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Lesnik C, Kaletsky R, Ashraf JM, Sohrabi S, Cota V, Sengupta T, Keyes W, Luo S, Murphy CT. Enhanced branched-chain amino acid metabolism improves age-related reproduction in C. elegans. Nat Metab 2024; 6:724-740. [PMID: 38418585 DOI: 10.1038/s42255-024-00996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Reproductive ageing is one of the earliest human ageing phenotypes, and mitochondrial dysfunction has been linked to oocyte quality decline; however, it is not known which mitochondrial metabolic processes are critical for oocyte quality maintenance with age. To understand how mitochondrial processes contribute to Caenorhabditis elegans oocyte quality, we characterized the mitochondrial proteomes of young and aged wild-type and long-reproductive daf-2 mutants. Here we show that the mitochondrial proteomic profiles of young wild-type and daf-2 worms are similar and share upregulation of branched-chain amino acid (BCAA) metabolism pathway enzymes. Reduction of the BCAA catabolism enzyme BCAT-1 shortens reproduction, elevates mitochondrial reactive oxygen species levels, and shifts mitochondrial localization. Moreover, bcat-1 knockdown decreases oocyte quality in daf-2 worms and reduces reproductive capability, indicating the role of this pathway in the maintenance of oocyte quality with age. Notably, oocyte quality deterioration can be delayed, and reproduction can be extended in wild-type animals both by bcat-1 overexpression and by supplementing with vitamin B1, a cofactor needed for BCAA metabolism.
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Affiliation(s)
- Chen Lesnik
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
- Faculty of Natural Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Jasmine M Ashraf
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Salman Sohrabi
- LSI Genomics, Princeton University, Princeton, NJ, USA
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, USA
| | - Vanessa Cota
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
- Department of Biology, Tacoma Community College, Tacoma, WA, USA
| | - Titas Sengupta
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
| | - William Keyes
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Shijing Luo
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- LSI Genomics, Princeton University, Princeton, NJ, USA.
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2
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Sengupta T, St. Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. PLoS Genet 2024; 20:e1011178. [PMID: 38547071 PMCID: PMC10977744 DOI: 10.1371/journal.pgen.1011178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024] Open
Abstract
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rebecca S. Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Renee J. Seto
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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Lesnik C, Kaletsky R, Ashraf JM, Sohrabi S, Cota V, Sengupta T, Keyes W, Luo S, Murphy CT. Enhanced Branched-Chain Amino Acid Metabolism Improves Age-Related Reproduction in C. elegans. bioRxiv 2024:2023.02.09.527915. [PMID: 38370685 PMCID: PMC10871302 DOI: 10.1101/2023.02.09.527915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Reproductive aging is one of the earliest human aging phenotypes, and mitochondrial dysfunction has been linked to oocyte quality decline. However, it is not known which mitochondrial metabolic processes are critical for oocyte quality maintenance with age. To understand how mitochondrial processes contribute to C. elegans oocyte quality, we characterized the mitochondrial proteomes of young and aged wild-type and long-reproductive daf-2 mutants. Here we show that the mitochondrial proteomic profiles of young wild-type and daf-2 worms are similar and share upregulation of branched-chain amino acid (BCAA) metabolism pathway enzymes. Reduction of the BCAA catabolism enzyme BCAT-1 shortens reproduction, elevates mitochondrial reactive oxygen species levels, and shifts mitochondrial localization. Moreover, bcat-1 knockdown decreases oocyte quality in daf-2 worms and reduces reproductive capability, indicating the role of this pathway in the maintenance of oocyte quality with age. Importantly, oocyte quality deterioration can be delayed, and reproduction can be extended in wild-type animals both by bcat-1 overexpression and by supplementing with Vitamin B1, a cofactor needed for BCAA metabolism.
