavenging lipid peroxidation products. There are three GPX4 isoforms: cytosolic (cGPX4), mitochondrial (mGPX4), and nuclear (nGPX4), with distinct spatiotemporal expression patterns during embryonic development and adult life. In addition to inducing the main phenotype of ferroptosis, the loss of GPX4 can in some cells trigger apoptosis, necroptosis, pyroptosis, or parthanatos, which mediates or accelerates developmental defects, tissue damage, and sterile inflammation. The interaction of GPX4 with the autophagic degradation pathway further modulates cell fate in response to oxidative stress. Impaired GPX4 function is implicated in tumorigenesis, neurodegeneration, infertility, inflammation, immune disorders, and ischemia-reperfusion injury. Additionally, the R152H mutation in GPX4 can promote the development of Sedaghatian-type spinal metaphyseal dysplasia, a rare and fatal disease in newborns. Here, we discuss the roles of classical GPX4 functions as well as emerging GPX4-regulated processes in cell death, autophagy, and disease.Abbreviations: AA: arachidonic acid; cGPX4: cytosolic GPX4; CMA: chaperone-mediated autophagy; DAMPs: danger/damage-associated molecular patterns; mGPX4: mitochondrial GPX4; nGPX4: nuclear GPX4; GSDMD-N: N-terminal fragment of GSDMD; I/R: ischemia-reperfusion; PLOOH: phospholipid hydroperoxide; PUFAs: polyunsaturated fatty acids; RCD: regulated cell death; ROS: reactive oxygen species; Se: selenium; SSMD: Sedaghatian-type spondylometaphyseal dysplasia; UPS: ubiquitin-proteasome system.
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Affiliation(s)
- Yangchun Xie
- Department of Oncology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Rui Kang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel J. Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daolin Tang
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX, USA
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6
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Salmain M, Gaschard M, Baroud M, Lepeltier E, Jaouen G, Passirani C, Vessières A. Thioredoxin Reductase and Organometallic Complexes: A Pivotal System to Tackle Multidrug Resistant Tumors? Cancers (Basel) 2023; 15:4448. [PMID: 37760418 PMCID: PMC10526406 DOI: 10.3390/cancers15184448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Cancers classified as multidrug-resistant (MDR) are a family of diseases with poor prognosis despite access to increasingly sophisticated treatments. Several mechanisms explain these resistances involving both tumor cells and their microenvironment. It is now recognized that a multi-targeting approach offers a promising strategy to treat these MDR tumors. Inhibition of thioredoxin reductase (TrxR), a key enzyme in maintaining redox balance in cells, is a well-identified target for this approach. Auranofin was the first inorganic gold complex to be described as a powerful inhibitor of TrxR. In this review, we will first recall the main results obtained with this metallodrug. Then, we will focus on organometallic complexes reported as TrxR inhibitors. These include gold(I), gold(III) complexes and metallocifens, i.e., organometallic complexes of Fe and Os derived from tamoxifen. In these families of complexes, similarities and differences in the molecular mechanisms of TrxR inhibition will be highlighted. Finally, the possible relationship between TrxR inhibition and cytotoxicity will be discussed and put into perspective with their mode of action.
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Affiliation(s)
- Michèle Salmain
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 Place Jussieu, F-75005 Paris, France; (M.S.); (M.G.); (G.J.); (A.V.)
| | - Marie Gaschard
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 Place Jussieu, F-75005 Paris, France; (M.S.); (M.G.); (G.J.); (A.V.)
| | - Milad Baroud
- Micro & Nanomedecines Translationnelles (MINT), University of Angers, Inserm, The National Center for Scientific Research (CNRS), SFR ICAT, F-49000 Angers, France; (M.B.); (E.L.)
| | - Elise Lepeltier
- Micro & Nanomedecines Translationnelles (MINT), University of Angers, Inserm, The National Center for Scientific Research (CNRS), SFR ICAT, F-49000 Angers, France; (M.B.); (E.L.)
| | - Gérard Jaouen
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 Place Jussieu, F-75005 Paris, France; (M.S.); (M.G.); (G.J.); (A.V.)
| | - Catherine Passirani
- Micro & Nanomedecines Translationnelles (MINT), University of Angers, Inserm, The National Center for Scientific Research (CNRS), SFR ICAT, F-49000 Angers, France; (M.B.); (E.L.)
| | - Anne Vessières
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire (IPCM), 4 Place Jussieu, F-75005 Paris, France; (M.S.); (M.G.); (G.J.); (A.V.)
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7
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Hoffman KS, Chung CZ, Mukai T, Krahn N, Jiang HK, Balasuriya N, O'Donoghue P, Söll D. Recoding UAG to selenocysteine in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1400-1410. [PMID: 37279998 PMCID: PMC10573291 DOI: 10.1261/rna.079658.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Unique chemical and physical properties are introduced by inserting selenocysteine (Sec) at specific sites within proteins. Recombinant and facile production of eukaryotic selenoproteins would benefit from a yeast expression system; however, the selenoprotein biosynthetic pathway was lost in the evolution of the kingdom Fungi as it diverged from its eukaryotic relatives. Based on our previous development of efficient selenoprotein production in bacteria, we designed a novel Sec biosynthesis pathway in Saccharomyces cerevisiae using Aeromonas salmonicida translation components. S. cerevisiae tRNASer was mutated to resemble A. salmonicida tRNASec to allow recognition by S. cerevisiae seryl-tRNA synthetase as well as A. salmonicida selenocysteine synthase (SelA) and selenophosphate synthetase (SelD). Expression of these Sec pathway components was then combined with metabolic engineering of yeast to enable the production of active methionine sulfate reductase enzyme containing genetically encoded Sec. Our report is the first demonstration that yeast is capable of selenoprotein production by site-specific incorporation of Sec.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Christina Z Chung
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Han-Kai Jiang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Nileeka Balasuriya
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 3K7, Canada
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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8
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Tijaro-Bulla S, Nyandwi SP, Cui H. Physiological and engineered tRNA aminoacylation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1789. [PMID: 37042417 DOI: 10.1002/wrna.1789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/11/2023] [Accepted: 03/21/2023] [Indexed: 04/13/2023]
Abstract
Aminoacyl-tRNA synthetases form the protein family that controls the interpretation of the genetic code, with tRNA aminoacylation being the key chemical step during which an amino acid is assigned to a corresponding sequence of nucleic acids. In consequence, aminoacyl-tRNA synthetases have been studied in their physiological context, in disease states, and as tools for synthetic biology to enable the expansion of the genetic code. Here, we review the fundamentals of aminoacyl-tRNA synthetase biology and classification, with a focus on mammalian cytoplasmic enzymes. We compile evidence that the localization of aminoacyl-tRNA synthetases can be critical in health and disease. In addition, we discuss evidence from synthetic biology which made use of the importance of subcellular localization for efficient manipulation of the protein synthesis machinery. This article is categorized under: RNA Processing Translation > Translation Regulation RNA Processing > tRNA Processing RNA Export and Localization > RNA Localization.
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Affiliation(s)
| | | | - Haissi Cui
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
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9
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Abstract
Methanogenic archaea are the only organisms that produce CH4 as part of their energy-generating metabolism. They are ubiquitous in oxidant-depleted, anoxic environments such as aquatic sediments, anaerobic digesters, inundated agricultural fields, the rumen of cattle, and the hindgut of termites, where they catalyze the terminal reactions in the degradation of organic matter. Methanogenesis is the only metabolism that is restricted to members of the domain Archaea. Here, we discuss the importance of model organisms in the history of methanogen research, including their role in the discovery of the archaea and in the biochemical and genetic characterization of methanogenesis. We also discuss outstanding questions in the field and newly emerging model systems that will expand our understanding of this uniquely archaeal metabolism.
