1
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Hain BA, Kimball SR, Waning DL. Preventing loss of sirt1 lowers mitochondrial oxidative stress and preserves C2C12 myotube diameter in an in vitro model of cancer cachexia. Physiol Rep 2024; 12:e16103. [PMID: 38946587 PMCID: PMC11215470 DOI: 10.14814/phy2.16103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/06/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Cancer cachexia is a multifactorial syndrome associated with advanced cancer that contributes to mortality. Cachexia is characterized by loss of body weight and muscle atrophy. Increased skeletal muscle mitochondrial reactive oxygen species (ROS) is a contributing factor to loss of muscle mass in cachectic patients. Mice inoculated with Lewis lung carcinoma (LLC) cells lose weight, muscle mass, and have lower muscle sirtuin-1 (sirt1) expression. Nicotinic acid (NA) is a precursor to nicotinamide dinucleotide (NAD+) which is exhausted in cachectic muscle and is a direct activator of sirt1. Mice lost body and muscle weight and exhibited reduced skeletal muscle sirt1 expression after inoculation with LLC cells. C2C12 myotubes treated with LLC-conditioned media (LCM) had lower myotube diameter. We treated C2C12 myotubes with LCM for 24 h with or without NA for 24 h. C2C12 myotubes treated with NA maintained myotube diameter, sirt1 expression, and had lower mitochondrial superoxide. We then used a sirt1-specific small molecule activator SRT1720 to increase sirt1 activity. C2C12 myotubes treated with SRT1720 maintained myotube diameter, prevented loss of sirt1 expression, and attenuated mitochondrial superoxide production. Our data provides evidence that NA may be beneficial in combating cancer cachexia by maintaining sirt1 expression and decreasing mitochondrial superoxide production.
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MESH Headings
- Animals
- Cachexia/etiology
- Cachexia/metabolism
- Cachexia/pathology
- Cachexia/prevention & control
- Sirtuin 1/metabolism
- Sirtuin 1/genetics
- Muscle Fibers, Skeletal/metabolism
- Muscle Fibers, Skeletal/drug effects
- Muscle Fibers, Skeletal/pathology
- Mice
- Oxidative Stress/drug effects
- Mice, Inbred C57BL
- Carcinoma, Lewis Lung/metabolism
- Carcinoma, Lewis Lung/pathology
- Carcinoma, Lewis Lung/complications
- Male
- Heterocyclic Compounds, 4 or More Rings/pharmacology
- Mitochondria, Muscle/metabolism
- Mitochondria, Muscle/drug effects
- Mitochondria, Muscle/pathology
- Cell Line
- Niacin/pharmacology
- Mitochondria/metabolism
- Mitochondria/drug effects
- Reactive Oxygen Species/metabolism
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Affiliation(s)
- Brian A. Hain
- Department of Cellular and Molecular PhysiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Penn State Cancer InstitutePenn State College of MedicineHersheyPennsylvaniaUSA
| | - Scot R. Kimball
- Department of Cellular and Molecular PhysiologyPenn State College of MedicineHersheyPennsylvaniaUSA
| | - David L. Waning
- Department of Cellular and Molecular PhysiologyPenn State College of MedicineHersheyPennsylvaniaUSA
- Penn State Cancer InstitutePenn State College of MedicineHersheyPennsylvaniaUSA
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2
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Huang Y, Ruan Q, Fang S, Duan Y, Zheng J, Xiang Z, Shen Y, Liu S, Ouyang G. Toxicity Assessment of Environmental Liquid Crystal Monomers: A Bacteriological Investigation on Escherichia coli and Staphylococcus epidermidis. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 38321847 DOI: 10.1021/acs.est.3c08281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
The widespread existence of liquid crystal monomers (LCMs) in various environmental matrices has been demonstrated, yet studies on the toxicological effects of LCMs are considerably scarce and are urgently needed to be conducted to assess the adverse impacts on ecology and human health. Here, we conducted a bacteriological study on two representative human commensal bacteria, Escherichia coli (E. coli) and Staphylococcus epidermidis (S. epidermidis), to investigate the effect of LCMs at human-relevant dosage and maximum environmental concentration on growth, metabolome, enzymatic activity, and mRNA expression. Microbial growth results exhibited that the highest inhibition ratio of LCMs on S. epidermidis reached 33.6% in our set concentration range, while the corresponding data on E. coli was only 14.3%. Additionally, LCMs showed more dose-dependent toxicity to S. epidermidis rather than E. coli. A novel in vivo solid-phase microextraction (SPME) fiber was applied to capture the in vivo metabolites of microorganisms. In vivo metabolomic analyses revealed that dysregulated fatty acid metabolism-related products of both bacteria accounted for >50% of the total number of differential substances, and the results also showed the species-specific and concentration-dependent metabolic dysregulation in LCM-exposed bacteria. The determination of enzymatic activity and mRNA relative expression levels related to oxidative stress confirmed our speculation that the adverse effects were related to the oxidative metabolism of fatty acids. This study complements the gaps in toxicity data for LCMs against bacteria and provides a new and important insight regarding metabolic dysregulation induced by environmental LCMs in human commensal bacteria.
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Affiliation(s)
- Yiquan Huang
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Qijun Ruan
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Shuting Fang
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Yingming Duan
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Jiating Zheng
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Zhangmin Xiang
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Yong Shen
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuqin Liu
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Gangfeng Ouyang
- KLGHEI of Environment and Energy Chemistry, School of Chemistry, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
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3
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Brunnsåker D, Kronström F, Tiukova IA, King RD. Interpreting protein abundance in Saccharomyces cerevisiae through relational learning. Bioinformatics 2024; 40:btae050. [PMID: 38273672 PMCID: PMC10868306 DOI: 10.1093/bioinformatics/btae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 01/27/2024] Open
Abstract
MOTIVATION Proteomic profiles reflect the functional readout of the physiological state of an organism. An increased understanding of what controls and defines protein abundances is of high scientific interest. Saccharomyces cerevisiae is a well-studied model organism, and there is a large amount of structured knowledge on yeast systems biology in databases such as the Saccharomyces Genome Database, and highly curated genome-scale metabolic models like Yeast8. These datasets, the result of decades of experiments, are abundant in information, and adhere to semantically meaningful ontologies. RESULTS By representing this knowledge in an expressive Datalog database we generated data descriptors using relational learning that, when combined with supervised machine learning, enables us to predict protein abundances in an explainable manner. We learnt predictive relationships between protein abundances, function and phenotype; such as α-amino acid accumulations and deviations in chronological lifespan. We further demonstrate the power of this methodology on the proteins His4 and Ilv2, connecting qualitative biological concepts to quantified abundances. AVAILABILITY AND IMPLEMENTATION All data and processing scripts are available at the following Github repository: https://github.com/DanielBrunnsaker/ProtPredict.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Filip Kronström
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Ievgeniia A Tiukova
- Department of Life Sciences, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm 106 91, Sweden
| | - Ross D King
- Department of Computer Science and Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
- The Alan Turing Institute, London NW1 2DB, United Kingdom
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4
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Goldkamp AK, Hagen DE. Implications of tRNA abundance on translation elongation across bovine tissues. Front Genet 2023; 14:1308048. [PMID: 38174049 PMCID: PMC10763252 DOI: 10.3389/fgene.2023.1308048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Translation is a crucial stage of gene expression. It may also act as an additional layer of regulation that plays an important role in gene expression and function. Highly expressed genes are believed to be codon-biased to support increased protein production, in which quickly translated codons correspond to highly abundant tRNAs. Synonymous SNPs, considered to be silent due to the degeneracy of the genetic code, may shift protein abundance and function through alterations in translational efficiency and suboptimal pairing to lowly abundant tRNAs. Methods: Here, we applied Quantitative Mature tRNA sequencing (QuantM-tRNAseq) and ribosome profiling across bovine tissues in order to investigate the relationship between tRNA expression and slowed translation. Results: Moreover, we have identified genes modulated at transcriptional and/or translational levels underlying tissue-specific biological processes. We have also successfully defined pausing sites that depict the regulatory information encoded within the open reading frame of transcripts, which could be related to translation rate and facilitate proper protein folding. This work offers an atlas of distinctive pausing sites across three bovine tissues, which provides an opportunity to predict codon optimality and understand tissue-specific mechanisms of regulating protein synthesis.
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Affiliation(s)
| | - Darren E. Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
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5
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Bishop DJ, Hoffman NJ, Taylor DF, Saner NJ, Lee MJC, Hawley JA. Discordant skeletal muscle gene and protein responses to exercise. Trends Biochem Sci 2023; 48:927-936. [PMID: 37709636 DOI: 10.1016/j.tibs.2023.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/07/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
The ability of skeletal muscle to adapt to repeated contractile stimuli is one of the most intriguing aspects of physiology. The molecular bases underpinning these adaptations involve increased protein activity and/or expression, mediated by an array of pre- and post-transcriptional processes, as well as translational and post-translational control. A longstanding dogma assumes a direct relationship between exercise-induced increases in mRNA levels and subsequent changes in the abundance of the proteins they encode. Drawing on the results of recent studies, we dissect and question the common assumption of a direct relationship between changes in the skeletal muscle transcriptome and proteome induced by repeated muscle contractions (e.g., exercise).
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Affiliation(s)
- David J Bishop
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia.
| | - Nolan J Hoffman
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
| | - Dale F Taylor
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Nicholas J Saner
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Matthew J-C Lee
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Australia
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6
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Lukanda MM, Dramadri IO, Adjei EA, Badji A, Arusei P, Gitonga HW, Wasswa P, Edema R, Ochwo-Ssemakula M, Tukamuhabwa P, Muthuri HM, Tusiime G. Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Genes (Basel) 2023; 14:1271. [PMID: 37372451 DOI: 10.3390/genes14061271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.
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Affiliation(s)
- Musondolya Mathe Lukanda
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Faculté des Sciences Agronomiques, Université Catholique du Graben, Butembo P.O. Box 29, Democratic Republic of the Congo
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Emmanuel Amponsah Adjei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Council for Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Arfang Badji
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Perpetua Arusei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Department of Biological Sciences, Moi University, Eldoret P.O. Box 3900-30100, Kenya
| | - Hellen Wairimu Gitonga
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Mildred Ochwo-Ssemakula
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Harun Murithi Muthuri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- International Institute of Tropical Agriculture (IITA), ILRI, Nairobi P.O. Box 30709-00100, Kenya
| | - Geoffrey Tusiime
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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7
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Oakley CA, Newson GI, Peng L, Davy SK. The Symbiodinium Proteome Response to Thermal and Nutrient Stresses. PLANT & CELL PHYSIOLOGY 2023; 64:433-447. [PMID: 36565060 PMCID: PMC10109209 DOI: 10.1093/pcp/pcac175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/18/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Coral bleaching is primarily caused by high sea surface temperatures, and nutrient enrichment of reefs is associated with lower resilience to thermal stress and ecological degradation. Excess inorganic nitrogen relative to phosphate has been proposed to sensitize corals to thermal bleaching. We assessed the physiological and proteomic responses of cultures of the dinoflagellate coral symbiont Symbiodinium microadriaticum to elevated temperature under low-nutrient, high-nutrient and phosphate-limited conditions. Elevated temperature induced reductions of many chloroplast proteins, particularly the light-harvesting complexes, and simultaneously increased the abundance of many chaperone proteins. Proteomes were similar when the N:P ratio was near the Redfield ratio, regardless of absolute N and P concentrations, but were strongly affected by phosphate limitation. Very high N:P inhibited Symbiodinium cell division while increasing the abundance of chloroplast proteins. The proteome response to phosphate limitation was greater than that to elevated temperature, as measured by the number of differentially abundant proteins. Increased physiological sensitivity to high temperatures under high nutrients or imbalanced N:P ratios was not apparent; however, oxidative stress response proteins were enriched among proteins responding to thermal stress under imbalanced N:P ratios. These data provide a detailed catalog of the effects of high temperatures and nutrients on a coral symbiont proteome.