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4
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Ange JS, Weng Y, Stevenson ME, Kaletsky R, Moore RS, Zhou S, Murphy CT. Adult Single-nucleus Neuronal Transcriptomes of Insulin Signaling Mutants Reveal Regulators of Behavior and Learning. bioRxiv 2024:2024.02.07.579364. [PMID: 38370779 PMCID: PMC10871314 DOI: 10.1101/2024.02.07.579364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The insulin/insulin-like signaling (IIS) pathway regulates many of C. elegans' adult functions, including learning and memory 1 . While whole-worm and tissue-specific transcriptomic analyses have identified IIS targets 2,3 , a higher-resolution single-cell approach is required to identify changes that confer neuron-specific improvements in the long-lived insulin receptor mutant, daf-2 . To understand how behaviors that are controlled by a small number of neurons change in daf-2 mutants, we used the deep resolution of single-nucleus RNA sequencing to define each neuron type's transcriptome in adult wild-type and daf-2 mutants. First, we found surprising differences between wild-type L4 larval neurons and young adult neurons in chemoreceptor expression, synaptic genes, and learning and memory genes. These Day 1 adult neuron transcriptomes allowed us to identify adult AWC-specific regulators of chemosensory function and to predict neuron-to-neuron peptide/receptor pairs. We then identified gene expression changes that correlate with daf-2's improved cognitive functions, particularly in the AWC sensory neuron that controls learning and associative memory 4 , and used behavioral assays to test their roles in cognitive function. Combining deep single-neuron transcriptomics, genetic manipulation, and behavioral analyses enabled us to identify genes that may function in a single adult neuron to control behavior, including conserved genes that function in learning and memory. One-Sentence Summary Single-nucleus sequencing of adult wild-type and daf-2 C. elegans neurons reveals functionally relevant transcriptional changes, including regulators of chemosensation, learning, and memory.
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Sengupta T, St. Ange J, Moore R, Kaletsky R, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. bioRxiv 2023:2023.07.20.549962. [PMID: 37503135 PMCID: PMC10370180 DOI: 10.1101/2023.07.20.549962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and its transgenerational inheritance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, like PA14, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure to GRb0427, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. Using bacterial small RNA sequencing, we identified Pv1, a small RNA from GRb0427, that matches the sequence of C. elegans maco-1. We find that Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina; this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance are functional in C. elegans' natural environment, and that different bacterial small RNA-mediated regulation systems evolved independently but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rebecca Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Sengupta T, Kaletsky R, Murphy CT. The Logic of Transgenerational Inheritance: Timescales of Adaptation. Annu Rev Cell Dev Biol 2023; 39:45-65. [PMID: 37339681 DOI: 10.1146/annurev-cellbio-020923-114620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Myriad mechanisms have evolved to adapt to changing environments. Environmental stimuli alter organisms' physiology to create memories of previous environments. Whether these environmental memories can cross the generational barrier has interested scientists for centuries. The logic of passing on information from generation to generation is not well understood. When is it useful to remember ancestral conditions, and when might it be deleterious to continue to respond to a context that may no longer exist? The key might be found in understanding the environmental conditions that trigger long-lasting adaptive responses. We discuss the logic that biological systems may use to remember environmental conditions. Responses spanning different generational timescales employ different molecular machineries and may result from differences in the duration or intensity of the exposure. Understanding the molecular components of multigenerational inheritance and the logic underlying beneficial and maladaptive adaptations is fundamental to understanding how organisms acquire and transmit environmental memories across generations.
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Affiliation(s)
- Titas Sengupta
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA;
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA;
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA;
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Stevenson ME, Bieri G, Kaletsky R, St Ange J, Remesal L, Pratt KJB, Zhou S, Weng Y, Murphy CT, Villeda SA. Neuronal activation of G αq EGL-30/GNAQ late in life rejuvenates cognition across species. Cell Rep 2023; 42:113151. [PMID: 37713310 PMCID: PMC10627507 DOI: 10.1016/j.celrep.2023.113151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/10/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Loss of cognitive function with age is devastating. EGL-30/GNAQ and Gαq signaling pathways are highly conserved between C. elegans and mammals, and murine Gnaq is enriched in hippocampal neurons and declines with age. We found that activation of EGL-30 in aged worms triples memory span, and GNAQ gain of function significantly improved memory in aged mice: GNAQ(gf) in hippocampal neurons of 24-month-old mice (equivalent to 70- to 80-year-old humans) rescued age-related impairments in well-being and memory. Single-nucleus RNA sequencing revealed increased expression of genes regulating synaptic function, axon guidance, and memory in GNAQ-treated mice, and worm orthologs of these genes were required for long-term memory extension in worms. These experiments demonstrate that C. elegans is a powerful model to identify mammalian regulators of memory, leading to the identification of a pathway that improves memory in extremely old mice. To our knowledge, this is the oldest age at which an intervention has improved age-related cognitive decline.