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Affiliation(s)
- Kyle C. Costa
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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10
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Giegé R, Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Res 2023; 51:1528-1570. [PMID: 36744444 PMCID: PMC9976931 DOI: 10.1093/nar/gkad007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023] Open
Abstract
tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.
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Affiliation(s)
- Richard Giegé
- Correspondence may also be addressed to Richard Giegé.
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11
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Selenoprotein: Potential Player in Redox Regulation in Chlamydomonas reinhardtii. Antioxidants (Basel) 2022; 11:antiox11081630. [PMID: 36009349 PMCID: PMC9404770 DOI: 10.3390/antiox11081630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/22/2022] Open
Abstract
Selenium (Se) is an essential micro-element for many organisms, including Chlamydomonas reinhardtii, and is required in trace amounts. It is obtained from the 21st amino acid selenocysteine (Sec, U), genetically encoded by the UGA codon. Proteins containing Sec are known as selenoproteins. In eukaryotes, selenoproteins are present in animals and algae, whereas fungi and higher plants lack them. The human genome contains 25 selenoproteins, most of which are involved in antioxidant defense activity, redox regulation, and redox signaling. In algae, 42 selenoprotein families were identified using various bioinformatics approaches, out of which C. reinhardtii is known to have 10 selenoprotein genes. However, the role of selenoproteins in Chlamydomonas is yet to be reported. Chlamydomonas selenoproteins contain conserved domains such as CVNVGC and GCUG, in the case of thioredoxin reductase, and CXXU in other selenoproteins. Interestingly, Sec amino acid residue is present in a catalytically active domain in Chlamydomonas selenoproteins, similar to human selenoproteins. Based on catalytical active sites and conserved domains present in Chlamydomonas selenoproteins, we suggest that Chlamydomonas selenoproteins could have a role in redox regulation and defense by acting as antioxidants in various physiological conditions.
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12
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Ursini F, Bosello Travain V, Cozza G, Miotto G, Roveri A, Toppo S, Maiorino M. A white paper on Phospholipid Hydroperoxide Glutathione Peroxidase (GPx4) forty years later. Free Radic Biol Med 2022; 188:117-133. [PMID: 35718302 DOI: 10.1016/j.freeradbiomed.2022.06.227] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 12/25/2022]
Abstract
The purification of a protein inhibiting lipid peroxidation led to the discovery of the selenoperoxidase GPx4 forty years ago. Thus, the evidence of the enzymatic activity was reached after identifying the biological effect and unambiguously defined the relationship between the biological function and the enzymatic activity. In the syllogism where GPx4 inhibits lipid peroxidation and its inhibition is lethal, cell death is operated by lipid peroxidation. Based on this rationale, this form of cell death emerged as regulated iron-enforced oxygen toxicity and was named ferroptosis in 2012. In the last decades, we learned that reduction of lipid hydroperoxides is indispensable and, in cooperation with prooxidant systems, controls the critical steady state of lipid peroxidation. This concept defined the GPx4 reaction as both the target for possible anti-cancer therapy and if insufficient, as cause of degenerative diseases. We know the reaction mechanism, but the details of the interaction at the membrane cytosol interface are still poorly defined. We know the gene structure, but the knowledge about expression control is still limited. The same holds true for post-transcriptional modifications. Reverse genetics indicate that GPx4 has a role in inflammation, immunity, and differentiation, but the observations emerging from these studies need a more specifically addressed biochemical evidence. Finally, the role of GPx4 in spermatogenesis disclosed an area unconnected to lipid peroxidation. In its mitochondrial and nuclear form, the peroxidase catalyzes the oxidation of protein thiols in two specific aspects of sperm maturation: stabilization of the mid-piece and chromatin compaction. Thus, although available evidence converges to the notion that GPx4 activity is vital due to the inhibition of lipid peroxidation, it is reasonable to foresee other unknown aspects of the GPx4 reaction to be disclosed.
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Affiliation(s)
- Fulvio Ursini
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy
| | | | - Giorgio Cozza
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy
| | - Giovanni Miotto
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy
| | - Antonella Roveri
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy
| | - Matilde Maiorino
- Department of Molecular Medicine, Viale G. Colombo, 3, University of Padova, 35121, Padova, Italy.
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13
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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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14
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Niu R, Yang Q, Dong Y, Hou Y, Liu G. Selenium metabolism and regulation of immune cells in immune-associated diseases. J Cell Physiol 2022; 237:3449-3464. [PMID: 35788930 DOI: 10.1002/jcp.30824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 11/06/2022]
Abstract
Selenium, as one of the essential microelements, plays an irreplaceable role in metabolism regulation and cell survival. Selenium metabolism and regulation have great effects on physiological systems especially the immune system. Therefore, selenium is tightly related to various diseases like cancer. Although recent research works have revealed much about selenium metabolism, the ways in which selenium regulates immune cells' functions and immune-associated diseases still remain much unclear. In this review, we will briefly introduce the regulatory role of selenium metabolism in immune cells and immune-associated diseases.
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Affiliation(s)
- Ruiying Niu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qiuli Yang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yingjie Dong
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yueru Hou
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
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15
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Noda Y, Okada S, Suzuki T. Regulation of A-to-I RNA editing and stop codon recoding to control selenoprotein expression during skeletal myogenesis. Nat Commun 2022; 13:2503. [PMID: 35523818 PMCID: PMC9076623 DOI: 10.1038/s41467-022-30181-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
Selenoprotein N (SELENON), a selenocysteine (Sec)-containing protein with high reductive activity, maintains redox homeostasis, thereby contributing to skeletal muscle differentiation and function. Loss-of-function mutations in SELENON cause severe neuromuscular disorders. In the early-to-middle stage of myoblast differentiation, SELENON maintains redox homeostasis and modulates endoplasmic reticulum (ER) Ca2+ concentration, resulting in a gradual reduction from the middle-to-late stages due to unknown mechanisms. The present study describes post-transcriptional mechanisms that regulate SELENON expression during myoblast differentiation. Part of an Alu element in the second intron of SELENON pre-mRNA is frequently exonized during splicing, resulting in an aberrant mRNA that is degraded by nonsense-mediated mRNA decay (NMD). In the middle stage of myoblast differentiation, ADAR1-mediated A-to-I RNA editing occurs in the U1 snRNA binding site at 5' splice site, preventing Alu exonization and producing mature mRNA. In the middle-to-late stage of myoblast differentiation, the level of Sec-charged tRNASec decreases due to downregulation of essential recoding factors for Sec insertion, thereby generating a premature termination codon in SELENON mRNA, which is targeted by NMD.
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Affiliation(s)
- Yuta Noda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enyacho, Izumo, Shimane, 693-8501, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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16
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Mukai T, Amikura K, Fu X, Söll D, Crnković A. Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems. Front Genet 2022; 12:794509. [PMID: 35047015 PMCID: PMC8762117 DOI: 10.3389/fgene.2021.794509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/18/2021] [Indexed: 01/23/2023] Open
Abstract
Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.