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Affiliation(s)
| | - Grace I Newson
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Lifeng Peng
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
| | - Simon K Davy
- School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington 6140, New Zealand
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8
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Kwolek-Mirek M, Dubicka-Lisowska A, Bednarska S, Zadrag-Tecza R, Kaszycki P. Changes in a Protein Profile Can Account for the Altered Phenotype of the Yeast Saccharomyces cerevisiae Mutant Lacking the Copper-Zinc Superoxide Dismutase. Metabolites 2023; 13:metabo13030459. [PMID: 36984899 PMCID: PMC10056615 DOI: 10.3390/metabo13030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Copper-zinc superoxide dismutase (SOD1) is an antioxidant enzyme that catalyzes the disproportionation of superoxide anion to hydrogen peroxide and molecular oxygen (dioxygen). The yeast Saccharomyces cerevisiae lacking SOD1 (Δsod1) is hypersensitive to the superoxide anion and displays a number of oxidative stress-related alterations in its phenotype. We compared proteomes of the wild-type strain and the Δsod1 mutant employing two-dimensional gel electrophoresis and detected eighteen spots representing differentially expressed proteins, of which fourteen were downregulated and four upregulated. Mass spectrometry-based identification enabled the division of these proteins into functional classes related to carbon metabolism, amino acid and protein biosynthesis, nucleotide biosynthesis, and metabolism, as well as antioxidant processes. Detailed analysis of the proteomic data made it possible to account for several important morphological, biochemical, and physiological changes earlier observed for the SOD1 mutation. An example may be the proposed additional explanation for methionine auxotrophy. It is concluded that protein comparative profiling of the Δsod1 yeast may serve as an efficient tool in the elucidation of the mutation-based systemic alterations in the resultant S. cerevisiae phenotype.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Aleksandra Dubicka-Lisowska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
| | - Sabina Bednarska
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Pawel Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
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9
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Benegiamo G, von Alvensleben GV, Rodríguez-López S, Goeminne LJ, Bachmann AM, Morel JD, Broeckx E, Ma JY, Carreira V, Youssef SA, Azhar N, Reilly DF, D’Aquino K, Mullican S, Bou-Sleiman M, Auwerx J. The genetic background shapes the susceptibility to mitochondrial dysfunction and NASH progression. J Exp Med 2023; 220:213867. [PMID: 36787127 PMCID: PMC9960245 DOI: 10.1084/jem.20221738] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/21/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a global health concern without treatment. The challenge in finding effective therapies is due to the lack of good mouse models and the complexity of the disease, characterized by gene-environment interactions. We tested the susceptibility of seven mouse strains to develop NASH. The severity of the clinical phenotypes observed varied widely across strains. PWK/PhJ mice were the most prone to develop hepatic inflammation and the only strain to progress to NASH with extensive fibrosis, while CAST/EiJ mice were completely resistant. Levels of mitochondrial transcripts and proteins as well as mitochondrial function were robustly reduced specifically in the liver of PWK/PhJ mice, suggesting a central role of mitochondrial dysfunction in NASH progression. Importantly, the NASH gene expression profile of PWK/PhJ mice had the highest overlap with the human NASH signature. Our study exposes the limitations of using a single mouse genetic background in metabolic studies and describes a novel NASH mouse model with features of the human NASH.
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Affiliation(s)
- Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Giorgia Benegiamo:
| | | | - Sandra Rodríguez-López
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ludger J.E. Goeminne
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Alexis M. Bachmann
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Jean-David Morel
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Ellen Broeckx
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | - Jing Ying Ma
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | - Nabil Azhar
- Janssen Research and Development, LLC, Raritan, NJ, USA
| | | | | | | | - Maroun Bou-Sleiman
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne, Lausanne, Switzerland,Correspondence to Johan Auwerx:
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10
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Shelke AD. Toxic Effect of Silver Nanoparticles on Liver, Gill and Muscle Tissues of Zebrafish <i>Danio rerio</i>. Toxicol Int 2023. [DOI: 10.18311/ti/2022/v29i4/29647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
The present study was aimed to evaluate the toxic effect of Silver nanoparticle on the liver, gill and muscle tissues of the Zebrafish, Danio rerio. The experiment was designed to understand the chronic toxicity of silver nanoparticles (AgNPs) in adult fish, Danio rerio. In the chronic toxicity study adult fish, Danio rerio were divided in to two groups. First group was experimental group in which fish were successively treated with a graded series of 0.3, 0.6, 0.9 mg/l an average 60 nm. PVP. coated AgNPs treatment were given for 21 days, at the end of experimental period, Reduced glutathione activity (GSH), Lipid peroxidation activity (LPO), Lactate dehydrogenase (LDH) and Total protein in liver, gill and muscle tissues were assayed. Second group were kept as a control which was free from AgNPs exposure. The levels of Reduced glutathione activity (GSH) and Total protein were found to be decreased were as Lipid peroxidation activity (LPO) and Lactate dehydrogenase activity (LDH) were found to be elevated in liver, gill and muscle tissue of AgNPs treated Zebrafish Danio rerio.
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11
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Menero-Valdés P, Lores-Padín A, Fernández B, Quarles CD, García M, González-Iglesias H, Pereiro R. Determination and localization of specific proteins in individual ARPE-19 cells by single cell and laser ablation ICP-MS using iridium nanoclusters as label. Talanta 2023; 253:123974. [PMID: 36195026 DOI: 10.1016/j.talanta.2022.123974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/13/2022] [Accepted: 09/25/2022] [Indexed: 12/13/2022]
Abstract
Single cell-inductively coupled plasma-mass spectrometry (sc-ICP-MS) and laser ablation (LA)-ICP-MS have been complementary employed to develop a comprehensive study of APOE and claudin-1 expression in ARPE-19 cells submitted to a glucose treatment (100 mM, 48 h) that induces oxidative stress conditions. Results were compared with control cells. The determination of the two proteins by ICP-MS was sequentially carried out using specific immunoprobes labelled with IrNCs that offer a huge amplification (1760 ± 90 atoms of Ir on average). A novel sample introduction system, the microFAST Single Cell set-up, was employed for sc-ICP-MS analysis. This introduction system resulted in a cellular transport efficiency of 85 ± 9% for ARPE-19 cells (91 ± 5% using a PtNPs standard). After the proper immunocytochemistry protocol with the specific IrNCs immunoprobes in cell suspensions (sc-ICP-MS), the mass of APOE and claudin-1 in individual ARPE-19 cells was obtained. Average detection limits per cell by sc-ICP-MS were 0.02 fg of APOE and 3 ag of claudin-1. The results of sample analyses obtained by sc-ICP-MS were validated with commercial ELISA kits. The distribution of both target proteins in individual cells (fixated in the chamber wall) was unveiled by LA-ICP-MS. The high amplification provided by the IrNCs immunoprobes allowed the identification of APOE and claudin-1 within individual ARPE-19 cells. High resolution images were obtained using a laser spot of 2 × 2 μm.
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Affiliation(s)
- Paula Menero-Valdés
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, Oviedo, 33006, Spain
| | - Ana Lores-Padín
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, Oviedo, 33006, Spain
| | - Beatriz Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, Oviedo, 33006, Spain.
| | - C Derrick Quarles
- Elemental Scientific, Inc., 7277 World Communications Drive, Omaha, NE, 68122, USA
| | - Montserrat García
- Instituto Oftalmológico Fernández-Vega, Avda. Dres. Fernández-Vega, 34, Oviedo, 33012, Spain; Department of Cellular Morphology and Biology, Faculty of Medicine, Julian Clavería, Oviedo, 33006, Spain
| | - Héctor González-Iglesias
- Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
| | - Rosario Pereiro
- Department of Physical and Analytical Chemistry, University of Oviedo, Julian Clavería 8, Oviedo, 33006, Spain.
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12
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Ferreira BL, Sousa MB, Leite GGF, Brunialti MKC, Nishiduka ES, Tashima AK, van der Poll T, Salomão R. Glucose metabolism is upregulated in the mononuclear cell proteome during sepsis and supports endotoxin-tolerant cell function. Front Immunol 2022; 13:1051514. [PMID: 36466921 PMCID: PMC9718365 DOI: 10.3389/fimmu.2022.1051514] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/01/2022] [Indexed: 07/24/2023] Open
Abstract
Metabolic adaptations shape immune cell function. In the acute response, a metabolic switch towards glycolysis is necessary for mounting a proinflammatory response. During the clinical course of sepsis, both suppression and activation of immune responses take place simultaneously. Leukocytes from septic patients present inhibition of cytokine production while other functions such as phagocytosis and production of reactive oxygen species (ROS) are preserved, similarly to the in vitro endotoxin tolerance model, where a first stimulation with lipopolysaccharide (LPS) affects the response to a second stimulus. Here, we sought to investigate how cellular metabolism is related to the modulation of immune responses in sepsis and endotoxin tolerance. Proteomic analysis in peripheral blood mononuclear cells (PBMCs) from septic patients obtained at intensive care unit admission showed an upregulation of proteins related to glycolysis, the pentose phosphate pathway (PPP), production of ROS and nitric oxide, and downregulation of proteins in the tricarboxylic acid cycle and oxidative phosphorylation compared to healthy volunteers. Using the endotoxin-tolerance model in PBMCs from healthy subjects, we observed increased lactate production in control cells upon LPS stimulation, while endotoxin-tolerant cells presented inhibited tumor necrosis factor-α and lactate production along with preserved phagocytic capacity. Inhibition of glycolysis and PPP led to impairment of phagocytosis and cytokine production both in control and in endotoxin-tolerant cells. These data indicate that glucose metabolism supports leukocyte functions even in a condition of endotoxin tolerance.
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Affiliation(s)
- Bianca Lima Ferreira
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mônica Bragança Sousa
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Milena Karina Colo Brunialti
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Erika Sayuri Nishiduka
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Alexandre Keiji Tashima
- Department of Biochemistry, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tom van der Poll
- Center of Experimental and Molecular Medicine, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
- Division of Infectious Diseases, Amsterdam Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Reinaldo Salomão
- Division of Infectious Diseases, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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13
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da Silva GB, Yamauchi MA, Bagatini MD. Oxidative stress in Hashimoto's thyroiditis: possible adjuvant therapies to attenuate deleterious effects. Mol Cell Biochem 2022; 478:949-966. [PMID: 36168075 DOI: 10.1007/s11010-022-04564-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022]
Abstract
A number of studies have shown that oxidative stress is related to the pathogenesis of several immunological diseases, such as Hashimoto's thyroiditis (HT), although there is no plausible mechanism to explain it. Thus, we aimed at hypothesizing and providing some possible mechanisms linking oxidative stress to autoimmunity aspects and its implications for HT, as well as adjuvant therapeutic proposals to mitigate the deleterious effects. Our hypothesis is that deficient eating habits, autoimmune regulator gene predisposing gene, dysbiosis and molecular mimicry, unfolded proteins and stress in the endoplasmic reticulum, and thymus involution appear to be the main potential factors leading to HT oxidative stress. Likewise, we show that the use of minerals selenium and zinc, vitamins D and C, as well as probiotics, can be interesting adjuvant therapies for the control of oxidative damage and poor prognosis of HT. Further clinical trials are needed to understand the real beneficial and side effects of these supplements.