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Affiliation(s)
- Morgan E Stevenson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Gregor Bieri
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan St Ange
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - L Remesal
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Karishma J B Pratt
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA
| | - Shiyi Zhou
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yifei Weng
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Bakar Aging Research Institute, San Francisco, CA 94143, USA.
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Cota V, Sohrabi S, Kaletsky R, Murphy CT. Oocyte mitophagy is critical for extended reproductive longevity. PLoS Genet 2022; 18:e1010400. [PMID: 36126046 PMCID: PMC9524673 DOI: 10.1371/journal.pgen.1010400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/30/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
Women’s reproductive cessation is the earliest sign of human aging and is caused by decreasing oocyte quality. Similarly, C. elegans’ reproduction declines in mid-adulthood and is caused by oocyte quality decline. Aberrant mitochondrial morphology is a hallmark of age-related dysfunction, but the role of mitochondrial morphology and dynamics in reproductive aging is unclear. We examined the requirements for mitochondrial fusion and fission in oocytes of both wild-type worms and the long-lived, long-reproducing insulin-like receptor mutant daf-2. We find that normal reproduction requires both fusion and fission, but that daf-2 mutants utilize a shift towards fission, but not fusion, to extend their reproductive span and oocyte health. daf-2 mutant oocytes’ mitochondria are punctate (fissioned) and this morphology is primed for mitophagy, as loss of the mitophagy regulator PINK-1 shortens daf-2’s reproductive span. daf-2 mutants maintain oocyte mitochondria quality with age at least in part through a shift toward punctate mitochondrial morphology and subsequent mitophagy. Supporting this model, Urolithin A, a metabolite that promotes mitophagy, extends reproductive span in wild-type mothers–even in mid-reproduction—by maintaining youthful oocytes with age. Our data suggest that promotion of mitophagy may be an effective strategy to maintain oocyte health with age. Female reproductive decline begins in a woman’s 30’s, and has become an increasingly important area of research as more women delay child bearing. Like women, the nematode C. elegans undergoes reproductive senescence starting in mid-life, and its reproductive span is determined by oocyte quality decline with age. One of the hallmarks of aging is an increase in mitochondrial dysfunction that can be driven by aberrant mitochondrial fission and fusion, the main regulators of metabolic function and mitochondrial dynamics. In this study we identified a mechanism that promotes reproductive longevity using mitochondrial fission and mitophagy, the trash compactor of dysfunctional mitochondria. This mechanism led us to test Urolithin A, a common metabolite that promotes mitophagy and extends lifespan in C. elegans, as a possible therapeutic to delay reproductive decline. We suggest promotion of mitophagy in oocytes as a new target to extend reproductive longevity through Urolithin A supplementation.
