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Li Y, Xu Y, Hu X, Li C, Wei L, Wang X, Jin Y, Hu Z. Water-Soluble Se-Containing Proteins from Chicken Alleviate DSS-Induced Ulcerative Colitis in Mice via Inhibiting TLR4/MyD88 Pathway and Protecting the Goblet Cell Pathway. Biol Trace Elem Res 2024; 202:3767-3780. [PMID: 37950138 DOI: 10.1007/s12011-023-03952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
The influence of water-soluble selenium-containing proteins (WSSeP) in chicken on ulcerative colitis (UC) is not known. This work aims to investigate the effect of two WSSeP including h-Se with 1.78 μg Se/g and l-Se with 1.04 μg Se/g on mice UC induced by dextran sodium sulfate (DSS) versus 5-aminosalicylic acid (5-ASA). Seventy C57BL/6 mice were randomly divided into seven groups: groups 1 and 7 were given normal saline. Group 2 to group 4 were administrated orally 500, 1500, and 3000 mg/kg/day h-Se, respectively. Group 5 was given 1500 mg/kg/day l-Se as the control of group 3. From day 14 to day 21, groups 2 to 7 were fed with 3% DSS. Synchronously, group 6 was fed with 150 mg/kg/day 5-ASA. On day 21, the disease activity index, colon length, the histopathological changes, the expressions of claudin-1, occludin, ZO-1, TLR4, and MyD88 in colons, the levels of inflammatory cytokines (IFN-γ, IL-1β, IL-6, TNF-α), and antioxidant markers (LPS, GSH-Px, SOD, MDA) in serum were determined. WSSeP can effectively improve the damages of DSS to the colon, thymus, and spleen, which present protein and Se dose-dependent. 1.50 g h-Se dose can significantly promote the expression levels of claudin-1, occludin, and ZO-1, to surround crypt gland and goblet and epithelial cells and inhibit the attack of DSS, suppress TLR4/MyD88 pathway, decrease the levels of IL-1β, IL-6, TNF-α, IFN-γ, LPS, and MDA, and increase the activities of GSH-Px and SOD, which are better than those of 5-ASA. Therefore, WSSeP would be a natural and potential anti-inflammatory agent for UC.
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Affiliation(s)
- Yuancheng Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Yanlong Xu
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Xin Hu
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Chenxi Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Lulu Wei
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Xinlei Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Yi Jin
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China
| | - Zhongqiu Hu
- College of Food Science and Engineering, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Laboratory of Quality & Safety Risk Assessment for Agro-Products (Yangling), Ministry of Agriculture and Rural Affairs of the People's Republic of China, Yangling, 712100, Shaanxi, China.
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Valentin-Alvarado LE, Appler KE, De Anda V, Schoelmerich MC, West-Roberts J, Kivenson V, Crits-Christoph A, Ly L, Sachdeva R, Greening C, Savage DF, Baker BJ, Banfield JF. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nat Commun 2024; 15:6384. [PMID: 39085194 PMCID: PMC11291895 DOI: 10.1038/s41467-024-49872-z] [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: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
The roles of Asgard archaea in eukaryogenesis and marine biogeochemical cycles are well studied, yet their contributions in soil ecosystems remain unknown. Of particular interest are Asgard archaeal contributions to methane cycling in wetland soils. To investigate this, we reconstructed two complete genomes for soil-associated Atabeyarchaeia, a new Asgard lineage, and a complete genome of Freyarchaeia, and predicted their metabolism in situ. Metatranscriptomics reveals expression of genes for [NiFe]-hydrogenases, pyruvate oxidation and carbon fixation via the Wood-Ljungdahl pathway. Also expressed are genes encoding enzymes for amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification and carbohydrate breakdown to acetate and formate. Overall, soil-associated Asgard archaea are predicted to include non-methanogenic acetogens, highlighting their potential role in carbon cycling in terrestrial environments.
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Affiliation(s)
- Luis E Valentin-Alvarado
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kathryn E Appler
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
| | - Valerie De Anda
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Environmental Systems Sciences; ETH Zürich, Zürich, Switzerland
| | - Jacob West-Roberts
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Veronika Kivenson
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Alexander Crits-Christoph
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Cultivarium, Watertown, MA, USA
| | - Lynn Ly
- Oxford Nanopore Technologies Inc, New York, NY, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia
- Securing Antarctica's Environmental Future, Monash University, Clayton, VIC, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, California, USA
- Howard Hughes Medical Institute, University of California, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
| | - Brett J Baker
- Department of Marine Science, University of Texas at Austin; Marine Science Institute, Port Aransas, TX, USA.
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, California, USA.
- Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
- Department of Microbiology, Biomedicine Discovery Institute; Monash University, Clayton, VIC, Australia.
- Earth and Planetary Science, University of California, Berkeley, CA, USA.
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Ko H, Pasternak JA, Mulligan MK, Hamonic G, Ramesh N, MacPhee DJ, Plastow GS, Harding JCS. A DIO2 missense mutation and its impact on fetal response to PRRSV infection. BMC Vet Res 2024; 20:255. [PMID: 38867209 PMCID: PMC11167750 DOI: 10.1186/s12917-024-04099-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Porcine reproductive and respiratory syndrome virus 2 (PRRSV-2) infection during late gestation substantially lowers fetal viability and survival. In a previous genome-wide association study, a single nucleotide polymorphism on chromosome 7 was significantly associated with probability of fetuses being viable in response to maternal PRRSV-2 infection at 21 days post maternal inoculation. The iodothyronine deiodinase 2 (DIO2) gene, located ~ 14 Kilobase downstream of this SNP, was selected as a priority candidate related to fetal susceptibility following maternal PRRSV-2 infection. Our objectives were to identify mutation(s) within the porcine DIO2 gene and to determine if they were associated with fetal outcomes after PRRSV-2 challenge. Sequencing of the DIO2, genotyping identified variants, and association of DIO2 genotypes with fetal phenotypes including DIO2 mRNA levels, viability, survival, viral loads, cortisol and thyroid hormone levels, and growth measurements were conducted. RESULTS A missense variant (p.Asn91Ser) was identified in the parental populations from two independent PRRSV-2 challenge trials. This variant was further genotyped to determine association with fetal PRRS outcomes. DIO2 mRNA levels in fetal heart and kidney differed by the genotypes of Asn91Ser substitution with significantly greater DIO2 mRNA expression in heterozygotes compared with wild-type homozygotes (P < 0.001 for heart, P = 0.002 for kidney). While Asn91Ser did not significantly alter fetal viability and growth measurements, interaction effects of the variant with fetal sex or trial were identified for fetal viability or crown rump length, respectively. However, this mutation was not related to dysregulation of the hypothalamic-pituitary-adrenal and thyroid axis, indicated by no differences in circulating cortisol, T4, and T3 levels in fetuses of the opposing genotypes following PRRSV-2 infection. CONCLUSIONS The present study suggests that a complex relationship among DIO2 genotype, DIO2 expression, fetal sex, and fetal viability may exist during the course of fetal PRRSV infection. Our study also proposes the increase in cortisol levels, indicative of fetal stress response, may lead to fetal complications, such as fetal compromise, fetal death, or premature farrowing, during PRRSV infection.
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Affiliation(s)
- Haesu Ko
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N5B4, Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G2H1, Canada
| | - J Alex Pasternak
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Margaret K Mulligan
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Glenn Hamonic
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N5B4, Canada
| | - Naresh Ramesh
- Department of Biology, West Virginia University Institute of Technology, Beckley, WV, 25801, USA
| | - Daniel J MacPhee
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N5B4, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G2H1, Canada
| | - John C S Harding
- Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N5B4, Canada.