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Affiliation(s)
- Gilnei Bruno da Silva
- Post Graduate Program in Biomedical Sciences, Universidade Federal da Fronteira Sul, Chapecó, Santa Catarina, 89815-899, Brazil
| | - Milena Ayumi Yamauchi
- Post Graduate Program in Biomedical Sciences, Universidade Federal da Fronteira Sul, Chapecó, Santa Catarina, 89815-899, Brazil
| | - Margarete Dulce Bagatini
- Post Graduate Program in Biomedical Sciences, Universidade Federal da Fronteira Sul, Chapecó, Santa Catarina, 89815-899, Brazil.
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14
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Chidananda AH, Khandelwal R, Jhamkhindikar A, Pawar AD, Sharma AK, Sharma Y. Secretagogin is a Ca 2+-dependent stress-responsive chaperone that may also play a role in aggregation-based proteinopathies. J Biol Chem 2022; 298:102285. [PMID: 35870554 PMCID: PMC9425029 DOI: 10.1016/j.jbc.2022.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Secretagogin (SCGN) is a three-domain hexa-EF-hand Ca2+-binding protein that plays a regulatory role in the release of several hormones. SCGN is expressed largely in pancreatic β-cells, certain parts of the brain, and also in neuroendocrine tissues. The expression of SCGN is altered in several diseases, such as diabetes, cancers, and neurodegenerative disorders; however, the precise associations that closely link SCGN expression to such pathophysiologies are not known. In this work, we report that SCGN is an early responder to cellular stress, and SCGN expression is temporally upregulated by oxidative stress and heat shock. We show the overexpression of SCGN efficiently prevents cells from heat shock and oxidative damage. We further demonstrate that in the presence of Ca2+, SCGN efficiently prevents the aggregation of a broad range of model proteins in vitro. Small-angle X-ray scattering (BioSAXS) studies further reveal that Ca2+ induces the conversion of a closed compact apo-SCGN conformation into an open extended holo-SCGN conformation via multistate intermediates, consistent with the augmentation of chaperone activity of SCGN. Furthermore, isothermal titration calorimetry establishes that Ca2+ enables SCGN to bind α-synuclein and insulin, two target proteins of SCGN. Altogether, our data not only demonstrate that SCGN is a Ca2+-dependent generic molecular chaperone involved in protein homeostasis with broad substrate specificity but also elucidate the origin of its altered expression in several cancers. We describe a plausible mechanism of how perturbations in Ca2+ homeostasis and/or deregulated SCGN expression would hasten the process of protein misfolding, which is a feature of many aggregation-based proteinopathies.
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Affiliation(s)
- Amrutha H Chidananda
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India
| | - Radhika Khandelwal
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Aditya Jhamkhindikar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India
| | - Asmita D Pawar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Indian Institute of Scientific and Education Research (IISER), Berhampur-760010, India
| | - Anand K Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India.
| | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India; Indian Institute of Scientific and Education Research (IISER), Berhampur-760010, India.
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15
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Simões V, Cizubu BK, Harley L, Zhou Y, Pajak J, Snyder NA, Bouvette J, Borgnia MJ, Arya G, Bartesaghi A, Silva GM. Redox-sensitive E2 Rad6 controls cellular response to oxidative stress via K63-linked ubiquitination of ribosomes. Cell Rep 2022; 39:110860. [PMID: 35613580 PMCID: PMC9215706 DOI: 10.1016/j.celrep.2022.110860] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 01/11/2023] Open
Abstract
Protein ubiquitination is an essential process that rapidly regulates protein synthesis, function, and fate in dynamic environments. Within its non-proteolytic functions, we showed that K63-linked polyubiquitinated conjugates heavily accumulate in yeast cells exposed to oxidative stress, stalling ribosomes at elongation. K63-ubiquitinated conjugates accumulate mostly because of redox inhibition of the deubiquitinating enzyme Ubp2; however, the role and regulation of ubiquitin-conjugating enzymes (E2) in this pathway remained unclear. Here, we show that the E2 Rad6 associates and modifies ribosomes during stress. We further demonstrate that Rad6 and its human homolog UBE2A are redox regulated by forming a reversible disulfide with the E1 ubiquitin-activating enzyme (Uba1). This redox regulation is part of a negative feedback regulation, which controls the levels of K63 ubiquitination under stress. Finally, we show that Rad6 activity is necessary to regulate translation, antioxidant defense, and adaptation to stress, thus providing an additional physiological role for this multifunctional enzyme.
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Affiliation(s)
- Vanessa Simões
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Lana Harley
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ye Zhou
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Joshua Pajak
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Nathan A Snyder
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC 27709, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Department of Biochemistry, and Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, NC 27708, USA.
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16
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Kavoor A, Kelly P, Ibba M. Escherichia coli alanyl-tRNA synthetase maintains proofreading activity and translational accuracy under oxidative stress. J Biol Chem 2022; 298:101601. [PMID: 35065077 PMCID: PMC8857464 DOI: 10.1016/j.jbc.2022.101601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that synthesize aminoacyl-tRNAs to facilitate translation of the genetic code. Quality control by aaRS proofreading and other mechanisms maintains translational accuracy, which promotes cellular viability. Systematic disruption of proofreading, as recently demonstrated for alanyl-tRNA synthetase (AlaRS), leads to dysregulation of the proteome and reduced viability. Recent studies showed that environmental challenges such as exposure to reactive oxygen species can also alter aaRS synthetic and proofreading functions, prompting us to investigate if oxidation might positively or negatively affect AlaRS activity. We found that while oxidation leads to modification of several residues in Escherichia coli AlaRS, unlike in other aaRSs, this does not affect proofreading activity against the noncognate substrates serine and glycine and only results in a 1.6-fold decrease in efficiency of cognate Ala-tRNAAla formation. Mass spectrometry analysis of oxidized AlaRS revealed that the critical proofreading residue in the editing site, Cys666, and three methionine residues (M217 in the active site, M658 in the editing site, and M785 in the C-Ala domain) were modified to cysteine sulfenic acid and methionine sulfoxide, respectively. Alanine scanning mutagenesis showed that none of the identified residues were solely responsible for the change in cognate tRNAAla aminoacylation observed under oxidative stress, suggesting that these residues may act as reactive oxygen species “sinks” to protect catalytically critical sites from oxidative damage. Combined, our results indicate that E. coli AlaRS proofreading is resistant to oxidative damage, providing an important mechanism of stress resistance that helps to maintain proteome integrity and cellular viability.
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Affiliation(s)
- Arundhati Kavoor
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA; Department of Microbiology, The Ohio State University, Columbus, Ohio, USA; Schmid College of Science and Technology, Chapman University, Orange, California, USA.
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17
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Srinivas P, Steiner RE, Pavelich IJ, Guerrero-Ferreira R, Juneja P, Ibba M, Dunham CM. Oxidation alters the architecture of the phenylalanyl-tRNA synthetase editing domain to confer hyperaccuracy. Nucleic Acids Res 2021; 49:11800-11809. [PMID: 34581811 PMCID: PMC8599791 DOI: 10.1093/nar/gkab856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/12/2022] Open
Abstract
High fidelity during protein synthesis is accomplished by aminoacyl-tRNA synthetases (aaRSs). These enzymes ligate an amino acid to a cognate tRNA and have proofreading and editing capabilities that ensure high fidelity. Phenylalanyl-tRNA synthetase (PheRS) preferentially ligates a phenylalanine to a tRNAPhe over the chemically similar tyrosine, which differs from phenylalanine by a single hydroxyl group. In bacteria that undergo exposure to oxidative stress such as Salmonella enterica serovar Typhimurium, tyrosine isomer levels increase due to phenylalanine oxidation. Several residues are oxidized in PheRS and contribute to hyperactive editing, including against mischarged Tyr-tRNAPhe, despite these oxidized residues not being directly implicated in PheRS activity. Here, we solve a 3.6 Å cryo-electron microscopy structure of oxidized S. Typhimurium PheRS. We find that oxidation results in widespread structural rearrangements in the β-subunit editing domain and enlargement of its editing domain. Oxidization also enlarges the phenylalanyl-adenylate binding pocket but to a lesser extent. Together, these changes likely explain why oxidation leads to hyperaccurate editing and decreased misincorporation of tyrosine. Taken together, these results help increase our understanding of the survival of S. Typhimurium during human infection.
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Affiliation(s)
- Pooja Srinivas
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Molecular and Systems Pharmacology Graduate Program, Emory University, Atlanta, GA 30322, USA.,Antibiotic Resistance Center, Emory University, Atlanta, GA 30322, USA
| | - Rebecca E Steiner
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Ian J Pavelich
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Antibiotic Resistance Center, Emory University, Atlanta, GA 30322, USA.,Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Ricardo Guerrero-Ferreira
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Puneet Juneja
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Christine M Dunham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Antibiotic Resistance Center, Emory University, Atlanta, GA 30322, USA
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18
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Structure and dynamics of UBA5-UFM1 complex formation showing new insights in the UBA5 activation mechanism. J Struct Biol 2021; 213:107796. [PMID: 34508858 DOI: 10.1016/j.jsb.2021.107796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/17/2021] [Accepted: 09/05/2021] [Indexed: 11/21/2022]
Abstract
Ubiquitin fold modifier 1 (UFM1) is an ubiquitin-like protein (Ubl) involved especially in endoplasmic stress response. Activation occurs via a three-step mechanism like other Ubls. Data obtained reveal that UFM1 regulates the oligomeric state of ubiquitin activating enzyme 5 (UBA5) to initiate the activation step. Mixtures of homodimers and heterotrimers are observed in solution at the equilibrium state, demonstrating that the UBA5-UFM1 complex undergoes several concentration dependent oligomeric translational states to form a final functional complex. The oligomerization state of unbound UBA5 is also concentration dependent and shifts from the monomeric to the dimeric state. Data describing different oligomeric states are complemented with binding studies that reveal a negative cooperativity for the complex formation and thereby provide more detailed insights into the complex formation mechanism.
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19
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Krzyzanowski D, Kruszewski M, Grzelak A. Differential Action of Silver Nanoparticles on ABCB1 (MDR1) and ABCC1 (MRP1) Activity in Mammalian Cell Lines. MATERIALS 2021; 14:ma14123383. [PMID: 34207361 PMCID: PMC8234686 DOI: 10.3390/ma14123383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 01/01/2023]
Abstract
Silver nanoparticles (AgNPs), due to their unique properties have been receiving immense attention in recent years. In addition to their antibacterial and antifungal activities, AgNPs also cause apoptosis, mitochondria disfunction, nucleic acid damage and show potent anticancer properties in both multidrug resistance (MDR) and sensitive tumors. The MDR phenomenon, caused by the presence of ATP-binding cassette (ABC) proteins, is responsible for the failure of chemotherapy. Thus, investigating the influence of widely used AgNPs on ABC transporters is crucial. In the present study, we have examined the cytotoxicity of silver nanoparticles of a nominal size of 20 nm (Ag20) on the cell lines of different tissue origins. In addition, we have checked the ATP-binding cassette transporters’ activity and expression under AgNP exposure. The results indicate that Ag20 shows a toxic effect on tested cells, as well as modulating the expression and transport activity of ABC proteins.
