101
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Na J, Jung J, Bang J, Lu Q, Carlson BA, Guo X, Gladyshev VN, Kim J, Hatfield DL, Lee BJ. Selenophosphate synthetase 1 and its role in redox homeostasis, defense and proliferation. Free Radic Biol Med 2018; 127:190-197. [PMID: 29715549 DOI: 10.1016/j.freeradbiomed.2018.04.577] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
Selenophosphate synthetase (SEPHS) synthesizes selenophosphate, the active selenium donor, using ATP and selenide as substrates. SEPHS was initially identified and isolated from bacteria and has been characterized in many eukaryotes and archaea. Two SEPHS paralogues, SEPHS1 and SEPHS2, occur in various eukaryotes, while prokaryotes and archaea have only one form of SEPHS. Between the two isoforms in eukaryotes, only SEPHS2 shows catalytic activity during selenophosphate synthesis. Although SEPHS1 does not contain any significant selenophosphate synthesis activity, it has been reported to play an essential role in regulating cellular physiology. Prokaryotic SEPHS contains a cysteine or selenocysteine (Sec) at the catalytic domain. However, in eukaryotes, SEPHS1 contains other amino acids such as Thr, Arg, Gly, or Leu at the catalytic domain, and SEPHS2 contains only a Sec. Sequence comparisons, crystal structure analyses, and ATP hydrolysis assays suggest that selenophosphate synthesis occurs in two steps. In the first step, ATP is hydrolyzed to produce ADP and gamma-phosphate. In the second step, ADP is further hydrolyzed and selenophosphate is produced using gamma-phosphate and selenide. Both SEPHS1 and SEPHS2 have ATP hydrolyzing activities, but Cys or Sec is required in the catalytic domain for the second step of reaction. The gene encoding SEPHS1 is divided by introns, and five different splice variants are produced by alternative splicing in humans. SEPHS1 mRNA is abundant in rapidly proliferating cells such as embryonic and cancer cells and its expression is induced by various stresses including oxidative stress and salinity stress. The disruption of the SEPHS1 gene in mice or Drosophila leads to the inhibition of cell proliferation, embryonic lethality, and morphological changes in the embryos. Targeted removal of SEPHS1 mRNA in insect, mouse, and human cells also leads to common phenotypic changes similar to those observed by in vivo gene knockout: the inhibition of cell growth/proliferation, the accumulation of hydrogen peroxide in mammals and an unidentified reactive oxygen species (ROS) in Drosophila, and the activation of a defense system. Hydrogen peroxide accumulation in SEPHS1-deficient cells is mainly caused by the down-regulation of genes involved in ROS scavenging, and leads to the inhibition of cell proliferation and survival. However, the mechanisms underlying SEPHS1 regulation of redox homeostasis are still not understood.
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Affiliation(s)
- Jiwoon Na
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jisu Jung
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeyoung Bang
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Qiao Lu
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bradley A Carlson
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiong Guo
- School of Public Health, Xi'an Jiaotong University, Xi'an 710061, PR China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Jinhong Kim
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Dolph L Hatfield
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Byeong Jae Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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102
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Abstract
Selenocysteine-containing proteins (selenoproteins) have been implicated in the regulation of various cell signaling pathways, many of which are linked to colorectal malignancies. In this in-depth excurse into the selenoprotein literature, we review possible roles for human selenoproteins in colorectal cancer, focusing on the typical hallmarks of cancer cells and their tumor-enabling characteristics. Human genome studies of single nucleotide polymorphisms in various genes coding for selenoproteins have revealed potential involvement of glutathione peroxidases, thioredoxin reductases, and other proteins. Cell culture studies with targeted down-regulation of selenoproteins and studies utilizing knockout/transgenic animal models have helped elucidate the potential roles of individual selenoproteins in this malignancy. Those selenoproteins, for which strong links to development or progression of colorectal cancer have been described, may be potential future targets for clinical interventions.
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Affiliation(s)
- Kristin M Peters
- Dept. of Biological Sciences, Towson University, 8000 York Rd, Towson, MD 21252, United States.
| | - Bradley A Carlson
- National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, United States.
| | - Vadim N Gladyshev
- Dept. of Medicine, Brigham & Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, United States.
| | - Petra A Tsuji
- Dept. of Biological Sciences, Towson University, 8000 York Rd, Towson, MD 21252, United States.
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103
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Zhou X, Sun D, Guang X, Ma S, Fang X, Mariotti M, Nielsen R, Gladyshev VN, Yang G. Molecular Footprints of Aquatic Adaptation Including Bone Mass Changes in Cetaceans. Genome Biol Evol 2018; 10:967-975. [PMID: 29608729 PMCID: PMC5952927 DOI: 10.1093/gbe/evy062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 01/04/2023] Open
Abstract
Cetaceans (whales, dolphins, and porpoises) are a group of specialized mammals that evolved from terrestrial ancestors and are fully adapted to aquatic habitats. Taking advantage of the recently sequenced finless porpoise genome, we conducted comparative analyses of the genomes of seven cetaceans and related terrestrial species to provide insight into the molecular bases of adaptation of these aquatic mammals. Changes in gene sequences were identified in main lineages of cetaceans, offering an evolutionary picture of cetacean genomes that reveal new pathways that could be associated with adaptation to aquatic lifestyle. We profiled bone microanatomical structures across 28 mammals, including representatives of cetaceans, pinnipeds, and sirenians. Subsequent phylogenetic comparative analyses revealed genes (including leptin, insulin-like growth factor 1, and collagen type I alpha 2 chain) with the root-to-tip substitution rate significantly correlated with bone compactness, implicating these genes could be involved in bone mass control. Overall, this study described adjustments of the genomes of cetaceans according to lifestyle, phylogeny, and bone mass.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
| | - Xuanmin Guang
- BGI-Shenzhen, Shenzhen, China.,The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Siming Ma
- Genome Institute of Singapore, Singapore
| | | | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, China
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104
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Golubev A, Hanson AD, Gladyshev VN. A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging. Antioxid Redox Signal 2018; 29:1003-1017. [PMID: 28874059 PMCID: PMC6104246 DOI: 10.1089/ars.2017.7105] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 08/09/2017] [Accepted: 08/31/2017] [Indexed: 12/18/2022]
Abstract
SIGNIFICANCE The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone. CRITICAL ISSUES Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch. FUTURE DIRECTIONS The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.
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Affiliation(s)
- Alexey Golubev
- Department of Carcinogenesis and Oncogerontology, Petrov Research Institute of Oncology, Saint Petersburg, Russia
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, Massachusetts
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow Russia
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105
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Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN. Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity. Aging Cell 2018; 17:e12740. [PMID: 29671950 PMCID: PMC6052463 DOI: 10.1111/acel.12740] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Abstract
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan-extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan-extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.
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Affiliation(s)
- Siming Ma
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Genome Institute of SingaporeA*STARSingapore CitySingapore
| | - Andrei S. Avanesov
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Emily Porter
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Byung Cheon Lee
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- College of Life Sciences and BiotechnologyKorea UniversitySeoulSouth Korea
| | - Marco Mariotti
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Nadezhda Zemskaya
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
| | - Roderic Guigo
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Alexey A. Moskalev
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
- Moscow Institute of Physics and TechnologyDolgoprudny, Moscow RegionRussia
- Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Belozersky Institute of Physico‐Chemical BiologyMoscow State UniversityMoscowRussia
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106
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Tang Q, Gu Y, Zhou X, Jin L, Guan J, Liu R, Li J, Long K, Tian S, Che T, Hu S, Liang Y, Yang X, Tao X, Zhong Z, Wang G, Chen X, Li D, Ma J, Wang X, Mai M, Jiang A, Luo X, Lv X, Gladyshev VN, Li X, Li M. Comparative transcriptomics of 5 high-altitude vertebrates and their low-altitude relatives. Gigascience 2018; 6:1-9. [PMID: 29149296 PMCID: PMC5729692 DOI: 10.1093/gigascience/gix105] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 10/24/2017] [Indexed: 01/22/2023] Open
Abstract
Background Species living at high altitude are subject to strong selective pressures due to inhospitable environments (e.g., hypoxia, low temperature, high solar radiation, and lack of biological production), making these species valuable models for comparative analyses of local adaptation. Studies that have examined high-altitude adaptation have identified a vast array of rapidly evolving genes that characterize the dramatic phenotypic changes in high-altitude animals. However, how high-altitude environment shapes gene expression programs remains largely unknown. Findings We generated a total of 910 Gb of high-quality RNA-seq data for 180 samples derived from 6 tissues of 5 agriculturally important high-altitude vertebrates (Tibetan chicken, Tibetan pig, Tibetan sheep, Tibetan goat, and yak) and their cross-fertile relatives living in geographically neighboring low-altitude regions. Of these, ∼75% reads could be aligned to their respective reference genomes, and on average ∼60% of annotated protein coding genes in each organism showed FPKM expression values greater than 0.5. We observed a general concordance in topological relationships between the nucleotide alignments and gene expression-based trees. Tissue and species accounted for markedly more variance than altitude based on either the expression or the alternative splicing patterns. Cross-species clustering analyses showed a tissue-dominated pattern of gene expression and a species-dominated pattern for alternative splicing. We also identified numerous differentially expressed genes that could potentially be involved in phenotypic divergence shaped by high-altitude adaptation. Conclusions These data serve as a valuable resource for examining the convergence and divergence of gene expression changes between species as they adapt or acclimatize to high-altitude environments.
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Affiliation(s)
- Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiuqiang Guan
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Rui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kereng Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Department of Animal Science, Texas A & M University, College Station, Texas, 77843 USA
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Mai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - An'an Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolin Luo
- Yak Research Institute, Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Pig Science Institute, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115 USA
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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107
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Zhang Y, Lee JH, Paull TT, Gehrke S, D'Alessandro A, Dou Q, Gladyshev VN, Schroeder EA, Steyl SK, Christian BE, Shadel GS. Mitochondrial redox sensing by the kinase ATM maintains cellular antioxidant capacity. Sci Signal 2018; 11:eaaq0702. [PMID: 29991649 PMCID: PMC6042875 DOI: 10.1126/scisignal.aaq0702] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mitochondria are integral to cellular energy metabolism and ATP production and are involved in regulating many cellular processes. Mitochondria produce reactive oxygen species (ROS), which not only can damage cellular components but also participate in signal transduction. The kinase ATM, which is mutated in the neurodegenerative, autosomal recessive disease ataxia-telangiectasia (A-T), is a key player in the nuclear DNA damage response. However, ATM also performs a redox-sensing function mediated through formation of ROS-dependent disulfide-linked dimers. We found that mitochondria-derived hydrogen peroxide promoted ATM dimerization. In HeLa cells, ATM dimers were localized to the nucleus and inhibited by the redox regulatory protein thioredoxin 1 (TRX1), suggesting the existence of a ROS-mediated, stress-signaling relay from mitochondria to the nucleus. ATM dimer formation did not affect its association with chromatin in the absence or presence of nuclear DNA damage, consistent with the separation of its redox and DNA damage signaling functions. Comparative analysis of U2OS cells expressing either wild-type ATM or the redox sensing-deficient C2991L mutant revealed that one function of ATM redox sensing is to promote glucose flux through the pentose phosphate pathway (PPP) by increasing the abundance and activity of glucose-6-phosphate dehydrogenase (G6PD), thereby increasing cellular antioxidant capacity. The PPP produces the coenzyme NADPH needed for a robust antioxidant response, including the regeneration of TRX1, indicating the existence of a regulatory feedback loop involving ATM and TRX1. We propose that loss of the mitochondrial ROS-sensing function of ATM may cause cellular ROS accumulation and oxidative stress in A-T.