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Zhu WS, Litterman AJ, Sekhon HS, Kageyama R, Arce MM, Taylor KE, Zhao W, Criswell LA, Zaitlen N, Erle DJ, Ansel KM. GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins. Genome Biol 2023; 24:281. [PMID: 38062486 PMCID: PMC10701951 DOI: 10.1186/s13059-023-03125-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam J Litterman
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Harshaan S Sekhon
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Robin Kageyama
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Wenxue Zhao
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Lindsey A Criswell
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - David J Erle
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
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Eight Unexpected Selenoprotein Families in Organometallic Biochemistry in Clostridium difficile, in ABC Transport, and in Methylmercury Biosynthesis. J Bacteriol 2023; 205:e0025922. [PMID: 36598231 PMCID: PMC9879109 DOI: 10.1128/jb.00259-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bioinformatics of a nine-gene locus, designated selenocysteine-assisted organometallic (SAO), was investigated after identifying six new selenoprotein families and constructing hidden Markov models (HMMs) that find and annotate members of those families. Four are selenoproteins in most SAO loci, including Clostridium difficile. They include two ABC transporter subunits, namely, permease SaoP, with selenocysteine (U) at the channel-gating position, and substrate-binding subunit SaoB. Cytosolic selenoproteins include SaoL, homologous to MerB organomercurial lyases from mercury resistance loci, and SaoT, related to thioredoxins. SaoL, SaoB, and surface protein SaoC (an occasional selenoprotein) share an unusual CU dipeptide motif, which is something rare in selenoproteins but found in selenoprotein variants of mercury resistance transporter subunit MerT. A nonselenoprotein, SaoE, shares homology with Cu/Zn efflux and arsenical efflux pumps. The organization of the SAO system suggests substrate interaction with surface-exposed selenoproteins, followed by import, metabolism that may cleave a carbon-to-heavy metal bond, and finally metal efflux. A novel type of mercury resistance is possible, but SAO instead may support fermentative metabolism, with selenocysteine-mediated formation of organometallic intermediates, followed by import, degradation, and metal efflux. Phylogenetic profiling shows SOA loci consistently co-occur with Stickland fermentation markers but even more consistently with 8Fe-9S cofactor-type double-cubane proteins. Hypothesizing that the SAO system forms organometallic intermediates, we investigated the known methylmercury formation protein families HgcA and HgcB. Both families contained overlooked selenoproteins. Most HgcAs have a CU motif N terminal to their previously accepted start sites. Seeking additional rare and overlooked selenoproteins may help reveal more cryptic aspects of microbial biochemistry. IMPORTANCE This work adds 8 novel prokaryotic selenoproteins to the 80 or so families previously known. It describes the SAO (selenocysteine-assisted organometallic) locus, with the most selenoproteins of any known system. The rare CU motif recurs throughout, suggesting the formation and degradation of organometallic compounds. That suggestion triggered a reexamination of HgcA and HcgB, which are methylmercury formation proteins that can adversely impact food safety. Both are selenoproteins, once corrected, with HgcA again showing a CU motif. The SAO system is plausibly a mercury resistance locus for selenium-dependent anaerobes. But instead, it may exploit heavy metals as cofactors in organometallic intermediate-forming pathways that circumvent high activation energies and facilitate the breakdown of otherwise poorly accessible nutrients. SAO could provide an edge that helps Clostridium difficile, an important pathogen, establish disease.
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Manta B, Makarova NE, Mariotti M. The selenophosphate synthetase family: A review. Free Radic Biol Med 2022; 192:63-76. [PMID: 36122644 DOI: 10.1016/j.freeradbiomed.2022.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/11/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022]
Abstract
Selenophosphate synthetases use selenium and ATP to synthesize selenophosphate. This is required for biological utilization of selenium, most notably for the synthesis of the non-canonical amino acid selenocysteine (Sec). Therefore, selenophosphate synthetases underlie all functions of selenoproteins, which include redox homeostasis, protein quality control, hormone regulation, metabolism, and many others. This protein family comprises two groups, SelD/SPS2 and SPS1. The SelD/SPS2 group represent true selenophosphate synthetases, enzymes central to selenium metabolism which are present in all Sec-utilizing organisms across the tree of life. Notably, many SelD/SPS2 proteins contain Sec as catalytic residue in their N-terminal flexible selenium-binding loop, while others replace it with cysteine (Cys). The SPS1 group comprises proteins originated through gene duplications of SelD/SPS2 in metazoa in which the Sec/Cys-dependent catalysis was disrupted. SPS1 proteins do not synthesize selenophosphate and are not required for Sec synthesis. They have essential regulatory functions related to redox homeostasis and pyridoxal phosphate, which affect signaling pathways for growth and differentiation. In this review, we summarize the knowledge about the selenophosphate synthetase family acquired through decades of research, encompassing their structure, mechanism, function, and evolution.
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Affiliation(s)
- Bruno Manta
- Laboratorio de Genómica Microbiana, Institut Pasteur Montevideo, Uruguay, Cátedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Uruguay
| | - Nadezhda E Makarova
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Avinguda Diagonal 643, Barcelona, 08028, Catalonia, Spain
| | - Marco Mariotti
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Avinguda Diagonal 643, Barcelona, 08028, Catalonia, Spain.
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Chung CZ, Krahn N. The selenocysteine toolbox: A guide to studying the 21st amino acid. Arch Biochem Biophys 2022; 730:109421. [DOI: 10.1016/j.abb.2022.109421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
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Zhang L, Zhang Y, Li S, Li C, Hu X, Li Z, Yue T, Hu Z. Effect of the selenized yeast added in feed on selenium-containing proteins of albumins in egg yolk. Food Chem 2022; 402:134435. [DOI: 10.1016/j.foodchem.2022.134435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 10/14/2022]
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Design of typical genes for heterologous gene expression. Sci Rep 2022; 12:9625. [PMID: 35688911 PMCID: PMC9187722 DOI: 10.1038/s41598-022-13089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Heterologous protein expression is an important method for analysing cellular functions of proteins, in genetic circuit engineering and in overexpressing proteins for biopharmaceutical applications and structural biology research. The degeneracy of the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, plays an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the influence of a profiled codon usage adaptation approach on protein expression levels in the eukaryotic model organism Saccharomyces cerevisiae. We selected green fluorescent protein (GFP) and human α-synuclein (αSyn) as representatives for stable and intrinsically disordered proteins and representing a benchmark and a challenging test case. A new approach was implemented to design typical genes resembling the codon usage of any subset of endogenous genes. Using this approach, synthetic genes for GFP and αSyn were generated, heterologously expressed and evaluated in yeast. We demonstrate that GFP is expressed at high levels, and that the toxic αSyn can be adapted to endogenous, low-level expression. The new software is publicly available as a web-application for performing host-specific protein adaptations to a set of the most commonly used model organisms ( https://odysseus.motorprotein.de ).
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Chemoproteomic interrogation of selenocysteine by low-pH isoTOP-ABPP. Methods Enzymol 2022; 662:187-225. [DOI: 10.1016/bs.mie.2021.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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SecMS analysis of selenoproteins with selenocysteine insertion sequence and beyond. Methods Enzymol 2022; 662:227-240. [DOI: 10.1016/bs.mie.2021.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Larval metamorphosis is inhibited by methimazole and propylthiouracil that reveals possible hormonal action in the mussel Mytilus coruscus. Sci Rep 2021; 11:19288. [PMID: 34588587 PMCID: PMC8481496 DOI: 10.1038/s41598-021-98930-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/16/2021] [Indexed: 11/08/2022] Open
Abstract
Larval metamorphosis in bivalves is a key event for the larva-to-juvenile transformation. Previously we have identified a thyroid hormone receptor (TR) gene that is crucial for larvae to acquire “competence” for the metamorphic transition in the mussel Mytilus courscus (Mc). The mechanisms of thyroid signaling in bivalves are still largely unknown. In the present study, we molecularly characterized the full-length of two iodothyronine deiodinase genes (McDx and McDy). Phylogenetic analysis revealed that deiodinases of molluscs (McDy, CgDx and CgDy) and vertebrates (D2 and D3) shared a node representing an immediate common ancestor, which resembled vertebrates D1 and might suggest that McDy acquired specialized function from vertebrates D1. Anti-thyroid compounds, methimazole (MMI) and propylthiouracil (PTU), were used to investigate their effects on larval metamorphosis and juvenile development in M. coruscus. Both MMI and PTU significantly reduced larval metamorphosis in response to the metamorphosis inducer epinephrine. MMI led to shell growth retardation in a concentration-dependent manner in juveniles of M. coruscus after 4 weeks of exposure, whereas PTU had no effect on juvenile growth. It is hypothesized that exposure to MMI and PTU reduced the ability of pediveliger larvae for the metamorphic transition to respond to the inducer. The effect of MMI and PTU on larval metamorphosis and development is most likely through a hormonal signal in the mussel M. coruscus, with the implications for exploring the origins and evolution of metamorphosis.
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Craig RJ, Yushenova IA, Rodriguez F, Arkhipova IR. An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates many invertebrate genomes. Mol Biol Evol 2021; 38:5005-5020. [PMID: 34320655 PMCID: PMC8557442 DOI: 10.1093/molbev/msab225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Penelope-like elements (PLEs) are an enigmatic clade of retrotransposons whose reverse transcriptases (RTs) share a most recent common ancestor with telomerase RTs. The single ORF of canonical endonuclease (EN)+ PLEs encodes RT and a C-terminal GIY–YIG EN that enables intrachromosomal integration, whereas EN− PLEs lack EN and are generally restricted to chromosome termini. EN+ PLEs have only been found in animals, except for one case of horizontal transfer to conifers, whereas EN− PLEs occur in several kingdoms. Here, we report a new, deep-branching PLE clade with a permuted domain order, whereby an N-terminal GIY–YIG EN is linked to a C-terminal RT by a short domain with a characteristic CxC motif. These N-terminal EN+ PLEs share a structural organization, including pseudo-LTRs and complex tandem/inverted insertions, with canonical EN+ PLEs from Penelope/Poseidon, Neptune, and Nematis clades, and show insertion bias for microsatellites, but lack canonical hammerhead ribozyme motifs. However, their phylogenetic distribution is much broader. The Naiads, found in numerous invertebrate phyla, can reach tens of thousands of copies per genome. In spiders and clams, Naiads independently evolved to encode selenoproteins containing multiple selenocysteines. Chlamys, which lack the CCHH motif universal to PLE ENs, occur in green algae, spike mosses (targeting ribosomal DNA), and slime molds. Unlike canonical PLEs, RTs of N-terminal EN+ PLEs contain the insertion-in-fingers domain (IFD), strengthening the link between PLEs and telomerases. Additionally, we describe Hydra, a novel metazoan C-terminal EN+ clade. Overall, we conclude that PLE diversity, taxonomic distribution, and abundance are comparable with non-LTR and LTR-retrotransposons.