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Affiliation(s)
- Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Xian Fu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Ana Crnković
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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17
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Minich WB. Selenium Metabolism and Biosynthesis of Selenoproteins in the Human Body. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S168-S102. [PMID: 35501994 PMCID: PMC8802287 DOI: 10.1134/s0006297922140139] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022]
Abstract
As an essential trace element, selenium (Se) plays a tremendous role in the functioning of the human organism being used for the biosynthesis of selenoproteins (proteins containing one or several selenocysteine residues). The functions of human selenoproteins in vivo are extremely diverse. Many selenoproteins have an antioxidant activity and, hence, play a key role in cell antioxidant defense and maintenance of redox homeostasis, which accounts for their involvement in diverse biological processes, such as signal transduction, proliferation, cell transformation and aging, ferroptosis, immune system functioning, etc. One of the critical functions of selenoenzymes is participation in the synthesis of thyroid hormones regulating basal metabolism in all body tissues. Over the last decades, optimization of population Se intake for prevention of diseases related to Se deficiency or excess has been recognized as a pressing issue in modern healthcare worldwide.
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Affiliation(s)
- Waldemar B Minich
- Institute of Experimental Endocrinology, Charite, Medical University, Berlin, D-10115, Germany.
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18
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Tsuji PA, Santesmasses D, Lee BJ, Gladyshev VN, Hatfield DL. Historical Roles of Selenium and Selenoproteins in Health and Development: The Good, the Bad and the Ugly. Int J Mol Sci 2021; 23:ijms23010005. [PMID: 35008430 PMCID: PMC8744743 DOI: 10.3390/ijms23010005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/25/2022] Open
Abstract
Selenium is a fascinating element that has a long history, most of which documents it as a deleterious element to health. In more recent years, selenium has been found to be an essential element in the diet of humans, all other mammals, and many other life forms. It has many health benefits that include, for example, roles in preventing heart disease and certain forms of cancer, slowing AIDS progression in HIV patients, supporting male reproduction, inhibiting viral expression, and boosting the immune system, and it also plays essential roles in mammalian development. Elucidating the molecular biology of selenium over the past 40 years generated an entirely new field of science which encompassed the many novel features of selenium. These features were (1) how this element makes its way into protein as the 21st amino acid in the genetic code, selenocysteine (Sec); (2) the vast amount of machinery dedicated to synthesizing Sec uniquely on its tRNA; (3) the incorporation of Sec into protein; and (4) the roles of the resulting Sec-containing proteins (selenoproteins) in health and development. One of the research areas receiving the most attention regarding selenium in health has been its role in cancer prevention, but further research has also exposed the role of this element as a facilitator of various maladies, including cancer.
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Affiliation(s)
- Petra A. Tsuji
- Department of Biological Sciences, Towson University, 8000 York Rd., Towson, MD 21252, USA
- Correspondence:
| | - Didac Santesmasses
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA; (D.S.); (V.N.G.)
| | - Byeong J. Lee
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Korea;
| | - Vadim N. Gladyshev
- Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA; (D.S.); (V.N.G.)
| | - Dolph L. Hatfield
- Scientist Emeritus, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
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19
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Fradejas-Villar N, Zhao W, Reuter U, Doengi M, Ingold I, Bohleber S, Conrad M, Schweizer U. Missense mutation in selenocysteine synthase causes cardio-respiratory failure and perinatal death in mice which can be compensated by selenium-independent GPX4. Redox Biol 2021; 48:102188. [PMID: 34794077 PMCID: PMC8605217 DOI: 10.1016/j.redox.2021.102188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/26/2021] [Accepted: 11/11/2021] [Indexed: 12/16/2022] Open
Abstract
Selenoproteins are a small family of proteins containing the trace element selenium in form of the rare amino acid selenocysteine (Sec), which is decoded by the UGA codon. In humans, a number of pathogenic variants in genes encoding distinct selenoproteins or selenoprotein biosynthesis factors have been identified. Pathogenic variants in selenocysteine synthase (SEPSECS), which catalyzes the last step in Sec-tRNA[Ser]Sec biosynthesis, were reported in children suffering from progressive cerebello-cerebral atrophy. To understand the pathomechanism associated with SEPSECS deficiency, we generated a novel mouse model recapitulating the respective human pathogenic p.Y334C variant in the murine Sepsecs gene (SepsecsY334C). Unlike in patients, pups homozygous for the p.Y334C variant died perinatally with signs of cardio-respiratory failure. Perinatal death is reminiscent of the Sedaghatian spondylometaphyseal dysplasia disorder in humans, which is caused by pathogenic variants in the gene encoding the selenoprotein and key ferroptosis regulator glutathione peroxidase 4 (GPX4). Protein expression levels of distinct selenoproteins in SepsecsY334C/Y334C mice were found to be generally reduced in brain and isolated cortical neurons, while transcriptomics analysis uncovered an upregulation of NRF2-regulated genes. Crossbreeding of SepsecsY334C/Y334C mice with mice harboring a targeted mutation of the catalytically active Sec to Cys in GPX4 rescued perinatal death of SepsecsY334C/Y334C mice, showing that the cardio-respiratory defects of SepsecsY334C/Y334C mice were caused by the lack of GPX4. Like in SepsecsY334C/Y334C mice, selenoprotein expression levels remained low and NRF2-regulated genes remained highly expressed in these compound mutant mice, indicating that selenium-independent GPX4, along with a sustained antioxidant response are sufficient to compensate for dysfunctional Sec-tRNA[Ser]Sec biosynthesis. Our findings imply that children with pathogenic variants in SEPSECS or GPX4 may even benefit from treatments that incompletely compensate for impaired GPX4 activity.
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Affiliation(s)
| | - Wenchao Zhao
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Uschi Reuter
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Michael Doengi
- Institut für Physiologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Irina Ingold
- Helmholtz Zentrum München, Institute of Metabolism and Cell Death, 85764, Neuherberg, Germany
| | - Simon Bohleber
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Bonn, Germany
| | - Marcus Conrad
- Helmholtz Zentrum München, Institute of Metabolism and Cell Death, 85764, Neuherberg, Germany; Pirogov Russian National Research Medical University, Laboratory of Experimental Oncology, Moscow, 117997, Russia
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Universitätsklinikum Bonn, Bonn, Germany.
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20
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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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21
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Shimizu A, Tobe R, Aono R, Inoue M, Hagita S, Kiriyama K, Toyotake Y, Ogawa T, Kurihara T, Goto K, Prakash NT, Mihara H. Initial Step of Selenite Reduction via Thioredoxin for Bacterial Selenoprotein Biosynthesis. Int J Mol Sci 2021; 22:ijms222010965. [PMID: 34681630 PMCID: PMC8538045 DOI: 10.3390/ijms222010965] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Many organisms reductively assimilate selenite to synthesize selenoprotein. Although the thioredoxin system, consisting of thioredoxin 1 (TrxA) and thioredoxin reductase with NADPH, can reduce selenite and is considered to facilitate selenite assimilation, the detailed mechanism remains obscure. Here, we show that selenite was reduced by the thioredoxin system from Pseudomonas stutzeri only in the presence of the TrxA (PsTrxA), and this system was specific to selenite among the oxyanions examined. Mutational analysis revealed that Cys33 and Cys36 residues in PsTrxA are important for selenite reduction. Free thiol-labeling assays suggested that Cys33 is more reactive than Cys36. Mass spectrometry analysis suggested that PsTrxA reduces selenite via PsTrxA-SeO intermediate formation. Furthermore, an in vivo formate dehydrogenase activity assay in Escherichia coli with a gene disruption suggested that TrxA is important for selenoprotein biosynthesis. The introduction of PsTrxA complemented the effects of TrxA disruption in E. coli cells, only when PsTrxA contained Cys33 and Cys36. Based on these results, we proposed the early steps of the link between selenite and selenoprotein biosynthesis via the formation of TrxA–selenium complexes.
