1
|
Martell J, Seo Y, Bak DW, Kingsley SF, Tissenbaum HA, Weerapana E. Global Cysteine-Reactivity Profiling during Impaired Insulin/IGF-1 Signaling in C. elegans Identifies Uncharacterized Mediators of Longevity. Cell Chem Biol 2016; 23:955-66. [PMID: 27499530 DOI: 10.1016/j.chembiol.2016.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022]
Abstract
In the nematode Caenorhabditis elegans, inactivating mutations in the insulin/IGF-1 receptor, DAF-2, result in a 2-fold increase in lifespan mediated by DAF-16, a FOXO-family transcription factor. Downstream protein activities that directly regulate longevity during impaired insulin/IGF-1 signaling (IIS) are poorly characterized. Here, we use global cysteine-reactivity profiling to identify protein activity changes during impaired IIS. Upon confirming that cysteine reactivity is a good predictor of functionality in C. elegans, we profiled cysteine-reactivity changes between daf-2 and daf-16;daf-2 mutants, and identified 40 proteins that display a >2-fold change. Subsequent RNAi-mediated knockdown studies revealed that lbp-3 and K02D7.1 knockdown caused significant increases in lifespan and dauer formation. The proteins encoded by these two genes, LBP-3 and K02D7.1, are implicated in intracellular fatty acid transport and purine metabolism, respectively. These studies demonstrate that cysteine-reactivity profiling can be complementary to abundance-based transcriptomic and proteomic studies, serving to identify uncharacterized mediators of C. elegans longevity.
Collapse
Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Yonghak Seo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Samuel F Kingsley
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heidi A Tissenbaum
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | |
Collapse
|
2
|
Warnhoff K, Murphy JT, Kumar S, Schneider DL, Peterson M, Hsu S, Guthrie J, Robertson JD, Kornfeld K. The DAF-16 FOXO transcription factor regulates natc-1 to modulate stress resistance in Caenorhabditis elegans, linking insulin/IGF-1 signaling to protein N-terminal acetylation. PLoS Genet 2014; 10:e1004703. [PMID: 25330323 PMCID: PMC4199503 DOI: 10.1371/journal.pgen.1004703] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 08/26/2014] [Indexed: 12/24/2022] Open
Abstract
The insulin/IGF-1 signaling pathway plays a critical role in stress resistance and longevity, but the mechanisms are not fully characterized. To identify genes that mediate stress resistance, we screened for C. elegans mutants that can tolerate high levels of dietary zinc. We identified natc-1, which encodes an evolutionarily conserved subunit of the N-terminal acetyltransferase C (NAT) complex. N-terminal acetylation is a widespread modification of eukaryotic proteins; however, relatively little is known about the biological functions of NATs. We demonstrated that loss-of-function mutations in natc-1 cause resistance to a broad-spectrum of physiologic stressors, including multiple metals, heat, and oxidation. The C. elegans FOXO transcription factor DAF-16 is a critical target of the insulin/IGF-1 signaling pathway that mediates stress resistance, and DAF-16 is predicted to directly bind the natc-1 promoter. To characterize the regulation of natc-1 by DAF-16 and the function of natc-1 in insulin/IGF-1 signaling, we analyzed molecular and genetic interactions with key components of the insulin/IGF-1 pathway. natc-1 mRNA levels were repressed by DAF-16 activity, indicating natc-1 is a physiological target of DAF-16. Genetic studies suggested that natc-1 functions downstream of daf-16 to mediate stress resistance and dauer formation. Based on these findings, we hypothesize that natc-1 is directly regulated by the DAF-16 transcription factor, and natc-1 is a physiologically significant effector of the insulin/IGF-1 signaling pathway that mediates stress resistance and dauer formation. These studies identify a novel biological function for natc-1 as a modulator of stress resistance and dauer formation and define a functionally significant downstream effector of the insulin/IGF-1 signaling pathway. Protein N-terminal acetylation mediated by the NatC complex may play an evolutionarily conserved role in regulating stress resistance.