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Affiliation(s)
- Damian Krzyzanowski
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, 91-738 Lodz, Poland
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland
- Correspondence:
| | - Marcin Kruszewski
- Centre for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
- Department of Molecular Biology and Translational Research, Institute of Rural Health, 20-090 Lublin, Poland
| | - Agnieszka Grzelak
- Department of Molecular Biophysics, University of Lodz, 90-237 Lodz, Poland;
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20
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Stress modulation as a means to improve yeasts for lignocellulose bioconversion. Appl Microbiol Biotechnol 2021; 105:4899-4918. [PMID: 34097119 DOI: 10.1007/s00253-021-11383-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
The second-generation (2G) fermentation environment for lignocellulose conversion presents unique challenges to the fermentative organism that do not necessarily exist in other industrial fermentations. While extreme osmotic, heat, and nutrient starvation stresses are observed in sugar- and starch-based fermentation environments, additional pre-treatment-derived inhibitor stress, potentially exacerbated by stresses such as pH and product tolerance, exist in the 2G environment. Furthermore, in a consolidated bioprocessing (CBP) context, the organism is also challenged to secrete enzymes that may themselves lead to unfolded protein response and other stresses. This review will discuss responses of the yeast Saccharomyces cerevisiae to 2G-specific stresses and stress modulation strategies that can be followed to improve yeasts for this application. We also explore published -omics data and discuss relevant rational engineering, reverse engineering, and adaptation strategies, with the view of identifying genes or alleles that will make positive contributions to the overall robustness of 2G industrial strains. KEYPOINTS: • Stress tolerance is a key driver to successful application of yeast strains in biorefineries. • A wealth of data regarding stress responses has been gained through omics studies. • Integration of this knowledge could inform engineering of fit for purpose strains.
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21
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Luo Z, Hu H, Liu S, Zhang Z, Li Y, Zhou L. Comprehensive analysis of the translatome reveals the relationship between the translational and transcriptional control in high fat diet-induced liver steatosis. RNA Biol 2021; 18:863-874. [PMID: 32967529 PMCID: PMC8081042 DOI: 10.1080/15476286.2020.1827193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Translational regulation plays a critical role in gene expression. However, there are few genome-wide studies on translational regulation in non-alcoholic fatty liver disease (NAFLD), which is a severe non-communicable epidemic worldwide. In this study, we performed RNC-mRNA (mRNAs bound to ribosome-nascent chain complex) sequencing and mRNA sequencing to probe the translation status of high-fat-diet (HFD) induced mouse fatty liver. Generally, in the HFD group compared to the control group, changes of translation ratios and changes in mRNA abundance had a negative correlation. The relative abundance of RNC-mRNAs and mRNAs were positively correlated, yet the former changed more slowly than the latter. However, the rate of change became more balanced when it came to the livers of mice that were fed the HFD plus lycopene, an antioxidant. This indicated relatively independent roles of translational modulation and transcriptional regulation. Furthermore, many genes were differentially regulated at the transcriptional or translational levels, suggesting a new screening strategy for functional genes. In conclusion, our analysis revealed the different and correlated role of translational control with transcriptional regulation in the HFD-induced mouse fatty liver relative to the control, which indicates critical roles of translational control for liver steatosis; thus, adding a new dimension towards a better understanding and improvement of treatment for NAFLD.
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Affiliation(s)
- Zupeng Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Hailong Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Siqi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Zhiwang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Yixing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
| | - Lei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning, P.R. China
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22
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Zhong N, Yao Y, Ma Y, Meng X, Sowanou A, Pei J. Effects of Fluoride on Oxidative Stress Markers of Lipid, Gene, and Protein in Rats. Biol Trace Elem Res 2021; 199:2238-2246. [PMID: 32789643 DOI: 10.1007/s12011-020-02336-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/06/2020] [Indexed: 12/20/2022]
Abstract
Endemic fluorosis is a systemic chronic disease caused by excessive intake of fluoride. It is widely accepted that oxidative stress is closely related to fluorosis; however, molecular mechanism of oxidative stress in fluorosis remains unclear. This study investigated the effects of fluoride (F) on oxidative stress markers of lipid, gene, and protein in rats for revealing molecular mechanism of oxidative stress in fluorosis. The results showed concentration and exposure time of fluoride both had a significant effect on MDA and 8-OHdG. Fluoride concentration significantly impacted AGEs level, but exposure time did not. AOPP was not statistically different among the groups. AGEs decreased with the increase of fluoride in the rats with 3 months of fluoride treatment. The correlation analysis showed the degree of dental fluorosis was significantly negatively correlated with 8-OHdG at 1 month and 3 months, and negatively correlated with AGEs at 3 months. In the rats with 100 mg/L of fluoride treatment, MDA was significant positively correlated with 8-OHdG, and negatively correlated with AGEs. 8-OHdG was significantly negatively correlated with AGEs in the control group and 100 mg/L fluoride group. Taken together, fluoride had different effects on oxidative stress markers of lipid, gene, and protein. Excessive fluoride could increase MDA content, and decrease 8-OHdG and AGEs. These findings suggest that oxidative stress involved in molecular pathogenesis of fluorosis is complicated, and needs to furtherly study in the future.
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Affiliation(s)
- Nan Zhong
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Yingjie Yao
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Yongzheng Ma
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Xinyue Meng
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Alphonse Sowanou
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China
| | - Junrui Pei
- Key Lab of Etiology and Epidemiology, Education Bureau of Heilongjiang Province & National Health Commission (23618504), Institute for Kaschin-Beck Disease Control, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, 150081, Heilongjiang Province, China.
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23
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Moro SG, Hermans C, Ruiz-Orera J, Albà MM. Impact of uORFs in mediating regulation of translation in stress conditions. BMC Mol Cell Biol 2021; 22:29. [PMID: 33992089 PMCID: PMC8126119 DOI: 10.1186/s12860-021-00363-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background A large fraction of genes contains upstream ORFs (uORFs) in the 5′ untranslated region (5’UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature dissociation of the two ribosomal units or ribosome stalling. However, it is currently unknown if most uORFs are inhibitory or if this activity is restricted to specific cases. Here we interrogate ribosome profiling data from three different stress experiments in yeast to gain novel insights into this question. Results By comparing ribosome occupancies in different conditions and experiments we obtain strong evidence that, in comparison to primary coding sequences (CDS), which undergo translational arrest during stress, the translation of uORFs is mostly unaffected by changes in the environment. As a result, the relative abundance of uORF-encoded peptides increases during stress. In general, the changes in the translational efficiency of regions containing uORFs do not seem to affect downstream translation. The exception are uORFs found in a subset of genes that are significantly up-regulated at the level of translation during stress; these uORFs tend to be translated at lower levels in stress conditions than in optimal growth conditions, facilitating the translation of the CDS during stress. We find new examples of uORF-mediated regulation of translation, including the Gcn4 functional homologue fil1 and ubi4 genes in S. pombe. Conclusion We find evidence that the relative amount of uORF-encoded peptides increases during stress. The increased translation of uORFs is however uncoupled from the general CDS translational repression observed during stress. In a subset of genes that encode proteins that need to be rapidly synthesized upon stress uORFs act as translational switches. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00363-9.
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Affiliation(s)
- Simone G Moro
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cedric Hermans
- Bioinformatics Knowledge Center, Howest University of Applied Sciences, Bruges, Belgium
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute (IMIM) and Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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24
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Spevak CC, Elias HK, Kannan L, Ali MAE, Martin GH, Selvaraj S, Eng WS, Ernlund A, Rajasekhar VK, Woolthuis CM, Zhao G, Ha CJ, Schneider RJ, Park CY. Hematopoietic Stem and Progenitor Cells Exhibit Stage-Specific Translational Programs via mTOR- and CDK1-Dependent Mechanisms. Cell Stem Cell 2021; 26:755-765.e7. [PMID: 32386556 DOI: 10.1016/j.stem.2019.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/16/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022]
Abstract
Hematopoietic stem cells (HSCs) require highly regulated rates of protein synthesis, but it is unclear if they or lineage-committed progenitors preferentially recruit transcripts to translating ribosomes. We utilized polysome profiling, RNA sequencing, and whole-proteomic approaches to examine the translatome in LSK (Lin-Sca-1+c-Kit+) and myeloid progenitor (MP; Lin-Sca-1-c-Kit+) cells. Our studies show that LSKs exhibit low global translation but high translational efficiencies (TEs) of mRNAs required for HSC maintenance. In contrast, MPs activate translation in an mTOR-independent manner due, at least in part, to proteasomal degradation of mTOR by the E3 ubiquitin ligase c-Cbl. In the near absence of mTOR, CDK1 activates eIF4E-dependent translation in MPs through phosphorylation of 4E-BP1. Aberrant activation of mTOR expression and signaling in c-Cbl-deficient MPs results in increased mature myeloid lineage output. Overall, our data demonstrate that hematopoietic stem and progenitor cells (HSPCs) undergo translational reprogramming mediated by previously uncharacterized mechanisms of translational regulation.
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Affiliation(s)
- Christina C Spevak
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Harold K Elias
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Lavanya Kannan
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Mohamed A E Ali
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Gaëlle H Martin
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | | | - William S Eng
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Amanda Ernlund
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Vinagolu K Rajasekhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Carolien M Woolthuis
- Department of Hematology, Cancer Research Center, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Guangjie Zhao
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Caryn J Ha
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Robert J Schneider
- Department of Microbiology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Christopher Y Park
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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25
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Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1647. [PMID: 33694288 DOI: 10.1002/wrna.1647] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Responsible for generating the proteome that controls phenotype, translation is the ultimate convergence point for myriad upstream signals that influence gene expression. System-wide adaptive translational reprogramming has recently emerged as a pillar of cellular adaptation. As classic regulators of mRNA stability and translation efficiency, foundational studies established the concept of collaboration and competition between RNA-binding proteins (RBPs) and noncoding RNAs (ncRNAs) on individual mRNAs. Fresh conceptual innovations now highlight stress-activated, evolutionarily conserved RBP networks and ncRNAs that increase the translation efficiency of populations of transcripts encoding proteins that participate in a common cellular process. The discovery of post-transcriptional functions for long noncoding RNAs (lncRNAs) was particularly intriguing given their cell-type-specificity and historical definition as nuclear-functioning epigenetic regulators. The convergence of RBPs, lncRNAs, and microRNAs on functionally related mRNAs to enable adaptive protein synthesis is a newer biological paradigm that highlights their role as "translatome (protein output) remodelers" and reinvigorates the paradigm of "RNA operons." Together, these concepts modernize our understanding of cellular stress adaptation and strategies for therapeutic development. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Regulation Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Jeffrey H S Man
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada.,Department of Respirology, University Health Network, Latner Thoracic Research Laboratories, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Philip A Marsden
- Keenan Research Centre, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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26
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Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach. Sci Rep 2021; 11:5495. [PMID: 33750851 PMCID: PMC7943770 DOI: 10.1038/s41598-021-84904-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Myopia, or short-sightedness, is a highly prevalent refractive disorder in which the eye's focal length is too short for its axial dimension in its relaxed state. High myopia is associated with increased risks of blinding ocular complications and abnormal eye shape. In addition to consistent findings on posterior segment anomalies in high myopia (e.g., scleral remodeling), more recent biometric and biomechanical data in myopic humans and animal models also indicate anterior segment anomalies (e.g., corneal biomechanical properties). Because the cornea is the anterior-most ocular tissue, providing essential refractive power and physiological stability, it is important to understand the biochemical signaling pathway during myopia development. This study first aimed to establish the entire chicken corneal proteome. Then, using the classical form deprivation paradigm to induce high myopia in chicks, state-of-the-art bioinformatics technologies were applied to identify eight differentially expressed proteins in the highly myopic cornea. These results provide strong foundation for future corneal research, especially those using chicken as an animal model for myopia development.
