1
|
Abstract
Professor Vadim N. Gladyshev is recognized here as a Redox Pioneer, because he has published an article on antioxidant/redox biology that has been cited more than 1000 times and 29 articles that have been cited more than 100 times. Gladyshev is world renowned for his characterization of the human selenoproteome encoded by 25 genes, identification of the majority of known selenoprotein genes in the three domains of life, and discoveries related to thiol oxidoreductases and mechanisms of redox control. Gladyshev's first faculty position was in the Department of Biochemistry, the University of Nebraska. There, he was a Charles Bessey Professor and Director of the Redox Biology Center. He then moved to the Department of Medicine at Brigham and Women's Hospital, Harvard Medical School, where he is Professor of Medicine and Director of the Center for Redox Medicine. His discoveries in redox biology relate to selenoenzymes, such as methionine sulfoxide reductases and thioredoxin reductases, and various thiol oxidoreductases. He is responsible for the genome-wide identification of catalytic redox-active cysteines and for advancing our understanding of the general use of cysteines by proteins. In addition, Gladyshev has characterized hydrogen peroxide metabolism and signaling and regulation of protein function by methionine-R-sulfoxidation. He has also made important contributions in the areas of aging and lifespan control and pioneered applications of comparative genomics in redox biology, selenium biology, and aging. Gladyshev's discoveries have had a profound impact on redox biology and the role of redox control in health and disease. He is a true Redox Pioneer. Antioxid. Redox Signal. 25, 1-9.
Collapse
Affiliation(s)
- Dolph L Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health , Bethesda, Maryland
| |
Collapse
|
2
|
Baranov PV, Atkins JF, Yordanova MM. Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nat Rev Genet 2015; 16:517-29. [PMID: 26260261 DOI: 10.1038/nrg3963] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The non-universality of the genetic code is now widely appreciated. Codes differ between organisms, and certain genes are known to alter the decoding rules in a site-specific manner. Recently discovered examples of decoding plasticity are particularly spectacular. These examples include organisms and organelles with disruptions of triplet continuity during the translation of many genes, viruses that alter the entire genetic code of their hosts and organisms that adjust their genetic code in response to changing environments. In this Review, we outline various modes of alternative genetic decoding and expand existing terminology to accommodate recently discovered manifestations of this seemingly sophisticated phenomenon.
Collapse
Affiliation(s)
- Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Ireland
| | - John F Atkins
- 1] School of Biochemistry and Cell Biology, University College Cork, Ireland. [2] Department of Human Genetics, University of Utah, 15 N 2030 E Rm. 7410, Salt Lake City, Utah 84112-5330, USA
| | | |
Collapse
|
3
|
Labunskyy VM, Hatfield DL, Gladyshev VN. Selenoproteins: molecular pathways and physiological roles. Physiol Rev 2014; 94:739-77. [PMID: 24987004 DOI: 10.1152/physrev.00039.2013] [Citation(s) in RCA: 793] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Selenium is an essential micronutrient with important functions in human health and relevance to several pathophysiological conditions. The biological effects of selenium are largely mediated by selenium-containing proteins (selenoproteins) that are present in all three domains of life. Although selenoproteins represent diverse molecular pathways and biological functions, all these proteins contain at least one selenocysteine (Sec), a selenium-containing amino acid, and most serve oxidoreductase functions. Sec is cotranslationally inserted into nascent polypeptide chains in response to the UGA codon, whose normal function is to terminate translation. To decode UGA as Sec, organisms evolved the Sec insertion machinery that allows incorporation of this amino acid at specific UGA codons in a process requiring a cis-acting Sec insertion sequence (SECIS) element. Although the basic mechanisms of Sec synthesis and insertion into proteins in both prokaryotes and eukaryotes have been studied in great detail, the identity and functions of many selenoproteins remain largely unknown. In the last decade, there has been significant progress in characterizing selenoproteins and selenoproteomes and understanding their physiological functions. We discuss current knowledge about how these unique proteins perform their functions at the molecular level and highlight new insights into the roles that selenoproteins play in human health.
