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Tan CH, Wang TY, Park H, Lomenick B, Chou TF, Sternberg PW. Single-tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles. Proc Natl Acad Sci U S A 2024; 121:e2322588121. [PMID: 38861598 PMCID: PMC11194598 DOI: 10.1073/pnas.2322588121] [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: 12/25/2023] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of biomolecules; lysosome-related organelles known as gut granules are important for many of these functions. Aspects of intestine biology are not well understood, including the export of the nutrients it imports and the molecules it synthesizes, as well as the complete functions and protein content of the gut granules. Here, we report a mass spectrometry (MS)-based proteomic analysis of the intestine of the Caenorhabditis elegans and of its gut granules. Overall, we identified approximately 5,000 proteins each in the intestine and the gonad and showed that most of these proteins can be detected in samples extracted from a single worm, suggesting the feasibility of individual-level genetic analysis using proteomes. Comparing proteomes and published transcriptomes of the intestine and the gonad, we identified proteins that appear to be synthesized in the intestine and then transferred to the gonad. To identify gut granule proteins, we compared the proteome of individual intestines deficient in gut granules to the wild type. The identified gut granule proteome includes proteins known to be exclusively localized to the granules and additional putative gut granule proteins. We selected two of these putative gut granule proteins for validation via immunohistochemistry, and our successful confirmation of both suggests that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single-tissue MS-based proteomic analysis in small organisms and in its future utility.
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Affiliation(s)
- Chieh-Hsiang Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Ting-Yu Wang
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Brett Lomenick
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
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2
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Cui F, Ma N, Han X, Chen N, Xi Y, Yuan W, Xu Y, Han J, Xu X, Tu Y. Effects of 60Co γ Irradiation on the Reproductive Function of Caenorhabditis elegans. Dose Response 2019; 17:1559325818820981. [PMID: 30733651 PMCID: PMC6343448 DOI: 10.1177/1559325818820981] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/07/2018] [Accepted: 11/18/2018] [Indexed: 12/15/2022] Open
Abstract
The effects of ionizing radiation on the reproductive system have always been a matter of great interest. Both artificial and naturally occurring ionizing radiation can directly or indirectly affect the reproductive system via the introduction of DNA single-strand and double-strand breaks, the excitation of water molecules, and the generation of free radicals. In order to quantitatively investigate the effects of ionizing radiation on reproductive function, 60Co γ irradiation was applied on a model organism, Caenorhabditis elegans (C. elegans). The egg-laying and embryo-hatching activities were observed for the parent (F0) and the first 2 progeny (F1 and F2) generations. The incidence rate of ovipositor malformation was also recorded. Acridine orange was used to detect the number of apoptotic germ cells. With the above metrics, the effects of 60Co γ irradiation on the reproductive function of C. elegans were systematically evaluated. The results showed that the postirradiation egg-laying and embryo-hatching activities of the F0 generation were increasingly suppressed by increasing doses of 60Co γ irradiation. Those of the F1 generation showed a trend toward recovery although also suppressed by the radiation to the F0 generation compared with the control. Those activities were restored to normal or near-normal levels for the F2 generation. The incidence rate of ovipositor malformation was greatly increased by 60Co γ irradiation according to radiation doses. Gamma irradiation by 60Co also substantially induced germ cell apoptosis, and the apoptosis rate increased with increasing radiation doses. Therefore, 60Co γ irradiation affects the reproductive function of C. elegans. The suppression on its reproductive function increases with increasing radiation doses. The reproductive functions of progeny generations are also affected and weakened.
