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Larance M, Pourkarimi E, Wang B, Brenes Murillo A, Kent R, Lamond AI, Gartner A. Global Proteomics Analysis of the Response to Starvation in C. elegans. Mol Cell Proteomics 2015; 14:1989-2001. [PMID: 25963834 PMCID: PMC4587315 DOI: 10.1074/mcp.m114.044289] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 12/31/2022] Open
Abstract
Periodic starvation of animals induces large shifts in metabolism but may also influence many other cellular systems and can lead to adaption to prolonged starvation conditions. To date, there is limited understanding of how starvation affects gene expression, particularly at the protein level. Here, we have used mass-spectrometry-based quantitative proteomics to identify global changes in the Caenorhabditis elegans proteome due to acute starvation of young adult animals. Measuring changes in the abundance of over 5,000 proteins, we show that acute starvation rapidly alters the levels of hundreds of proteins, many involved in central metabolic pathways, highlighting key regulatory responses. Surprisingly, we also detect changes in the abundance of chromatin-associated proteins, including specific linker histones, histone variants, and histone posttranslational modifications associated with the epigenetic control of gene expression. To maximize community access to these data, they are presented in an online searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).
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Affiliation(s)
- Mark Larance
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Ehsan Pourkarimi
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Bin Wang
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Alejandro Brenes Murillo
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Robert Kent
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Angus I Lamond
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
| | - Anton Gartner
- From the ‡Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St, Dundee, United Kingdom, DD15EH
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Measuring Food Intake and Nutrient Absorption in Caenorhabditis elegans. Genetics 2015; 200:443-54. [PMID: 25903497 PMCID: PMC4492371 DOI: 10.1534/genetics.115.175851] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/16/2015] [Indexed: 12/19/2022] Open
Abstract
Caenorhabditiselegans has emerged as a powerful model to study the genetics of feeding, food-related behaviors, and metabolism. Despite the many advantages of C. elegans as a model organism, direct measurement of its bacterial food intake remains challenging. Here, we describe two complementary methods that measure the food intake of C. elegans. The first method is a microtiter plate-based bacterial clearing assay that measures food intake by quantifying the change in the optical density of bacteria over time. The second method, termed pulse feeding, measures the absorption of food by tracking de novo protein synthesis using a novel metabolic pulse-labeling strategy. Using the bacterial clearance assay, we compare the bacterial food intake of various C. elegans strains and show that long-lived eat mutants eat substantially more than previous estimates. To demonstrate the applicability of the pulse-feeding assay, we compare the assimilation of food for two C. elegans strains in response to serotonin. We show that serotonin-increased feeding leads to increased protein synthesis in a SER-7-dependent manner, including proteins known to promote aging. Protein content in the food has recently emerged as critical factor in determining how food composition affects aging and health. The pulse-feeding assay, by measuring de novo protein synthesis, represents an ideal method to unequivocally establish how the composition of food dictates protein synthesis. In combination, these two assays provide new and powerful tools for C. elegans research to investigate feeding and how food intake affects the proteome and thus the physiology and health of an organism.
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54
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Age-related proteostasis and metabolic alterations in Caspase-2-deficient mice. Cell Death Dis 2015; 6:e1615. [PMID: 25611376 PMCID: PMC4669765 DOI: 10.1038/cddis.2014.567] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 12/21/2022]
Abstract
Ageing is a complex biological process for which underlying biochemical changes are still largely unknown. We performed comparative profiling of the cellular proteome and metabolome to understand the molecular basis of ageing in Caspase-2-deficient (Casp2−/−) mice that are a model of premature ageing in the absence of overt disease. Age-related changes were determined in the liver and serum of young (6–9 week) and aged (18–24 month) wild-type and Casp2−/− mice. We identified perturbed metabolic pathways, decreased levels of ribosomal and respiratory complex proteins and altered mitochondrial function that contribute to premature ageing in the Casp2−/− mice. We show that the metabolic profile changes in the young Casp2−/− mice resemble those found in aged wild-type mice. Intriguingly, aged Casp2−/− mice were found to have reduced blood glucose and improved glucose tolerance. These results demonstrate an important role for caspase-2 in regulating proteome and metabolome remodelling during ageing.
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55
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Roth DM, Hutt DM, Tong J, Bouchecareilh M, Wang N, Seeley T, Dekkers JF, Beekman JM, Garza D, Drew L, Masliah E, Morimoto RI, Balch WE. Modulation of the maladaptive stress response to manage diseases of protein folding. PLoS Biol 2014; 12:e1001998. [PMID: 25406061 PMCID: PMC4236052 DOI: 10.1371/journal.pbio.1001998] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/07/2014] [Indexed: 12/31/2022] Open
Abstract
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function. To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitrypsin deficiency (AATD), Niemann-Pick type C1 disease (NPC1), Alzheimer's disease (AD), and cystic fibrosis (CF). Using distinct models, including patient-derived cell lines and primary epithelium, mouse brain tissue, and Caenorhabditis elegans, we found that chronic expression of misfolded proteins not only triggers the sustained activation of the heat shock response (HSR) pathway, but that this sustained activation is maladaptive. In diseased cells, maladaptation alters protein structure-function relationships, impacts protein folding in the cytosol, and further exacerbates the disease state. We show that down-regulation of this maladaptive stress response (MSR), through silencing of HSF1, the master regulator of the HSR, restores cellular protein folding and improves the disease phenotype. We propose that restoration of a more physiological proteostatic environment will strongly impact the management and progression of loss-of-function and gain-of-toxic-function phenotypes common in human disease.
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Affiliation(s)
- Daniela Martino Roth
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Darren M. Hutt
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jiansong Tong
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Marion Bouchecareilh
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ning Wang
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - Theo Seeley
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Johanna F. Dekkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
- Laboratory of Translational Immunology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands
| | - Dan Garza
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Lawrence Drew
- Proteostasis Therapeutics Inc., Cambridge, Massachusetts, United States of America
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, California, United States of America
| | - Richard I. Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois, United States of America
| | - William E. Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, United States of America
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, United States of America
- The Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
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DAF-16 target identification in C. elegans: past, present and future. Biogerontology 2014; 16:221-34. [PMID: 25156270 PMCID: PMC4361755 DOI: 10.1007/s10522-014-9527-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/13/2014] [Indexed: 12/28/2022]
Abstract
In C. elegans, mutations in the conserved insulin/IGF-1 signaling (IIS) pathway lead to a robust extension in lifespan, improved late life health, and protection from age-related disease. These effects are mediated by the FoxO transcription factor DAF-16 which lies downstream of the IIS kinase cascade. Identifying and functionally testing DAF-16 target genes has been a focal point of ageing research for the last 10 years. Here, I review the recent advances in identifying and understanding IIS/DAF-16 targets. These studies continue to reveal the intricate nature of the IIS/DAF-16 gene regulation network and are helping us to understand the mechanisms that control lifespan. Ageing and age related disease is an area of intense public interest, and the biochemical characterization of the genes involved will be critical for identifying drugs to improve the health of our ageing population.
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