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Affiliation(s)
- Rory J Craig
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
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Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME COMMUNICATIONS 2021; 1:30. [PMID: 36739331 PMCID: PMC9723677 DOI: 10.1038/s43705-021-00032-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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Affiliation(s)
- Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Gagen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
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De Lise F, Strazzulli A, Iacono R, Curci N, Di Fenza M, Maurelli L, Moracci M, Cobucci-Ponzano B. Programmed Deviations of Ribosomes From Standard Decoding in Archaea. Front Microbiol 2021; 12:688061. [PMID: 34149676 PMCID: PMC8211752 DOI: 10.3389/fmicb.2021.688061] [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: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic code decoding, initially considered to be universal and immutable, is now known to be flexible. In fact, in specific genes, ribosomes deviate from the standard translational rules in a programmed way, a phenomenon globally termed recoding. Translational recoding, which has been found in all domains of life, includes a group of events occurring during gene translation, namely stop codon readthrough, programmed ± 1 frameshifting, and ribosome bypassing. These events regulate protein expression at translational level and their mechanisms are well known and characterized in viruses, bacteria and eukaryotes. In this review we summarize the current state-of-the-art of recoding in the third domain of life. In Archaea, it was demonstrated and extensively studied that translational recoding regulates the decoding of the 21st and the 22nd amino acids selenocysteine and pyrrolysine, respectively, and only one case of programmed -1 frameshifting has been reported so far in Saccharolobus solfataricus P2. However, further putative events of translational recoding have been hypothesized in other archaeal species, but not extensively studied and confirmed yet. Although this phenomenon could have some implication for the physiology and adaptation of life in extreme environments, this field is still underexplored and genes whose expression could be regulated by recoding are still poorly characterized. The study of these recoding episodes in Archaea is urgently needed.
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Affiliation(s)
- Federica De Lise
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Andrea Strazzulli
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Roberta Iacono
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Nicola Curci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy
| | - Mauro Di Fenza
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Luisa Maurelli
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy
| | - Marco Moracci
- Institute of Biosciences and BioResources - National Research Council of Italy, Naples, Italy.,Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Naples, Italy.,Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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16
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Leitsch D, Mbouaka AL, Köhsler M, Müller N, Walochnik J. An unusual thioredoxin system in the facultative parasite Acanthamoeba castellanii. Cell Mol Life Sci 2021; 78:3673-3689. [PMID: 33599799 PMCID: PMC8038987 DOI: 10.1007/s00018-021-03786-x] [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: 11/30/2020] [Revised: 01/08/2021] [Accepted: 02/02/2021] [Indexed: 01/25/2023]
Abstract
The free-living amoeba Acanthamoeba castellanii occurs worldwide in soil and water and feeds on bacteria and other microorganisms. It is, however, also a facultative parasite and can cause serious infections in humans. The annotated genome of A. castellanii (strain Neff) suggests the presence of two different thioredoxin reductases (TrxR), of which one is of the small bacterial type and the other of the large vertebrate type. This combination is highly unusual. Similar to vertebrate TrxRases, the gene coding for the large TrxR in A. castellanii contains a UGA stop codon at the C-terminal active site, suggesting the presence of selenocysteine. We characterized the thioredoxin system in A. castellanii in conjunction with glutathione reductase (GR), to obtain a more complete understanding of the redox system in A. castellanii and the roles of its components in the response to oxidative stress. Both TrxRases localize to the cytoplasm, whereas GR localizes to the cytoplasm and the large organelle fraction. We could only identify one thioredoxin (Trx-1) to be indeed reduced by one of the TrxRases, i.e., by the small TrxR. This thioredoxin, in turn, could reduce one of the two peroxiredoxins tested and also methionine sulfoxide reductase A (MsrA). Upon exposure to hydrogen peroxide and diamide, only the small TrxR was upregulated in expression at the mRNA and protein levels, but not the large TrxR. Our results show that the small TrxR is involved in the A. castellanii's response to oxidative stress. The role of the large TrxR, however, remains elusive.
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Affiliation(s)
- David Leitsch
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria.
| | - Alvie Loufouma Mbouaka
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Martina Köhsler
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
| | - Norbert Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, 3012, Bern, Switzerland
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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Mayasich SA, Korte JJ, Denny JS, Hartig PC, Olker JH, DeGoey P, O'Flanagan J, Degitz SJ, Hornung MW. Xenopus laevis and human type 3 iodothyronine deiodinase enzyme cross-species sensitivity to inhibition by ToxCast chemicals. Toxicol In Vitro 2021; 73:105141. [PMID: 33713820 DOI: 10.1016/j.tiv.2021.105141] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/12/2021] [Accepted: 03/08/2021] [Indexed: 11/15/2022]
Abstract
Deiodinase enzymes are critical for tissue-specific and temporal control of activation or inactivation of thyroid hormones during vertebrate development, including amphibian metamorphosis. We previously screened ToxCast chemicals for inhibitory activity toward human recombinant Type 3 iodothyronine deiodinase enzyme (hDIO3) and subsequently produced Xenopus laevis recombinant dio3 enzyme (Xldio3) with the goals to identify specific chemical inhibitors of Xldio3, to evaluate cross-species sensitivity and explore whether the human assay results are predictive of the amphibian. We identified a subset of 356 chemicals screened against hDIO3 to test against Xldio3, initially at a single concentration (200 μM), and further tested 79 in concentration-response mode. Most chemicals had IC50 values lower for hDIO3 than for Xldio3 and many had steep Hill slopes (a potential indication of non-specific inhibition). However, eight of the most potent chemicals are likely specific inhibitors, with IC50 values of 14 μM or less, Hill slopes near -1 and curves not significantly different between species likely due to conservation of catalytically active amino acids. Controlling for assay conditions, human in vitro screening results can be predictive of activity in the amphibian assay. This study lays the groundwork for future studies using recombinant non-mammalian proteins to test cross-species sensitivity to chemicals. DISCLAIMER: The views expressed in this paper are those of the authors and do not necessarily reflect the views or policies of the U.S. Environmental Protection Agency. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.
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Affiliation(s)
- Sally A Mayasich
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA; Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Joseph J Korte
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Jeffrey S Denny
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Phillip C Hartig
- Public Health and Integrated Toxicology Division, Center for Public Health and Environmental Assessment, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Jennifer H Olker
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Philip DeGoey
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Joseph O'Flanagan
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA; Oak Ridge Associated Universities, Oak Ridge, TN, USA
| | - Sigmund J Degitz
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA
| | - Michael W Hornung
- Great Lakes Toxicology and Ecology Division, Center for Computational Toxicology and Ecology, Office of Research and Development, U.S. Environmental Protection Agency, Duluth, MN, USA.
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18
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Xu XJ, Zhang DG, Zhao T, Xu YH, Luo Z. Characterization and expression analysis of seven selenoprotein genes in yellow catfish Pelteobagrus fulvidraco to dietary selenium levels. J Trace Elem Med Biol 2020; 62:126600. [PMID: 32622174 DOI: 10.1016/j.jtemb.2020.126600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Selenium (Se) appears in the selenoproteins in the form of selenocysteine (Sec) and is important for the growth and development of vertebrates. The present study characterized seven selenoproteins, consisting of the GPX1, GPX3, GPX4, SELENOW, SELENOP, TXNRD2 and TXNRD3 cDNAs in various tissues of yellow catfish, explored their regulation to dietary Se addition. METHODS 3' and 5' RACE PCR were used to clone full-length cDNA sequences of seven selenoprotein genes (GPX1, GPX3, GPX4, SELENOW, SELENOP, TXNRD2 and TXNRD3). Their molecular characterizations were analyzed, including conservative motifs and the SECIS elements. The phylogenetic trees were generated through neighbor-joining (NJ) method with MEGA 6.0 with 1000 bootstrap replications. Quantitative real-time PCR was used to explore their mRNA tissue distribution in the heart, anterior intestine, dorsal muscle, head kidney, gill, liver, brain, spleen and mesenteric fat. Yellow catfish (mixed sex) were fed diets with dietary Se contents at 0.03 (low Se), 0.25 (adequate Se) and 6.39 (high Se) mg Se/kg, respectively, for 12 weeks, and their spleen, kidney, testis and brain were used for the determination of the mRNA levels of the seven selenoproteins. RESULTS The seven selenoproteins had similar domains to their corresponding members of other vertebrates. They were widely expressed in nine tissues, including heart, liver, brain, spleen, head kidney, dorsal muscle, mesenteric fat, anterior intestine and gill, but showed tissue-dependent expression patterns. Dietary Se addition affected the expression of the seven genes in spleen, kidney, testis and brain tissues of yellow catfish. CONCLUSION Taken together, our study demonstrated the characterization, expression and regulation of seven selenoproteins, which increased our understanding of the biological functions of Se and selenoproteins in fish.
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Affiliation(s)
- Xiao-Jian Xu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Dian-Guang Zhang
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Zhao
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Huan Xu
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Luo
- Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Fishery College, Huazhong Agricultural University, Wuhan 430070, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China.