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Affiliation(s)
- Yichong Zhang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ji-Hoon Lee
- Howard Hughes Medical Institute, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Howard Hughes Medical Institute, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Sarah Gehrke
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045, USA
| | - Qianhui Dou
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02155, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02155, USA
| | | | - Samantha K Steyl
- Department of Chemistry, Appalachian State University, Boone, NC 28608, USA
| | - Brooke E Christian
- Department of Chemistry, Appalachian State University, Boone, NC 28608, USA.
| | - Gerald S Shadel
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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108
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Abstract
Cancer researchers have traditionally used the mouse and the rat as staple model organisms. These animals are very short-lived, reproduce rapidly and are highly prone to cancer. They have been very useful for modelling some human cancer types and testing experimental treatments; however, these cancer-prone species offer little for understanding the mechanisms of cancer resistance. Recent technological advances have expanded bestiary research to non-standard model organisms that possess unique traits of very high value to humans, such as cancer resistance and longevity. In recent years, several discoveries have been made in non-standard mammalian species, providing new insights on the natural mechanisms of cancer resistance. These include mechanisms of cancer resistance in the naked mole rat, blind mole rat and elephant. In each of these species, evolution took a different path, leading to novel mechanisms. Many other long-lived mammalian species display cancer resistance, including whales, grey squirrels, microbats, cows and horses. Understanding the molecular mechanisms of cancer resistance in all these species is important and timely, as, ultimately, these mechanisms could be harnessed for the development of human cancer therapies.
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Affiliation(s)
- Andrei Seluanov
- University of Rochester, Department of Biology, Rochester, NY, USA
| | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vera Gorbunova
- University of Rochester, Department of Biology, Rochester, NY, USA.
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109
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Lee SG, Mikhalchenko AE, Yim SH, Gladyshev VN. A naked mole rat iPSC line expressing drug-inducible mouse pluripotency factors developed from embryonic fibroblasts. Stem Cell Res 2018; 31:197-200. [PMID: 30107334 DOI: 10.1016/j.scr.2018.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/17/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022] Open
Abstract
Naked mole rats (NMRs, Heterocephalus glaber) are long-lived, cancer-resistant rodents. Here, we report the development of an induced pluripotent stem cell (iPSC) line generated from immortalized NMR embryonic fibroblasts transduced with a doxycycline-inducible mouse OSKM polycistronic vector. This iPSC line was shown to express pluripotency-associated markers, form embryoid bodies, differentiate in vitro to the derivatives of three germ layers, and exhibit normal karyotype. The ability of iPSCs to differentiate in vivo was supported by the contribution to interspecific chimera upon injection into mouse blastocysts. This NMR iPSC line may be a useful tool in cancer and aging research.
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Affiliation(s)
- Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksei E Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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110
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Samokhin AO, Stephens T, Wertheim BM, Wang RS, Vargas SO, Yung LM, Cao M, Brown M, Arons E, Dieffenbach PB, Fewell JG, Matar M, Bowman FP, Haley KJ, Alba GA, Marino SM, Kumar R, Rosas IO, Waxman AB, Oldham WM, Khanna D, Graham BB, Seo S, Gladyshev VN, Yu PB, Fredenburgh LE, Loscalzo J, Leopold JA, Maron BA. NEDD9 targets COL3A1 to promote endothelial fibrosis and pulmonary arterial hypertension. Sci Transl Med 2018; 10:eaap7294. [PMID: 29899023 PMCID: PMC6223025 DOI: 10.1126/scitranslmed.aap7294] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 05/23/2018] [Indexed: 12/12/2022]
Abstract
Germline mutations involving small mothers against decapentaplegic-transforming growth factor-β (SMAD-TGF-β) signaling are an important but rare cause of pulmonary arterial hypertension (PAH), which is a disease characterized, in part, by vascular fibrosis and hyperaldosteronism (ALDO). We developed and analyzed a fibrosis protein-protein network (fibrosome) in silico, which predicted that the SMAD3 target neural precursor cell expressed developmentally down-regulated 9 (NEDD9) is a critical ALDO-regulated node underpinning pathogenic vascular fibrosis. Bioinformatics and microscale thermophoresis demonstrated that oxidation of Cys18 in the SMAD3 docking region of NEDD9 impairs SMAD3-NEDD9 protein-protein interactions in vitro. This effect was reproduced by ALDO-induced oxidant stress in cultured human pulmonary artery endothelial cells (HPAECs), resulting in impaired NEDD9 proteolytic degradation, increased NEDD9 complex formation with Nk2 homeobox 5 (NKX2-5), and increased NKX2-5 binding to COL3A1 Up-regulation of NEDD9-dependent collagen III expression corresponded to changes in cell stiffness measured by atomic force microscopy. HPAEC-derived exosomal signaling targeted NEDD9 to increase collagen I/III expression in human pulmonary artery smooth muscle cells, identifying a second endothelial mechanism regulating vascular fibrosis. ALDO-NEDD9 signaling was not affected by treatment with a TGF-β ligand trap and, thus, was not contingent on TGF-β signaling. Colocalization of NEDD9 with collagen III in HPAECs was observed in fibrotic pulmonary arterioles from PAH patients. Furthermore, NEDD9 ablation or inhibition prevented fibrotic vascular remodeling and pulmonary hypertension in animal models of PAH in vivo. These data identify a critical TGF-β-independent posttranslational modification that impairs SMAD3-NEDD9 binding in HPAECs to modulate vascular fibrosis and promote PAH.
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Affiliation(s)
- Andriy O Samokhin
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Thomas Stephens
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bradley M Wertheim
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Rui-Sheng Wang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sara O Vargas
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lai-Ming Yung
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Minwei Cao
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marcel Brown
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elena Arons
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Paul B Dieffenbach
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Majed Matar
- Celsion Corporation, Lawrenceville, NJ 08648, USA
| | - Frederick P Bowman
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kathleen J Haley
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - George A Alba
- Department of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stefano M Marino
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Biotechnology, Akdeniz University, Konyaaltı, Antalya 07058, Turkey
| | - Rahul Kumar
- Program in Translational Lung Research, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ivan O Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Aaron B Waxman
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - William M Oldham
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dinesh Khanna
- Division of Rheumatology, University of Michigan Scleroderma Program, Ann Arbor, MI 48109, USA
| | - Brian B Graham
- Program in Translational Lung Research, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sachiko Seo
- Department of Hematology and Oncology, National Cancer Research Center East, Kashiwa-shi, Chiba-ken 277-8577, Japan
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Paul B Yu
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Laura E Fredenburgh
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jane A Leopold
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
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111
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Sziráki A, Tyshkovskiy A, Gladyshev VN. Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction. Aging Cell 2018; 17:e12738. [PMID: 29575528 PMCID: PMC5946071 DOI: 10.1111/acel.12738] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2018] [Indexed: 01/08/2023] Open
Abstract
Aging is characterized by numerous molecular changes, such as accumulation of molecular damage and altered gene expression, many of which are linked to DNA methylation. Here, we characterize the blood DNA methylome across 16 age groups of mice and report numerous global, region‐ and site‐specific features, as well as the associated dynamics of methylation changes. Transition of the methylome throughout lifespan was not uniform, with many sites showing accelerated changes in late life. The associated genes and promoters were enriched for aging‐related pathways, pointing to a fundamental link between DNA methylation and control of the aging process. Calorie restriction both shifted the overall methylation pattern and was accompanied by its gradual age‐related remodeling, the latter contributing to the lifespan‐extending effect. With age, both highly and poorly methylated sites trended toward intermediate levels, and aging was accompanied by an accelerated increase in entropy, consistent with damage accumulation. However, the entropy effects differed for the sites that increased, decreased and did not change methylation with age. Many sites trailed behind, whereas some followed or even exceeded the entropy trajectory and altered the developmental DNA methylation pattern. The patterns we observed in certain genomic regions were conserved between humans and mice, suggesting common principles of functional DNA methylome remodeling and its critical role in aging. The highly resolved DNA methylome remodeling provides an excellent model for understanding systemic changes that characterize the aging process.
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Affiliation(s)
- András Sziráki
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston MA USA
| | - Alexander Tyshkovskiy
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston MA USA
- Center for Data-Intensive Biomedicine and Biotechnology; Skolkovo Institute of Science and Technology; Moscow Russia
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston MA USA
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112
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Zhou X, Guang X, Sun D, Xu S, Li M, Seim I, Jie W, Yang L, Zhu Q, Xu J, Gao Q, Kaya A, Dou Q, Chen B, Ren W, Li S, Zhou K, Gladyshev VN, Nielsen R, Fang X, Yang G. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater. Nat Commun 2018; 9:1276. [PMID: 29636446 PMCID: PMC5893588 DOI: 10.1038/s41467-018-03722-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/07/2018] [Indexed: 12/20/2022] Open
Abstract
Cetaceans (whales, dolphins, and porpoises) are a group of mammals adapted to various aquatic habitats, from oceans to freshwater rivers. We report the sequencing, de novo assembly and analysis of a finless porpoise genome, and the re-sequencing of an additional 48 finless porpoise individuals. We use these data to reconstruct the demographic history of finless porpoises from their origin to the occupation into the Yangtze River. Analyses of selection between marine and freshwater porpoises identify genes associated with renal water homeostasis and urea cycle, such as urea transporter 2 and angiotensin I-converting enzyme 2, which are likely adaptations associated with the difference in osmotic stress between ocean and rivers. Our results strongly suggest that the critically endangered Yangtze finless porpoises are reproductively isolated from other porpoise populations and harbor unique genetic adaptations, supporting that they should be considered a unique incipient species. Whales, dolphins and porpoises are adapted to various aquatic habitats. Here, Zhou et al. show that polymorphisms associated with renal function and the urea cycle have undergone selection in the freshwater Yangtze finless porpoise and provide genomic evidence of incipient speciation.