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Affiliation(s)
- Atsuki Shimizu
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
| | - Ryuta Tobe
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
| | - Riku Aono
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
| | - Masao Inoue
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
- R-GIRO, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan
| | - Satoru Hagita
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
| | - Kaito Kiriyama
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
| | - Yosuke Toyotake
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Kyoto, Japan; (Y.T.); (T.O.); (T.K.)
| | - Takuya Ogawa
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Kyoto, Japan; (Y.T.); (T.O.); (T.K.)
| | - Tatsuo Kurihara
- Institute for Chemical Research, Kyoto University, Gokasho, Uji 611-0011, Kyoto, Japan; (Y.T.); (T.O.); (T.K.)
| | - Kei Goto
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan;
| | - N. Tejo Prakash
- School of Energy and Environment, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India;
| | - Hisaaki Mihara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan; (A.S.); (R.T.); (R.A.); (M.I.); (S.H.); (K.K.)
- Correspondence: ; Tel.: +81-(0)77-561-2732
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22
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Vallée Y, Youssef-Saliba S. Sulfur Amino Acids: From Prebiotic Chemistry to Biology and Vice Versa. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1472-7914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractTwo sulfur-containing amino acids are included in the list of the 20 classical protein amino acids. A methionine residue is introduced at the start of the synthesis of all current proteins. Cysteine, thanks to its thiol function, plays an essential role in a very large number of catalytic sites. Here we present what is known about the prebiotic synthesis of these two amino acids and homocysteine, and we discuss their introduction into primitive peptides and more elaborate proteins.1 Introduction2 Sulfur Sources3 Prebiotic Synthesis of Cysteine4 Prebiotic Synthesis of Methionine5 Homocysteine and Its Thiolactone6 Methionine and Cystine in Proteins7 Prebiotic Scenarios Using Sulfur Amino Acids8 Introduction of Cys and Met in the Genetic Code9 Conclusion
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23
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Wang Y, Liu P, Chang J, Xu Y, Wang J. Site-Specific Selenocysteine Incorporation into Proteins by Genetic Engineering. Chembiochem 2021; 22:2918-2924. [PMID: 33949764 DOI: 10.1002/cbic.202100124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/03/2021] [Indexed: 01/23/2023]
Abstract
Selenocysteine (Sec), a rare naturally proteinogenic amino acid, is the major form of essential trace element selenium in living organisms. Selenoproteins, with one or several Sec residues, are found in all three domains of life. Many selenoproteins play a role in critical cellular functions such as maintaining cell redox homeostasis. Sec is usually encoded by an in-frame stop codon UGA in the selenoprotein mRNA, and its incorporation in vivo is highly species-dependent and requires the reprogramming of translation. This mechanistic complexity of selenoprotein synthesis poses a big challenge to produce synthetic selenoproteins. To understand the functions of natural as well as engineered selenoproteins, many strategies have recently been developed to overcome the inherent barrier for recombinant selenoprotein production. In this review, we will describe the progress in selenoprotein production methodology.
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Affiliation(s)
- Yuchuan Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
| | - Pengcheng Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Jiao Chang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China
| | - Yunping Xu
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China
| | - Jiangyun Wang
- Shenzhen Institute of Transfusion Medicine Shenzhen Blood Center, Shenzhen, Futian District, 518052, P. R. China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, Chaoyang District, 100101, P. R. China.,Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 1068 Xueyuan Avenue, Shenzhen, Nanshan District, 518055, P. R. China
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24
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Wells M, Basu P, Stolz JF. The physiology and evolution of microbial selenium metabolism. Metallomics 2021; 13:6261189. [PMID: 33930157 DOI: 10.1093/mtomcs/mfab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/27/2022]
Abstract
Selenium is an essential trace element whose compounds are widely metabolized by organisms from all three domains of life. Moreover, phylogenetic evidence indicates that selenium species, along with iron, molybdenum, tungsten, and nickel, were metabolized by the last universal common ancestor of all cellular lineages, primarily for the synthesis of the 21st amino acid selenocysteine. Thus, selenium metabolism is both environmentally ubiquitous and a physiological adaptation of primordial life. Selenium metabolic reactions comprise reductive transformations both for assimilation into macromolecules and dissimilatory reduction of selenium oxyanions and elemental selenium during anaerobic respiration. This review offers a comprehensive overview of the physiology and evolution of both assimilatory and dissimilatory selenium metabolism in bacteria and archaea, highlighting mechanisms of selenium respiration. This includes a thorough discussion of our current knowledge of the physiology of selenocysteine synthesis and incorporation into proteins in bacteria obtained from structural biology. Additionally, this is the first comprehensive discussion in a review of the incorporation of selenium into the tRNA nucleoside 5-methylaminomethyl-2-selenouridine and as an inorganic cofactor in certain molybdenum hydroxylase enzymes. Throughout, conserved mechanisms and derived features of selenium metabolism in both domains are emphasized and discussed within the context of the global selenium biogeochemical cycle.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Partha Basu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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25
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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26
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Zhang C, Qiu Z, Zhang L, Pang Q, Yang Z, Qin JK, Liang H, Zhao S. Design and synthesis of a ratiometric photoacoustic imaging probe activated by selenol for visual monitoring of pathological progression of autoimmune hepatitis. Chem Sci 2021; 12:4883-4888. [PMID: 34163738 PMCID: PMC8179563 DOI: 10.1039/d0sc06573k] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/17/2021] [Indexed: 12/19/2022] Open
Abstract
Photoacoustic (PA) imaging with both the high contrast of optical imaging and the high spatial resolution of ultrasound imaging has been regarded as a robust biomedical imaging technique. Autoimmune hepatitis (AIH) is the second largest liver inflammatory disease after viral hepatitis, but its pathogenesis is not fully understood probably due to the lack of an effective in vivo monitoring approach. In this work, an innovative selenol-activated ratiometric PA imaging probe APSel was developed for visual monitoring of pathological progress of AIH. Selenols including selenocysteine (Sec, the major form of Se-containing species in vivo) have been demonstrated to have an effective antioxidant role in inflammation. The reaction of APSel with selenol results in a blue shift of the PA spectrum peak from 860 nm to 690 nm, which enables the ratiometric PA imaging. The APSel probe displays high sensitivity and selectivity to Sec and other selenols. The APSel probe was then employed for ratiometric PA imaging of selenol in cells, and for monitoring the development of AIH in a murine model by tracking the changes of selenol level. The results revealed that the level of selenol was closely correlated with the development of AIH. The proposed APSel, as the first example of a selenol-responsive PA imaging probe, provides a new tool and approach to study and diagnose AIH diseases.