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19
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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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20
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Abstract
Background Selenium is an essential trace element, and selenocysteine (Sec, U) is its predominant form in vivo. Proteins that contain Sec are selenoproteins, whose special structural features include not only the TGA codon encoding Sec but also the SECIS element in mRNA and the conservation of the Sec-flanking region. These unique features have led to the development of a series of bioinformatics methods to predict and research selenoprotein genes. There have been some studies and reports on the evolution and distribution of selenoprotein genes in prokaryotes and multicellular eukaryotes, but the systematic analysis of single-cell eukaryotes, especially algae, has been very limited. Results In this study, we predicted selenoprotein genes in 137 species of algae by using a program we previously developed. More than 1000 selenoprotein genes were obtained. A database website was built to record these algae selenoprotein genes (www.selenoprotein.com). These genes belong to 42 selenoprotein families, including three novel selenoprotein gene families. Conclusions This study reveals the primordial state of the eukaryotic selenoproteome. It is an important clue to explore the significance of selenium for primordial eukaryotes and to determine the complete evolutionary spectrum of selenoproteins in all life forms.
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21
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Santesmasses D, Mariotti M, Gladyshev VN. Bioinformatics of Selenoproteins. Antioxid Redox Signal 2020; 33:525-536. [PMID: 32031018 PMCID: PMC7409585 DOI: 10.1089/ars.2020.8044] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/13/2022]
Abstract
Significance: Bioinformatics has brought important insights into the field of selenium research. The progress made in the development of computational tools in the last two decades, coordinated with growing genome resources, provided new opportunities to study selenoproteins. The present review discusses existing tools for selenoprotein gene finding and other bioinformatic approaches to study the biology of selenium. Recent Advances: The availability of complete selenoproteomes allowed assessing a global distribution of the use of selenocysteine (Sec) across the tree of life, as well as studying the evolution of selenoproteins and their biosynthetic pathway. Beyond gene identification and characterization, human genetic variants in selenoprotein genes were used to examine adaptations to selenium levels in diverse human populations and to estimate selective constraints against gene loss. Critical Issues: The synthesis of selenoproteins is essential for development in mice. In humans, several mutations in selenoprotein genes have been linked to rare congenital disorders. And yet, the mechanism of Sec insertion and the regulation of selenoprotein synthesis in mammalian cells are not completely understood. Future Directions: Omics technologies offer new possibilities to study selenoproteins and mechanisms of Sec incorporation in cells, tissues, and organisms.
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Affiliation(s)
- Didac Santesmasses
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts, USA
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22
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Reshma R, Kumari S, Arumugam M. Structural elucidation of selenocysteine insertion machinery of microalgal selenoprotein T and its transcriptional analysis. Biotechnol Appl Biochem 2020; 68:636-647. [PMID: 32579774 DOI: 10.1002/bab.1974] [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: 04/10/2020] [Accepted: 06/21/2020] [Indexed: 11/06/2022]
Abstract
Essential trace element selenium in association with selenoproteins, which is found in almost all organisms except higher plants and fungi, is involved in various biological functions. Advancement in the field of whole genome sequencing and data analyzing bioinformatic tools led to the accumulation of genome information of organisms. However, selenoproteins are unique and it needs specialized genomics tool for its identification as well as characterization. In this study, the presence of selenoprotein T (SelT) from Scenedesmus quadricauda was shown for the first time with experimental evidence and compared with SelT of marine microalgae Nannochloropsis oceanica. Along with SelT, all the associated machineries required to synthesize the selenoproteins were also identified. Also, the present study tried to explicate the evolutionary relatedness of SelT of these two organisms with other known bacteria and eukaryotes. Transcript level analysis in S. quadricauda under endoplasmic reticulum stress showed a 1.2 ± 0.28-fold increase in SelT expression. Thus, it provided the first experimental evidence on SelT expression from microalgae.
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Affiliation(s)
- Ragini Reshma
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sunitha Kumari
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Muthu Arumugam
- Microbial Processes and Technology Division, National Institute for Interdisciplinary Science and Technology (NIIST), Council of Scientific and Industrial Research (CSIR), Trivandrum, Kerala, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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23
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Cubas-Gaona LL, de Francisco P, Martín-González A, Gutiérrez JC. Tetrahymena Glutathione Peroxidase Family: A Comparative Analysis of These Antioxidant Enzymes and Differential Gene Expression to Metals and Oxidizing Agents. Microorganisms 2020; 8:microorganisms8071008. [PMID: 32635666 PMCID: PMC7409322 DOI: 10.3390/microorganisms8071008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/21/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022] Open
Abstract
In the present work, an extensive analysis of the putative glutathione peroxidases (GPx) of the eukaryotic microorganism model Tetrahymena thermophila is carried out. A comparative analysis with GPx present in other Tetrahymena species and other very taxonomically diverse ciliates is also performed. A majority of ciliate GPx have replaced the selenocysteine (Sec) by Cys in its catalytic center, so they can be considered as phospholipid hydroperoxide glutathione peroxidases (PHGPx). Selenocysteine insertion sequence (SECIS) elements have been detected in several ciliate GPx that do not incorporate Sec in their amino acid sequences, and conversely, in other ciliate GPx with Sec, no SECIS elements are detected. These anomalies are analyzed and discussed. From the phylogenetic analysis using the ciliate GPx amino acid sequences, the existence of extensive intra- and interspecific gene duplications that produced multiple GPx isoforms in each species is inferred. The ancestral character of the selenoproteins is also corroborated. The analysis by qRT-PCR of six selected T. thermophila GPx genes has shown a quantitative differential expression between them, depending on the stressor (oxidizing agents, apoptotic inducer or metals) and the time of exposure.
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Affiliation(s)
| | - Patricia de Francisco
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850 Madrid, Spain;
| | - Ana Martín-González
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología. C/. José Antonio Nováis, 12. Universidad Complutense (UCM), 28040 Madrid, Spain;
| | - Juan Carlos Gutiérrez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología. C/. José Antonio Nováis, 12. Universidad Complutense (UCM), 28040 Madrid, Spain;
- Correspondence:
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Shtratnikova VY, Schelkunov MI, Penin AA, Logacheva MD. Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing. PeerJ 2020; 8:e9309. [PMID: 32601550 PMCID: PMC7307570 DOI: 10.7717/peerj.9309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 05/17/2020] [Indexed: 01/05/2023] Open
Abstract
Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.
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Affiliation(s)
- Viktoria Yu Shtratnikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Moscow, Russia.,Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Aleksey A Penin
- Laboratory of Plant Genomics, Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
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25
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Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity. Proc Natl Acad Sci U S A 2020; 117:10789-10796. [PMID: 32358195 PMCID: PMC7245117 DOI: 10.1073/pnas.2001387117] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Oxidation of cysteine thiols by physiological reactive oxygen species (ROS) initiates thermogenesis in brown and beige adipose tissues. Cellular selenocysteines, where sulfur is replaced with selenium, exhibit enhanced reactivity with ROS. Despite their critical roles in physiology, methods for broad and direct detection of proteogenic selenocysteines are limited. Here we developed a mass spectrometric method to interrogate incorporation of selenium into proteins. Unexpectedly, this approach revealed facultative incorporation of selenium as selenocysteine or selenomethionine into proteins that lack canonical encoding for selenocysteine. Selenium was selectively incorporated into regulatory sites on key metabolic proteins, including as selenocysteine-replacing cysteine at position 253 in uncoupling protein 1 (UCP1). This facultative utilization of selenium was initiated by increasing cellular levels of organic, but not inorganic, forms of selenium. Remarkably, dietary selenium supplementation elevated facultative incorporation into UCP1, elevated energy expenditure through thermogenic adipose tissue, and protected against obesity. Together, these findings reveal the existence of facultative protein selenation, which correlates with impacts on thermogenic adipocyte function and presumably other biological processes as well.