Collapse
Affiliation(s)
- Vyacheslav M Labunskyy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Dolph L Hatfield
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; and Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| |
Collapse
|
4
|
Lobanov AV, Turanov AA, Hatfield DL, Gladyshev VN. Dual functions of codons in the genetic code. Crit Rev Biochem Mol Biol 2010; 45:257-65. [PMID: 20446809 DOI: 10.3109/10409231003786094] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3'-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.
Collapse
Affiliation(s)
- Alexey V Lobanov
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | | | | |
Collapse
|
5
|
Lukashenko NP. Expanding genetic code: Amino acids 21 and 22, selenocysteine and pyrrolysine. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410080016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
6
|
Das S, Mukherjee R, Sahoo S, Thakkar R, Chakrabarti J. Structural Clones of UAG Decoding RNA. J Biomol Struct Dyn 2009; 27:381-90. [DOI: 10.1080/07391102.2009.10507324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
7
|
|
8
|
Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol 2008; 8:R198. [PMID: 17880704 PMCID: PMC2375036 DOI: 10.1186/gb-2007-8-9-r198] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2006] [Revised: 09/18/2007] [Accepted: 09/19/2007] [Indexed: 12/23/2022] Open
Abstract
In silico and metabolic labeling studies of the selenoproteomes of several eukaryotes revealed distinct selenoprotein patterns as well as an ancient origin of selenoproteins and massive, independent losses in land plants, fungi, nematodes, insects and some protists, suggesting that the environment plays an important role in selenoproteome evolution. Background Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all. Results We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified by metabolic labeling of O. tauri and D. discoideum with 75Se. More than half of the selenoprotein families were shared by unicellular eukaryotes and mammals, consistent with their ancient origin. Further analyses identified massive, independent selenoprotein losses in land plants, fungi, nematodes, insects and some protists. Comparative analyses of selenoprotein-rich and -deficient organisms revealed that aquatic organisms generally have large selenoproteomes, whereas several groups of terrestrial organisms reduced their selenoproteomes through loss of selenoprotein genes and replacement of Sec with cysteine. Conclusion Our data suggest many selenoproteins originated at the base of the eukaryotic domain and show that the environment plays an important role in selenoproteome evolution. In particular, aquatic organisms apparently retained and sometimes expanded their selenoproteomes, whereas the selenoproteomes of some terrestrial organisms were reduced or completely lost. These findings suggest a hypothesis that, with the exception of vertebrates, aquatic life supports selenium utilization, whereas terrestrial habitats lead to reduced use of this trace element due to an unknown environmental factor.
Collapse
Affiliation(s)
- Alexey V Lobanov
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Dmitri E Fomenko
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Yan Zhang
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| | - Aniruddha Sengupta
- Section on the Molecular Biology of Selenium, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dolph L Hatfield
- Section on the Molecular Biology of Selenium, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vadim N Gladyshev
- Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA
| |
Collapse
|
9
|
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics 2007; 8:225. [PMID: 17597547 PMCID: PMC1914089 DOI: 10.1186/1471-2105-8-225] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 06/28/2007] [Indexed: 11/20/2022] Open
Abstract
Background Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. Recently, a computational study addressed this question and reported that no tRNA gene for unknown amino acid was found in genome sequences available. However, performance of the tRNA prediction program on an unknown tRNA family, which may have atypical sequence and structure, is unclear, thereby rendering their result inconclusive. A protein-level study will provide independent insight into the novel amino acid. Results Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes. Since our prediction method relies only on the conservation patterns of primary sequences, it also provides an opportunity to search novel selenoproteins and other readthrough proteins. It successfully recovered many of currently known selenoproteins and pyrrolysine proteins. However, no promising candidate for the 23rd amino acid was detected, and only one novel selenoprotein was predicted. Conclusion Our result suggests that the unknown amino acid encoded by stop codons does not exist, or its phylogenetic distribution is rather limited, which is in agreement with the previous study on tRNA. The method described here can be used in future studies to explore novel readthrough events from complete genomes, which are rapidly growing.