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Affiliation(s)
- Vanessa Cota
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Salman Sohrabi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- LSI Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- LSI Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Coleen T. Murphy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- LSI Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail:
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9
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McIntyre LM, Huertas F, Morse AM, Kaletsky R, Murphy CT, Kalia V, Miller GW, Moskalenko O, Conesa A, Mor DE. GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease. Sci Rep 2022; 12:3268. [PMID: 35228596 PMCID: PMC8885929 DOI: 10.1038/s41598-022-07238-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 01/24/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson’s disease (PD) is a disabling neurodegenerative disorder in which multiple cell types, including dopaminergic and cholinergic neurons, are affected. The mechanisms of neurodegeneration in PD are not fully understood, limiting the development of therapies directed at disease-relevant molecular targets. C. elegans is a genetically tractable model system that can be used to disentangle disease mechanisms in complex diseases such as PD. Such mechanisms can be studied combining high-throughput molecular profiling technologies such as transcriptomics and metabolomics. However, the integrative analysis of multi-omics data in order to unravel disease mechanisms is a challenging task without advanced bioinformatics training. Galaxy, a widely-used resource for enabling bioinformatics analysis by the broad scientific community, has poor representation of multi-omics integration pipelines. We present the integrative analysis of gene expression and metabolite levels of a C. elegans PD model using GAIT-GM, a new Galaxy tool for multi-omics data analysis. Using GAIT-GM, we discovered an association between branched-chain amino acid metabolism and cholinergic neurons in the C. elegans PD model. An independent follow-up experiment uncovered cholinergic neurodegeneration in the C. elegans model that is consistent with cholinergic cell loss observed in PD. GAIT-GM is an easy to use Galaxy-based tool for generating novel testable hypotheses of disease mechanisms involving gene-metabolite relationships.
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Affiliation(s)
- Lauren M McIntyre
- University of Florida Genetics Institute, Gainesville, FL, USA. .,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA.
| | - Francisco Huertas
- University of Florida Genetics Institute, Gainesville, FL, USA.,Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32610, USA
| | - Alison M Morse
- University of Florida Genetics Institute, Gainesville, FL, USA.,Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Rachel Kaletsky
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Vrinda Kalia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Gary W Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Olexander Moskalenko
- University of Florida Research Computing, University of Florida, Gainesville, FL, 32610, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32610, USA. .,Institute for Integrative Systems Biology, Spanish National Research Council, 46980, Paterna, Spain.
| | - Danielle E Mor
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, GA, 30912, USA.
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Abstract
Animal experiences, including learned behaviors, can be passed down to several generations of progeny in a phenomenon known as transgenerational epigenetic inheritance. Yet, little is known regarding the molecular mechanisms regulating physiologically relevant transgenerational memories. Here, we present a method for Caenorhabditis elegans in which worms learn to avoid the pathogen Pseudomonas aeruginosa (PA14). Unlike previous protocols, this training paradigm, either using PA14 lawns or through exposure to a PA14 small RNA (P11), induces memory in four generations of progeny. For complete details on the use and execution of this protocol, please refer to Moore et al. (2019) and Kaletsky et al. (2020). Protocol for C. elegans transgenerational pathogen avoidance memory training Trained worms are tested for pathogen avoidance learning using choice assays Several generations of progeny from trained mothers are propagated and tested
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Affiliation(s)
- Rebecca S Moore
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.,LSI Genomics, Princeton University, Princeton, NJ 08544, USA
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11
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Sohrabi S, Mor DE, Kaletsky R, Keyes W, Murphy CT. High-throughput behavioral screen in C. elegans reveals Parkinson's disease drug candidates. Commun Biol 2021; 4:203. [PMID: 33589689 PMCID: PMC7884385 DOI: 10.1038/s42003-021-01731-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 12/18/2020] [Indexed: 12/17/2022] Open
Abstract
We recently linked branched-chain amino acid transferase 1 (BCAT1) dysfunction with the movement disorder Parkinson's disease (PD), and found that RNAi-mediated knockdown of neuronal bcat-1 in C. elegans causes abnormal spasm-like 'curling' behavior with age. Here we report the development of a machine learning-based workflow and its application to the discovery of potentially new therapeutics for PD. In addition to simplifying quantification and maintaining a low data overhead, our simple segment-train-quantify platform enables fully automated scoring of image stills upon training of a convolutional neural network. We have trained a highly reliable neural network for the detection and classification of worm postures in order to carry out high-throughput curling analysis without the need for user intervention or post-inspection. In a proof-of-concept screen of 50 FDA-approved drugs, enasidenib, ethosuximide, metformin, and nitisinone were identified as candidates for potential late-in-life intervention in PD. These findings point to the utility of our high-throughput platform for automated scoring of worm postures and in particular, the discovery of potential candidate treatments for PD.
