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Falsztyn IB, Taylor SM, Baugh LR. Developmental and conditional regulation of DAF-2/INSR ubiquitination in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595723. [PMID: 38854056 PMCID: PMC11160630 DOI: 10.1101/2024.05.24.595723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Insulin/IGF signaling (IIS) regulates developmental and metabolic plasticity. Conditional regulation of insulin-like peptide expression and secretion promotes different phenotypes in different environments. However, IIS can also be regulated by other, less-understood mechanisms. For example, stability of the only known insulin/IGF receptor in C. elegans, DAF-2/INSR, is regulated by CHIP-dependent ubiquitination. Disruption of chn-1/CHIP reduces longevity in C. elegans by increasing DAF-2/INSR abundance and IIS activity in adults. Likewise, mutation of a ubiquitination site causes daf-2(gk390525) to display gain-of-function phenotypes in adults. However, we show that this allele displays loss-of-function phenotypes in larvae, and that its effect on IIS activity transitions from negative to positive during development. In contrast, the allele acts like a gain-of-function in larvae cultured at high temperature, inhibiting temperature-dependent dauer formation. Disruption of chn-1/CHIP causes an increase in IIS activity in starved L1 larvae, unlike daf-2(gk390525). CHN-1/CHIP ubiquitinates DAF-2/INSR at multiple sites. These results suggest that the sites that are functionally relevant to negative regulation of IIS vary in larvae and adults, at different temperatures, and in nutrient-dependent fashion, revealing additional layers of IIS regulation.
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Affiliation(s)
| | - Seth M. Taylor
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L. Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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Cerón J. Caenorhabditis elegans for research on cancer hallmarks. Dis Model Mech 2023; 16:dmm050079. [PMID: 37278614 PMCID: PMC10259857 DOI: 10.1242/dmm.050079] [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] [Indexed: 06/07/2023] Open
Abstract
After decades of research, our knowledge of the complexity of cancer mechanisms, elegantly summarized as 'hallmarks of cancer', is expanding, as are the therapeutic opportunities that this knowledge brings. However, cancer still needs intense research to diminish its tremendous impact. In this context, the use of simple model organisms such as Caenorhabditis elegans, in which the genetics of the apoptotic pathway was discovered, can facilitate the investigation of several cancer hallmarks. Amenable for genetic and drug screens, convenient for fast and efficient genome editing, and aligned with the 3Rs ('Replacement, Reduction and Refinement') principles for ethical animal research, C. elegans plays a significant role in unravelling the intricate network of cancer mechanisms and presents a promising option in clinical diagnosis and drug discovery.
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Affiliation(s)
- Julián Cerón
- Modeling Human Diseases in C. elegans Group – Genes, Disease and Therapy Program, Bellvitge Biomedical Research Institute – IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
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Webster AK, Chitrakar R, Powell M, Chen J, Fisher K, Tanny RE, Stevens L, Evans K, Wei A, Antoshechkin I, Andersen EC, Baugh LR. Using population selection and sequencing to characterize natural variation of starvation resistance in C. elegans. eLife 2022; 11:80204. [PMID: 35727141 PMCID: PMC9262388 DOI: 10.7554/elife.80204] [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: 05/11/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. Uncovering the genetic basis of complex, quantitative traits such as starvation resistance is technically challenging. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in C. elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strains using standard assays. We performed genome-wide association (GWA) with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance, and we created near isogenic lines (NILs) to validate the effect of these QTL on the trait. These QTL contain numerous candidate genes including several members of the Insulin/EGF Receptor-L Domain (irld) family. We used genome editing to show that four different irld genes have modest effects on starvation resistance. Natural variants of irld-39 and irld-52 affect starvation resistance, and increased resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS, though they may act through other mechanisms as well. This work demonstrates efficacy of using MIP-seq to dissect a complex trait and it suggests that irld genes are natural modifiers of starvation resistance in C. elegans.
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Affiliation(s)
- Amy K Webster
- Department of Biology, Duke University, Durham, United States
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, United States
| | - Maya Powell
- Department of Biology, Duke University, Durham, United States
| | - Jingxian Chen
- Department of Biology, Duke University, Durham, United States
| | - Kinsey Fisher
- Department of Biology, Duke University, Durham, United States
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Lewis Stevens
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Kathryn Evans
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Angela Wei
- Department of Biology, Duke University, Durham, United States
| | - Igor Antoshechkin
- Division of Biology, California Institute of Technology, Pasadena, United States
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, United States
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Wittes J, Greenwald I. Genetic analysis of DAF-18/PTEN missense mutants for the ability to maintain quiescence of the somatic gonad and germ line in Caenorhabditis elegans dauer larvae. G3 (BETHESDA, MD.) 2022; 12:jkac093. [PMID: 35451467 PMCID: PMC9157151 DOI: 10.1093/g3journal/jkac093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022]
Abstract
The mammalian tumor suppressor PTEN has well-established lipid phosphatase and protein phosphatase activities. DAF-18, the Caenorhabditis elegans ortholog of PTEN, has a high degree of conservation in the catalytic domain, and human PTEN complements a null allele of daf-18, suggesting conserved protein function. Insights gleaned from studies of mammalian PTEN have been applied to studies of DAF-18 in C. elegans, including predicted enzymatic properties of mutants. Here, we characterize DAF-18 missense mutants previously treated as selectively disrupting either protein or lipid phosphatase activity in genetic assays to connect distinct phenotypes to specific enzymatic activities of DAF-18/PTEN. We analyze the ability of these mutants to maintain quiescence of the somatic gonad and germ line in dauer larvae, a state of diapause during which development is suspended. We show that transgenes expressing either the putative lipid phosphatase-deficient or putative protein phosphatase-deficient form fail to complement a daf-18 null allele, and that the corresponding homozygous endogenous missense mutant alleles fail to maintain developmental quiescence. We also show that the endogenous daf-18 missense alleles fail to complement each other, suggesting that one or both of the missense forms are not activity-selective. Furthermore, homozygous daf-18 missense mutants have a more severe phenotype than a daf-18 null mutant, suggesting the presence of functionally compromised mutant DAF-18 is more deleterious than the absence of DAF-18. We discuss how these genetic properties complicate the interpretation of genetic assays to associate specific enzymatic activities with specific phenotypes.
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Affiliation(s)
- Julia Wittes
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Iva Greenwald
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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