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Affiliation(s)
- Xuming Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Medical School, Boston, MA, 02115, USA
| | - Xuanmin Guang
- BGI-Shenzhen, 518083, Shenzhen, China.,The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Di Sun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, 611130, Chengdu, China
| | - Inge Seim
- Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD, 4102, Australia
| | | | | | | | - Jiabao Xu
- BGI-Shenzhen, 518083, Shenzhen, China
| | - Qiang Gao
- BGI-Shenzhen, 518083, Shenzhen, China
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Medical School, Boston, MA, 02115, USA
| | - Qianhui Dou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Medical School, Boston, MA, 02115, USA
| | - Bingyao Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shuaicheng Li
- Department of Computer Sciences, City University of Hong Kong, 999077, Hong Kong, China
| | - Kaiya Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard Medical School, Boston, MA, 02115, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
| | | | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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113
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Yordanova MM, Loughran G, Zhdanov AV, Mariotti M, Kiniry SJ, O'Connor PBF, Andreev DE, Tzani I, Saffert P, Michel AM, Gladyshev VN, Papkovsky DB, Atkins JF, Baranov PV. AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation. Nature 2018; 553:356-360. [PMID: 29310120 DOI: 10.1038/nature25174] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/28/2017] [Indexed: 11/09/2022]
Abstract
In addition to acting as template for protein synthesis, messenger RNA (mRNA) often contains sensory sequence elements that regulate this process. Here we report a new mechanism that limits the number of complete protein molecules that can be synthesized from a single mRNA molecule of the human AMD1 gene encoding adenosylmethionine decarboxylase 1 (AdoMetDC). A small proportion of ribosomes translating AMD1 mRNA stochastically read through the stop codon of the main coding region. These readthrough ribosomes then stall close to the next in-frame stop codon, eventually forming a ribosome queue, the length of which is proportional to the number of AdoMetDC molecules that were synthesized from the same AMD1 mRNA. Once the entire spacer region between the two stop codons is filled with queueing ribosomes, the queue impinges upon the main AMD1 coding region halting its translation. Phylogenetic analysis suggests that this mechanism is highly conserved in vertebrates and existed in their common ancestor. We propose that this mechanism is used to count and limit the number of protein molecules that can be synthesized from a single mRNA template. It could serve to safeguard from dysregulated translation that may occur owing to errors in transcription or mRNA damage.
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Affiliation(s)
- Martina M Yordanova
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Alexander V Zhdanov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Marco Mariotti
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Stephen J Kiniry
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Dmitry E Andreev
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ioanna Tzani
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Paul Saffert
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Audrey M Michel
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Dmitry B Papkovsky
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland.,Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
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114
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Abstract
The sulfur-containing amino acid methionine (Met) plays critical roles in protein synthesis, methylation, and sulfur metabolism. Both in its free form and in the form of an amino acid residue, it can be oxidized to the R and S diastereomers of methionine sulfoxide (MetO). Organisms evolved methionine sulfoxide reductases (MSRs) to reduce MetO to Met, with the MSRs type A (MSRA) and type B (MSRB) being specific for the S and R forms of MetO, respectively. In mammals, the selenoprotein MSRB1 plays an important protein repair function, and its expression is tightly regulated by dietary selenium. In this chapter, we describe a protocol for determining the concentration of protein-based Met-R-O and its analysis in HEK293 cells using a genetically encoded ratiometric fluorescent biosensor MetROx. We also describe the procedure for quantifying MSR activities in cell extracts using specific substrates and a reverse phase HPLC-based method.
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Affiliation(s)
- Lionel Tarrago
- Laboratoire de Bioénergétique Cellulaire, Institut de Biosciences et Biotechnologies Aix-Marseille (BIAM), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 13108, Saint-Paul-lès-Durance, France. .,UMR 7265, Centre National de Recherche Scientifique, Saint-Paul-lès-Durance, France. .,Aix Marseille Université, Marseille, France.
| | - Emmanuel Oheix
- Centrale Marseille, CNRS, iSm2 UMR 7313, Aix-Marseille Université, 13397, Marseille, France
| | - Zalán Péterfi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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115
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Salinas G, Gao W, Wang Y, Bonilla M, Yu L, Novikov A, Virginio VG, Ferreira HB, Vieites M, Gladyshev VN, Gambino D, Dai S. The Enzymatic and Structural Basis for Inhibition of Echinococcus granulosus Thioredoxin Glutathione Reductase by Gold(I). Antioxid Redox Signal 2017; 27:1491-1504. [PMID: 28463568 PMCID: PMC5678357 DOI: 10.1089/ars.2016.6816] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 04/11/2017] [Accepted: 04/12/2017] [Indexed: 01/04/2023]
Abstract
AIMS New drugs are needed to treat flatworm infections that cause severe human diseases such as schistosomiasis. The unique flatworm enzyme thioredoxin glutathione reductase (TGR), structurally different from the human enzyme, is a key drug target. Structural studies of the flatworm Echinococcus granulosus TGR, free and complexed with AuI-MPO, a novel gold inhibitor, together with inhibition assays were performed. RESULTS AuI-MPO is a potent TGR inhibitor that achieves 75% inhibition at a 1:1 TGR:Au ratio and efficiently kills E. granulosus in vitro. The structures revealed salient insights: (i) unique monomer-monomer interactions, (ii) distinct binding sites for thioredoxin and the glutaredoxin (Grx) domain, (iii) a single glutathione disulfide reduction site in the Grx domain, (iv) rotation of the Grx domain toward the Sec-containing redox active site, and (v) a single gold atom bound to Cys519 and Cys573 in the AuI-TGR complex. Structural modeling suggests that these residues are involved in the stabilization of the Sec-containing C-terminus. Consistently, Cys→Ser mutations in these residues decreased TGR activities. Mass spectroscopy confirmed these cysteines are the primary binding site. INNOVATION The identification of a primary site for gold binding and the structural model provide a basis for gold compound optimization through scaffold adjustments. CONCLUSIONS The structural study revealed that TGR functions are achieved not only through a mobile Sec-containing redox center but also by rotation of the Grx domain and distinct binding sites for Grx domain and thioredoxin. The conserved Cys519 and Cys573 residues targeted by gold assist catalysis through stabilization of the Sec-containing redox center. Antioxid. Redox Signal. 27, 1491-1504.
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Affiliation(s)
- Gustavo Salinas
- Worm Biology Lab, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
| | - Wei Gao
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado
- School of Science, Beijing Forestry University, Beijing, China
| | - Yang Wang
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Mariana Bonilla
- Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, Universidad de la República, Montevideo, Uruguay
- Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Uruguay
| | - Long Yu
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Andrey Novikov
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Veridiana G. Virginio
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Henrique B. Ferreira
- Laboratório de Genômica Estrutural e Funcional, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marisol Vieites
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Vadim N. Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dinorah Gambino
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Montevideo, Uruguay
| | - Shaodong Dai
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado Denver, School of Medicine, Aurora, Colorado
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116
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Patrick A, Seluanov M, Hwang C, Tam J, Khan T, Morgenstern A, Wiener L, Vazquez JM, Zafar H, Wen R, Muratkalyeva M, Doerig K, Zagorulya M, Cole L, Catalano S, Lobo Ladd AA, Coppi AA, Coşkun Y, Tian X, Ablaeva J, Nevo E, Gladyshev VN, Zhang ZD, Vijg J, Seluanov A, Gorbunova V. Sensitivity of primary fibroblasts in culture to atmospheric oxygen does not correlate with species lifespan. Aging (Albany NY) 2017; 8:841-7. [PMID: 27163160 PMCID: PMC4931838 DOI: 10.18632/aging.100958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/26/2016] [Indexed: 01/01/2023]
Abstract
Differences in the way human and mouse fibroblasts experience senescence in culture had long puzzled researchers. While senescence of human cells is mediated by telomere shortening, Parrinello et al. demonstrated that senescence of mouse cells is caused by extreme oxygen sensitivity. It was hypothesized that the striking difference in oxygen sensitivity between mouse and human cells explains their different rates of aging. To test if this hypothesis is broadly applicable, we cultured cells from 16 rodent species with diverse lifespans in 3% and 21% oxygen and compared their growth rates. Unexpectedly, fibroblasts derived from laboratory mouse strains were the only cells demonstrating extreme sensitivity to oxygen. Cells from hamster, muskrat, woodchuck, capybara, blind mole rat, paca, squirrel, beaver, naked mole rat and wild-caught mice were mildly sensitive to oxygen, while cells from rat, gerbil, deer mouse, chipmunk, guinea pig and chinchilla showed no difference in the growth rate between 3% and 21% oxygen. We conclude that, although the growth of primary fibroblasts is generally improved by maintaining cells in 3% oxygen, the extreme oxygen sensitivity is a peculiarity of laboratory mouse strains, possibly related to their very long telomeres, and fibroblast oxygen sensitivity does not directly correlate with species' lifespan.
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Affiliation(s)
- Alison Patrick
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Chaewon Hwang
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Jonathan Tam
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Tanya Khan
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Ari Morgenstern
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lauren Wiener
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Juan M Vazquez
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Hiba Zafar
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Robert Wen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | | - Katherine Doerig
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Maria Zagorulya
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Lauren Cole
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Sophia Catalano
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Aliny Ab Lobo Ladd
- Laboratory of Stochastic Stereology and Chemical Anatomy (LSSCA), Department of Surgery, College of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, Brazil
| | - A Augusto Coppi
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Yüksel Coşkun
- Science Faculty, Biology Department, Dicle University, 21280 Diyarbakır, Turkey
| | - Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa 31905, Israel
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
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117
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Lee SG, Mikhalchenko AE, Yim SH, Lobanov AV, Park JK, Choi KH, Bronson RT, Lee CK, Park TJ, Gladyshev VN. Naked Mole Rat Induced Pluripotent Stem Cells and Their Contribution to Interspecific Chimera. Stem Cell Reports 2017; 9:1706-1720. [PMID: 29107591 PMCID: PMC5829328 DOI: 10.1016/j.stemcr.2017.09.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 12/16/2022] Open
Abstract
Naked mole rats (NMRs) are exceptionally long-lived, cancer-resistant rodents. Identifying the defining characteristics of these traits may shed light on aging and cancer mechanisms. Here, we report the generation of induced pluripotent stem cells (iPSCs) from NMR fibroblasts and their contribution to mouse-NMR chimeric embryos. Efficient reprogramming could be observed under N2B27+2i conditions. The iPSCs displayed a characteristic morphology, expressed pluripotent markers, formed embryoid bodies, and showed typical differentiation patterns. Interestingly, NMR embryonic fibroblasts and the derived iPSCs had propensity for a tetraploid karyotype and were resistant to forming teratomas, but within mouse blastocysts they contributed to both interspecific placenta and fetus. Gene expression patterns of NMR iPSCs were more similar to those of human than mouse iPSCs. Overall, we uncovered unique features of NMR iPSCs and report a mouse-NMR chimeric model. The iPSCs and associated cell culture systems can be used for a variety of biological and biomedical applications.