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Affiliation(s)
- Fengmei Cui
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Nan Ma
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Xiaojing Han
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Department of Hematology and Oncology, The First Affiliated Hospital of Suzhou University, Suzhou, China
| | - Na Chen
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Yue Xi
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Weiye Yuan
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Yufan Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Jianfang Han
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Xiaoyan Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
| | - Yu Tu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Soochow University, Suzhou, China.,Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Suzhou, China
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3
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Moll L, Roitenberg N, Bejerano-Sagie M, Boocholez H, Carvalhal Marques F, Volovik Y, Elami T, Siddiqui AA, Grushko D, Biram A, Lampert B, Achache H, Ravid T, Tzur YB, Cohen E. The insulin/IGF signaling cascade modulates SUMOylation to regulate aging and proteostasis in Caenorhabditis elegans. eLife 2018; 7:38635. [PMID: 30403374 PMCID: PMC6277199 DOI: 10.7554/elife.38635] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 11/06/2018] [Indexed: 12/02/2022] Open
Abstract
Although aging-regulating pathways were discovered a few decades ago, it is not entirely clear how their activities are orchestrated, to govern lifespan and proteostasis at the organismal level. Here, we utilized the nematode Caenorhabditis elegans to examine whether the alteration of aging, by reducing the activity of the Insulin/IGF signaling (IIS) cascade, affects protein SUMOylation. We found that IIS activity promotes the SUMOylation of the germline protein, CAR-1, thereby shortening lifespan and impairing proteostasis. In contrast, the expression of mutated CAR-1, that cannot be SUMOylated at residue 185, extends lifespan and enhances proteostasis. A mechanistic analysis indicated that CAR-1 mediates its aging-altering functions, at least partially, through the notch-like receptor glp-1. Our findings unveil a novel regulatory axis in which SUMOylation is utilized to integrate the aging-controlling functions of the IIS and of the germline and provide new insights into the roles of SUMOylation in the regulation of organismal aging. Aging may seem inescapable, but there are many factors, from diet to genetic mutations, that can affect this process. In fact, scientists have started to uncover the mechanisms that control and influence this slow decline. For example, in the small worm Caenorhabditis elegans, removing the germs cells – which give rise to eggs – extends the lifespan. Similarly, interfering with the activity of the Insulin/IGF-1 signaling (IIS) pathway leads to a longer life for the animals. However, it is unclear whether these two mechanisms work together, or if they operate in parallel. To explore this, Moll, Roitenberg et al. first looked at how the IIS pathway regulates a type of protein modification known as SUMOylation in C. elegans. Reducing the activity of the IIS pathway slowed down aging in the worms. It also decreased the levels of SUMOylation of certain proteins, including CAR-1, which is found in the structures that produce germ cells. Further experiments showed that stopping the SUMOylation of CAR-1 extended the lifespan of the animals. In fact, replacing the protein with a mutated version of CAR-1 that cannot accept the SUMO element makes the worms live longer and resist a toxic protein that causes Alzheimer’s disease in humans. These results therefore show that, in C. elegans, the IIS pathway and a mechanism that involves CAR-1 in germ cells work together to determine the pace of aging. Further studies are now needed to dissect how the IIS pathway influences SUMOylation, and whether the findings hold true in mammals.
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Affiliation(s)
- Lorna Moll
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Noa Roitenberg
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Michal Bejerano-Sagie
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Hana Boocholez
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Filipa Carvalhal Marques
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Yuli Volovik
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Tayir Elami
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Atif Ahmed Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Danielle Grushko
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
| | - Adi Biram
- Departments of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bar Lampert
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hana Achache
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tommer Ravid
- Departments of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonatan B Tzur
- Departments of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University School of Medicine, Jerusalem, Israel
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4
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Ankney JA, Muneer A, Chen X. Relative and Absolute Quantitation in Mass Spectrometry-Based Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:49-77. [PMID: 29894226 DOI: 10.1146/annurev-anchem-061516-045357] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mass spectrometry-based quantitative proteomics is a powerful tool for gaining insights into function and dynamics of biological systems. However, peptides with different sequences have different ionization efficiencies, and their intensities in a mass spectrum are not correlated with their abundances. Therefore, various label-free or stable isotope label-based quantitation methods have emerged to assist mass spectrometry to perform comparative proteomic experiments, thus enabling nonbiased identification of thousands of proteins differentially expressed in healthy versus diseased cells. Here, we discuss the most widely used label-free and metabolic-, enzymatic-, and chemical labeling-based proteomic strategies for relative and absolute quantitation. We summarize the specific strengths and weaknesses of each technique in terms of quantification accuracy, proteome coverage, multiplexing capability, and robustness. Applications of each strategy for solving specific biological complexities are also presented.