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Affiliation(s)
- Salman Sohrabi
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Danielle E Mor
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - William Keyes
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.
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12
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Mor DE, Sohrabi S, Kaletsky R, Keyes W, Tartici A, Kalia V, Miller GW, Murphy CT. Metformin rescues Parkinson's disease phenotypes caused by hyperactive mitochondria. Proc Natl Acad Sci U S A 2020; 117:26438-26447. [PMID: 33024014 PMCID: PMC7585014 DOI: 10.1073/pnas.2009838117] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Metabolic dysfunction occurs in many age-related neurodegenerative diseases, yet its role in disease etiology remains poorly understood. We recently discovered a potential causal link between the branched-chain amino acid transferase BCAT-1 and the neurodegenerative movement disorder Parkinson's disease (PD). RNAi-mediated knockdown of Caenorhabditis elegans bcat-1 is known to recapitulate PD-like features, including progressive motor deficits and neurodegeneration with age, yet the underlying mechanisms have remained unknown. Using transcriptomic, metabolomic, and imaging approaches, we show here that bcat-1 knockdown increases mitochondrial respiration and induces oxidative damage in neurons through mammalian target of rapamycin-independent mechanisms. Increased mitochondrial respiration, or "mitochondrial hyperactivity," is required for bcat-1(RNAi) neurotoxicity. Moreover, we show that post-disease-onset administration of the type 2 diabetes medication metformin reduces mitochondrial respiration to control levels and significantly improves both motor function and neuronal viability. Taken together, our findings suggest that mitochondrial hyperactivity may be an early event in the pathogenesis of PD, and that strategies aimed at reducing mitochondrial respiration may constitute a surprising new avenue for PD treatment.
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Affiliation(s)
- Danielle E Mor
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Salman Sohrabi
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - William Keyes
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Alp Tartici
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544
| | - Vrinda Kalia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Gary W Miller
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544;
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
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13
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Abstract
Multicellular organisms are composed of distinct cells and tissues that coordinate highly orchestrated responses to environmental challenges, including those that arise with age. Since C. elegans is a premier model system used to study the molecular and cellular regulators of adult and aging phenotypes, cell type- and tissue-specific approaches are needed to characterize the genome-wide expression changes associated with these responses. Here we describe a method for the FACS-based isolation and RNA sequencing of dissociated cells from adult C. elegans. This technique is amenable to profiling the cell- and tissue-specific gene expression changes in C. elegans mutants, including aging models, such as the daf-2/insulin-like signaling (IIS) pathway, and in wild-type animals with age.
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Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Coleen T Murphy
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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14
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Abstract
Presynaptic protein synthesis is important in the adult central nervous system; however, the nervous system-wide set of mRNAs localized to presynaptic areas has yet to be identified in any organism. Here we differentially labeled somatic and synaptic compartments in adult C. elegans with fluorescent proteins, and isolated synaptic and somatic regions from the same population of animals. We used this technique to determine the nervous system-wide presynaptic transcriptome by deep sequencing. Analysis of the synaptic transcriptome reveals that synaptic transcripts are predicted to have specialized functions in neurons. Differential expression analysis identified 542 genes enriched in synaptic regions relative to somatic regions, with synaptic functions conserved in higher organisms. We find that mRNAs for pumilio RNA-binding proteins are abundant in synaptic regions, which we confirmed through high-sensitivity in situ hybridization. Presynaptic PUMILIOs regulate associative memory. Our approach enables the identification of new mechanisms that regulate synaptic function and behavior.
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Affiliation(s)
- Rachel N Arey
- Department of Molecular and Cellular Biology and Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ, 08544, USA.