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Affiliation(s)
- Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksei E Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jin-Kyu Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea
| | - Kwang-Hwan Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea
| | - Roderick T Bronson
- Rodent Histopathology Laboratory, Harvard Medical School, Boston MA 02115, USA
| | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 151-921, Korea; Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon-do 232-916, Korea
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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118
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Ma S, Gladyshev VN. Molecular signatures of longevity: Insights from cross-species comparative studies. Semin Cell Dev Biol 2017; 70:190-203. [PMID: 28800931 PMCID: PMC5807068 DOI: 10.1016/j.semcdb.2017.08.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/31/2017] [Accepted: 08/03/2017] [Indexed: 01/26/2023]
Abstract
Much of the current research on longevity focuses on the aging process within a single species. Several molecular players (e.g. IGF1 and MTOR), pharmacological compounds (e.g. rapamycin and metformin), and dietary approaches (e.g. calorie restriction and methionine restriction) have been shown to be important in regulating and modestly extending lifespan in model organisms. On the other hand, natural lifespan varies much more significantly across species. Within mammals alone, maximum lifespan differs more than 100 fold, but the underlying regulatory mechanisms remain poorly understood. Recent comparative studies are beginning to shed light on the molecular signatures associated with exceptional longevity. These include genome sequencing of microbats, naked mole rat, blind mole rat, bowhead whale and African turquoise killifish, and comparative analyses of gene expression, metabolites, lipids and ions across multiple mammalian species. Together, they point towards several putative strategies for lifespan regulation and cancer resistance, as well as the pathways and metabolites associated with longevity variation. In particular, longevity may be achieved by both lineage-specific adaptations and common mechanisms that apply across the species. Comparing the resulting cross-species molecular signatures with the within-species lifespan extension strategies will improve our understanding of mechanisms of longevity control and provide a starting point for novel and effective interventions.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Genome Institute of Singapore, A*STAR, Singapore, 138672, Singapore
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; Laboratory of Systems Biology of Aging, Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119234, Russia.
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119
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Ke Z, Mallik P, Johnson AB, Luna F, Nevo E, Zhang ZD, Gladyshev VN, Seluanov A, Gorbunova V. Translation fidelity coevolves with longevity. Aging Cell 2017; 16:988-993. [PMID: 28707419 PMCID: PMC5595694 DOI: 10.1111/acel.12628] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/26/2022] Open
Abstract
Whether errors in protein synthesis play a role in aging has been a subject of intense debate. It has been suggested that rare mistakes in protein synthesis in young organisms may result in errors in the protein synthesis machinery, eventually leading to an increasing cascade of errors as organisms age. Studies that followed generally failed to identify a dramatic increase in translation errors with aging. However, whether translation fidelity plays a role in aging remained an open question. To address this issue, we examined the relationship between translation fidelity and maximum lifespan across 17 rodent species with diverse lifespans. To measure translation fidelity, we utilized sensitive luciferase‐based reporter constructs with mutations in an amino acid residue critical to luciferase activity, wherein misincorporation of amino acids at this mutated codon re‐activated the luciferase. The frequency of amino acid misincorporation at the first and second codon positions showed strong negative correlation with maximum lifespan. This correlation remained significant after phylogenetic correction, indicating that translation fidelity coevolves with longevity. These results give new life to the role of protein synthesis errors in aging: Although the error rate may not significantly change with age, the basal rate of translation errors is important in defining lifespan across mammals.
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Affiliation(s)
- Zhonghe Ke
- Department of Biology; University of Rochester; Rochester NY USA
| | - Pramit Mallik
- Department of Biology; University of Rochester; Rochester NY USA
| | - Adam B. Johnson
- Department of Biology; University of Rochester; Rochester NY USA
| | - Facundo Luna
- Instituto de Investigaciones Marinas y Costeras; CONICET-UNMdP; Mar del Plata Argentina
| | - Eviatar Nevo
- Institute of Evolution; University of Haifa; Haifa 3498838 Israel
| | - Zhengdong D. Zhang
- Department of Genetics; Albert Einstein College of Medicine; Bronx NY USA
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine, Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Andrei Seluanov
- Department of Biology; University of Rochester; Rochester NY USA
| | - Vera Gorbunova
- Department of Biology; University of Rochester; Rochester NY USA
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120
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Abstract
Protein function can be regulated via post-translational modifications by numerous enzymatic and non-enzymatic mechanisms, including oxidation of cysteine and methionine residues. Redox-dependent regulatory mechanisms have been identified for nearly every cellular process, but the major paradigm has been that cellular components are oxidized (damaged) by reactive oxygen species (ROS) in a relatively unspecific way, and then reduced (repaired) by designated reductases. While this scheme may work with cysteine, it cannot be ascribed to other residues, such as methionine, whose reaction with ROS is too slow to be biologically relevant. However, methionine is clearly oxidized in vivo and enzymes for its stereoselective reduction are present in all three domains of life. Here, we revisit the chemistry and biology of methionine oxidation, with emphasis on its generation by enzymes from the monooxygenase family. Particular attention is placed on MICALs, a recently discovered family of proteins that harbor an unusual flavin-monooxygenase domain with an NADPH-dependent methionine sulfoxidase activity. Based on structural and kinetic information we provide a rational framework to explain MICAL mechanism, inhibition, and regulation. Methionine residues that are targeted by MICALs are reduced back by methionine sulfoxide reductases, suggesting that reversible methionine oxidation may be a general mechanism analogous to the regulation by phosphorylation by kinases/phosphatases. The identification of new enzymes that catalyze the oxidation of methionine will open a new area of research at the forefront of redox signaling.
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Affiliation(s)
- Bruno Manta
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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121
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Lee BC, Lee SG, Choo MK, Kim JH, Lee HM, Kim S, Fomenko DE, Kim HY, Park JM, Gladyshev VN. Selenoprotein MsrB1 promotes anti-inflammatory cytokine gene expression in macrophages and controls immune response in vivo. Sci Rep 2017; 7:5119. [PMID: 28698597 PMCID: PMC5506048 DOI: 10.1038/s41598-017-05230-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/25/2017] [Indexed: 12/14/2022] Open
Abstract
Post-translational redox modification of methionine residues often triggers a change in protein function. Emerging evidence points to this reversible protein modification being an important regulatory mechanism under various physiological conditions. Reduction of oxidized methionine residues is catalyzed by methionine sulfoxide reductases (Msrs). Here, we show that one of these enzymes, a selenium-containing MsrB1, is highly expressed in immune-activated macrophages and contributes to shaping cellular and organismal immune responses. In particular, lipopolysaccharide (LPS) induces expression of MsrB1, but not other Msrs. Genetic ablation of MsrB1 did not preclude LPS-induced intracellular signaling in macrophages, but resulted in attenuated induction of anti-inflammatory cytokines, such as interleukin (IL)-10 and the IL-1 receptor antagonist. This anomaly was associated with excessive pro-inflammatory cytokine production as well as an increase in acute tissue inflammation in mice. Together, our findings suggest that MsrB1 controls immune responses by promoting anti-inflammatory cytokine expression in macrophages. MsrB1-dependent reduction of oxidized methionine in proteins may be a heretofore unrecognized regulatory event underlying immunity and inflammatory disease, and a novel target for clinical applications.
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Affiliation(s)
- Byung Cheon Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea.
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Min-Kyung Choo
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Ji Hyung Kim
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Hae Min Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Sorah Kim
- College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Dmitri E Fomenko
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, NE, 68588, USA
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, 42415, South Korea
| | - Jin Mo Park
- Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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122
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Peters KM, Carlson BA, Canter JE, Tobe R, Seifried HE, Yu Y, Cao L, Gladyshev VN, Davis CD, Hatfield DL, Tsuji PA. Potential Role of the 15kDa Selenoprotein in Colorectal Inflammation. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.206.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Previously, systemic knockout (KO) of the ER-resident 15kDa selenoprotein (Sep15, SelenoF) protected mice against the formation of chemically-induced pre-neoplastic lesions and suggested modulation of inflammatory pathways. Our objective is to elucidate the potential role of SelenoF in the early steps of colon tumorigenesis by assaying gene expression of KO mice and littermate controls (WT) that were either treated with 2% dextran sulfate sodium (DSS) to induce colitis or given water (control). Based on previous results, we hypothesize that SelenoF expression is inversely correlated with a protective interferon (IFN)-γ pro-inflammatory response. Microarray analyses of colonic mucosa suggest that knockout of SelenoF expression itself caused more significant gene expression changes than DSS treatment (inflammation). Gene pathway analyses indicated galectin-6 was the highest up-regulated gene in DSS-treated (133-fold) and untreated (30-fold) KO compared to WT mice. The top significantly changed network included genes involved in the differentiation of T-lymphocytes. Colonic gene expression changes in SelenoF-KO mice, as validated with qPCR, included up-regulation of guanylate-binding protein 1 (p=0.004), and a down-regulation of T-box transcription factor 21 (p=0.08). Interestingly, a decrease in IFN-γ levels (p=0.026) was detected in the serum of KO compared to WT mice, whereas the opposite trend was shown in colonic mucosa. Thus, our preliminary analyses indicate that SelenoF may indeed influence the expression of inflammatory genes in the colon. Its contribution to the regulation of colitis will continue to be elucidated.
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Abstract
The chemical potentialities of metabolites far exceed metabolic requirements. The required potentialities are realized mostly through enzymatic catalysis. The rest are realized spontaneously through organic reactions that (i) occur wherever appropriate reactants come together, (ii) are so typical that many have proper names (e.g. Michael addition, Amadori rearrangement, and Pictet-Spengler reaction), and (iii) often have damaging consequences. There are many more causes of non-enzymatic damage to metabolites than reactive oxygen species and free radical processes (the "usual suspects"). Endogenous damage accumulation in non-renewable macromolecules and spontaneously polymerized material is sufficient to account for aging and differentiates aging from wear-and-tear of inanimate objects by deriving it from metabolism, the essential attribute of life.
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Affiliation(s)
- Alexey Golubev
- From the Department of Biochemistry, Saint-Petersburg State University, Saint Petersburg 199034, Russia,
| | - Andrew D Hanson
- the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, and
| | - Vadim N Gladyshev
- the Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
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124
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Petkovich DA, Podolskiy DI, Lobanov AV, Lee SG, Miller RA, Gladyshev VN. Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions. Cell Metab 2017; 25:954-960.e6. [PMID: 28380383 PMCID: PMC5578459 DOI: 10.1016/j.cmet.2017.03.016] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/09/2017] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Abstract
The DNA methylation levels of certain CpG sites are thought to reflect the pace of human aging. Here, we developed a robust predictor of mouse biological age based on 90 CpG sites derived from partial blood DNA methylation profiles. The resulting clock correctly determines the age of mouse cohorts, detects the longevity effects of calorie restriction and gene knockouts, and reports rejuvenation of fibroblast-derived iPSCs. The data show that mammalian DNA methylomes are characterized by CpG sites that may represent the organism's biological age. They are scattered across the genome, they are distinct in human and mouse, and their methylation gradually changes with age. The clock derived from these sites represents a biomarker of aging and can be used to determine the biological age of organisms and evaluate interventions that alter the rate of aging.