Collapse
Affiliation(s)
- Kurt Warnhoff
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - John T. Murphy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sandeep Kumar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Daniel L. Schneider
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle Peterson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Simon Hsu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James Guthrie
- Research Reactor Center, University of Missouri, Columbia, Missouri, United States of America
| | - J. David Robertson
- Research Reactor Center, University of Missouri, Columbia, Missouri, United States of America
- Department of Chemistry, University of Missouri, Columbia, Missouri, United States of America
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| |
Collapse
|
3
|
Wojakowska A, Muth D, Narożna D, Mądrzak C, Stobiecki M, Kachlicki P. Changes of phenolic secondary metabolite profiles in the reaction of narrow leaf lupin ( Lupinus angustifolius) plants to infections with Colletotrichum lupini fungus or treatment with its toxin. Metabolomics 2013; 9:575-589. [PMID: 23678343 PMCID: PMC3651525 DOI: 10.1007/s11306-012-0475-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/15/2012] [Indexed: 12/16/2022]
Abstract
Plant interactions with environmental factors cause changes in the metabolism and regulation of biochemical and physiological processes. Plant defense against pathogenic microorganisms depends on an innate immunity system that is activated as a result of infection. There are two mechanisms of triggering this system: basal immunity activated as a result of a perception of microbe-associated molecular patterns through pattern recognition receptors situated on the cell surface and effector-triggered immunity (ETI). An induced biosynthesis of bioactive secondary metabolites, in particular phytoalexins, is one of the mechanisms of plant defense to fungal infection. Results of the study on narrow leaf lupin (Lupinus angustifolius L.) plants infected with the anthracnose fungus Colletotrichum lupini and treated with fungal phytotoxic metabolites are described in the paper. The C. lupini phytotoxins were isolated from liquid cultures, purified and partially characterized with physicochemical methods. Accumulation of secondary metabolites on leaf surface and within the tissues of plants either infected, treated with the fungal phytotoxin or submitted to both treatments was studied using GC-MS and LC-MS, respectively. Substantial differences in isoflavone aglycones and glycoconjugate profiles occurred in response to different ways of plant treatment.
Collapse
Affiliation(s)
- Anna Wojakowska
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Dorota Muth
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Dorota Narożna
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Poznań University of Life Science, ul. Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Cezary Mądrzak
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Poznań University of Life Science, ul. Wojska Polskiego 28, 60-637 Poznan, Poland
| | - Maciej Stobiecki
- Institute of Bioorganic Chemistry PAS, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Piotr Kachlicki
- Institute of Plant Genetics PAS, Strzeszyńska 34, 60-479 Poznań, Poland
| |
Collapse
|
4
|
Neri C. Role and Therapeutic Potential of the Pro-Longevity Factor FOXO and Its Regulators in Neurodegenerative Disease. Front Pharmacol 2012; 3:15. [PMID: 22363285 PMCID: PMC3281233 DOI: 10.3389/fphar.2012.00015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/25/2012] [Indexed: 12/25/2022] Open
Abstract
Studies in simple model organisms have yielded crucial insights into the genetic and molecular aspects of longevity. FOXO, which is most notable for its association with longevity, and its upstream regulators such as sirtuins have received particular attention in translational research because these genes modulate cell survival in several models of neurodegenerative diseases. There is a large amount of knowledge on the pathways that regulate FOXO activity and genes that may be regulated by FOXO. However, for the same reason that the FOXO network is a complex stress response system, its therapeutic potential to develop disease-modifying strategies requires further examination. Although the FOXO network contains druggable genes such as sirtuins and AMPK, whether they should be activated or inhibited and whether protection against the early or late phases of neuronal cell decline might require opposite therapeutic strategies remains unclear. Additionally, the mode of action of small compound molecules believed to act on FOXO network targets was questioned. This review recapitulates essential facts and questions about the promises of FOXO and its interactors in neurodegenerative disease.