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Affiliation(s)
- Chaobang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Zhidong Qiu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Qiufang Pang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Zhengmin Yang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Jiang-Ke Qin
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Hong Liang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University Guilin 541004 China
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27
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Smejda M, Kądziołka D, Radczuk N, Krutyhołowa R, Chramiec-Głąbik A, Kędracka-Krok S, Jankowska U, Biela A, Glatt S. Same but different - Molecular comparison of human KTI12 and PSTK. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:118945. [PMID: 33417976 DOI: 10.1016/j.bbamcr.2020.118945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/23/2020] [Indexed: 11/18/2022]
Abstract
Kti12 and PSTK are closely related and highly similar proteins implicated in different aspects of tRNA metabolism. Kti12 has been identified as an essential regulatory factor of the Elongator complex, involved in the modification of uridine bases in eukaryotic tRNAs. PSTK phosphorylates the tRNASec-bound amino acid serine, which is required to synthesize selenocysteine. Kti12 and PSTK have previously been studied independently in various organisms, but only appear simultaneously in some animalia, including humans. As Kti12- and PSTK-related pathways are clinically relevant, it is of prime importance to understand their biological functions and mutual relationship in humans. Here, we use different tRNA substrates to directly compare the enzymatic activities of purified human KTI12 and human PSTK proteins. Our complementary Co-IP and BioID2 approaches in human cells confirm that Elongator is the main interaction partner of KTI12 but additionally indicate potential links to proteins involved in vesicular transport, RNA metabolism and deubiquitination. Moreover, we identify and validate a yet uncharacterized interaction between PSTK and γ-taxilin. Foremost, we demonstrate that human KTI12 and PSTK do not share interactors or influence their respective biological functions. Our data provide a comprehensive analysis of the regulatory networks controlling the activity of the human Elongator complex and selenocysteine biosynthesis.
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Affiliation(s)
- Marta Smejda
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Dominika Kądziołka
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Natalia Radczuk
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rościsław Krutyhołowa
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Sylwia Kędracka-Krok
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Urszula Jankowska
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Anna Biela
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland.
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28
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Wells M, Stolz JF. Microbial selenium metabolism: a brief history, biogeochemistry and ecophysiology. FEMS Microbiol Ecol 2020; 96:5921172. [DOI: 10.1093/femsec/fiaa209] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/02/2023] Open
Abstract
ABSTRACTSelenium is an essential trace element for organisms from all three domains of life. Microorganisms, in particular, mediate reductive transformations of selenium that govern the element's mobility and bioavailability in terrestrial and aquatic environments. Selenium metabolism is not just ubiquitous but an ancient feature of life likely extending back to the universal common ancestor of all cellular lineages. As with the sulfur biogeochemical cycle, reductive transformations of selenium serve two metabolic functions: assimilation into macromolecules and dissimilatory reduction during anaerobic respiration. This review begins with a historical overview of how research in both aspects of selenium metabolism has developed. We then provide an overview of the global selenium biogeochemical cycle, emphasizing the central role of microorganisms in the cycle. This serves as a basis for a robust discussion of current models for the evolution of the selenium biogeochemical cycle over geologic time, and how knowledge of the evolution and ecophysiology of selenium metabolism can enrich and refine these models. We conclude with a discussion of the ecophysiological function of selenium-respiring prokaryotes within the cycle, and the tantalizing possibility of oxidative selenium transformations during chemolithoautotrophic growth.
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Affiliation(s)
- Michael Wells
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - John F Stolz
- Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15282, USA
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29
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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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30
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Schoenmakers E, Chatterjee K. Human Disorders Affecting the Selenocysteine Incorporation Pathway Cause Systemic Selenoprotein Deficiency. Antioxid Redox Signal 2020; 33:481-497. [PMID: 32295391 PMCID: PMC7409586 DOI: 10.1089/ars.2020.8097] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significance: Generalized selenoprotein deficiency has been associated with mutations in SECISBP2, SEPSECS, and TRU-TCA1-1, 3 factors that are crucial for incorporation of the amino acid selenocysteine (Sec) into at least 25 human selenoproteins. SECISBP2 and TRU-TCA1-1 defects are characterized by a multisystem phenotype due to deficiencies of antioxidant and tissue-specific selenoproteins, together with abnormal thyroid hormone levels reflecting impaired hormone metabolism by deiodinase selenoenzymes. SEPSECS mutations are associated with a predominantly neurological phenotype with progressive cerebello-cerebral atrophy. Recent Advances: The recent identification of individuals with defects in genes encoding components of the selenocysteine insertion pathway has delineated complex and multisystem disorders, reflecting a lack of selenoproteins in specific tissues, oxidative damage due to lack of oxidoreductase-active selenoproteins and other pathways whose nature is unclear. Critical Issues: Abnormal thyroid hormone metabolism in patients can be corrected by triiodothyronine (T3) treatment. No specific therapies for other phenotypes (muscular dystrophy, male infertility, hearing loss, neurodegeneration) exist as yet, but their severity often requires supportive medical intervention. Future Directions: These disorders provide unique insights into the role of selenoproteins in humans. The long-term consequences of reduced cellular antioxidant capacity remain unknown, and future surveillance of patients may reveal time-dependent phenotypes (e.g., neoplasia, aging) or consequences of deficiency of selenoproteins whose function remains to be elucidated. The role of antioxidant therapies requires evaluation. Antioxid. Redox Signal. 33, 481-497.
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Affiliation(s)
- Erik Schoenmakers
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, United Kingdom
| | - Krishna Chatterjee
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge, United Kingdom
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31
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Abstract
The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code. Synthetases help to ensure accurate translation of the genetic code by using both highly accurate cognate substrate recognition and stringent proofreading of noncognate products. While alterations in the quality control mechanisms of synthetases are generally detrimental to cellular viability, recent studies suggest that in some instances such changes facilitate adaption to stress conditions. Beyond their central role in translation, synthetases are also emerging as key players in an increasing number of other cellular processes, with far-reaching consequences in health and disease. The biochemical versatility of the synthetases has also proven pivotal in efforts to expand the genetic code, further emphasizing the wide-ranging roles of the aminoacyl-tRNA synthetase family in synthetic and natural biology.
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Affiliation(s)
- Miguel Angel Rubio Gomez
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael Ibba
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
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32
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Peeler JC, Falco JA, Kelemen RE, Abo M, Chartier BV, Edinger LC, Chen J, Chatterjee A, Weerapana E. Generation of Recombinant Mammalian Selenoproteins through Genetic Code Expansion with Photocaged Selenocysteine. ACS Chem Biol 2020; 15:1535-1540. [PMID: 32330002 DOI: 10.1021/acschembio.0c00147] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Selenoproteins contain the amino acid selenocysteine (Sec) and are found in all domains of life. The functions of many selenoproteins are poorly understood, partly due to difficulties in producing recombinant selenoproteins for cell-biological evaluation. Endogenous mammalian selenoproteins are produced through a noncanonical translation mechanism requiring suppression of the UGA stop codon and a Sec insertion sequence (SECIS) element in the 3' untranslated region of the mRNA. Here, recombinant selenoproteins are generated in mammalian cells through genetic code expansion, circumventing the requirement for the SECIS element and selenium availability. An engineered orthogonal E. coli leucyl-tRNA synthetase/tRNA pair is used to incorporate a photocaged Sec (DMNB-Sec) at the UAG amber stop codon. DMNB-Sec is successfully incorporated into GFP and uncaged by irradiation of living cells. Furthermore, DMNB-Sec is used to generate the native selenoprotein methionine-R-sulfoxide reductase B1 (MsrB1). Importantly, MsrB1 is shown to be catalytically active after uncaging, constituting the first use of genetic code expansion to generate a functional selenoprotein in mammalian systems. The ability to site-specifically introduce Sec directly in mammalian cells, and temporally modulate selenoprotein activity, will aid in the characterization of mammalian selenoprotein function.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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33
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Abstract
The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.