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26
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Abstract
Selenoproteins are the family of proteins that contain the amino acid selenocysteine. Many selenoproteins, including glutathione peroxidases and thioredoxin reductases, play a role in maintaining cellular redox homeostasis. There are a number of examples of homologues of selenoproteins that utilize cysteine residues, raising the question of why selenocysteines are utilized. One hypothesis is that incorporation of selenocysteine protects against irreversible overoxidation, typical of cysteine-containing homologues under high oxidative stress. Studies of selenocysteine function are hampered by challenges both in detection and in recombinant expression of selenoproteins. In fact, about half of the 25 known human selenoproteins remain uncharacterized. Historically, selenoproteins were first detected via labeling with radioactive 75Se or by use of inductively coupled plasma-mass spectrometry to monitor nonradioactive selenium. More recently, tandem mass-spectrometry techniques have been developed to detect selenocysteine-containing peptides. For example, the isotopic distribution of selenium has been used as a unique signature to identify selenium-containing peptides from unenriched proteome samples. Additionally, selenocysteine-containing proteins and peptides were selectively enriched using thiol-reactive electrophiles by exploiting the increased reactivity of selenols relative to thiols, especially under low pH conditions. Importantly, the reactivity-based enrichment of selenoproteins can differentiate between oxidized and reduced selenoproteins, providing insight into the activity state. These mass spectrometry-based selenoprotein detection approaches have enabled (1) production of selenoproteome expression atlases, (2) identification of aging-associated changes in selenoprotein expression, (3) characterization of selenocysteine reactivity across the selenoprotein family, and (4) interrogation of selenoprotein targets of small-molecule drugs. Further investigations of selenoprotein function would benefit from recombinant expression of selenoproteins. However, the endogenous mechanism of selenoprotein production makes recombinant expression challenging. Primarily, selenocysteine is biosynthesized on its own tRNA, is dependent on multiple enzymatic steps, and is highly sensitive to selenium concentrations. Furthermore, selenocysteine is encoded by the stop codon UGA, and suppression of that stop codon requires a selenocysteine insertion sequence element in the selenoprotein mRNA. In order to circumvent the low efficiency of the endogenous machinery, selenoproteins have been produced in vitro through native chemical ligation and expressed protein ligation. Attempts have also been made to engineer the endogenous machinery for increased efficiency, including recoding the selenocysteine codon, and engineering the tRNA and the selenocysteine insertion sequence element. Alternatively, genetic code expansion can be used to generate selenoproteins. This approach allows for selenoprotein production directly within its native cellular environment, while bypassing the endogenous selenocysteine incorporation machinery. Furthermore, by incorporating a caged selenocysteine by genetic code expansion, selenoprotein activity can be spatially and temporally controlled. Genetic code expansion has allowed for the expression and uncaging of human selenoproteins in E. coli and more recently in mammalian cells. Together, advances in selenoprotein detection and expression should enable a better understanding of selenoprotein function and provide insight into the necessity for selenocysteine production.
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Affiliation(s)
- Jennifer C. Peeler
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Eranthie Weerapana
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
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27
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Processive Recoding and Metazoan Evolution of Selenoprotein P: Up to 132 UGAs in Molluscs. J Mol Biol 2019; 431:4381-4407. [PMID: 31442478 DOI: 10.1016/j.jmb.2019.08.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023]
Abstract
Selenoproteins typically contain a single selenocysteine, the 21st amino acid, encoded by a context-redefined UGA. However, human selenoprotein P (SelenoP) has a redox-functioning selenocysteine in its N-terminal domain and nine selenium transporter-functioning selenocysteines in its C-terminal domain. Here we show that diverse SelenoP genes are present across metazoa with highly variable numbers of Sec-UGAs, ranging from a single UGA in certain insects, to 9 in common spider, and up to 132 in bivalve molluscs. SelenoP genes were shaped by a dynamic evolutionary process linked to selenium usage. Gene evolution featured modular expansions of an ancestral multi-Sec domain, which led to particularly Sec-rich SelenoP proteins in many aquatic organisms. We focused on molluscs, and chose Pacific oyster Magallana gigas as experimental model. We show that oyster SelenoP mRNA with 46 UGAs is translated full-length in vivo. Ribosome profiling indicates that selenocysteine specification occurs with ∼5% efficiency at UGA1 and approaches 100% efficiency at distal 3' UGAs. We report genetic elements relevant to its expression, including a leader open reading frame and an RNA structure overlapping the initiation codon that modulates ribosome progression in a selenium-dependent manner. Unlike their mammalian counterparts, the two SECIS elements in oyster SelenoP (3'UTR recoding elements) do not show functional differentiation in vitro. Oysters can increase their tissue selenium level up to 50-fold upon supplementation, which also results in extensive changes in selenoprotein expression.
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28
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Rajput B, Pruitt KD, Murphy TD. RefSeq curation and annotation of stop codon recoding in vertebrates. Nucleic Acids Res 2019; 47:594-606. [PMID: 30535227 PMCID: PMC6344875 DOI: 10.1093/nar/gky1234] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 12/03/2018] [Indexed: 12/23/2022] Open
Abstract
Recoding of stop codons as amino acid-specifying codons is a co-translational event that enables C-terminal extension of a protein. Synthesis of selenoproteins requires recoding of internal UGA stop codons to the 21st non-standard amino acid selenocysteine (Sec) and plays a vital role in human health and disease. Separately, canonical stop codons can be recoded to specify standard amino acids in a process known as stop codon readthrough (SCR), producing extended protein isoforms with potential novel functions. Conventional computational tools cannot distinguish between the dual functionality of stop codons as stop signals and sense codons, resulting in misannotation of selenoprotein gene products and failure to predict SCR. Manual curation is therefore required to correctly represent recoded gene products and their functions. Our goal was to provide accurately curated and annotated datasets of selenoprotein and SCR transcript and protein records to serve as annotation standards and to promote basic and biomedical research. Gene annotations were curated in nine vertebrate model organisms and integrated into NCBI's Reference Sequence (RefSeq) dataset, resulting in 247 selenoprotein genes encoding 322 selenoproteins, and 93 genes exhibiting SCR encoding 94 SCR isoforms.
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Affiliation(s)
- Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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29
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Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida. Int J Mol Sci 2019; 20:ijms20123020. [PMID: 31226841 PMCID: PMC6627142 DOI: 10.3390/ijms20123020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 11/17/2022] Open
Abstract
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.
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30
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Kumar D, Embers M, Mather TN, Karim S. Is selenoprotein K required for Borrelia burgdorferi infection within the tick vector Ixodes scapularis? Parasit Vectors 2019; 12:289. [PMID: 31174589 PMCID: PMC6555942 DOI: 10.1186/s13071-019-3548-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background Tick selenoproteins are involved in regulating oxidative and endoplasmic reticulum stress during prolonged tick feeding on mammalian hosts. How selenoproteins are activated upon tick-borne pathogen infection is yet to be defined. Methods To examine the functional role of selenoprotein K in Borrelia burgdorferi infection within the tick host Ixodes scapularis, RNA interference (RNAi)-based gene silencing was performed. Results Selenoprotein K is an endoplasmic reticulum (ER)-resident protein and a component of the ERAD complex involved in ER homeostasis. A qRT-PCR assay revealed the significant upregulation of selenogene K (selenoK) expression in B. burgdorferi-infected tick tissues. Silencing of the selenoK transcript significantly depleted B. burgdorferi copies within the infected tick tissues. Upon selenoK knockdown, another component of the ERAD complex, selenoprotein S (selenoS), was significantly upregulated, suggesting a compensatory mechanism to maintain ER homeostasis within the tick tissues. Knockdown of selenoK also upregulated ER stress-related unfolded protein response (UPR) pathway components, ATF6 and EIF2. Conclusions The exact mechanisms that contribute to depletion of B. burgdorferi upon selenoK knockdown is yet to be determined, but this study suggests that selenoK may play a vital role in the survival of B. burgdorferi within the tick host. Electronic supplementary material The online version of this article (10.1186/s13071-019-3548-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepak Kumar
- Department of of Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA
| | - Monica Embers
- Division of Immunology, Tulane National Primate Research Center, Covington, LA, 70455, USA
| | - Thomas N Mather
- Center for Vector-Borne Disease, University of Rhode Island, Kingston, RI, 02881, USA
| | - Shahid Karim
- Department of of Cell and Molecular Biology, School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, 39406, USA.
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31
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Abstract
Challenging the paradigm of SECIS-dependent selenoprotein translation, in this issue of Cell Chemical BiologyGuo et al. (2018) introduce a new selenoprotein profiling platform with which they identify novel selenoproteins apparently lacking SECIS. With increased interest in covalent targeting of reactive Sec residues in drug discovery, their method adds a valuable contribution toward expanding the druggable human proteome.
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32
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Mariotti M, Salinas G, Gabaldón T, Gladyshev VN. Utilization of selenocysteine in early-branching fungal phyla. Nat Microbiol 2019; 4:759-765. [PMID: 30742068 DOI: 10.1038/s41564-018-0354-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
Selenoproteins are a diverse group of proteins containing selenocysteine (Sec)-the twenty-first amino acid-incorporated during translation via a unique recoding mechanism1,2. Selenoproteins fulfil essential roles in many organisms1, yet are not ubiquitous across the tree of life3-7. In particular, fungi were deemed devoid of selenoproteins4,5,8. However, we show here that Sec is utilized by nine species belonging to diverse early-branching fungal phyla, as evidenced by the genomic presence of both Sec machinery and selenoproteins. Most fungal selenoproteins lack consensus Sec recoding signals (SECIS elements9) but exhibit other RNA structures, suggesting altered mechanisms of Sec insertion in fungi. Phylogenetic analyses support a scenario of vertical inheritance of the Sec trait within eukaryotes and fungi. Sec was then lost in numerous independent events in various fungal lineages. Notably, Sec was lost at the base of Dikarya, resulting in the absence of selenoproteins in Saccharomyces cerevisiae and other well-studied fungi. Our results indicate that, despite scattered occurrence, selenoproteins are found in all kingdoms of life.