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Affiliation(s)
- Daniel A Petkovich
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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125
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Payne NC, Geissler A, Button A, Sasuclark AR, Schroll AL, Ruggles EL, Gladyshev VN, Hondal RJ. Comparison of the redox chemistry of sulfur- and selenium-containing analogs of uracil. Free Radic Biol Med 2017; 104:249-261. [PMID: 28108278 PMCID: PMC5328918 DOI: 10.1016/j.freeradbiomed.2017.01.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/13/2017] [Accepted: 01/16/2017] [Indexed: 11/16/2022]
Abstract
Selenium is present in proteins in the form of selenocysteine, where this amino acid serves catalytic oxidoreductase functions. The use of selenocysteine in nature is strongly associated with redox catalysis. However, selenium is also found in a 2-selenouridine moiety at the wobble position of tRNAGlu, tRNAGln and tRNALys. It is thought that the modifications of the wobble position of the tRNA improves the selectivity of the codon-anticodon pair as a result of the physico-chemical changes that result from substitution of sulfur and selenium for oxygen. Both selenocysteine and 2-selenouridine have widespread analogs, cysteine and thiouridine, where sulfur is used instead. To examine the role of selenium in 2-selenouridine, we comparatively analyzed the oxidation reactions of sulfur-containing 2-thiouracil-5-carboxylic acid (s2c5Ura) and its selenium analog 2-selenouracil-5-carboxylic acid (se2c5Ura) using 1H-NMR spectroscopy, 77Se-NMR spectroscopy, and liquid chromatography-mass spectrometry. Treatment of s2c5Ura with hydrogen peroxide led to oxidized intermediates, followed by irreversible desulfurization to form uracil-5-carboxylic acid (c5Ura). In contrast, se2c5Ura oxidation resulted in a diselenide intermediate, followed by conversion to the seleninic acid, both of which could be readily reduced by ascorbate and glutathione. Glutathione and ascorbate only minimally prevented desulfurization of s2c5Ura, whereas very little deselenization of se2c5Ura occurred in the presence of the same antioxidants. In addition, se2c5Ura but not s2c5Ura showed glutathione peroxidase activity, further suggesting that oxidation of se2c5Ura is readily reversible, while oxidation of s2c5Ura is not. The results of the study of these model nucleobases suggest that the use of 2-selenouridine is related to resistance to oxidative inactivation that otherwise characterizes 2-thiouridine. As the use of selenocysteine in proteins also confers resistance to oxidation, our findings suggest a common mechanism for the use of selenium in biology.
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Affiliation(s)
- N Connor Payne
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Andrew Geissler
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Aileen Button
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Alexandru R Sasuclark
- Department of Chemistry, St. Michael's College, 1 Winooski Park, Colchester, VT 05439, United States
| | - Alayne L Schroll
- Department of Chemistry, St. Michael's College, 1 Winooski Park, Colchester, VT 05439, United States
| | - Erik L Ruggles
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Robert J Hondal
- Department of Biochemistry, 89 Beaumont Ave, Given Building Room B413, Burlington, VT 05405, United States.
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126
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Lee SG, Kaya A, Avanesov AS, Podolskiy DI, Song EJ, Go DM, Jin GD, Hwang JY, Kim EB, Kim DY, Gladyshev VN. Age-associated molecular changes are deleterious and may modulate life span through diet. Sci Adv 2017; 3:e1601833. [PMID: 28232953 PMCID: PMC5315447 DOI: 10.1126/sciadv.1601833] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/29/2016] [Indexed: 05/15/2023]
Abstract
Transition through life span is accompanied by numerous molecular changes, such as dysregulated gene expression, altered metabolite levels, and accumulated molecular damage. These changes are thought to be causal factors in aging; however, because they are numerous and are also influenced by genotype, environment, and other factors in addition to age, it is difficult to characterize the cumulative effect of these molecular changes on longevity. We reasoned that age-associated changes, such as molecular damage and tissue composition, may influence life span when used in the diet of organisms that are closely related to those that serve as a dietary source. To test this possibility, we used species-specific culture media and diets that incorporated molecular extracts of young and old organisms and compared the influence of these diets on the life span of yeast, fruitflies, and mice. In each case, the "old" diet or medium shortened the life span for one or both sexes. These findings suggest that age-associated molecular changes, such as cumulative damage and altered dietary composition, are deleterious and causally linked with aging and may affect life span through diet.
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Affiliation(s)
- Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioinspired Science, Ewha Womans University, Seoul 03760, South Korea
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrei S. Avanesov
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Dmitriy I. Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eun Ju Song
- Ewha Laboratory Animal Genomic Center, Institute of Molecular Life Sciences and Technology, Office of Research Affairs, Ewha Womans University, Seoul 03760, South Korea
- Department of Veterinary Physiology, College of Veterinary Medicine, BK21 PLUS Creative Veterinary Research Center, Seoul National University, Seoul 08826, South Korea
| | - Du-Min Go
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea
| | - Gwi-Deuk Jin
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Jae Yeon Hwang
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Eun Bae Kim
- Department of Animal Life Science, Kangwon National University, Chuncheon 24341, South Korea
- Division of Applied Animal Science, Kangwon National University, Chuncheon 24341, South Korea
| | - Dae-Yong Kim
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Seoul National University, Seoul 08826, South Korea
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author.
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127
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Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 2017; 24:61-68. [PMID: 27870834 PMCID: PMC5295771 DOI: 10.1038/nsmb.3330] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
Abstract
The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3' mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a 'stop codon' is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.
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Affiliation(s)
- Alexei V. Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Stephen M. Heaphy
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Anton A. Turanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Sandra Pucciarelli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Raghul R. Devaraj
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Fang Xie
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Richard D. Smith
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Dolph L. Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
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128
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Heo JY, Cha HN, Kim KY, Lee E, Kim SJ, Kim YW, Kim JY, Lee IK, Gladyshev VN, Kim HY, Park SY. Methionine sulfoxide reductase B1 deficiency does not increase high-fat diet-induced insulin resistance in mice. Free Radic Res 2016; 51:24-37. [PMID: 27838938 DOI: 10.1080/10715762.2016.1261133] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methionine-S-sulfoxide reductase (MsrA) protects against high-fat diet-induced insulin resistance due to its antioxidant effects. To determine whether its counterpart, methionine-R-sulfoxide reductase (MsrB) has similar effects, we compared MsrB1 knockout and wild-type mice using a hyperinsulinemic-euglycemic clamp technique. High-fat feeding for eight weeks increased body weights, fat masses, and plasma levels of glucose, insulin, and triglycerides to similar extents in wild-type and MsrB1 knockout mice. Intraperitoneal glucose tolerance test showed no difference in blood glucose levels between the two genotypes after eight weeks on the high-fat diet. The hyperglycemic-euglycemic clamp study showed that glucose infusion rates and whole body glucose uptakes were decreased to similar extents by the high-fat diet in both wild-type and MsrB1 knockout mice. Hepatic glucose production and glucose uptake of skeletal muscle were unaffected by MsrB1 deficiency. The high-fat diet-induced oxidative stress in skeletal muscle and liver was not aggravated in MsrB1-deficient mice. Interestingly, whereas MsrB1 deficiency reduced JNK protein levels to a great extent in skeletal muscle and liver, it markedly elevated phosphorylation of JNK, suggesting the involvement of MsrB1 in JNK protein activation. However, this JNK phosphorylation based on a p-JNK/JNK level did not positively correlate with insulin resistance in MsrB1-deficient mice. Taken together, our results show that, in contrast to MsrA deficiency, MsrB1 deficiency does not increase high-fat diet-induced insulin resistance in mice.
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Affiliation(s)
- Jung-Yoon Heo
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
| | - Hye-Na Cha
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
| | - Ki Young Kim
- b Department of Biochemistry and Molecular Biology, College of Medicine , Yeungnam University , Daegu , Republic of Korea
| | - Eujin Lee
- b Department of Biochemistry and Molecular Biology, College of Medicine , Yeungnam University , Daegu , Republic of Korea
| | - Suk-Jeong Kim
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
| | - Yong-Woon Kim
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
| | - Jong-Yeon Kim
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
| | - In-Kyu Lee
- c Department of Internal Medicine, School of Medicine , Kyungpook National University , Daegu , Republic of Korea
| | - Vadim N Gladyshev
- d Division of Genetics, Department of Medicine Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Hwa-Young Kim
- b Department of Biochemistry and Molecular Biology, College of Medicine , Yeungnam University , Daegu , Republic of Korea
| | - So-Young Park
- a Department of Physiology , College of Medicine, Yeungnam University , Daegu , Republic of Korea
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Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN. Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. eLife 2016; 5:e19130. [PMID: 27874830 PMCID: PMC5148604 DOI: 10.7554/elife.19130] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022] Open
Abstract
Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Akhil Upneja
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Andrzej Galecki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, United States
| | - Yi-Miau Tsai
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Sasha Raskind
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, United States
| | | | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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130
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Gladyshev TV, Gladyshev VN. A Disease or Not a Disease? Aging As a Pathology. Trends Mol Med 2016; 22:995-996. [PMID: 27793599 DOI: 10.1016/j.molmed.2016.09.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 12/01/2022]
Abstract
The debate on the relationship between aging and disease is centered on whether aging is a normal/natural/physiological process or it represents a pathology. Considering this relationship from medical, molecular, social, and historical perspectives, we argue that aging is neither a disease, nor a non-disease. Instead, it combines all age-related diseases and their preclinical forms, in addition to other pathological changes.
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Affiliation(s)
| | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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131
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Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. Selenoprotein Gene Nomenclature. J Biol Chem 2016; 291:24036-24040. [PMID: 27645994 DOI: 10.1074/jbc.m116.756155] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4, and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine sulfoxide reductase B1), and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15-kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV), and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing, and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates.