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34
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Zhang L, Shi Y, Sheng Z, Zhang Y, Kai X, Li M, Yin X. Bioluminescence Imaging of Selenocysteine in Vivo with a Highly Sensitive Probe. ACS Sens 2019; 4:3147-3155. [PMID: 31701738 DOI: 10.1021/acssensors.9b01268] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Selenocysteine (Sec), a vital member of reactive selenium species, is closely implicated in diverse pathophysiological states, including cancer, cardiovascular diseases, diabetes, neurodegenerative diseases, and male infertility. Monitoring Sec in vivo is of significant interest for understanding the physiological roles of Sec and the mechanisms of human diseases associated with abnormal levels of Sec. However, no bioluminescence probe for real-time monitoring of Sec in vivo has been reported. Herein, we present a novel bioluminescent probe BF-1 as an effective tool for the determination of Sec in living cells and in vivo for the first time. BF-1 has advantages of high sensitivity (a detection limit of 8 nM), remarkable bioluminescence enhancement (580-fold), reasonable selectivity, low cytotoxicity, and high signal-to-noise ratio imaging feasibility of Sec in living cells and mice. More importantly, BF-1 affords high sensitivity for monitoring Sec stimulated by Na2SeO3 in tumor-bearing mice. These results demonstrate that our new probe could serve as a powerful tool to selectively monitor Sec in vivo, thus providing a valuable approach for exploring the physiological and pathological functions and anticancer mechanisms of selenium.
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Affiliation(s)
- Ling Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
| | - Yanfen Shi
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
| | - Zhijia Sheng
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
| | - Yiran Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
| | - Xiaoning Kai
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, School of Pharmacy, Shandong University, Jinan 250012, PR China
| | - Xiaoxing Yin
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, School of Pharmacy, Xuzhou Medical University, Xuzhou 221002, PR China
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35
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Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Res 2019; 47:4814-4830. [PMID: 30916349 PMCID: PMC6511879 DOI: 10.1093/nar/gkz190] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/14/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Posttranscriptional RNA modifications occur in all domains of life. Modifications of anticodon bases are of particular importance for ribosomal decoding and proteome homeostasis. The Elongator complex modifies uridines in the wobble position and is highly conserved in eukaryotes. Despite recent insights into Elongator's architecture, the structure and function of its regulatory factor Kti12 have remained elusive. Here, we present the crystal structure of Kti12′s nucleotide hydrolase domain trapped in a transition state of ATP hydrolysis. The structure reveals striking similarities to an O-phosphoseryl-tRNA kinase involved in the selenocysteine pathway. Both proteins employ similar mechanisms of tRNA binding and show tRNASec-dependent ATPase activity. In addition, we demonstrate that Kti12 binds directly to Elongator and that ATP hydrolysis is crucial for Elongator to maintain proper tRNA anticodon modification levels in vivo. In summary, our data reveal a hitherto uncharacterized link between two translational control pathways that regulate selenocysteine incorporation and affect ribosomal tRNA selection via specific tRNA modifications.
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Affiliation(s)
- Rościsław Krutyhołowa
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Rene Zabel
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | | | - Mark Helm
- Institut für Pharmazie und Biochemie, Universität Mainz, Mainz, Germany
| | - Michael J R Stark
- Centre for Gene Regulation & Expression, University of Dundee, Dundee, UK
| | - Karin D Breunig
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Raffael Schaffrath
- Institut für Biologie, FG Mikrobiologie, Universität Kassel, Kassel, Germany
| | - Sebastian Glatt
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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Tymoshok NO, Kharchuk MS, Kaplunenko VG, Bityutskyy VS, Tsekhmistrenko SI, Tsekhmistrenko OS, Spivak MY, Melnichenko ОМ. Evaluation of effects of selenium nanoparticles on Bacillus subtilis. REGULATORY MECHANISMS IN BIOSYSTEMS 2019. [DOI: 10.15421/021980] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The present study was performed to characterize of selenium nanoparticles (Nano-Se) which were synthesized by pulsed laser ablation in liquids to obtain the aqueous selenium citrate solution. The study was conducted using bacteriological and electronic-microscopic methods. Transmission electron microscopy (TEM) and spectroscopy analyses demonstrated that nano-selenium particles obtained by the method of selenium ablation had the size of 4–8 nm. UV-Visible Spectrum colloidal solution Nano-Se exhibited absorption maxima at 210 nm. To clarify some effects of the action of Nano-Se on Bacillus subtilis, we investigated the interaction of Nano-Se with B. subtilis IMV B-7392 before and after incubation with Nano-Se, examining TEM images. It has been shown that exposure to B. subtilis IMV B-7392 in the presence of Nano-Se is accompanied by the rapid uptake of Nano-Se by bacterial culture. TEM analysis found that the electron-dense Nano-Se particles were located in the intracellular spaces of B. subtilis IMV B-7392. That does not lead to changes in cultural and morphological characteristics of B. subtilis IMV B-7392. Using TEM, it has been shown that penetration of nanoparticles in the internal compartments is accompanied with transient porosity of the cell membrane of B. subtilis IMV B-7392 without rupturing it. The effective concentration of Nano-Se 0.2 × 10–3 mg/mL was found to increase the yield of biologically active substances of B. subtilis. In order to create probiotic nano-selenium containing products, the nutrient medium of B. subtilis IMV B-7392 was enriched with Nano-Se at 0.2 × 10–3 mg/mL. It was found that particles Nano-Se are non-toxic to the culture and did not exhibit bactericidal or bacteriostatic effects. The experimentally demonstrated ability of B. subtilis to absorb selenium nanoparticles has opened up the possibility of using Nano-Se as suitable drug carriers.
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Selenocysteine β-Lyase: Biochemistry, Regulation and Physiological Role of the Selenocysteine Decomposition Enzyme. Antioxidants (Basel) 2019; 8:antiox8090357. [PMID: 31480609 PMCID: PMC6770646 DOI: 10.3390/antiox8090357] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022] Open
Abstract
The enzyme selenocysteine β-lyase (SCLY) was first isolated in 1982 from pig livers, followed by its identification in bacteria. SCLY works as a homodimer, utilizing pyridoxal 5'-phosphate as a cofactor, and catalyzing the specific decomposition of the amino acid selenocysteine into alanine and selenide. The enzyme is thought to deliver its selenide as a substrate for selenophosphate synthetases, which will ultimately be reutilized in selenoprotein synthesis. SCLY subcellular localization is unresolved, as it has been observed both in the cytosol and in the nucleus depending on the technical approach used. The highest SCLY expression and activity in mammals is found in the liver and kidneys. Disruption of the Scly gene in mice led to obesity, hyperinsulinemia, glucose intolerance, and hepatic steatosis, with SCLY being suggested as a participant in the regulation of energy metabolism in a sex-dependent manner. With the physiological role of SCLY still not fully understood, this review attempts to discuss the available literature regarding SCLY in animals and provides avenues for possible future investigation.
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Hoffman KS, Vargas-Rodriguez O, Bak DW, Mukai T, Woodward LK, Weerapana E, Söll D, Reynolds NM. A cysteinyl-tRNA synthetase variant confers resistance against selenite toxicity and decreases selenocysteine misincorporation. J Biol Chem 2019; 294:12855-12865. [PMID: 31296657 DOI: 10.1074/jbc.ra119.008219] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/03/2019] [Indexed: 11/06/2022] Open
Abstract
Selenocysteine (Sec) is the 21st genetically encoded amino acid in organisms across all domains of life. Although structurally similar to cysteine (Cys), the Sec selenol group has unique properties that are attractive for protein engineering and biotechnology applications. Production of designer proteins with Sec (selenoproteins) at desired positions is now possible with engineered translation systems in Escherichia coli However, obtaining pure selenoproteins at high yields is limited by the accumulation of free Sec in cells, causing undesired incorporation of Sec at Cys codons due to the inability of cysteinyl-tRNA synthetase (CysRS) to discriminate against Sec. Sec misincorporation is toxic to cells and causes protein aggregation in yeast. To overcome this limitation, here we investigated a CysRS from the selenium accumulator plant Astragalus bisulcatus that is reported to reject Sec in vitro Sequence analysis revealed a rare His → Asn variation adjacent to the CysRS catalytic pocket. Introducing this variation into E. coli and Saccharomyces cerevisiae CysRS increased resistance to the toxic effects of selenite and selenomethionine (SeMet), respectively. Although the CysRS variant could still use Sec as a substrate in vitro, we observed a reduction in the frequency of Sec misincorporation at Cys codons in vivo We surmise that the His → Asn variation can be introduced into any CysRS to provide a fitness advantage for strains burdened by Sec misincorporation and selenium toxicity. Our results also support the notion that the CysRS variant provides higher specificity for Cys as a mechanism for plants to grow in selenium-rich soils.