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Affiliation(s)
- Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Gustavo Salinas
- Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay.,Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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33
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Zhang Y, Ying H, Xu Y. Comparative genomics and metagenomics of the metallomes. Metallomics 2019; 11:1026-1043. [DOI: 10.1039/c9mt00023b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent achievements and advances in comparative genomic and metagenomic analyses of trace metals were reviewed and discussed.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
| | - Huimin Ying
- Department of Endocrinology
- Hangzhou Xixi Hospital
- Hangzhou
- P. R. China
| | - Yinzhen Xu
- Shenzhen Key Laboratory of Marine Bioresources and Ecology
- College of Life Sciences and Oceanography
- Shenzhen University
- Shenzhen
- P. R. China
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34
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The genomics of selenium: Its past, present and future. Biochim Biophys Acta Gen Subj 2018; 1862:2427-2432. [DOI: 10.1016/j.bbagen.2018.05.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/29/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022]
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35
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Shetty SP, Sturts R, Vetick M, Copeland PR. Processive incorporation of multiple selenocysteine residues is driven by a novel feature of the selenocysteine insertion sequence. J Biol Chem 2018; 293:19377-19386. [PMID: 30323062 DOI: 10.1074/jbc.ra118.005211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/05/2018] [Indexed: 11/06/2022] Open
Abstract
RNA stem loop structures have been frequently shown to regulate essential cellular processes. The selenocysteine insertion sequence (SECIS) element, found in the 3' UTRs of all selenoprotein mRNAs, is an example of such a structure, as it is required for the incorporation of the 21st amino acid, selenocysteine (Sec). Selenoprotein synthesis poses a mechanistic challenge because Sec is incorporated during translation in response to a stop codon (UGA). Although it is known that a SECIS-binding protein (SBP2) is required for Sec insertion, the mechanism of action remains elusive. Additional complexity is present in the synthesis of selenoprotein P (SELENOP), which is the only selenoprotein that contains multiple UGA codons and possesses two SECIS elements in its 3' UTR. Thus, full-length SELENOP synthesis requires processive Sec incorporation. Using zebrafish Selenop, in vitro translation assays, and 75Se labeling in HEK293 cells, we found here that processive Sec incorporation is an intrinsic property of the SECIS elements. Specifically, we identified critical features of SECIS elements that are required for processive Sec incorporation. A screen of the human SECIS elements revealed that most of these elements support processive Sec incorporation in vitro; however, we also found that the processivity of Sec incorporation into Selenop in cells is tightly regulated. We propose a model for processive Sec incorporation that involves differential recruitment of SECIS-binding proteins.
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Affiliation(s)
- Sumangala P Shetty
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Ryan Sturts
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Vetick
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Paul R Copeland
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
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36
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Gao J, Yang F, Che J, Han Y, Wang Y, Chen N, Bak DW, Lai S, Xie X, Weerapana E, Wang C. Selenium-Encoded Isotopic Signature Targeted Profiling. ACS CENTRAL SCIENCE 2018; 4:960-970. [PMID: 30159393 PMCID: PMC6107865 DOI: 10.1021/acscentsci.8b00112] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Indexed: 05/09/2023]
Abstract
Selenium (Se), as an essential trace element, plays crucial roles in many organisms including humans. The biological functions of selenium are mainly mediated by selenoproteins, a unique class of selenium-containing proteins in which selenium is inserted in the form of selenocysteine. Due to their low abundance and uneven tissue distribution, detection of selenoproteins within proteomes is very challenging, and therefore functional studies of these proteins are limited. In this study, we developed a computational method, named as selenium-encoded isotopic signature targeted profiling (SESTAR), which utilizes the distinct natural isotopic distribution of selenium to assist detection of trace selenium-containing signals from shotgun-proteomic data. SESTAR can detect femtomole quantities of synthetic selenopeptides in a benchmark test and dramatically improved detection of native selenoproteins from tissue proteomes in a targeted profiling mode. By applying SESTAR to screen publicly available datasets from Human Proteome Map, we provide a comprehensive picture of selenoprotein distributions in human primary hematopoietic cells and tissues. We further demonstrated that SESTAR can aid chemical-proteomic strategies to identify additional selenoprotein targets of RSL3, a canonical inducer of cell ferroptosis. We believe SESTAR not only serves as a powerful tool for global profiling of native selenoproteomes, but can also work seamlessly with chemical-proteomic profiling strategies to enhance identification of target proteins, post-translational modifications, or protein-protein interactions.
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Affiliation(s)
- Jinjun Gao
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fan Yang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Jinteng Che
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Han
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Yankun Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Nan Chen
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Daniel W. Bak
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Shuchang Lai
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiao Xie
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
| | - Eranthie Weerapana
- Department
of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Chu Wang
- Synthetic
and Functional Biomolecules Center; Beijing National Laboratory for
Molecular Sciences; Key Laboratory of Bioorganic Chemistry and Molecular
Engineering of the Ministry of Education; College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Peking−Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- E-mail:
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37
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A Quantitative Chemoproteomic Platform to Monitor Selenocysteine Reactivity within a Complex Proteome. Cell Chem Biol 2018; 25:1157-1167.e4. [PMID: 29983274 DOI: 10.1016/j.chembiol.2018.05.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 03/09/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
Mammalian selenocysteine (Sec)-containing proteins, selenoproteins, are important to (patho)physiological processes, including redox homeostasis. Sec residues have been recalcitrant to mass spectrometry-based chemoproteomic methods that enrich for reactive cysteine (Cys) residues with electrophilic chemical probes, despite confirmed reactivity of Sec with these electrophiles. Highly abundant Cys peptides likely suppress low-abundant Sec peptides. By exploiting the decreased pKa of Sec relative to Cys, we have developed a chemoproteomic platform that relies on low pH (pH 5.75) electrophile labeling, reducing Cys reactivity and enhancing identification of Sec-containing peptides across mouse tissues and cell lines. The utility of this Sec-profiling platform is underscored by evaluation of the selectivity of auranofin, an inhibitor of the selenoprotein, thioredoxin reductase, against both reactive Cys- and Sec-containing proteins. Platform limitations pertain to the non-physiological low-pH conditions that could perturb protein structure and function. Future work necessitates the discovery of Sec-selective electrophiles that function at physiological pH.
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38
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Xie X, Chen M, Zhu A. Molecular characterization and functional analysis of two phospholipid hydroperoxide isoforms from Larimichthys crocea under Vibrio parahaemolyticus challenge. FISH & SHELLFISH IMMUNOLOGY 2018; 78:259-269. [PMID: 29702237 DOI: 10.1016/j.fsi.2018.04.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
Glutathione peroxidases family is a key role in the antioxidant system in oxybiotic organisms for cell redox homeostasis. One of their members, phospholipid hydroperoxide glutathione peroxidase (GPx4) have unique monomeric structure and can directly react with complex lipid and membrane-bound peroxides under the presence of glutathione(GSH). In this paper, two complete GPx4 cDNAs (designated as LcGPx4a and LcGPx4b) from Larimichthys crocea are identified by rapid amplification of cDNA ends. The cDNA of LcGPx4a was consisted of a 5'-untranslated region (UTR) of 258 bp, a 3'-UTR of 330 bp, and an open reading frame (ORF) of 561 bp encoding 186 amino acid (aa) polypeptides. And the full-length sequence of LcGPx4b was 1164 bp with a 5'-UTR of 34 bp, a 3'-UTR of 551 bp and an ORF of 576 bp encoding a polypeptide of 191 aa residues with a predicted signal peptide of 15 aa. The characteristic selenocysteine insertion (SECIS) sequence was detected in the 3'UTR of the two sequences with 78 bp in length. The conserved active site of selenocysteine (Sec) encoded by TGA was also identified and formed a tetrad functional structure with glutamine, tryptophan, and asparagine in LcGPx4a and LcGPx4b. Two signature site motifs ("LRILAFPSNQFGNQEPG" and "LRILGFPCNQFGGQEPG") were both conserved in the deduced amino acid of LcGPx4a and LcGPx4b. The genomic structure analysis revealed that the two sequences both had 7 exons and 6 introns, and the Sec opal codon and SECIS element were located at the third and seventh exons, respectively. LcGPx4a and LcGPx4b both have a wide distribution in 9 tissues with various relative expression levels and a highest expression pattern in the liver. Under Vibrio parahaemolyticus challenge, their relative expression levels were altered in the liver, spleen, kidney, and head kidney but with different magnitudes and response time. LcGPx4a and LcGPx4b showed a significantly up-regulated trend in the spleen during experimental period. Above results suggested that LcGPx4a and LcGPx4b were two conserved immune molecules and might play a role in the immune response of fish with a tissue-depemdent manners.
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Affiliation(s)
- Xiaoze Xie
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mengnan Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Aiyi Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China.
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39
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Translation regulation of mammalian selenoproteins. Biochim Biophys Acta Gen Subj 2018; 1862:2480-2492. [PMID: 29751099 DOI: 10.1016/j.bbagen.2018.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/28/2018] [Accepted: 05/04/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Interest in selenium research has considerably grown over the last decades owing to the association of selenium deficiencies with an increased risk of several human diseases, including cancers, cardiovascular disorders and infectious diseases. The discovery of a genetically encoded 21st amino acid, selenocysteine, is a fascinating breakthrough in molecular biology as it is the first addition to the genetic code deciphered in the 1960s. Selenocysteine is a structural and functional analog of cysteine, where selenium replaces sulfur, and its presence is critical for the catalytic activity of selenoproteins. SCOPE OF REVIEW The insertion of selenocysteine is a non-canonical translational event, based on the recoding of a UGA codon in selenoprotein mRNAs, normally used as a stop codon in other cellular mRNAs. Two RNA molecules and associated partners are crucial components of the selenocysteine insertion machinery, the Sec-tRNA[Ser]Sec devoted to UGA codon recognition and the SECIS elements located in the 3'UTR of selenoprotein mRNAs. MAJOR CONCLUSIONS The translational UGA recoding event is a limiting stage of selenoprotein expression and its efficiency is regulated by several factors. GENERAL SIGNIFICANCE The control of selenoproteome expression is crucial for redox homeostasis and antioxidant defense of mammalian organisms. In this review, we summarize current knowledge on the co-translational insertion of selenocysteine into selenoproteins, and its layers of regulation.