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27
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Wasinger VC, Curnoe D, Boel C, Machin N, Goh HM. The Molecular Floodgates of Stress-Induced Senescence Reveal Translation, Signalling and Protein Activity Central to the Post-Mortem Proteome. Int J Mol Sci 2020; 21:ijms21176422. [PMID: 32899302 PMCID: PMC7504133 DOI: 10.3390/ijms21176422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
The transitioning of cells during the systemic demise of an organism is poorly understood. Here, we present evidence that organismal death is accompanied by a common and sequential molecular flood of stress-induced events that propagate the senescence phenotype, and this phenotype is preserved in the proteome after death. We demonstrate activation of “death” pathways involvement in diseases of ageing, with biochemical mechanisms mapping onto neurological damage, embryonic development, the inflammatory response, cardiac disease and ultimately cancer with increased significance. There is sufficient bioavailability of the building blocks required to support the continued translation, energy, and functional catalytic activity of proteins. Significant abundance changes occur in 1258 proteins across 1 to 720 h post-mortem of the 12-week-old mouse mandible. Protein abundance increases concord with enzyme activity, while mitochondrial dysfunction is evident with metabolic reprogramming. This study reveals differences in protein abundances which are akin to states of stress-induced premature senescence (SIPS). The control of these pathways is significant for a large number of biological scenarios. Understanding how these pathways function during the process of cellular death holds promise in generating novel solutions capable of overcoming disease complications, maintaining organ transplant viability and could influence the findings of proteomics through “deep-time” of individuals with no historically recorded cause of death.
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Affiliation(s)
- Valerie C. Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia
- Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia; (C.B.); (N.M.); (H.M.G.)
- Correspondence: (V.C.W.); (D.C.)
| | - Darren Curnoe
- Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia; (C.B.); (N.M.); (H.M.G.)
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales Sydney, Kensington, NSW 2052, Australia
- Correspondence: (V.C.W.); (D.C.)
| | - Ceridwen Boel
- Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia; (C.B.); (N.M.); (H.M.G.)
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales Sydney, Kensington, NSW 2052, Australia
| | - Naomi Machin
- Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia; (C.B.); (N.M.); (H.M.G.)
| | - Hsiao Mei Goh
- Palaeontology, Geobiology and Earth Archives Research Centre, University of New South Wales Sydney, Kensington, NSW 2052, Australia; (C.B.); (N.M.); (H.M.G.)
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales Sydney, Kensington, NSW 2052, Australia
- Centre for Global Archaeological Research, University Sains Malaysia, Penang 11800, Malaysia
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28
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Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress. Proc Natl Acad Sci U S A 2020; 117:22157-22166. [PMID: 32855298 DOI: 10.1073/pnas.2005301117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Subpopulations of ribosomes are responsible for fine tuning the control of protein synthesis in dynamic environments. K63 ubiquitination of ribosomes has emerged as a new posttranslational modification that regulates protein synthesis during cellular response to oxidative stress. K63 ubiquitin, a type of ubiquitin chain that functions independently of the proteasome, modifies several sites at the surface of the ribosome, however, we lack a molecular understanding on how this modification affects ribosome structure and function. Using cryoelectron microscopy (cryo-EM), we resolved the first three-dimensional (3D) structures of K63 ubiquitinated ribosomes from oxidatively stressed yeast cells at 3.5-3.2 Å resolution. We found that K63 ubiquitinated ribosomes are also present in a polysome arrangement, similar to that observed in yeast polysomes, which we determined using cryoelectron tomography (cryo-ET). We further showed that K63 ubiquitinated ribosomes are captured uniquely at the rotated pretranslocation stage of translation elongation. In contrast, cryo-EM structures of ribosomes from mutant cells lacking K63 ubiquitin resolved at 4.4-2.7 Å showed 80S ribosomes represented in multiple states of translation, suggesting that K63 ubiquitin regulates protein synthesis at a selective stage of elongation. Among the observed structural changes, ubiquitin mediates the destabilization of proteins in the 60S P-stalk and in the 40S beak, two binding regions of the eukaryotic elongation factor eEF2. These changes would impact eEF2 function, thus, inhibiting translocation. Our findings help uncover the molecular effects of K63 ubiquitination on ribosomes, providing a model of translation control during oxidative stress, which supports elongation halt at pretranslocation.
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29
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Stultz LK, Hunsucker A, Middleton S, Grovenstein E, O'Leary J, Blatt E, Miller M, Mobley J, Hanson PK. Proteomic analysis of the S. cerevisiae response to the anticancer ruthenium complex KP1019. Metallomics 2020; 12:876-890. [PMID: 32329475 PMCID: PMC7362344 DOI: 10.1039/d0mt00008f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Like platinum-based chemotherapeutics, the anticancer ruthenium complex indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(iii)], or KP1019, damages DNA, induces apoptosis, and causes tumor regression in animal models. Unlike platinum-based drugs, KP1019 showed no dose-limiting toxicity in a phase I clinical trial. Despite these advances, the mechanism(s) and target(s) of KP1019 remain unclear. For example, the drug may damage DNA directly or by causing oxidative stress. Likewise, KP1019 binds cytosolic proteins, suggesting DNA is not the sole target. Here we use the budding yeast Saccharomyces cerevisiae as a model in a proteomic study of the cellular response to KP1019. Mapping protein level changes onto metabolic pathways revealed patterns consistent with elevated synthesis and/or cycling of the antioxidant glutathione, suggesting KP1019 induces oxidative stress. This result was supported by increased fluorescence of the redox-sensitive dye DCFH-DA and increased KP1019 sensitivity of yeast lacking Yap1, a master regulator of the oxidative stress response. In addition to oxidative and DNA stress, bioinformatic analysis revealed drug-dependent increases in proteins involved ribosome biogenesis, translation, and protein (re)folding. Consistent with proteotoxic effects, KP1019 increased expression of a heat-shock element (HSE) lacZ reporter. KP1019 pre-treatment also sensitized yeast to oxaliplatin, paralleling prior research showing that cancer cell lines with elevated levels of translation machinery are hypersensitive to oxaliplatin. Combined, these data suggest that one of KP1019's many targets may be protein metabolism, which opens up intriguing possibilities for combination therapy.
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Affiliation(s)
- Laura K Stultz
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Alexandra Hunsucker
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Sydney Middleton
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Evan Grovenstein
- Department of Biology, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Jacob O'Leary
- Department of Chemistry, Birmingham-Southern College, Birmingham, AL 35254, USA
| | - Eliot Blatt
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - Mary Miller
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - James Mobley
- Department of Surgery, University of Alabama at Birmingham, School of Medicine, Birmingham, AL 35294, USA
| | - Pamela K Hanson
- Department of Biology, Furman University, Greenville, SC 29613, USA.
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30
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Ayres JC, Porto HKP, de Andrade DML, Junior JB, Ribeiro MTL, Rocha ML. Paracetamol-induced metabolic and cardiovascular changes are prevented by exercise training. Basic Clin Pharmacol Toxicol 2020; 127:516-524. [PMID: 32573044 DOI: 10.1111/bcpt.13460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022]
Abstract
Paracetamol (PAR) is the most frequently consumed non-prescription drug, yet it is well known to induce toxicity. Here, we have evaluated the effects of exercise training on vascular dysfunction induced by PAR. Rats were distributed among four groups: (a) Sedentary; (b) Exercise; (c) Sedentary+PAR; and (d) Exercise+PAR. The exercise comprised swimming 50 min/d, 5 d/wk for 6 weeks (+PAR in the last 2 weeks, at 400 mg/kg/d/p.o.). After killing, the rats' blood and aortas were collected for biochemical analysis of hepatic transaminases, TBARs reaction, glutathione, glutathione reductase, SOD, and catalase. In vitro vascular relaxation was measured using acetylcholine and sodium nitroprusside in the presence or absence of tiron (an antioxidant). Vascular protein expression (eNOS and sGC) also were analysed. Increased transaminases after PAR treatment were found to be reduced by exercise. Vasodilation was impaired by PAR only in the sedentary group. Exercise prevented alterations in lipoperoxidation and glutathione levels after PAR exposure. Glutaathione reductase and SOD also were increased by PAR but were normalized in the exercised group. Catalase activity and protein expressions did not change in any group. PAR treatment caused impairment in both vasodilation and redox balance; however, exercise training prevented the vascular and redox system dysfunction induced by PAR treatment.
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Affiliation(s)
- Júlio Cesar Ayres
- Laboratory of Pharmacology, Faculty of Pharmacy, Federal University of Goias, Goiânia, Brazil
| | | | | | - José Britto Junior
- Laboratory of Pharmacology, Faculty of Pharmacy, Federal University of Goias, Goiânia, Brazil
| | | | - Matheus Lavorenti Rocha
- Laboratory of Pharmacology, Faculty of Pharmacy, Federal University of Goias, Goiânia, Brazil
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31
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Bush JT, Chan MC, Mohammed S, Schofield CJ. Quantitative MS-Based Proteomics: Comparing the MCF-7 Cellular Response to Hypoxia and a 2-Oxoglutarate Analogue. Chembiochem 2020; 21:1647-1655. [PMID: 31919953 PMCID: PMC7317498 DOI: 10.1002/cbic.201900719] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/19/2022]
Abstract
The hypoxia-inducible factors (HIFs) are key transcription factors in determining cellular responses involving alterations in protein levels in response to limited oxygen availability in animal cells. 2-Oxoglutarate-dependent oxygenases play key roles in regulating levels of HIF and its transcriptional activity. We describe MS-based proteomics studies in which we compared the results of subjecting human breast cancer MCF-7 cells to hypoxia or treating them with a cell-penetrating derivative (dimethyl N-oxalylglycine; DMOG) of the stable 2OG analogue N-oxalylglycine. The proteomic results are consistent with reported transcriptomic analyses and support the proposed key roles of 2OG-dependent HIF prolyl- and asparaginyl-hydroxylases in the hypoxic response. Differences between the data sets for hypoxia and DMOG might reflect context-dependent effects or HIF-independent effects of DMOG.
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Affiliation(s)
- Jacob T. Bush
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: GSKMedicines Research CentreGunnels Wood RoadStevenageSG1 2NYUK
| | - Mun Chiang Chan
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: Department of Molecular MedicineFaculty of MedicineUniversity of Malaya, Jalan Universiti50603Kuala LumpurMalaysia
| | - Shabaz Mohammed
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Christopher J. Schofield
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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32
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Ho JJD, Balukoff NC, Theodoridis PR, Wang M, Krieger JR, Schatz JH, Lee S. A network of RNA-binding proteins controls translation efficiency to activate anaerobic metabolism. Nat Commun 2020; 11:2677. [PMID: 32472050 PMCID: PMC7260222 DOI: 10.1038/s41467-020-16504-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/30/2020] [Indexed: 01/30/2023] Open
Abstract
Protein expression evolves under greater evolutionary constraint than mRNA levels, and translation efficiency represents a primary determinant of protein levels during stimuli adaptation. This raises the question as to the translatome remodelers that titrate protein output from mRNA populations. Here, we uncover a network of RNA-binding proteins (RBPs) that enhances the translation efficiency of glycolytic proteins in cells responding to oxygen deprivation. A system-wide proteomic survey of translational engagement identifies a family of oxygen-regulated RBPs that functions as a switch of glycolytic intensity. Tandem mass tag-pulse SILAC (TMT-pSILAC) and RNA sequencing reveals that each RBP controls a unique but overlapping portfolio of hypoxic responsive proteins. These RBPs collaborate with the hypoxic protein synthesis apparatus, operating as a translation efficiency checkpoint that integrates upstream mRNA signals to activate anaerobic metabolism. This system allows anoxia-resistant animals and mammalian cells to initiate anaerobic glycolysis and survive hypoxia. We suggest that an oxygen-sensitive RBP cluster controls anaerobic metabolism to confer hypoxia tolerance. mRNA translation efficiency is regulated in response to stimuli. Here the authors employ mass spectrometry analysis of ribosome fractions and show that under hypoxia, oxygen-sensitive RNA binding proteins enhance the translation efficiency of glycolysis pathway transcripts.