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Affiliation(s)
- J Astor Ankney
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Adil Muneer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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5
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Subasic D, Stoeger T, Eisenring S, Matia-González AM, Imig J, Zheng X, Xiong L, Gisler P, Eberhard R, Holtackers R, Gerber AP, Pelkmans L, Hengartner MO. Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev 2017; 30:2213-2225. [PMID: 27798844 PMCID: PMC5088569 DOI: 10.1101/gad.285726.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/16/2016] [Indexed: 12/03/2022]
Abstract
In this study, Subasic et al. investigated the post-transcriptional control of caspases. The authors describe four conserved RNA-binding proteins (RBPs) that sequentially repress the CED-3 caspase in distinct regions of the C. elegans germline and identify seven RBPs that regulate human caspase-3 expression and/or activation, suggesting that translational inhibition of executioner caspases by RBPs might be a general strategy used widely across the animal kingdom to control apoptosis. Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3′ untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3′ UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
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Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Stoeger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Systems Biology PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Seline Eisenring
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ana M Matia-González
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Lei Xiong
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Pascal Gisler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ralf Eberhard
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - René Holtackers
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - André P Gerber
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Lucas Pelkmans
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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6
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Husson SJ, Moyson S, Valkenborg D, Baggerman G, Mertens I. Proteomics applications in Caenorhabditis elegans research. Biochem Biophys Res Commun 2015; 468:519-24. [DOI: 10.1016/j.bbrc.2015.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 01/04/2023]
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7
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Rhoads TW, Prasad A, Kwiecien NW, Merrill AE, Zawack K, Westphall MS, Schroeder FC, Kimble J, Coon JJ. NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans. Mol Cell Proteomics 2015; 14:2922-35. [PMID: 26392051 DOI: 10.1074/mcp.m115.049684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Indexed: 01/05/2023] Open
Abstract
The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.
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Affiliation(s)
| | - Aman Prasad
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | | | | | - Kelson Zawack
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | | | - Frank C Schroeder
- ‡‡Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14853
| | - Judith Kimble
- ‖Biochemistry, and **Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Joshua J Coon
- From the Departments of ‡Chemistry, §Biomolecular Chemistry, ¶Genome Center,
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Kassahun H, Nilsen H. Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. WORM 2013; 2:e27337. [PMID: 24744987 DOI: 10.4161/worm.27337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/25/2013] [Indexed: 01/04/2023]
Abstract
Oxidative stress promotes human aging and contributes to common neurodegenerative diseases. Endogenous DNA damage induced by oxidative stress is believed to be an important promoter of neurodegenerative diseases. Although a large amount of evidence correlates a reduced DNA repair capacity with aging and neurodegenerative disease, there is little direct evidence of causality. Moreover, the contribution of oxidative DNA damage to the aging process is poorly understood. We have used the nematode Caenorhabditis elegans to study the contribution of oxidative DNA damage and repair to aging. C. elegans is particularly well suited to tackle this problem because it has a minimum complexity DNA repair system, which enables us to circumvent the important limitation presented by the extensive redundancy of DNA repair enzymes in mammals.
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Affiliation(s)
- Henok Kassahun
- The Biotechnology Centre; University of Oslo; Oslo, Norway
| | - Hilde Nilsen
- The Biotechnology Centre; University of Oslo; Oslo, Norway
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9
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Arczewska KD, Tomazella GG, Lindvall JM, Kassahun H, Maglioni S, Torgovnick A, Henriksson J, Matilainen O, Marquis BJ, Nelson BC, Jaruga P, Babaie E, Holmberg CI, Bürglin TR, Ventura N, Thiede B, Nilsen H. Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. Nucleic Acids Res 2013; 41:5368-81. [PMID: 23580547 PMCID: PMC3664812 DOI: 10.1093/nar/gkt225] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transcription-blocking oxidative DNA damage is believed to contribute to aging and to underlie activation of oxidative stress responses and down-regulation of insulin-like signaling (ILS) in Nucleotide Excision Repair (NER) deficient mice. Here, we present the first quantitative proteomic description of the Caenorhabditis elegans NER-defective xpa-1 mutant and compare the proteome and transcriptome signatures. Both methods indicated activation of oxidative stress responses, which was substantiated biochemically by a bioenergetic shift involving increased steady-state reactive oxygen species (ROS) and Adenosine triphosphate (ATP) levels. We identify the lesion-detection enzymes of Base Excision Repair (NTH-1) and global genome NER (XPC-1 and DDB-1) as upstream requirements for transcriptomic reprogramming as RNA-interference mediated depletion of these enzymes prevented up-regulation of genes over-expressed in the xpa-1 mutant. The transcription factors SKN-1 and SLR-2, but not DAF-16, were identified as effectors of reprogramming. As shown in human XPA cells, the levels of transcription-blocking 8,5'-cyclo-2'-deoxyadenosine lesions were reduced in the xpa-1 mutant compared to the wild type. Hence, accumulation of cyclopurines is unlikely to be sufficient for reprogramming. Instead, our data support a model where the lesion-detection enzymes NTH-1, XPC-1 and DDB-1 play active roles to generate a genomic stress signal sufficiently strong to result in transcriptomic reprogramming in the xpa-1 mutant.
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Affiliation(s)
- Katarzyna D Arczewska
- The Biotechnology Centre, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway
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