Collapse
|
10
|
Cathopoulis T, Chuawong P, Hendrickson TL. Novel tRNA aminoacylation mechanisms. MOLECULAR BIOSYSTEMS 2007; 3:408-18. [PMID: 17533454 DOI: 10.1039/b618899k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In nature, ribosomally synthesized proteins can contain at least 22 different amino acids: the 20 common amino acids as well as selenocysteine and pyrrolysine. Each of these amino acids is inserted into proteins codon-specifically via an aminoacyl-transfer RNA (aa-tRNA). In most cases, these aa-tRNAs are biosynthesized directly by a set of highly specific and accurate aminoacyl-tRNA synthetases (aaRSs). However, in some cases aaRSs with relaxed or novel substrate specificities cooperate with other enzymes to generate specific canonical and non-canonical aminoacyl-tRNAs.
Collapse
MESH Headings
- Amino Acyl-tRNA Synthetases/metabolism
- Aspartate-tRNA Ligase/metabolism
- Bacteria/enzymology
- RNA, Transfer, Amino Acyl/biosynthesis
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Asn/biosynthesis
- RNA, Transfer, Asn/chemistry
- RNA, Transfer, Cys/biosynthesis
- RNA, Transfer, Cys/chemistry
- RNA, Transfer, Gln/biosynthesis
- RNA, Transfer, Gln/chemistry
- Transfer RNA Aminoacylation
Collapse
Affiliation(s)
- Terry Cathopoulis
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | | | | |
Collapse
|
11
|
Lobanov AV, Gromer S, Salinas G, Gladyshev VN. Selenium metabolism in Trypanosoma: characterization of selenoproteomes and identification of a Kinetoplastida-specific selenoprotein. Nucleic Acids Res 2006; 34:4012-24. [PMID: 16914442 PMCID: PMC1557815 DOI: 10.1093/nar/gkl541] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Proteins containing the 21st amino acid selenocysteine (Sec) are present in the three domains of life. However, within lower eukaryotes, particularly parasitic protists, the dependence on the trace element selenium is variable as many organisms lost the ability to utilize Sec. Herein, we analyzed the genomes of Trypanosoma and Leishmania for the presence of genes coding for Sec-containing proteins. The selenoproteomes of these flagellated protozoa have three selenoproteins, including distant homologs of mammalian SelK and SelT, and a novel multidomain selenoprotein designated SelTryp. In SelK and SelTryp, Sec is near the C-terminus, and in all three selenoproteins, it is within predicted redox motifs. SelTryp has neither Sec- nor cysteine-containing homologs in the human host and appears to be a Kinetoplastida-specific protein. The use of selenium for protein synthesis was verified by metabolically labeling Trypanosoma cells with 75Se. In addition, genes coding for components of the Sec insertion machinery were identified in the Kinetoplastida genomes. Finally, we found that Trypanosoma brucei brucei cells were highly sensitive to auranofin, a compound that specifically targets selenoproteins. Overall, these data establish that Trypanosoma, Leishmania and likely other Kinetoplastida utilize and depend on the trace element selenium, and this dependence is due to occurrence of selenium in at least three selenoproteins.
Collapse
Affiliation(s)
| | - Stephan Gromer
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 504D-69120 Heidelberg, Germany
| | - Gustavo Salinas
- Cátedra de Inmunología, Facultad de Química/Ciencias, Instituto de HigieneAvenida Alfredo Navarro 3051, Montevideo, CP 11600, Uruguay
| | - Vadim N. Gladyshev
- To whom correspondence should be addressed. Tel: +1 402 472 4948; Fax: +1 402 472 7842;
| |
Collapse
|
12
|
Hatfield DL, Carlson BA, Xu XM, Mix H, Gladyshev VN. Selenocysteine Incorporation Machinery and the Role of Selenoproteins in Development and Health. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:97-142. [PMID: 16891170 DOI: 10.1016/s0079-6603(06)81003-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Dolph L Hatfield
- Molecular Biology of Selenium Section, Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | | | | | | |
Collapse
|