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Affiliation(s)
- Vadim N Gladyshev
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, .,the Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142
| | - Elias S Arnér
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Marla J Berry
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | | | - Elspeth A Bruford
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Raymond F Burk
- the Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Bradley A Carlson
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - Sergi Castellano
- the Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurent Chavatte
- the Centre International de Recherche en Infectiologie, CIRI, INSERM U1111, and CNRS/ENS UMR5308, 69007 Lyon, France
| | - Marcus Conrad
- the Helmholtz Zentrum München, Institute of Developmental Genetics, 85764 Neuherberg, Germany
| | - Paul R Copeland
- the Department of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854
| | - Alan M Diamond
- the Department of Pathology, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Donna M Driscoll
- the Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Ana Ferreiro
- the Pathophysiology of Striated Muscles Laboratory, Unit of Functional and Adaptive Biology (BFA), University Paris Diderot, Sorbonne Paris Cité, BFA, UMR CNRS 8251, 75250 Paris, France.,the AP-HP, Centre de Référence Maladies Neuromusculaires Paris-Est, Groupe Hospitalier Pitié-Salpêtrière, 75013 Paris, France
| | - Leopold Flohé
- the Universidad de la República, Facultad de Medicina, Departamento de Bioquímica, 11800 Montevideo, Uruguay.,the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Fiona R Green
- the Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Roderic Guigó
- the Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain.,the Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Diane E Handy
- the Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115
| | - Dolph L Hatfield
- the Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland 20892
| | - John Hesketh
- the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the Human Nutrition Research Centre, Newcastle University, Newcastle-upon-Tyne NE1 7RU, United Kingdom.,the The Medical School, Newcastle University, Newcastle-upon-Tyne NE2 4HH, United Kingdom
| | - Peter R Hoffmann
- the Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii 96813
| | - Arne Holmgren
- the Department of Medical Biochemistry and Biophysics (MBB), Division of Biochemistry, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Robert J Hondal
- the Department of Biochemistry, University of Vermont, Burlington, Vermont 05405
| | - Michael T Howard
- the Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112
| | - Kaixun Huang
- the Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, Peoples Republic of China
| | - Hwa-Young Kim
- the Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu 42415, South Korea
| | - Ick Young Kim
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Josef Köhrle
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Alain Krol
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France
| | | | - Byeong Jae Lee
- the School of Biological Sciences, Seoul National University, Seoul 151-742, South Korea
| | - Byung Cheon Lee
- the College of Life Sciences and Biotechnology, Korea University, Seoul 02841, South Korea
| | - Xin Gen Lei
- the Department of Animal Science, Cornell University, Ithaca, New York 14853
| | - Qiong Liu
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
| | - Alain Lescure
- the Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, 67084 Strasbourg, France.,the Centre National de la Recherche Scientifique, 75794 Paris, France
| | - Alexei V Lobanov
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Joseph Loscalzo
- the Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - Matilde Maiorino
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Marco Mariotti
- From the Department of Medicine, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | - K Sandeep Prabhu
- the Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Margaret P Rayman
- the Department of Nutritional Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Sharon Rozovsky
- the Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Gustavo Salinas
- the Cátedra de Inmunología, Facultad de Química, Instituto de Higiene, CP11600 Montevideo, Uruguay
| | - Edward E Schmidt
- the Department of Microbiology and Immunology, Montana State University, Bozeman, Montana 59717
| | - Lutz Schomburg
- the Institute for Experimental Endocrinology, Charité-Universitaetsmedizin Berlin, D-13353 Berlin, Germany
| | - Ulrich Schweizer
- the Rheinische Friedrich-Wilhelms Universität Bonn, Institut für Biochemie und Molekularbiologie, 53115 Bonn, Germany
| | - Miljan Simonović
- the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Roger A Sunde
- the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706
| | - Petra A Tsuji
- the Department of Biological Sciences, Towson University, Towson, Maryland 21252, and
| | - Susan Tweedie
- the HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute-European Molecular Biology Laboratory (EMBL-EBI), Hinxton CB10 1SD, United Kingdom
| | - Fulvio Ursini
- the Department of Molecular Medicine, University of Padova, I-35121 Padova, Italy
| | - Philip D Whanger
- the Department of Environmental and Molecular Toxicology, College of Agricultural Sciences, Oregon State University, Corvallis, Oregon 97331
| | - Yan Zhang
- the Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Science, Shenzhen University, Shenzhen, 518060, Guangdong Province, Peoples Republic of China
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132
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Li M, Chen L, Tian S, Lin Y, Tang Q, Zhou X, Li D, Yeung CKL, Che T, Jin L, Fu Y, Ma J, Wang X, Jiang A, Lan J, Pan Q, Liu Y, Luo Z, Guo Z, Liu H, Zhu L, Shuai S, Tang G, Zhao J, Jiang Y, Bai L, Zhang S, Mai M, Li C, Wang D, Gu Y, Wang G, Lu H, Li Y, Zhu H, Li Z, Li M, Gladyshev VN, Jiang Z, Zhao S, Wang J, Li R, Li X. Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies. Genome Res 2016; 27:865-874. [PMID: 27646534 PMCID: PMC5411780 DOI: 10.1101/gr.207456.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/16/2016] [Indexed: 01/15/2023]
Abstract
Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.
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Affiliation(s)
- Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lei Chen
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Shilin Tian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Novogene Bioinformatics Institute, Beijing 100089, China
| | - Yu Lin
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | | | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuhua Fu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Anan Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Lan
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Qi Pan
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Yingkai Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zonggang Luo
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Zongyi Guo
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Haifeng Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Surong Shuai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiugang Zhao
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yanzhi Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Miaomiao Mai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Changchun Li
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dawei Wang
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Yiren Gu
- Sichuan Animal Science Academy, Chengdu 610066, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.,Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Yan Li
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Haihao Zhu
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Zongwen Li
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Shuhong Zhao
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinyong Wang
- Key Laboratory of Pig Industry Sciences (Ministry of Agriculture), Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing 100089, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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133
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Gerashchenko MV, Gladyshev VN. Ribonuclease selection for ribosome profiling. Nucleic Acids Res 2016; 45:e6. [PMID: 27638886 PMCID: PMC5314788 DOI: 10.1093/nar/gkw822] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/14/2016] [Accepted: 09/06/2016] [Indexed: 11/14/2022] Open
Abstract
Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised. However, ribosome coverage patterns of individual transcripts had little in common between the ribonucleases. We further examined their potency at converting polysomes to monosomes across other commonly used model organisms, including bacteria, nematodes and fruit flies. In some cases, ribonuclease treatment completely degraded ribosome populations. Ribonuclease T1 was the only enzyme that preserved ribosomal integrity while thoroughly converting polysomes to monosomes in all examined species. This study provides a guide for ribonuclease selection in ribosome profiling experiments across most common model systems.
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Affiliation(s)
- Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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134
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Zhou X, Meng X, Liu Z, Chang J, Wang B, Li M, Wengel POT, Tian S, Wen C, Wang Z, Garber PA, Pan H, Ye X, Xiang Z, Bruford MW, Edwards SV, Cao Y, Yu S, Gao L, Cao Z, Liu G, Ren B, Shi F, Peterfi Z, Li D, Li B, Jiang Z, Li J, Gladyshev VN, Li R, Li M. Population Genomics Reveals Low Genetic Diversity and Adaptation to Hypoxia in Snub-Nosed Monkeys. Mol Biol Evol 2016; 33:2670-81. [PMID: 27555581 DOI: 10.1093/molbev/msw150] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Snub-nosed monkeys (genus Rhinopithecus) are a group of endangered colobines endemic to South Asia. Here, we re-sequenced the whole genomes of 38 snub-nosed monkeys representing four species within this genus. By conducting population genomic analyses, we observed a similar load of deleterious variation in snub-nosed monkeys living in both smaller and larger populations and found that genomic diversity was lower than that reported in other primates. Reconstruction of Rhinopithecus evolutionary history suggested that episodes of climatic variation over the past 2 million years, associated with glacial advances and retreats and population isolation, have shaped snub-nosed monkey demography and evolution. We further identified several hypoxia-related genes under selection in R. bieti (black snub-nosed monkey), a species that exploits habitats higher than any other nonhuman primate. These results provide the first detailed and comprehensive genomic insights into genetic diversity, demography, genetic burden, and adaptation in this radiation of endangered primates.
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Affiliation(s)
- Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Xuehong Meng
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhijin Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jiang Chang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Boshi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Pablo Orozco-Ter Wengel
- Biodiversity and Sustainable Places Research Institute, Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Ziming Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Paul A Garber
- Department of Anthropology, University of Illinois at Urbana-Champaign Program in Ecology and Evolutionary Biology, University of Illinois at Urbana-Champaign
| | - Huijuan Pan
- College of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Xinping Ye
- School of Life Sciences, Shaanxi Normal University, XiXi'an, China
| | - Zuofu Xiang
- College of Life Science and Technology, Central South University of Forestry and Technology, Changsha, China
| | - Michael W Bruford
- Biodiversity and Sustainable Places Research Institute, Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University
| | - Yinchuan Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Lianju Gao
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhisheng Cao
- Novogene Bioinformatics Institute, Beijing, China
| | - Guangjian Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Baoping Ren
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fanglei Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zalan Peterfi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Dayong Li
- College of Life Sciences, China West Normal University, Nanchong, Sichuan, China
| | - Baoguo Li
- College of Life Sciences, Northwest University, Xi'an, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Junsheng Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, Beijing, China
| | - Ming Li
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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135
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Abstract
Two recent stimulating publications have examined the causes of cancer, comparing 'bad luck' versus environment as main risk factors for cancer incidence. However, bringing aging into the picture might question the entire debate.
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Affiliation(s)
- Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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136
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Podolskiy DI, Lobanov AV, Kryukov GV, Gladyshev VN. Analysis of cancer genomes reveals basic features of human aging and its role in cancer development. Nat Commun 2016; 7:12157. [PMID: 27515585 PMCID: PMC4990632 DOI: 10.1038/ncomms12157] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 06/07/2016] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations have long been implicated in aging and disease, but their impact on fitness and function is difficult to assess. Here by analysing human cancer genomes we identify mutational patterns associated with aging. Our analyses suggest that age-associated mutation load and burden double approximately every 8 years, similar to the all-cause mortality doubling time. This analysis further reveals variance in the rate of aging among different human tissues, for example, slightly accelerated aging of the reproductive system. Age-adjusted mutation load and burden correlate with the corresponding cancer incidence and precede it on average by 15 years, pointing to pre-clinical cancer development times. Behaviour of mutation load also exhibits gender differences and late-life reversals, explaining some gender-specific and late-life patterns in cancer incidence rates. Overall, this study characterizes some features of human aging and offers a mechanism for age being a risk factor for the onset of cancer. Somatic mutations are associated with disease, including cancer. Here, the authors analyse cancer genomic data and show that somatic mutations increase with age and that cancer incidence lags 15 years behind this increase, later in life, mutation and cancer incidence are reduced.
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Affiliation(s)
- Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexei V Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute, Cambridge, Massachusetts 02142, USA
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137
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Heaphy SM, Mariotti M, Gladyshev VN, Atkins JF, Baranov PV. Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum. Mol Biol Evol 2016; 33:2885-2889. [PMID: 27501944 PMCID: PMC5062323 DOI: 10.1093/molbev/msw166] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3′ end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.