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Affiliation(s)
- J J David Ho
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Nathan C Balukoff
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Phaedra R Theodoridis
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Miling Wang
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jonathan R Krieger
- The SickKids Proteomics, Analytics, Robotics & Chemical Biology Centre (SPARC Biocentre), The Hospital for Sick Children, Toronto, ON, M5G 1X8, Canada.,Bioinformatics Solutions Inc., Waterloo, ON, N2L 6J2, Canada
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Division of Hematology, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA. .,Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA. .,Department of Urology, Miller School of Medicine, University of Miami, Miami, 33136, USA.
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33
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Risner ML, McGrady NR, Pasini S, Lambert WS, Calkins DJ. Elevated ocular pressure reduces voltage-gated sodium channel NaV1.2 protein expression in retinal ganglion cell axons. Exp Eye Res 2020; 190:107873. [PMID: 31734278 PMCID: PMC6957720 DOI: 10.1016/j.exer.2019.107873] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/16/2019] [Accepted: 11/13/2019] [Indexed: 01/05/2023]
Abstract
Glaucoma is an age-related neurodegenerative disease that is commonly associated with sensitivity to intraocular pressure. The disease selectively targets retinal ganglion cells (RGCs) and constituent axons. RGC axons are rich in voltage-gated sodium channels, which are essential for action potential initiation and regeneration. Here, we identified voltage-dependent sodium channel, NaV1.2, in the retina, examined how this channel contributes to RGC light responses, and monitored NaV1.2 mRNA and protein expression in the retina during progression of modeled glaucoma. We found NaV1.2 is predominately localized in ganglion cell intraretinal axons with dispersed expression in the outer and inner plexiform layers. We showed Phrixotoxin-3, a potent NaV1.2 channel blocker, significantly decreased RGC electrical activity in a dose-dependent manner with an IC50 of 40 nM. Finally, we found four weeks of raised intraocular pressure (30% above baseline) significantly increased NaV1.2 mRNA expression but reduced NaV1.2 protein level in the retina up to 57% (p < 0.001). Following prolonged intraocular pressure elevation, NaV1.2 protein expression particularly diminished at distal sections of ganglion cell intraretinal axons (p ≤ 0.01). Our results suggest NaV1.2 might be a therapeutic target during disease progression to maintain RGC excitability, preserving presynaptic connections through action potential backpropagation.
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Affiliation(s)
- Michael L Risner
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, 11435 Medical Research Building IV, 2215B Garland Ave, Nashville, TN, 37232-0654, USA
| | - Nolan R McGrady
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, 11435 Medical Research Building IV, 2215B Garland Ave, Nashville, TN, 37232-0654, USA
| | - Silvia Pasini
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, 11435 Medical Research Building IV, 2215B Garland Ave, Nashville, TN, 37232-0654, USA
| | - Wendi S Lambert
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, 11435 Medical Research Building IV, 2215B Garland Ave, Nashville, TN, 37232-0654, USA
| | - David J Calkins
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, 11435 Medical Research Building IV, 2215B Garland Ave, Nashville, TN, 37232-0654, USA.
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34
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Manohar S, Jacob S, Wang J, Wiechecki KA, Koh HW, Simões V, Choi H, Vogel C, Silva GM. Polyubiquitin Chains Linked by Lysine Residue 48 (K48) Selectively Target Oxidized Proteins In Vivo. Antioxid Redox Signal 2019; 31:1133-1149. [PMID: 31482721 PMCID: PMC6798811 DOI: 10.1089/ars.2019.7826] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Aims: Ubiquitin is a highly conserved protein modifier that heavily accumulates during the oxidative stress response. Here, we investigated the role of the ubiquitination system, particularly at the linkage level, in the degradation of oxidized proteins. The function of ubiquitin in the removal of oxidized proteins remains elusive because of the wide range of potential targets and different roles that polyubiquitin chains play. Therefore, we describe in detail the dynamics of the K48 ubiquitin response as the canonical signal for protein degradation. We identified ubiquitin targets and defined the relationship between protein ubiquitination and oxidation during the stress response. Results: Combining oxidized protein isolation, linkage-specific ubiquitination screens, and quantitative proteomics, we found that K48 ubiquitin accumulated at both the early and late phases of the stress response. We further showed that a fraction of oxidized proteins are conjugated with K48 ubiquitin. We identified ∼750 ubiquitinated proteins and ∼400 oxidized proteins that were modified during oxidative stress, and around half of which contain both modifications. These proteins were highly abundant and function in translation and energy metabolism. Innovation and Conclusion: Our work showed for the first time that K48 ubiquitin modifies a large fraction of oxidized proteins, demonstrating that oxidized proteins can be targeted by the ubiquitin/proteasome system. We suggest that oxidized proteins that rapidly accumulate during stress are subsequently ubiquitinated and degraded during the late phase of the response. This delay between oxidation and ubiquitination may be necessary for reprogramming protein dynamics, restoring proteostasis, and resuming cell growth.
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Affiliation(s)
- Sandhya Manohar
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Samson Jacob
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Jade Wang
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Keira A. Wiechecki
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Hiromi W.L. Koh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vanessa Simões
- Department of Biology, Duke University, Durham, North Carolina
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christine Vogel
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York
| | - Gustavo M. Silva
- Department of Biology, Duke University, Durham, North Carolina
- Address correspondence to: Dr. Gustavo M. Silva, Department of Biology, Duke University, 130 Science Drive, Durham, NC 27708
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35
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Blevins WR, Tavella T, Moro SG, Blasco-Moreno B, Closa-Mosquera A, Díez J, Carey LB, Albà MM. Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast. Sci Rep 2019; 9:11005. [PMID: 31358845 PMCID: PMC6662803 DOI: 10.1038/s41598-019-47424-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed to directly influence protein abundances. However, the correlation between RNA-Seq and proteomics data is in general quite limited owing to differences in protein stability and translational regulation. Here we perform RNA-Seq, ribosome profiling and proteomics analyses in baker's yeast cells grown in rich media and oxidative stress conditions to examine gene expression regulation at various levels. With the exception of a small set of genes involved in the maintenance of the redox state, which are regulated at the transcriptional level, modulation of protein expression is largely driven by changes in the relative ribosome density across conditions. The majority of shifts in mRNA abundance are compensated by changes in the opposite direction in the number of translating ribosomes and are predicted to result in no net change at the protein level. We also identify a subset of mRNAs which is likely to undergo specific translational repression during stress and which includes cell cycle control genes. The study suggests that post-transcriptional buffering of gene expression may be more common than previously anticipated.
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Affiliation(s)
- William R Blevins
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Teresa Tavella
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Dipartimento di Farmacia e Biotecnologie (FaBiT), Università di Bologna, Bologna, Italy
| | - Simone G Moro
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bernat Blasco-Moreno
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain
| | - Adrià Closa-Mosquera
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain.,John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Juana Díez
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain
| | - Lucas B Carey
- Health and Experimental Sciences Department, Universitat Pompeu Fabra(UPF), Barcelona, Spain.,Center for Quantitative Biology and Peking-Tsinghua Joint Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM)-Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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36
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de Witt RN, Kroukamp H, Volschenk H. Proteome response of two natural strains of Saccharomyces cerevisiae with divergent lignocellulosic inhibitor stress tolerance. FEMS Yeast Res 2019; 19:5145847. [PMID: 30371771 DOI: 10.1093/femsyr/foy116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022] Open
Abstract
Strains of Saccharomyces cerevisiae with improved tolerance to plant hydrolysates are of utmost importance for the cost-competitive production of value-added chemicals and fuels. However, engineering strategies are constrained by a lack of understanding of the yeast response to complex inhibitor mixtures. Natural S. cerevisiae isolates display niche-specific phenotypic and metabolic diversity, encoded in their DNA, which has evolved to overcome external stresses, utilise available resources and ultimately thrive in their challenging environments. Industrial and laboratory strains, however, lack these adaptations due to domestication. Natural strains can serve as a valuable resource to mitigate engineering constraints by studying the molecular mechanisms involved in phenotypic variance and instruct future industrial strain improvement to lignocellulosic hydrolysates. We, therefore, investigated the proteomic changes between two natural S. cerevisiae isolates when exposed to a lignocellulosic inhibitor mixture. Comparative shotgun proteomics revealed that isolates respond by regulating a similar core set of proteins in response to inhibitor stress. Furthermore, superior tolerance was linked to NAD(P)/H and energy homeostasis, concurrent with inhibitor and reactive oxygen species detoxification processes. We present several candidate proteins within the redox homeostasis and energy management cellular processes as possible targets for future modification and study. Data are available via ProteomeXchange with identifier PXD010868.
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Affiliation(s)
- R N de Witt
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch, 7600, Western Cape, South Africa
| | - H Kroukamp
- Department of Molecular Sciences, Macquarie University, Balaclava Rd, North Ryde NSW 2109, Australia
| | - H Volschenk
- Department of Microbiology, Stellenbosch University, De Beer Street, Stellenbosch, 7600, Western Cape, South Africa
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37
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Solé M, Monge M, André M, Quero C. A proteomic analysis of the statocyst endolymph in common cuttlefish (Sepia officinalis): an assessment of acoustic trauma after exposure to sound. Sci Rep 2019; 9:9340. [PMID: 31249355 PMCID: PMC6597576 DOI: 10.1038/s41598-019-45646-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/11/2019] [Indexed: 12/21/2022] Open
Abstract
Recent studies, both in laboratory and sea conditions, have demonstrated damage after sound exposure in the cephalopod statocyst sensory epithelium, which secretes endolymph protein. Here, the proteomic analysis of the endolymph was performed before and after sound exposure to assess the effects of exposure to low intensity, low frequency sounds on the statocyst endolymph of the Mediterranean common cuttlefish (Sepia officinalis), determining changes in the protein composition of the statocyst endolymph immediately and 24 h after sound exposure. Significant differences in protein expression were observed, especially 24 h after exposure. A total of 37 spots were significantly different in exposed specimens, 17 of which were mostly related to stress and cytoskeletal structure. Among the stress proteins eight spots corresponding to eight hemocyanin isoforms were under-expressed possible due to lower oxygen consumption. In addition, cytoskeletal proteins such as tubulin alpha chain and intermediate filament protein were also down-regulated after exposure. Thus, endolymph analysis in the context of acoustic stress allowed us to establish the effects at the proteome level and identify the proteins that are particularly sensitive to this type of trauma.