Collapse
Affiliation(s)
- Christian Neri
- Laboratory of Neuronal Cell Biology and Pathology, Unit 894, INSERM Paris, France
| |
Collapse
|
5
|
Smith GR, Shanley DP. Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PLoS One 2010; 5:e11092. [PMID: 20567500 PMCID: PMC2886341 DOI: 10.1371/journal.pone.0011092] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 05/01/2010] [Indexed: 01/10/2023] Open
Abstract
FOXO transcription factors are an important, conserved family of regulators of cellular processes including metabolism, cell-cycle progression, apoptosis and stress resistance. They are required for the efficacy of several of the genetic interventions that modulate lifespan. FOXO activity is regulated by multiple post-translational modifications (PTMs) that affect its subcellular localization, half-life, DNA binding and transcriptional activity. Here, we show how a mathematical modelling approach can be used to simulate the effects, singly and in combination, of these PTMs. Our model is implemented using the Systems Biology Markup Language (SBML), generated by an ancillary program and simulated in a stochastic framework. The use of the ancillary program to generate the SBML is necessary because the possibility that many regulatory PTMs may be added, each independently of the others, means that a large number of chemically distinct forms of the FOXO molecule must be taken into account, and the program is used to generate them. Although the model does not yet include detailed representations of events upstream and downstream of FOXO, we show how it can qualitatively, and in some cases quantitatively, reproduce the known effects of certain treatments that induce various single and multiple PTMs, and allows for a complex spatiotemporal interplay of effects due to the activation of multiple PTM-inducing treatments. Thus, it provides an important framework to integrate current knowledge about the behaviour of FOXO. The approach should be generally applicable to other proteins experiencing multiple regulations.
Collapse
Affiliation(s)
- Graham R. Smith
- Henry Wellcome Laboratory for Biogerontology, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daryl P. Shanley
- Henry Wellcome Laboratory for Biogerontology, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| |
Collapse
|
6
|
Vermeirssen V, Joshi A, Michoel T, Bonnet E, Casneuf T, Van de Peer Y. Transcription regulatory networks in Caenorhabditis elegans inferred through reverse-engineering of gene expression profiles constitute biological hypotheses for metazoan development. MOLECULAR BIOSYSTEMS 2009; 5:1817-30. [PMID: 19763340 DOI: 10.1039/b908108a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Differential gene expression governs the development, function and pathology of multicellular organisms. Transcription regulatory networks study differential gene expression at a systems level by mapping the interactions between regulatory proteins and target genes. While microarray transcription profiles are the most abundant data for gene expression, it remains challenging to correctly infer the underlying transcription regulatory networks. The reverse-engineering algorithm LeMoNe (learning module networks) uses gene expression profiles to extract ensemble transcription regulatory networks of coexpression modules and their prioritized regulators. Here we apply LeMoNe to a compendium of microarray studies of the worm Caenorhabditis elegans. We obtain 248 modules with a regulation program for 5020 genes and 426 regulators and a total of 24 012 predicted transcription regulatory interactions. Through GO enrichment analysis, comparison with the gene-gene association network WormNet and integration of other biological data, we show that LeMoNe identifies functionally coherent coexpression modules and prioritizes regulators that relate to similar biological processes as the module genes. Furthermore, we can predict new functional relationships for uncharacterized genes and regulators. Based on modules involved in molting, meiosis and oogenesis, ciliated sensory neurons and mitochondrial metabolism, we illustrate the value of LeMoNe as a biological hypothesis generator for differential gene expression in greater detail. In conclusion, through reverse-engineering of C. elegans expression data, we obtained transcription regulatory networks that can provide further insight into metazoan development.
Collapse
|
7
|
Affiliation(s)
- Debopriya Das
- Life Sciences Division, Ernest O Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
| | | | | |
Collapse
|