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Affiliation(s)
- Stephen M Heaphy
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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138
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Gladyshev VN. Aging: progressive decline in fitness due to the rising deleteriome adjusted by genetic, environmental, and stochastic processes. Aging Cell 2016; 15:594-602. [PMID: 27060562 PMCID: PMC4933668 DOI: 10.1111/acel.12480] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2016] [Indexed: 01/11/2023] Open
Abstract
Different theories posit that aging is caused by molecular damage, genetic programs, continued development, hyperfunction, antagonistic pleiotropy alleles, mutations, trade‐offs, incomplete repair, etc. Here, I discuss that these ideas can be conceptually unified as they capture particular facets of aging, while being incomplete. Their respective deleterious effects impact fitness at different levels of biological organization, adjusting progression through aging, rather than causing it. Living is associated with a myriad of deleterious processes, both random and deterministic, which are caused by imperfectness, exhibit cumulative properties, and represent the indirect effects of biological functions at all levels, from simple molecules to systems. From this, I derive the deleteriome, which encompasses cumulative deleterious age‐related changes and represents the biological age. The organismal deleteriome consists of the deleteriomes of cells, organs, and systems, which change along roughly synchronized trajectories and may be assessed through biomarkers of aging. Aging is then a progressive decline in fitness due to the increasing deleteriome, adjusted by genetic, environmental, and stochastic processes. This model allows integration of diverse aging concepts, provides insights into the nature of aging, and suggests how lifespan may be adjusted during evolution and in experimental models.
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Affiliation(s)
- Vadim N. Gladyshev
- Division of Genetics Department of Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA 02115 USA
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139
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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140
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Péterfi Z, Tarrago L, Gladyshev VN. Practical guide for dynamic monitoring of protein oxidation using genetically encoded ratiometric fluorescent biosensors of methionine sulfoxide. Methods 2016; 109:149-157. [PMID: 27345570 DOI: 10.1016/j.ymeth.2016.06.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 11/30/2022] Open
Abstract
In cells, physiological and pathophysiological conditions may lead to the formation of methionine sulfoxide (MetO). This oxidative modification of methionine exists in the form of two diastereomers, R and S, and may occur in both free amino acid and proteins. MetO is reduced back to methionine by methionine sulfoxide reductases (MSRs). Methionine oxidation was thought to be a nonspecific modification affecting protein functions and methionine availability. However, recent findings suggest that cyclic methionine oxidation and reduction is a posttranslational modification that actively regulates protein function akin to redox regulation by cysteine oxidation and phosphorylation. Methionine oxidation is thus an important mechanism that could play out in various physiological contexts. However, detecting MetO generation and MSR functions remains challenging because of the lack of tools and reagents to detect and quantify this protein modification. We recently developed two genetically encoded diasterospecific fluorescent sensors, MetSOx and MetROx, to dynamically monitor MetO in living cells. Here, we provide a detailed procedure for their use in bacterial and mammalian cells using fluorimetric and fluorescent imaging approaches. This method can be adapted to dynamically monitor methionine oxidation in various cell types and under various conditions.
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Affiliation(s)
- Zalán Péterfi
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lionel Tarrago
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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141
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Carlson BA, Tobe R, Yefremova E, Tsuji PA, Hoffmann VJ, Schweizer U, Gladyshev VN, Hatfield DL, Conrad M. Glutathione peroxidase 4 and vitamin E cooperatively prevent hepatocellular degeneration. Redox Biol 2016; 9:22-31. [PMID: 27262435 PMCID: PMC4900515 DOI: 10.1016/j.redox.2016.05.003] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 02/07/2023] Open
Abstract
The selenoenzyme glutathione peroxidase 4 (Gpx4) is an essential mammalian glutathione peroxidase, which protects cells against detrimental lipid peroxidation and governs a novel form of regulated necrotic cell death, called ferroptosis. To study the relevance of Gpx4 and of another vitally important selenoprotein, cytosolic thioredoxin reductase (Txnrd1), for liver function, mice with conditional deletion of Gpx4 in hepatocytes were studied, along with those lacking Txnrd1 and selenocysteine (Sec) tRNA (Trsp) in hepatocytes. Unlike Txnrd1- and Trsp-deficient mice, Gpx4−/− mice died shortly after birth and presented extensive hepatocyte degeneration. Similar to Txnrd1-deficient livers, Gpx4−/− livers manifested upregulation of nuclear factor (erythroid-derived)-like 2 (Nrf2) response genes. Remarkably, Gpx4−/− pups born from mothers fed a vitamin E-enriched diet survived, yet this protection was reversible as subsequent vitamin E deprivation caused death of Gpx4-deficient mice ~4 weeks thereafter. Abrogation of selenoprotein expression in Gpx4−/− mice did not result in viable mice, indicating that the combined deficiency aggravated the loss of Gpx4 in liver. By contrast, combined Trsp/Txnrd1-deficient mice were born, but had significantly shorter lifespans than either single knockout, suggesting that Txnrd1 plays an important role in supporting liver function of mice lacking Trsp. In sum our study demonstrates that the ferroptosis regulator Gpx4 is critical for hepatocyte survival and proper liver function, and that vitamin E can compensate for its loss by protecting cells against deleterious lipid peroxidation. Conditional Gpx4 loss causes hepatocellular degeneration and early death of mice. Dietary vitamin E supplementation rescues death of liver-specific Gpx4 null mice. Nutritional vitamin E content in diet may severely impact experimental outcome.
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Affiliation(s)
- Bradley A Carlson
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryuta Tobe
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena Yefremova
- Helmholtz Zentrum München, Institute for Developmental Genetics, Neuherberg, Germany
| | - Petra A Tsuji
- Department of Biological Sciences, Towson University, Towson, MD, USA
| | - Victoria J Hoffmann
- Office of the Director Diagnostic and Research Services Branch, National Institutes of Health, Bethesda, MD, USA
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dolph L Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Marcus Conrad
- Helmholtz Zentrum München, Institute for Developmental Genetics, Neuherberg, Germany.
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142
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Bisio H, Bonilla M, Manta B, Graña M, Salzman V, Aguilar PS, Gladyshev VN, Comini MA, Salinas G. A New Class of Thioredoxin-Related Protein Able to Bind Iron-Sulfur Clusters. Antioxid Redox Signal 2016; 24:205-216. [PMID: 26381228 PMCID: PMC6913166 DOI: 10.1089/ars.2015.6377] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
AIMS Members of the thioredoxin (Trx) protein family participate mainly in redox pathways and have not been associated with Fe/S binding, in contrast to some closely related glutaredoxins (Grxs). Cestode parasites possess an unusual diversity of Trxs and Trx-related proteins with unexplored functions. In this study, we addressed the biochemical characterization of a new class of Trx-related protein (IsTRP) and a classical monothiol Grx (EgGrx5) from the human pathogen Echinococcus granulosus. RESULTS The dimeric form of IsTRP coordinates Fe2S2 in a glutathione-independent manner; instead, Fe/S binding relies on the CXXC motif conserved among Trxs. This novel binding mechanism allows holo-IsTRP to be highly resistant to oxidation. IsTRP lacks canonical reductase activities. Mitochondrially targeted IsTRP aids growth of a Grx5 null yeast strain. Similar complementation assays performed with EgGrx5 revealed functional conservation for class II Grxs, despite the presence of nonconserved structural elements. IsTRP is a cestode lineage-specific protein highly expressed in the gravid adult worm, which releases the infective stage critical for dissemination. INNOVATION IsTRP is the first member from the Trx family to be reported to bind Fe/S. We disclose a novel mechanism of Fe/S coordination within the Trx folding unit, which renders the cluster highly resistant to oxidation-mediated disassembly. CONCLUSION We demonstrate that IsTRP defines a new protein family within the Trx superfamily, confirm the conservation of function for class II Grx from nonphylogenetically related species, and highlight the versatility of the Trx folding unit to acquire Fe/S binding as a recurrent emergent function. Antioxid. Redox Signal. 00, 000-000.
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Affiliation(s)
- Hugo Bisio
- 1 Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Bonilla
- 2 Redox Biology of Trypanosomes Laboratory, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Bruno Manta
- 2 Redox Biology of Trypanosomes Laboratory, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Martín Graña
- 3 Bioinformatics Unit, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Valentina Salzman
- 4 Cellular Membranes Laboratory, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Pablo S Aguilar
- 4 Cellular Membranes Laboratory, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Vadim N Gladyshev
- 5 Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School , Boston, Massachusetts
| | - Marcelo A Comini
- 2 Redox Biology of Trypanosomes Laboratory, Institut Pasteur de Montevideo , Montevideo, Uruguay
| | - Gustavo Salinas
- 1 Worm Biology Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay .,6 Cátedra de Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República , Montevideo, Uruguay
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143
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Lee BC, Kaya A, Gladyshev VN. Methionine restriction and life-span control. Ann N Y Acad Sci 2015; 1363:116-24. [PMID: 26663138 DOI: 10.1111/nyas.12973] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 10/10/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023]
Abstract
Dietary restriction (DR) without malnutrition is associated with longevity in various organisms. However, it has also been shown that reduced calorie intake is often ineffective in extending life span. Selecting optimal dietary regimens for DR studies is complicated, as the same regimen may lead to different outcomes depending on genotype and environmental factors. Recent studies suggested that interventions such as moderate protein restriction with or without adequate nutrition (e.g., particular amino acids or carbohydrates) may have additional beneficial effects mediated by certain metabolic and hormonal factors implicated in the biology of aging, regardless of total calorie intake. In particular, it was shown that restriction of a single amino acid, methionine, can mimic the effects of DR and extend life span in various model organisms. We discuss the beneficial effects of a methionine-restricted diet, the molecular pathways involved, and the use of this regimen in longevity interventions.
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Affiliation(s)
- Byung Cheon Lee
- College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Alaattin Kaya
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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144
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Malinouski M, Hasan NM, Zhang Y, Seravalli J, Lin J, Avanesov A, Lutsenko S, Gladyshev VN. Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism. Nat Commun 2015; 5:3301. [PMID: 24522796 PMCID: PMC5578452 DOI: 10.1038/ncomms4301] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/23/2014] [Indexed: 11/09/2022] Open
Abstract
Trace elements are essential for human metabolism and dysregulation of their homoeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundamental differences in the regulation of different trace elements. Specifically, selenium levels are controlled through the selenocysteine machinery and expression of abundant selenoproteins; copper balance is affected by lipid metabolism and requires machinery involved in protein trafficking and post-translational modifications; and the iron levels are influenced by iron import and expression of the iron/haeme-containing enzymes. Our approach can be applied to a variety of disease models and/or nutritional conditions, and the generated data set opens new directions for studies of human trace element metabolism.