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Trace Elements and Healthcare: A Bioinformatics Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1005:63-98. [PMID: 28916929 DOI: 10.1007/978-981-10-5717-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals. The relationship between individual elements and several diseases based on recent large-scale systematic studies such as genome-wide association studies and case-control studies is discussed. Lastly, developments of ionomics and its recent application in human health are also introduced.
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Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME JOURNAL 2018; 12:1021-1031. [PMID: 29445130 DOI: 10.1038/s41396-018-0060-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/12/2017] [Accepted: 01/10/2018] [Indexed: 12/21/2022]
Abstract
Thorarchaeota are a new archaeal phylum within the Asgard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudflat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, fix inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen fixation, nitrite reduction, and arsenic detoxification. Interestingly, these Thorarchaeotal genomes are inferred to contain the tetrahydromethanopterin and tetrahydrofolate Wood-Ljungdahl (WL) pathways for CO2 reduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisphosphate carboxylase-like proteins (normally without RuBisCO activity) and a near-complete Calvin-Benson-Bassham cycle. The existence of eukaryotic selenocysteine insertion sequences and many genes for proteins previously considered eukaryote-specific in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryotic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their roles in ecosystems.
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Pallotti S, Pediconi D, Subramanian D, Molina MG, Antonini M, Morelli MB, Renieri C, La Terza A. Evidence of post-transcriptional readthrough regulation in FGF5 gene of alpaca. Gene 2018; 647:121-128. [PMID: 29307854 DOI: 10.1016/j.gene.2018.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/23/2017] [Accepted: 01/02/2018] [Indexed: 02/08/2023]
Abstract
Two different phenotypes are described in alpaca, identified as suri and huacaya, which differ in the type of fleece. The huacaya fleece is characterized by compact, soft and highly crimped fibers, while the suri fleece is longer, straight, less-crimped and lustrous. In our study, the Fibroblast growth factor 5 (FGF5) was investigated as a possible candidate gene for hair length in alpaca (Vicugna pacos). As previously identified in other mammals, our results show that the alpaca FGF5 gene gives rise to a short (FGF5S) and a long (FGF5) isoform. Interestingly, in the long isoform, we observed a point mutation (i.e., a transition C>T at position 499 downstream of the ATG codon) that is able to generate a premature termination codon (PTC). The highly conserved nucleotide and amino acid sequence after PTC suggested a readthrough event (RT) that was confirmed by western blot analysis. The analysis of cDNA sequence revealed motifs and structures of mRNA undergoing RT. In fact, the event is positively influenced by particular signals harbored by the transcript. To the best of our knowledge, this is the first case of a readthrough event on PTC reported for the FGF5 gene and the first case of this translational mechanism in alpaca.
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Affiliation(s)
- Stefano Pallotti
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, (MC), Italy.
| | - Dario Pediconi
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, (MC), Italy.
| | | | - María Gabriela Molina
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Universidad Católica de Córdoba, Argentina
| | - Marco Antonini
- ENEA C.R. Casaccia Biotec-Agro, S.M. di Galeria, 00060 Roma, Italy
| | - Maria Beatrice Morelli
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, (MC), Italy
| | - Carlo Renieri
- School of Pharmacy, University of Camerino, Via Gentile III da Varano, 62032 Camerino, (MC), Italy
| | - Antonietta La Terza
- School of Bioscience and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, (MC), Italy.
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Mariotti M. SECISearch3 and Seblastian: In-Silico Tools to Predict SECIS Elements and Selenoproteins. Methods Mol Biol 2018; 1661:3-16. [PMID: 28917033 DOI: 10.1007/978-1-4939-7258-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The computational identification of selenoprotein genes is complicated by the dual meaning of the UGA codon as stop and selenocysteine. SECIS elements are RNA structures essential for selenocysteine incorporation, which have been used as markers for selenoprotein genes in many bioinformatics studies. The most widely used tool for eukaryotic SECIS finding has been recently improved to its third generation, SECISearch3. This program is also a component of Seblastian, a pipeline for the identification of selenoprotein genes that employs SECIS finding as the first step. This chapter constitutes a practical guide to use SECISearch3 and Seblastian, which can be run via webservers at http://seblastian.crg.eu / or http://gladyshevlab.org/SelenoproteinPredictionServer/ .
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Affiliation(s)
- Marco Mariotti
- Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA. .,Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Institut Hospital del Mar d'Investigacions Mediques (IMIM), Barcelona, Spain.
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Chen W, Colon R, Louda JW, Del Rey FR, Durham M, Rein KS. Brevetoxin (PbTx-2) influences the redox status and NPQ of Karenia brevis by way of thioredoxin reductase. HARMFUL ALGAE 2018; 71:29-39. [PMID: 29306394 PMCID: PMC5994908 DOI: 10.1016/j.hal.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 06/07/2023]
Abstract
The Florida red tide dinoflagellate, Karenia brevis, is the major harmful algal bloom dinoflagellate of the Gulf of Mexico and plays a destructive role in the region. Blooms of K. brevis can produce brevetoxins: ladder-shaped polyether (LSP) compounds, which can lead to adverse human health effects, such as reduced respiratory function through inhalation exposure, or neurotoxic shellfish poisoning through consumption of contaminated shellfish. The endogenous role of the brevetoxins remains uncertain. Recent work has shown that some forms of NADPH dependent thioredoxin reductase (NTR) are inhibited by brevetoxin-2 (PbTx-2). The study presented herein reveals that high toxin and low toxin K. brevis, which have a ten-fold difference in toxin content, also show a significant difference in their ability, not only to produce brevetoxin, but also in their cellular redox status and distribution of xanthophyll cycle pigments. These differences are likely due to the inhibition of NTR by brevetoxin. The work could shed light on the physiological role that brevetoxin fills for K. brevis.
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Affiliation(s)
- Wei Chen
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8thStreet, Miami, FL 33199, United States.
| | - Ricardo Colon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8thStreet, Miami, FL 33199, United States.
| | - J William Louda
- Department of Chemistry and Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 United States.
| | - Freddy Rodriguez Del Rey
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8thStreet, Miami, FL 33199, United States.
| | - Michaella Durham
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8thStreet, Miami, FL 33199, United States.
| | - Kathleen S Rein
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8thStreet, Miami, FL 33199, United States.
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45
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Xie X, Chen M, Zhu A. Identification and characterization of two selenium-dependent glutathione peroxidase 1 isoforms from Larimichthys crocea. FISH & SHELLFISH IMMUNOLOGY 2017; 71:411-422. [PMID: 28964863 DOI: 10.1016/j.fsi.2017.09.067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/18/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Glutathione peroxidases, a vital family of antioxidant enzymes in oxybiotic organisms, are involved in anti-pathogen immune response. In this study, two complete selenium-dependent glutathione peroxidase 1 cDNAs (designated as LcGPx1a and LcGPx1b) were obtained from the large yellow croaker Larimichthys crocea by rapid amplification of cDNA ends. The full-length sequence of LcGPx1a was 917 bp with a 5'-untranslated region (UTR) of 52 bp, a 3'-UTR of 289 bp, and an open reading frame of 576 bp encoding 191 amino acid (aa) polypeptides. The cDNA of LcGPx1b was composed of 884 bp with a 5'-UTR of 59 bp, a 3'-UTR of 258 bp, and an open reading frame of 567 bp encoding 188 aa polypeptides. The conserved selenocysteine insertion sequence was detected in the 3'-UTR of both isoforms, which can classify types I and II. Protein sequence analysis revealed that both isoforms included a selenocysteine encoded by an opal codon (TGA) and formed the functioning tetrad site with glutamine, tryptophan, and asparagine. Three conservative motifs, including one active site motif ("GKVVLIENVASLUGTT") and two signature site motifs ("LVILGVPCNQFGHQENC" and "V(A/S)WNFEKFLI"), were conserved both in sequence and location. Multiple alignments revealed that they exhibited a high level of identities with GPx1 from other organisms, especially in the abovementioned conserved amino acid sequence motifs. Tissue expression analysis indicated that LcGPx1a and LcGPx1b had a wide distribution in nine tissues with various abundances. The transcript level of LcGPx1a was not significantly different among the nine tissues, whereas that of LcGPx1b was higher in the kidney and head kidney than in the other tissues. After Vibrio parahaemolyticus stimulation, the expression levels of LcGPx1a and LcGPx1b were unanimously altered in the liver, spleen, kidney, and head kidney but with different magnitudes and response time. LcGPx1a and LcGPx1b showed distinct expression trends in the liver, where LcGPx1b was induced and LcGPx1a was depressed in response to pathogen infection. These results indicate that LcGPx1a and LcGPx1b display functional diversities and play crucial roles in mediating the immune response of fish.