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Affiliation(s)
- Kyle S Hoffman
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Laura K Woodward
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.,Department of Chemistry, Yale University, New Haven, Connecticut 06511
| | - Noah M Reynolds
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
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39
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Lee KJ, Kang D, Park HS. Site-Specific Labeling of Proteins Using Unnatural Amino Acids. Mol Cells 2019; 42:386-396. [PMID: 31122001 PMCID: PMC6537655 DOI: 10.14348/molcells.2019.0078] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/02/2019] [Indexed: 12/11/2022] Open
Abstract
Labeling of a protein with a specific dye or tag at defined positions is a critical step in tracing the subtle behavior of the protein and assessing its cellular function. Over the last decade, many strategies have been developed to achieve selective labeling of proteins in living cells. In particular, the site-specific unnatural amino acid (UAA) incorporation technique has gained increasing attention since it enables attachment of various organic probes to a specific position of a protein in a more precise way. In this review, we describe how the UAA incorporation technique has expanded our ability to achieve site-specific labeling and visualization of target proteins for functional analyses in live cells.
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Affiliation(s)
- Kyung Jin Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Deokhee Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Hee-Sung Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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40
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Versatility of Synthetic tRNAs in Genetic Code Expansion. Genes (Basel) 2018; 9:genes9110537. [PMID: 30405060 PMCID: PMC6267555 DOI: 10.3390/genes9110537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022] Open
Abstract
Transfer RNA (tRNA) is a dynamic molecule used by all forms of life as a key component of the translation apparatus. Each tRNA is highly processed, structured, and modified, to accurately deliver amino acids to the ribosome for protein synthesis. The tRNA molecule is a critical component in synthetic biology methods for the synthesis of proteins designed to contain non-canonical amino acids (ncAAs). The multiple interactions and maturation requirements of a tRNA pose engineering challenges, but also offer tunable features. Major advances in the field of genetic code expansion have repeatedly demonstrated the central importance of suppressor tRNAs for efficient incorporation of ncAAs. Here we review the current status of two fundamentally different translation systems (TSs), selenocysteine (Sec)- and pyrrolysine (Pyl)-TSs. Idiosyncratic requirements of each of these TSs mandate how their tRNAs are adapted and dictate the techniques used to select or identify the best synthetic variants.
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41
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Rother M, Quitzke V. Selenoprotein synthesis and regulation in Archaea. Biochim Biophys Acta Gen Subj 2018; 1862:2451-2462. [DOI: 10.1016/j.bbagen.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 01/23/2023]
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42
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Quitzke V, Fersch J, Seyhan D, Rother M. Selenium-dependent gene expression in Methanococcus maripaludis: Involvement of the transcriptional regulator HrsM. Biochim Biophys Acta Gen Subj 2018; 1862:2441-2450. [DOI: 10.1016/j.bbagen.2018.03.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 01/23/2023]
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43
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Bywater RP. Why twenty amino acid residue types suffice(d) to support all living systems. PLoS One 2018; 13:e0204883. [PMID: 30321190 PMCID: PMC6188899 DOI: 10.1371/journal.pone.0204883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/17/2018] [Indexed: 11/21/2022] Open
Abstract
It is well known that proteins are built up from an alphabet of 20 different amino acid types. These suffice to enable the protein to fold into its operative form relevant to its required functional roles. For carrying out these allotted functions, there may in some cases be a need for post-translational modifications and it has been established that an additional three types of amino acid have at some point been recruited into this process. But it still remains the case that the 20 residue types referred to are the major building blocks in all terrestrial proteins, and probably "universally". Given this fact, it is surprising that no satisfactory answer has been given to the two questions: "why 20?" and "why just these 20?". Furthermore, a suggestion is made as to how these 20 map to the codon repertoire which in principle has the capacity to cater for 64 different residue types. Attempts are made in this paper to answer these questions by employing a combination of quantum chemical and chemoinformatic tools which are applied to the standard 20 amino acid types as well as 3 “non-standard” types found in nature, a set of fictitious but feasible analog structures designed to test the need for greater coverage of function space and the collection of candidate alternative structures found either on meteorites or in experiments designed to reconstruct pre-life scenarios.
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44
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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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45
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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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46
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Njoroge RN, Unno K, Zhao JC, Naseem AF, Anker JF, McGee WA, Nonn L, Abdulkadir SA. Organoids model distinct Vitamin E effects at different stages of prostate cancer evolution. Sci Rep 2017; 7:16285. [PMID: 29176677 PMCID: PMC5701195 DOI: 10.1038/s41598-017-16459-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/13/2017] [Indexed: 11/09/2022] Open
Abstract
Vitamin E increased prostate cancer risk in the Selenium and Vitamin E Cancer Prevention Trial (SELECT) through unknown mechanisms while Selenium showed no efficacy. We determined the effects of the SELECT supplements on benign (primary), premalignant ( RWPE-1) and malignant (LNCaP) prostate epithelial organoids. While the supplements decreased proliferation and induced cell death in cancer organoids, they had no effect on the benign organoids. In contrast, Vitamin E enhanced cell proliferation and survival in the premalignant organoids in a manner that recapitulated the SELECT results. Indeed, while Vitamin E induced a pro-proliferative gene expression signature, Selenium alone or combined with Vitamin E produced an anti-proliferative signature. The premalignant organoids also displayed significant downregulation of glucose transporter and glycolytic gene expression pointing to metabolic alterations. Detached RWPE-1 cells had low ATP levels due to diminished glucose uptake and glycolysis which was rescued by Vitamin E through the activation of fatty acid oxidation (FAO). FAO inhibition abrogated the ATP rescue, diminished survival of the inner matrix detached cells, restoring the normal hollow lumen morphology in Vitamin E treated organoids. Organoid models therefore clarify the paradoxical findings from SELECT and demonstrate that Vitamin E promotes tumorigenesis in the early stages of prostate cancer evolution.