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Affiliation(s)
- Mikalai Malinouski
- 1] Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Nesrin M Hasan
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Yan Zhang
- 1] Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Javier Seravalli
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Jie Lin
- 1] Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China [2] Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrei Avanesov
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Vadim N Gladyshev
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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145
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Ma S, Lee SG, Kim EB, Park TJ, Seluanov A, Gorbunova V, Buffenstein R, Seravalli J, Gladyshev VN. Organization of the Mammalian Ionome According to Organ Origin, Lineage Specialization, and Longevity. Cell Rep 2015; 13:1319-1326. [PMID: 26549444 DOI: 10.1016/j.celrep.2015.10.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/19/2015] [Accepted: 10/05/2015] [Indexed: 12/16/2022] Open
Abstract
Trace elements are essential to all mammals, but their distribution and utilization across species and organs remains unclear. Here, we examined 18 elements in the brain, heart, kidney, and liver of 26 mammalian species and report the elemental composition of these organs, the patterns of utilization across the species, and their correlation with body mass and longevity. Across the organs, we observed distinct distribution patterns for abundant elements, transition metals, and toxic elements. Some elements showed lineage-specific patterns, including reduced selenium utilization in African mole rats, and positive correlation between the number of selenocysteine residues in selenoprotein P and the selenium levels in liver and kidney across mammals. Body mass was linked positively to zinc levels, whereas species lifespan correlated positively with cadmium and negatively with selenium. This study provides insights into the variation of mammalian ionome by organ physiology, lineage specialization, body mass, and longevity.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea; Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, Kangwon-do 200-701, Republic of Korea
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Javier Seravalli
- Redox Biology Center and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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146
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Turanov AA, Everley RA, Hybsier S, Renko K, Schomburg L, Gygi SP, Hatfield DL, Gladyshev VN. Regulation of Selenocysteine Content of Human Selenoprotein P by Dietary Selenium and Insertion of Cysteine in Place of Selenocysteine. PLoS One 2015; 10:e0140353. [PMID: 26452064 PMCID: PMC4599804 DOI: 10.1371/journal.pone.0140353] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/24/2015] [Indexed: 11/27/2022] Open
Abstract
Selenoproteins are a unique group of proteins that contain selenium in the form of selenocysteine (Sec) co-translationally inserted in response to a UGA codon with the help of cis- and trans-acting factors. Mammalian selenoproteins contain single Sec residues, with the exception of selenoprotein P (SelP) that has 7–15 Sec residues depending on species. Assessing an individual’s selenium status is important under various pathological conditions, which requires a reliable selenium biomarker. Due to a key role in organismal selenium homeostasis, high Sec content, regulation by dietary selenium, and availability of robust assays in human plasma, SelP has emerged as a major biomarker of selenium status. Here, we found that Cys is present in various Sec positions in human SelP. Treatment of cells expressing SelP with thiophosphate, an analog of the selenium donor for Sec synthesis, led to a nearly complete replacement of Sec with Cys, whereas supplementation of cells with selenium supported Sec insertion. SelP isolated directly from human plasma had up to 8% Cys inserted in place of Sec, depending on the Sec position. These findings suggest that a change in selenium status may be reflected in both SelP concentration and its Sec content, and that availability of the SelP-derived selenium for selenoprotein synthesis may be overestimated under conditions of low selenium status due to replacement of Sec with Cys.
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Affiliation(s)
- Anton A. Turanov
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Robert A. Everley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Sandra Hybsier
- Institute for Experimental Endocrinology, Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Kostja Renko
- Institute for Experimental Endocrinology, Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lutz Schomburg
- Institute for Experimental Endocrinology, Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, 02115, United States of America
| | - Dolph L. Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, 02115, United States of America
- * E-mail:
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147
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Abstract
SIGNIFICANCE Protein structure and function can be regulated via post-translational modifications by numerous enzymatic and nonenzymatic mechanisms. Regulation involving oxidation of sulfur-containing residues emerged as a key mechanism of redox control. Unraveling the participants and principles of such regulation is necessary for understanding the biological significance of redox control of cellular processes. RECENT ADVANCES Reversible oxidation of methionine residues by monooxygenases of the Mical family and subsequent reduction of methionine sulfoxides by a selenocysteine-containing methionine sulfoxide reductase B1 (MsrB1) was found to control the assembly and disassembly of actin in mammals, and the Mical/MsrB pair similarly regulates actin in fruit flies. This finding has opened up new avenues for understanding the use of stereospecific methionine oxidation in regulating cellular processes and the roles of MsrB1 and Micals in regulation of actin dynamics. CRITICAL ISSUES So far, Micals have been the only known partners of MsrB1, and actin is the only target. It is important to identify additional substrates of Micals and characterize other Mical-like enzymes. FUTURE DIRECTIONS Oxidation of methionine, reviewed here, is an emerging but not well-established mechanism. Studies suggest that methionine oxidation is a form of oxidative damage of proteins, a modification that alters protein structure or function, a tool in redox signaling, and a mechanism that controls protein function. Understanding the functional impact of reversible oxidation of methionine will require identification of targets, substrates, and regulators of Micals and Msrs. Linking the biological processes, in which these proteins participate, might also lead to insights into disease conditions, which involve regulation of actin by Micals and Msrs.
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Affiliation(s)
- Alaattin Kaya
- 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital , Harvard Medical School, Boston, Massachusetts
| | - Byung Cheon Lee
- 2 College of Life Sciences and Biotechnology, Korea University , Seoul, South Korea
| | - Vadim N Gladyshev
- 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital , Harvard Medical School, Boston, Massachusetts
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148
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Ma S, Yim SH, Lee SG, Kim EB, Lee SR, Chang KT, Buffenstein R, Lewis KN, Park TJ, Miller RA, Clish CB, Gladyshev VN. Organization of the Mammalian Metabolome according to Organ Function, Lineage Specialization, and Longevity. Cell Metab 2015; 22:332-43. [PMID: 26244935 PMCID: PMC4758382 DOI: 10.1016/j.cmet.2015.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 04/15/2015] [Accepted: 07/02/2015] [Indexed: 12/24/2022]
Abstract
Biological diversity among mammals is remarkable. Mammalian body weights range seven orders of magnitude and lifespans differ more than 100-fold among species. While genetic, dietary, and pharmacological interventions can be used to modulate these traits in model organisms, it is unknown how they are determined by natural selection. By profiling metabolites in brain, heart, kidney, and liver tissues of 26 mammalian species representing ten taxonomical orders, we report metabolite patterns characteristic of organs, lineages, and species longevity. Our data suggest different rates of metabolite divergence across organs and reveal patterns representing organ-specific functions and lineage-specific physiologies. We identified metabolites that correlated with species lifespan, some of which were previously implicated in longevity control. We also compared the results with metabolite changes in five long-lived mouse models and observed some similar patterns. Overall, this study describes adjustments of the mammalian metabolome according to lifespan, phylogeny, and organ and lineage specialization.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Eun Bae Kim
- Department of Bioinspired Science, Ewha Womans University, Seoul 120-750, Republic of Korea; Department of Animal Life Science, Kangwon National University, Chuncheon 200-701, Republic of Korea
| | - Sang-Rae Lee
- The National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Kyu-Tae Chang
- The National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang, Cheongwon, Chungbuk 363-883, Republic of Korea
| | - Rochelle Buffenstein
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Kaitlyn N Lewis
- Department of Physiology and The Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, USA
| | - Thomas J Park
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA.
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149
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Seim I, Ma S, Zhou X, Gerashchenko MV, Lee SG, Suydam R, George JC, Bickham JW, Gladyshev VN. The transcriptome of the bowhead whale Balaena mysticetus reveals adaptations of the longest-lived mammal. Aging (Albany NY) 2015; 6:879-99. [PMID: 25411232 PMCID: PMC4247388 DOI: 10.18632/aging.100699] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mammals vary dramatically in lifespan, by at least two-orders of magnitude, but the molecular basis for this difference remains largely unknown. The bowhead whale Balaena mysticetus is the longest-lived mammal known, with an estimated maximal lifespan in excess of two hundred years. It is also one of the two largest animals and the most cold-adapted baleen whale species. Here, we report the first genome-wide gene expression analyses of the bowhead whale, based on the de novo assembly of its transcriptome. Bowhead whale or cetacean-specific changes in gene expression were identified in the liver, kidney and heart, and complemented with analyses of positively selected genes. Changes associated with altered insulin signaling and other gene expression patterns could help explain the remarkable longevity of bowhead whales as well as their adaptation to a lipid-rich diet. The data also reveal parallels in candidate longevity adaptations of the bowhead whale, naked mole rat and Brandt's bat. The bowhead whale transcriptome is a valuable resource for the study of this remarkable animal, including the evolution of longevity and its important correlates such as resistance to cancer and other diseases.
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Affiliation(s)
- Inge Seim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xuming Zhou
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Suydam
- Department of Wildlife Management, North Slope Borough, Barrow, AK 99723, USA
| | - John C George
- Department of Wildlife Management, North Slope Borough, Barrow, AK 99723, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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150
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Gould NS, Evans P, Martínez-Acedo P, Marino SM, Gladyshev VN, Carroll KS, Ischiropoulos H. Site-Specific Proteomic Mapping Identifies Selectively Modified Regulatory Cysteine Residues in Functionally Distinct Protein Networks. ACTA ACUST UNITED AC 2015; 22:965-75. [PMID: 26165157 DOI: 10.1016/j.chembiol.2015.06.010] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/03/2015] [Accepted: 06/05/2015] [Indexed: 12/21/2022]
Abstract
S-Acylation, S-glutathionylation, S-nitrosylation, and S-sulfenylation are prominent, chemically distinct modifications that regulate protein function, redox sensing, and trafficking. Although the biological significance of these modifications is increasingly appreciated, their integration in the proteome remains unknown. Novel mass spectrometry-based technologies identified 2,596 predominately unique sites in 1,319 mouse liver proteins under physiological conditions. Structural analysis localized the modifications in unique, evolutionary conserved protein segments, outside commonly annotated functional regions. Contrary to expectations, propensity for modification did not correlate with biophysical properties that regulate cysteine reactivity. However, the in vivo chemical reactivity is fine-tuned for specificity, demonstrated by the nominal complementation between the four modifications and quantitative proteomics which showed that a reduction in S-nitrosylation is not correlated with increased S-glutathionylation. A comprehensive survey uncovered clustering of modifications within biologically related protein networks. The data provide the first evidence for the occurrence of distinct, endogenous protein networks that undergo redox signaling through specific cysteine modifications.
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Affiliation(s)
- Neal S Gould
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Perry Evans
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Stefano M Marino
- Department of Agricultural Biotechnology, Akdeniz University, Antalya 07985, Turkey
| | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kate S Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Harry Ischiropoulos
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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