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Affiliation(s)
- M Solé
- Laboratory of Applied Bioacoustics, Technical University of Catalonia, Barcelona TECH, 08800, Rambla exposició s/n, Vilanova i la Geltrú, Barcelona, Spain
| | - M Monge
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Edifici Collserola, 08035, Barcelona, Spain
| | - M André
- Laboratory of Applied Bioacoustics, Technical University of Catalonia, Barcelona TECH, 08800, Rambla exposició s/n, Vilanova i la Geltrú, Barcelona, Spain.
| | - C Quero
- Department of Biological Chemistry and Molecular Modelling, IQAC (CSIC), Jordi Girona 18, 08034, Barcelona, Spain.
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38
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Steiner RE, Ibba M. Regulation of tRNA-dependent translational quality control. IUBMB Life 2019; 71:1150-1157. [PMID: 31135095 DOI: 10.1002/iub.2080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/01/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023]
Abstract
Translation is the most error-prone process in protein synthesis; however, it is important that accuracy is maintained because erroneous translation has been shown to affect all domains of life. Translational quality control is maintained by both proteins and RNA through intricate processes. The aminoacyl-tRNA synthetases help maintain high levels of translational accuracy through the esterification of tRNA and proofreading mechanisms. tRNA is often recognized by an aminoacyl-tRNA synthetase in a sequence and structurally dependent manner, sometimes involving modified nucleotides. Additionally, some proofreading mechanisms of aminoacyl-tRNA synthetases require tRNA elements for hydrolysis of a noncognate aminoacyl-tRNA. Finally, tRNA is also important for proper decoding of the mRNA message by codon and anticodon pairing. Here, recent developments regarding the importance of tRNA in maintenance of translational accuracy are reviewed. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1150-1157, 2019.
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Affiliation(s)
- Rebecca E Steiner
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Michael Ibba
- The Ohio State University Biochemistry Program, The Ohio State University, Columbus, OH, USA.,Center for RNA Biology, The Ohio State University, Columbus, OH, USA.,Department of Microbiology, The Ohio State University, Columbus, OH, USA
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39
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Li H, Zhang W, Zhang H, Xie Y, Sun C, Di C, Si J, Gan L, Yan J. Mitochondrial proteomics reveals the mechanism of spermatogenic cells apoptosis induced by carbon ion radiation in zebrafish. J Cell Physiol 2019; 234:22439-22449. [DOI: 10.1002/jcp.28808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/20/2019] [Accepted: 04/24/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Hongyan Li
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
- School of Nuclear Science and Technology University of Chinese Academy of Sciences Beijing China
| | - Weihong Zhang
- Department of Ultrasonography Gansu Wuwei Tumor Hospital Wuwei China
| | - Hong Zhang
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
- School of Nuclear Science and Technology University of Chinese Academy of Sciences Beijing China
- Department of Science and Technology Gansu Wuwei Tumor Hospital Wuwei China
| | - Yi Xie
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
| | - Chao Sun
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
| | - Cuixia Di
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
| | - Jing Si
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
| | - Lu Gan
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
| | - Junfang Yan
- Department of Radiation Medicine, Institute of Modern Physics Chinese Academy of Sciences Lanzhou China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences Institute of Modern Physics Lanzhou China
- Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine Institute of Modern Physics, Chinese Academy of Sciences Lanzhou China
- School of Nuclear Science and Technology University of Chinese Academy of Sciences Beijing China
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40
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Oxidation of phenylalanyl-tRNA synthetase positively regulates translational quality control. Proc Natl Acad Sci U S A 2019; 116:10058-10063. [PMID: 31036643 DOI: 10.1073/pnas.1901634116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate translation of the genetic code is maintained in part by aminoacyl-tRNA synthetases (aaRS) proofreading mechanisms that ensure correct attachment of a cognate amino acid to a transfer RNA (tRNA). During environmental stress, such as oxidative stress, demands on aaRS proofreading are altered by changes in the availability of cytoplasmic amino acids. For example, oxidative stress increases levels of cytotoxic tyrosine isomers, noncognate amino acids normally excluded from translation by the proofreading activity of phenylalanyl-tRNA synthetase (PheRS). Here we show that oxidation of PheRS induces a conformational change, generating a partially unstructured protein. This conformational change does not affect Phe or Tyr activation or the aminoacylation activity of PheRS. However, in vitro and ex vivo analyses reveal that proofreading activity to hydrolyze Tyr-tRNAPhe is increased during oxidative stress, while the cognate Phe-tRNAPhe aminoacylation activity is unchanged. In HPX-, Escherichia coli that lack reactive oxygen-scavenging enzymes and accumulate intracellular H2O2, we found that PheRS proofreading is increased by 11%, thereby providing potential protection against hazardous cytoplasmic m-Tyr accumulation. These findings show that in response to oxidative stress, PheRS proofreading is positively regulated without negative effects on the enzyme's housekeeping activity in translation. Our findings also illustrate that while the loss of quality control and mistranslation may be beneficial under some conditions, increased proofreading provides a mechanism for the cell to appropriately respond to environmental changes during oxidative stress.
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41
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Exposure to acetaminophen impairs vasodilation, increases oxidative stress and changes arterial morphology of rats. Arch Toxicol 2019; 93:1955-1964. [PMID: 31020376 DOI: 10.1007/s00204-019-02463-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 04/18/2019] [Indexed: 12/16/2022]
Abstract
Acetaminophen (APAP) is one of the most widely consumed drugs in the world. Studies have shown renal and hepatic damage as the direct result of high oxidative stress induced by APAP. Since the cardiovascular system is sensitive to oxidative stress and literature describes increased cardiovascular dysfunction in APAP consumers, this work aimed to evaluate harmful effects of APAP on the vascular system. Rats were exposed to APAP (400 mg/kg/day in drinking water) for 14 days. Plasma and aortas were collected and stored in - 80 °C and a selection of arteries was prepared for isometric tension recordings, morphological, immunohistochemical and protein expression analysis. The APAP-treated group presented increased transaminases (ALT/AST) and malondialdehyde levels in the plasma compared to controls. Lipid peroxidation, glutathione reductase and superoxide dismutase levels were increased in the plasma and arteries of the APAP group. Nevertheless, glutathione level was reduced as compared to control group. The vasodilation response to acetylcholine and sodium nitroprusside (0.1 nM to 10 µM) was also impaired after APAP treatment; however, the vascular relaxation was restored after treatment with vitamin C (100 µM). Arteries from the APAP group presented reduced wall thickness, collagen deposition, elastic fibers and increased immunoreactivity to nitrotyrosine. eNOS and sGC protein expression remained unchanged and were at similar levels as controls. These findings showed higher oxidative stress and impaired vasodilation in rats exposed to APAP. Furthermore, arteries presented reduced cell layers, collagen, elastin deposition and significantly increased immunoreactivity to nitrotyrosine after APAP treatment.
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42
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Zapalska-Sozoniuk M, Chrobak L, Kowalczyk K, Kankofer M. Is it useful to use several "omics" for obtaining valuable results? Mol Biol Rep 2019; 46:3597-3606. [PMID: 30989558 DOI: 10.1007/s11033-019-04793-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 04/02/2019] [Indexed: 01/23/2023]
Abstract
The integration of cell communication and the transfer of signals from stimuli via transcription to translation and further to activation of new protein is crucial for appropriate metabolism and function of living organisms. The overall elucidation and the examination of these complex processes require multistep laboratory approaches in order to obtain results which will not only detect particular stage but also indicate the mechanisms lying upon this process. Such results will be reliable because they will cover multidirectional methods and approaches. The analysis of currently available results already provided with the conclusion that often single omics approach does not correspond with other expected information and may bring misinterpretations. That is why the integration of several "omics" is useful for searching entire explanations and answers as well as appropriate interpretation of obtained complex results. The hypothesis was stated that "from transcriptomics can not be concluded to proteomics". This review focuses on the reasons for the integration of transcriptomic, proteomic and other-omics analysis. Moreover it also describes the examples of clinical meanings and mentions some methods used in these approaches.
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Affiliation(s)
- Magdalena Zapalska-Sozoniuk
- Departament of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, Akademicka Street 12, 20-033, Lublin, Poland
| | - Lukasz Chrobak
- Departament of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, Akademicka Street 12, 20-033, Lublin, Poland
| | - Krzysztof Kowalczyk
- Institute of Plant Genetics, Breeding and Biotechnology, Faculty of Agrobioengineering, University of Life Sciences in Lublin, Akademicka Street 15, 20-950, Lublin, Poland
| | - Marta Kankofer
- Departament of Biochemistry, Faculty of Veterinary Medicine, University of Life Science in Lublin, Akademicka Street 12, 20-033, Lublin, Poland.
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43
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Sonawane AR, Weiss ST, Glass K, Sharma A. Network Medicine in the Age of Biomedical Big Data. Front Genet 2019; 10:294. [PMID: 31031797 PMCID: PMC6470635 DOI: 10.3389/fgene.2019.00294] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 03/19/2019] [Indexed: 12/13/2022] Open
Abstract
Network medicine is an emerging area of research dealing with molecular and genetic interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale biomedical data generation offers a unique opportunity to assess the effect and impact of cellular heterogeneity and environmental perturbations on the observed phenotype. Marrying the two, network medicine with biomedical data provides a framework to build meaningful models and extract impactful results at a network level. In this review, we survey existing network types and biomedical data sources. More importantly, we delve into ways in which the network medicine approach, aided by phenotype-specific biomedical data, can be gainfully applied. We provide three paradigms, mainly dealing with three major biological network archetypes: protein-protein interaction, expression-based, and gene regulatory networks. For each of these paradigms, we discuss a broad overview of philosophies under which various network methods work. We also provide a few examples in each paradigm as a test case of its successful application. Finally, we delineate several opportunities and challenges in the field of network medicine. We hope this review provides a lexicon for researchers from biological sciences and network theory to come on the same page to work on research areas that require interdisciplinary expertise. Taken together, the understanding gained from combining biomedical data with networks can be useful for characterizing disease etiologies and identifying therapeutic targets, which, in turn, will lead to better preventive medicine with translational impact on personalized healthcare.
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Affiliation(s)
- Abhijeet R. Sonawane
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Boston, MA, United States
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44
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Yang SK, Yusoff K, Ajat M, Thomas W, Abushelaibi A, Akseer R, Lim SHE, Lai KS. Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil. PLoS One 2019; 14:e0214326. [PMID: 30939149 PMCID: PMC6445408 DOI: 10.1371/journal.pone.0214326] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/10/2019] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae (KP) remains the most prevalent nosocomial pathogen and carries the carbapenemase (KPC) gene which confers resistance towards carbapenem. Thus, it is necessary to discover novel antimicrobials to address the issue of antimicrobial resistance in such pathogens. Natural products such as essential oils are a promising source due to their complex composition. Essential oils have been shown to be effective against pathogens, but the overall mechanisms have yet to be fully explained. Understanding the molecular mechanisms of essential oil towards KPC-KP cells would provide a deeper understanding of their potential use in clinical settings. Therefore, we aimed to investigate the mode of action of essential oil against KPC-KP cells from a proteomic perspective by comparing the overall proteome profile of KPC-KP cells treated with cinnamon bark (Cinnamomum verum J. Presl) essential oil (CBO) at their sub-inhibitory concentration of 0.08% (v/v). A total of 384 proteins were successfully identified from the non-treated cells, whereas only 242 proteins were identified from the CBO-treated cells. Proteins were then categorized based on their biological processes, cellular components and molecular function prior to pathway analysis. Pathway analysis showed that CBO induced oxidative stress in the KPC-KP cells as indicated by the abundance of oxidative stress regulator proteins such as glycyl radical cofactor, catalase peroxidase and DNA mismatch repair protein. Oxidative stress is likely to oxidize and disrupt the bacterial membrane as shown by the loss of major membrane proteins. Several genes selected for qRT-PCR analysis validated the proteomic profile and were congruent with the proteomic abundance profiles. In conclusion, KPC-KP cells exposed to CBO undergo oxidative stress that eventually disrupts the bacterial membrane possibly via interaction with the phospholipid bilayer. Interestingly, several pathways involved in the bacterial membrane repair system were also affected by oxidative stress, contributing to the loss of cells viability.