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Affiliation(s)
- Rose N Njoroge
- Northwestern University, Feinberg School of Medicine, Department of Urology, Chicago, IL, 60611, USA
| | - Kenji Unno
- Northwestern University, Feinberg School of Medicine, Department of Urology, Chicago, IL, 60611, USA
| | - Jonathan C Zhao
- Division of Hematology/Oncology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Anum F Naseem
- Northwestern University, Feinberg School of Medicine, Department of Urology, Chicago, IL, 60611, USA
| | - Jonathan F Anker
- Northwestern University, Feinberg School of Medicine, Department of Urology, Chicago, IL, 60611, USA
| | - Warren A McGee
- Department of Neurology, Northwestern University, Chicago, IL, USA
| | - Larisa Nonn
- Department of Pathology, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Sarki A Abdulkadir
- Northwestern University, Feinberg School of Medicine, Department of Urology, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. .,Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
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47
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Holman KM, Puppala AK, Lee JW, Lee H, Simonović M. Insights into substrate promiscuity of human seryl-tRNA synthetase. RNA (NEW YORK, N.Y.) 2017; 23:1685-1699. [PMID: 28808125 PMCID: PMC5648036 DOI: 10.1261/rna.061069.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
Seryl-tRNA synthetase (SerRS) attaches L-serine to the cognate serine tRNA (tRNASer) and the noncognate selenocysteine tRNA (tRNASec). The latter activity initiates the anabolic cycle of selenocysteine (Sec), proper decoding of an in-frame Sec UGA codon, and synthesis of selenoproteins across all domains of life. While the accuracy of SerRS is important for overall proteome integrity, it is its substrate promiscuity that is vital for the integrity of the selenoproteome. This raises a question as to what elements in the two tRNA species, harboring different anticodon sequences and adopting distinct folds, facilitate aminoacylation by a common aminoacyl-tRNA synthetase. We sought to answer this question by analyzing the ability of human cytosolic SerRS to bind and act on tRNASer, tRNASec, and 10 mutant and chimeric constructs in which elements of tRNASer were transposed onto tRNASec We show that human SerRS only subtly prefers tRNASer to tRNASec, and that discrimination occurs at the level of the serylation reaction. Surprisingly, the tRNA mutants predicted to adopt either the 7/5 or 8/5 fold are poor SerRS substrates. In contrast, shortening of the acceptor arm of tRNASec by a single base pair yields an improved SerRS substrate that adopts an 8/4 fold. We suggest that an optimal tertiary arrangement of structural elements within tRNASec and tRNASer dictate their utility for serylation. We also speculate that the extended acceptor-TΨC arm of tRNASec evolved as a compromise for productive binding to SerRS while remaining the major recognition element for other enzymes involved in Sec and selenoprotein synthesis.
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MESH Headings
- Base Sequence
- Binding Sites
- Cytosol/enzymology
- Humans
- Kinetics
- Models, Molecular
- Mutagenesis
- Nucleic Acid Conformation
- RNA Folding
- RNA, Transfer, Amino Acid-Specific/chemistry
- RNA, Transfer, Amino Acid-Specific/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/genetics
- RNA, Transfer, Ser/metabolism
- Serine-tRNA Ligase/metabolism
- Substrate Specificity
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Affiliation(s)
- Kaitlyn M Holman
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Anupama K Puppala
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Jonathan W Lee
- College of Liberal Arts and Sciences, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, College of Medicine, The University of Illinois at Chicago, Chicago, Illinois 60607, USA
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48
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Schweizer U, Fradejas‐Villar N. Why 21? The significance of selenoproteins for human health revealed by inborn errors of metabolism. FASEB J 2016; 30:3669-3681. [DOI: 10.1096/fj.201600424] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/18/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Ulrich Schweizer
- Institut für Biochemie und MolekularbiologieRheinische Friedrich‐Wilhelms‐Universitfät Bonn Bonn Germany
| | - Noelia Fradejas‐Villar
- Institut für Biochemie und MolekularbiologieRheinische Friedrich‐Wilhelms‐Universitfät Bonn Bonn Germany
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49
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Efficient Sulfide Assimilation in Methanosarcina acetivorans Is Mediated by the MA1715 Protein. J Bacteriol 2016; 198:1974-83. [PMID: 27137504 DOI: 10.1128/jb.00141-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/26/2016] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED Conserved genes essential to sulfur assimilation and trafficking in aerobic organisms are missing in many methanogens, most of which inhabit highly sulfidic, anaerobic environmental niches. This suggests that methanogens possess distinct pathways for the synthesis of key metabolites and intermediates, including cysteine, homocysteine, and protein persulfide groups. Prior work identified a novel tRNA-dependent two-step pathway for cysteine biosynthesis and a new metabolic transformation by which sulfur is inserted into aspartate semialdehyde to produce homocysteine. Homocysteine biosynthesis requires two of the three proteins previously identified in our laboratory by a comprehensive bioinformatics approach. Here, we show that the third protein identified in silico, the ApbE-like protein COG2122, facilitates sulfide assimilation in Methanosarcina acetivorans Knockout strains lacking the gene encoding COG2122 are severely impaired for growth when sulfide is provided as the sole sulfur source. However, rapid growth is recovered upon supplementation with cysteine, homocysteine, or cystathionine, suggesting that COG2122 is required for efficient biosynthesis of both cysteine and homocysteine. Deletion of the gene encoding COG2122 does not influence the extent of sulfur modifications in tRNA or the prevalence of iron-sulfur clusters, indicating that the function of COG2122 could be limited to sulfide assimilation for cysteine and homocysteine biosynthesis alone. IMPORTANCE We have found that the conserved M. acetivorans ma1715 gene, which encodes an ApbE-like protein, is required for optimal growth with sulfide as the sole sulfur source and supports both cysteine and homocysteine biosynthesis in vivo Together with related functional-genomics studies in methanogens, these findings make a key contribution to elucidating the novel pathways of sulfide assimilation and sulfur trafficking in anaerobic microorganisms that existed before the advent of oxygenic photosynthesis. The data suggest that the MA1715 protein is particularly important to sustaining robust physiological function when ambient sulfide concentrations are low. Phylogenetic analysis shows that MA1715 and other recently discovered methanogen sulfur-trafficking proteins share an evolutionary history with enzymes in the methanogenesis pathway. The newly characterized genes thus likely formed an essential part of the core metabolic machinery of the ancestral euryarchaeote.
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50
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Iwama K, Sasaki M, Hirabayashi S, Ohba C, Iwabuchi E, Miyatake S, Nakashima M, Miyake N, Ito S, Saitsu H, Matsumoto N. Milder progressive cerebellar atrophy caused by biallelic SEPSECS mutations. J Hum Genet 2016; 61:527-31. [PMID: 26888482 DOI: 10.1038/jhg.2016.9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/20/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022]
Abstract
Cerebellar atrophy is recognized in various types of childhood neurological disorders with clinical and genetic heterogeneity. Genetic analyses such as whole exome sequencing are useful for elucidating the genetic basis of these conditions. Pathological recessive mutations in Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase (SEPSECS) have been reported in a total of 11 patients with pontocerebellar hypoplasia type 2, progressive cerebellocerebral atrophy or progressive encephalopathy, yet detailed clinical features are limited to only four patients. We identified two new families with progressive cerebellar atrophy, and by whole exome sequencing detected biallelic SEPSECS mutations: c.356A>G (p.Asn119Ser) and c.77delG (p.Arg26Profs*42) in family 1, and c.356A>G (p.Asn119Ser) and c.467G>A (p.Arg156Gln) in family 2. Their development was slightly delayed regardless of normal brain magnetic resonance imaging (MRI) in infancy. The progression of clinical symptoms in these families is evidently slower than in previously reported cases, and the cerebellar atrophy milder by brain MRI, indicating that SEPSECS mutations are also involved in milder late-onset cerebellar atrophy.
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Affiliation(s)
- Kazuhiro Iwama
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Yokohama City University, Yokohama, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | - Chihiro Ohba
- Department of Clinical Neurology and Stroke Medicine, Yokohama City University, Yokohama, Japan
| | - Emi Iwabuchi
- Department of Child Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Mitsuko Nakashima
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Shuichi Ito
- Department of Pediatrics, Yokohama City University, Yokohama, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
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