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Affiliation(s)
- Xiaoze Xie
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Mengnan Chen
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China
| | - Aiyi Zhu
- National Engineering Research Center of Marine Facilities Aquaculture, Zhejiang Ocean University, Zhoushan 316022, PR China.
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Wu S, Mariotti M, Santesmasses D, Hill KE, Baclaocos J, Aparicio-Prat E, Li S, Mackrill J, Wu Y, Howard MT, Capecchi M, Guigó R, Burk RF, Atkins JF. Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements. Open Biol 2017; 6:rsob.160241. [PMID: 27881738 PMCID: PMC5133445 DOI: 10.1098/rsob.160241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 01/04/2023] Open
Abstract
Dynamic redefinition of the 10 UGAs in human and mouse selenoprotein P (Sepp1) mRNAs to specify selenocysteine instead of termination involves two 3' UTR structural elements (SECIS) and is regulated by selenium availability. In addition to the previously known human Sepp1 mRNA poly(A) addition site just 3' of SECIS 2, two further sites were identified with one resulting in 10-25% of the mRNA lacking SECIS 2. To address function, mutant mice were generated with either SECIS 1 or SECIS 2 deleted or with the first UGA substituted with a serine codon. They were fed on either high or selenium-deficient diets. The mutants had very different effects on the proportions of shorter and longer product Sepp1 protein isoforms isolated from plasma, and on viability. Spatially and functionally distinctive effects of the two SECIS elements on UGA decoding were inferred. We also bioinformatically identify two selenoprotein S mRNAs with different 5' sequences predicted to yield products with different N-termini. These results provide insights into SECIS function and mRNA processing in selenoprotein isoform diversity.
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Affiliation(s)
- Sen Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, People's Republic of China
| | - Marco Mariotti
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Didac Santesmasses
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Kristina E Hill
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Janinah Baclaocos
- Department of Biochemistry, University College Cork, Cork, Republic of Ireland
| | - Estel Aparicio-Prat
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Shuping Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, People's Republic of China
| | - John Mackrill
- Department of Physiology, University College Cork, Cork, Republic of Ireland
| | - Yuanyuan Wu
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Michael T Howard
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Mario Capecchi
- Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
| | - Roderic Guigó
- Center for Genomic Regulation, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Raymond F Burk
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - John F Atkins
- Department of Biochemistry, University College Cork, Cork, Republic of Ireland .,Department of Human Genetics, University of Utah, Salt Lake City, UT 8412-5330, USA
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Santesmasses D, Mariotti M, Guigó R. Computational identification of the selenocysteine tRNA (tRNASec) in genomes. PLoS Comput Biol 2017; 13:e1005383. [PMID: 28192430 PMCID: PMC5330540 DOI: 10.1371/journal.pcbi.1005383] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 02/28/2017] [Accepted: 01/26/2017] [Indexed: 12/11/2022] Open
Abstract
Selenocysteine (Sec) is known as the 21st amino acid, a cysteine analogue with selenium replacing sulphur. Sec is inserted co-translationally in a small fraction of proteins called selenoproteins. In selenoprotein genes, the Sec specific tRNA (tRNASec) drives the recoding of highly specific UGA codons from stop signals to Sec. Although found in organisms from the three domains of life, Sec is not universal. Many species are completely devoid of selenoprotein genes and lack the ability to synthesize Sec. Since tRNASec is a key component in selenoprotein biosynthesis, its efficient identification in genomes is instrumental to characterize the utilization of Sec across lineages. Available tRNA prediction methods fail to accurately predict tRNASec, due to its unusual structural fold. Here, we present Secmarker, a method based on manually curated covariance models capturing the specific tRNASec structure in archaea, bacteria and eukaryotes. We exploited the non-universality of Sec to build a proper benchmark set for tRNASec predictions, which is not possible for the predictions of other tRNAs. We show that Secmarker greatly improves the accuracy of previously existing methods constituting a valuable tool to identify tRNASec genes, and to efficiently determine whether a genome contains selenoproteins. We used Secmarker to analyze a large set of fully sequenced genomes, and the results revealed new insights in the biology of tRNASec, led to the discovery of a novel bacterial selenoprotein family, and shed additional light on the phylogenetic distribution of selenoprotein containing genomes. Secmarker is freely accessible for download, or online analysis through a web server at http://secmarker.crg.cat. Most proteins are made of twenty amino acids. However, there is a small group of proteins that incorporate a 21st amino acid, Selenocysteine (Sec). These proteins are called selenoproteins and are present in some, but not all, species from the three domains of life. Sec is inserted in selenoproteins in response to the UGA codon, normally a stop codon. A Sec specific tRNA (tRNASec), which only exists in the organisms that synthesize selenoproteins recognizes the UGA codon. tRNASec is not only indispensable for Sec incorporation into selenoproteins, but also for Sec synthesis, since Sec is synthesized on its own tRNA. The structure of tRNASec differs from that of canonical tRNAs, and general tRNA detection methods fail to accurately predict it. We developed Secmarker, a tRNASec specific identification tool based on the characteristic structural features of the tRNASec. Our benchmark shows that Secmarker produces nearly flawless tRNASec predictions. We used Secmarker to scan all currently available genome sequences. The analysis of the highly accurate predictions obtained revealed new insights into the biology of tRNASec.
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Affiliation(s)
- Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
- * E-mail: (DS); (MM)
| | - Marco Mariotti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (DS); (MM)
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigacions Mèdiques (IMIM), Barcelona, Spain
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48
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Zhu SY, Li XN, Sun XC, Lin J, Li W, Zhang C, Li JL. Biochemical characterization of the selenoproteome in Gallus gallus via bioinformatics analysis: structure–function relationships and interactions of binding molecules. Metallomics 2017; 9:124-131. [DOI: 10.1039/c6mt00254d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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49
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Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M. Evolutionary Dynamics of Abundant Stop Codon Readthrough. Mol Biol Evol 2016; 33:3108-3132. [PMID: 27604222 PMCID: PMC5100048 DOI: 10.1093/molbev/msw189] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translational stop codon readthrough emerged as a major regulatory mechanism affecting hundreds of genes in animal genomes, based on recent comparative genomics and ribosomal profiling evidence, but its evolutionary properties remain unknown. Here, we leverage comparative genomic evidence across 21 Anopheles mosquitoes to systematically annotate readthrough genes in the malaria vector Anopheles gambiae, and to provide the first study of abundant readthrough evolution, by comparison with 20 Drosophila species. Using improved comparative genomics methods for detecting readthrough, we identify evolutionary signatures of conserved, functional readthrough of 353 stop codons in the malaria vector, Anopheles gambiae, and of 51 additional Drosophila melanogaster stop codons, including several cases of double and triple readthrough and of readthrough of two adjacent stop codons. We find that most differences between the readthrough repertoires of the two species arose from readthrough gain or loss in existing genes, rather than birth of new genes or gene death; that readthrough-associated RNA structures are sometimes gained or lost while readthrough persists; that readthrough is more likely to be lost at TAA and TAG stop codons; and that readthrough is under continued purifying evolutionary selection in mosquito, based on population genetic evidence. We also determine readthrough-associated gene properties that predate readthrough, and identify differences in the characteristic properties of readthrough genes between clades. We estimate more than 600 functional readthrough stop codons in mosquito and 900 in fruit fly, provide evidence of readthrough control of peroxisomal targeting, and refine the phylogenetic extent of abundant readthrough as following divergence from centipede.
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Affiliation(s)
- Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Clara S Chan
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
| | - Robert M Waterhouse
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, Geneva, Switzerland.,Swiss Institute of Bioinformatics, rue Michel-Servet 1, Geneva, Switzerland
| | | | | | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA .,Broad Institute of MIT and Harvard, Cambridge, MA
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50
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Mariotti M, Lobanov AV, Manta B, Santesmasses D, Bofill A, Guigó R, Gabaldón T, Gladyshev VN. Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems. Mol Biol Evol 2016; 33:2441-53. [PMID: 27413050 PMCID: PMC4989117 DOI: 10.1093/molbev/msw122] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess similar sets of selenoproteins, Sec biosynthesis is more similar among archaea and eukaryotes. However, SECIS elements are completely different in the three domains of life. Here, we analyze the archaeon Lokiarchaeota that resolves the relationships among Sec insertion systems. This organism has selenoproteins representing five protein families, three of which have multiple Sec residues. Remarkably, these archaeal selenoprotein genes possess conserved RNA structures that strongly resemble the eukaryotic SECIS element, including key eukaryotic protein-binding sites. These structures also share similarity with the SECIS element in archaeal selenoprotein VhuD, suggesting a relation of direct descent. These results identify Lokiarchaeota as an intermediate form between the archaeal and eukaryotic Sec-encoding systems and clarify the evolution of the Sec insertion system.
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Affiliation(s)
- Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Bruno Manta
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Didac Santesmasses
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Andreu Bofill
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain Universitat Pompeu Fabra (UPF); and Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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