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Affiliation(s)
- Shun-Kai Yang
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mokrish Ajat
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Warren Thomas
- Perdana University-Royal College of Surgeons in Ireland, School of Medicine, Perdana University, Serdang, Selangor, Malaysia
| | - Aisha Abushelaibi
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Riaz Akseer
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Swee-Hua Erin Lim
- Perdana University-Royal College of Surgeons in Ireland, School of Medicine, Perdana University, Serdang, Selangor, Malaysia
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi, United Arab Emirates
| | - Kok-Song Lai
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- * E-mail:
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45
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Cziesielski MJ, Liew YJ, Cui G, Schmidt-Roach S, Campana S, Marondedze C, Aranda M. Multi-omics analysis of thermal stress response in a zooxanthellate cnidarian reveals the importance of associating with thermotolerant symbionts. Proc Biol Sci 2019; 285:rspb.2017.2654. [PMID: 29669898 PMCID: PMC5936724 DOI: 10.1098/rspb.2017.2654] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/22/2018] [Indexed: 01/07/2023] Open
Abstract
Corals and their endosymbiotic dinoflagellates of the genus Symbiodinium have a fragile relationship that breaks down under heat stress, an event known as bleaching. However, many coral species have adapted to high temperature environments such as the Red Sea (RS). To investigate mechanisms underlying temperature adaptation in zooxanthellate cnidarians we compared transcriptome- and proteome-wide heat stress response (24 h at 32°C) of three strains of the model organism Aiptasia pallida from regions with differing temperature profiles; North Carolina (CC7), Hawaii (H2) and the RS. Correlations between transcript and protein levels were generally low but inter-strain comparisons highlighted a common core cnidarian response to heat stress, including protein folding and oxidative stress pathways. RS anemones showed the strongest increase in antioxidant gene expression and exhibited significantly lower reactive oxygen species (ROS) levels in hospite. However, comparisons of antioxidant gene and protein expression between strains did not show strong differences, indicating similar antioxidant capacity across the strains. Subsequent analysis of ROS production in isolated symbionts confirmed that the observed differences of ROS levels in hospite were symbiont-driven. Our findings indicate that RS anemones do not show increased antioxidant capacity but may have adapted to higher temperatures through association with more thermally tolerant symbionts.
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Affiliation(s)
- Maha J Cziesielski
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Yi Jin Liew
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Guoxin Cui
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Sebastian Schmidt-Roach
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Sara Campana
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Claudius Marondedze
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Manuel Aranda
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia
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46
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Bertoldo JB, Terenzi H, Hüttelmaier S, Bernardes GJL. Posttranslational Chemical Mutagenesis: To Reveal the Role of Noncatalytic Cysteine Residues in Pathogenic Bacterial Phosphatases. Biochemistry 2018; 57:6144-6152. [DOI: 10.1021/acs.biochem.8b00639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jean B. Bertoldo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Institut für Molekulare Medizin, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Stra 3a, 06108 Halle, Germany
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-970 Florianópolis, SC, Brazil
| | - Stefan Hüttelmaier
- Institut für Molekulare Medizin, Medizinische Fakultät, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Stra 3a, 06108 Halle, Germany
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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Crawford RA, Pavitt GD. Translational regulation in response to stress in Saccharomyces cerevisiae. Yeast 2018; 36:5-21. [PMID: 30019452 PMCID: PMC6492140 DOI: 10.1002/yea.3349] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/08/2018] [Accepted: 06/25/2018] [Indexed: 12/19/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae must dynamically alter the composition of its proteome in order to respond to diverse stresses. The reprogramming of gene expression during stress typically involves initial global repression of protein synthesis, accompanied by the activation of stress‐responsive mRNAs through both translational and transcriptional responses. The ability of specific mRNAs to counter the global translational repression is therefore crucial to the overall response to stress. Here we summarize the major repressive mechanisms and discuss mechanisms of translational activation in response to different stresses in S. cerevisiae. Taken together, a wide range of studies indicate that multiple elements act in concert to bring about appropriate translational responses. These include regulatory elements within mRNAs, altered mRNA interactions with RNA‐binding proteins and the specialization of ribosomes that each contribute towards regulating protein expression to suit the changing environmental conditions.
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Affiliation(s)
- Robert A Crawford
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Michael Smith Building, Dover Street, Manchester, M13 9PT, UK
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48
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Nguyen TM, Kabotyanski EB, Dou Y, Reineke LC, Zhang P, Zhang XHF, Malovannaya A, Jung SY, Mo Q, Roarty KP, Chen Y, Zhang B, Neilson JR, Lloyd RE, Perou CM, Ellis MJ, Rosen JM. FGFR1-Activated Translation of WNT Pathway Components with Structured 5' UTRs Is Vulnerable to Inhibition of EIF4A-Dependent Translation Initiation. Cancer Res 2018; 78:4229-4240. [PMID: 29844125 PMCID: PMC6072612 DOI: 10.1158/0008-5472.can-18-0631] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/26/2018] [Accepted: 05/23/2018] [Indexed: 11/16/2022]
Abstract
Cooperativity between WNT and FGF signaling is well documented in embryonic development and cancer progression, but the molecular mechanisms underlying this cross-talk remain elusive. In this study, we interrogated the dynamics of RNA levels, ribosome occupancy, and protein expression as a function of inducible FGF signaling in mouse mammary glands with constitutive WNT hyperactivation. Multiomics correlation analysis revealed a substantial discrepancy between RNA and ribosome occupancy levels versus protein levels. However, this discrepancy decreased as cells became premalignant and dynamically responded to FGF signaling, implicating the importance of stringent gene regulation in nontransformed cells. Analysis of individual genes demonstrated that acute FGF hyperactivation increased translation of many stem cell self-renewal regulators, including WNT signaling components, and decreased translation of genes regulating cellular senescence. WNT pathway components translationally upregulated by FGF signaling had long and structured 5' UTRs with a high frequency of polypurine sequences, several of which harbored (CGG)4 motifs that can fold into either stable G-quadruplexes or other stable secondary structures. The FGF-mediated increase in translation of WNT pathway components was compromised by silvestrol, an inhibitor of EIF4A that clamps EIF4A to polypurine sequences to block 43S scanning and inhibits its RNA-unwinding activity important for translation initiation. Moreover, silvestrol treatment significantly delayed FGF-WNT-driven tumorigenesis. Taken together, these results suggest that FGF signaling selectively enhances translation of structured mRNAs, particularly WNT signaling components, and highlight their vulnerability to inhibitors that target the RNA helicase EIF4A.Significance: The RNA helicase EIF4A may serve as a therapeutic target for breast cancers that require FGF and WNT signaling. Cancer Res; 78(15); 4229-40. ©2018 AACR.
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Affiliation(s)
- Tuan M Nguyen
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Elena B Kabotyanski
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Lucas C Reineke
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Anna Malovannaya
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Houston, Texas
| | - Sung Yun Jung
- Verna & Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, Texas
| | - Qianxing Mo
- Dan L Duncan Comprehensive Cancer Center, Houston, Texas
| | - Kevin P Roarty
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Joel R Neilson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas
| | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Matthew J Ellis
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Houston, Texas
| | - Jeffrey M Rosen
- Graduate Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
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49
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Exposure of Drosophila melanogaster to Mancozeb Induces Oxidative Damage and Modulates Nrf2 and HSP70/83. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:5456928. [PMID: 30116484 PMCID: PMC6079323 DOI: 10.1155/2018/5456928] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/09/2018] [Accepted: 05/31/2018] [Indexed: 12/21/2022]
Abstract
Mancozeb (MZ), a manganese- and zinc-containing ethylene-bis-dithiocarbamate, is a broad-spectrum fungicide. Harmful effects of this fungicide have been reported in nontarget organisms via a not fully understood mechanism. Drosophila melanogaster has provided remarkable contributions for toxicological studies. This work was aimed at evaluating the biochemical targets and implication of oxidative stress in MZ-mediated toxicity in drosophilas. Exposure of flies for fifteen days to MZ at 5 and 10 mg/mL through the diet impaired locomotor performance and induced fly mortality. In parallel, it caused lipid peroxidation and reactive oxygen species (ROS) formation and Mn overload. MZ inhibited superoxide dismutase and inducted catalase and glutathione S-transferase activities. Nitric oxide and reduced glutathione levels were significantly decreased by MZ. Heat shock proteins (HSP70 and HSP83) and Nrf2 mRNA levels were significantly augmented in MZ-exposed flies. Our study reinforced the use of Drosophila melanogaster as a reliable model for the study of biochemical targets of pesticides, and based on our data, MZ induced oxidative damage and Mn accumulation in a concentration-dependent manner. An adaptative cellular state was inducted by the lower concentration of pesticide, possibly contributing to the slighter damage observed.
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50
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Zhou YY, Chun RKM, Wang JC, Zuo B, Li KK, Lam TC, Liu Q, To CH. Proteomic analysis of chick retina during early recovery from lens‑induced myopia. Mol Med Rep 2018; 18:59-66. [PMID: 29749514 PMCID: PMC6059693 DOI: 10.3892/mmr.2018.8954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/06/2018] [Indexed: 12/13/2022] Open
Abstract
Myopia development has been extensively studied from different perspectives. Myopia recovery is also considered important for understanding the development of myopia. However, despite several previous studies, retinal proteomics during recovery from myopia is still relatively unknown. Therefore, the aim of the present study was to investigate the changes in protein profiles of chicken retinas during early recovery from lens-induced myopia to evaluate the signals involved in the adjustment of this refractive disorder. Three-day old chickens wore glasses for 7 days (−10D lens over the right eye and a plano lens as control over the left eye), followed by 24 h without lenses. Protein expression in the retina was measured by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Pro-Q Diamond phosphoprotein staining 2D gel electrophoresis was used to analyze phosphoprotein profiles. Protein spots with significant differences (P<0.05) were analyzed by mass spectrometry. The minus lens-treated eye became myopic, however following 24 h recovery, less myopia was observed. 2D-DIGE proteomic analysis demonstrated that three identified protein spots were upregulated at least 1.2-fold in myopic recovery retinas compared with those of the controls, Ras related protein Rab-11B, S-antigen retina and pineal gland and 26S proteasome non-ATPase regulatory subunit 14. Pro-Q Diamond images further revealed three protein spots with significant changes (at least 1.8-fold): β-tubulin was downregulated, while peroxiredoxin 4 and ubiquitin carboxyl-terminal hydrolase-L1 were upregulated in the recovery retinas compared with the control eye retinas. The present study detected previously unreported protein changes in recovering eyes, therefore revealing their potential involvement in retinal remodeling during eye ball reforge.
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Affiliation(s)
- Yun Yun Zhou
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Rachel Ka Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Jian Chao Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710049, P.R. China
| | - Bing Zuo
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - King Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Quan Liu
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Chi-Ho To
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
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