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15
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Moore RS, Kaletsky R, Murphy CT. Piwi/PRG-1 Argonaute and TGF-β Mediate Transgenerational Learned Pathogenic Avoidance. Cell 2019; 177:1827-1841.e12. [PMID: 31178117 DOI: 10.1016/j.cell.2019.05.024] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/04/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2022]
Abstract
The ability to inherit learned information from parents could be evolutionarily beneficial, enabling progeny to better survive dangerous conditions. We discovered that, after C. elegans have learned to avoid the pathogenic bacteria Pseudomonas aeruginosa (PA14), they pass this learned behavior on to their progeny, through either the male or female germline, persisting through the fourth generation. Expression of the TGF-β ligand DAF-7 in the ASI sensory neurons correlates with and is required for this transgenerational avoidance behavior. Additionally, the Piwi Argonaute homolog PRG-1 and its downstream molecular components are required for transgenerational inheritance of both avoidance behavior and ASI daf-7 expression. Animals whose parents have learned to avoid PA14 display a PA14 avoidance-based survival advantage that is also prg-1 dependent, suggesting an adaptive response. Transgenerational epigenetic inheritance of pathogenic learning may optimize progeny decisions to increase survival in fluctuating environmental conditions.
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Affiliation(s)
- Rebecca S Moore
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA.
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16
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Kaletsky R, Murphy CT. Gut feelings: microRNAs tune protein quality control and ageing to odours. Nat Metab 2019; 1:306-307. [PMID: 32694717 DOI: 10.1038/s42255-019-0042-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology and LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Coleen T Murphy
- Department of Molecular Biology and LSI Genomics, Princeton University, Princeton, NJ, USA.
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17
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Kaletsky R, Murphy CT. Publisher Correction: Gut feelings: microRNAs tune protein quality control and ageing to odours. Nat Metab 2019; 1:416. [PMID: 32694726 DOI: 10.1038/s42255-019-0050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of the article originally published, the study by Finger et al. was incorrectly described in one sentence in the third paragraph as implicating the microRNA mir-73 in the regulation of proteostasis; mir-71 was the correct microRNA. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology and LSI Genomics, Princeton University, Princeton, NJ, USA
| | - Coleen T Murphy
- Department of Molecular Biology and LSI Genomics, Princeton University, Princeton, NJ, USA.
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18
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Yao V, Kaletsky R, Keyes W, Mor DE, Wong AK, Sohrabi S, Murphy CT, Troyanskaya OG. An integrative tissue-network approach to identify and test human disease genes. Nat Biotechnol 2018; 36:nbt.4246. [PMID: 30346941 PMCID: PMC7021177 DOI: 10.1038/nbt.4246] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023]
Abstract
Effective discovery of causal disease genes must overcome the statistical challenges of quantitative genetics studies and the practical limitations of human biology experiments. Here we developed diseaseQUEST, an integrative approach that combines data from human genome-wide disease studies with in silico network models of tissue- and cell-type-specific function in model organisms to prioritize candidates within functionally conserved processes and pathways. We used diseaseQUEST to predict candidate genes for 25 different diseases and traits, including cancer, longevity, and neurodegenerative diseases. Focusing on Parkinson's disease (PD), a diseaseQUEST-directed Caenhorhabditis elegans behavioral screen identified several candidate genes, which we experimentally verified and found to be associated with age-dependent motility defects mirroring PD clinical symptoms. Furthermore, knockdown of the top candidate gene, bcat-1, encoding a branched chain amino acid transferase, caused spasm-like 'curling' and neurodegeneration in C. elegans, paralleling decreased BCAT1 expression in PD patient brains. diseaseQUEST is modular and generalizable to other model organisms and human diseases of interest.
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Affiliation(s)
- Victoria Yao
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - William Keyes
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Danielle E Mor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Aaron K Wong
- Flatiron Institute, Simons Foundation, New York, New York, USA
| | - Salman Sohrabi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, New Jersey, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
- Flatiron Institute, Simons Foundation, New York, New York, USA
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19
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Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, Troyanskaya OG, Murphy CT. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet 2018; 14:e1007559. [PMID: 30096138 PMCID: PMC6105014 DOI: 10.1371/journal.pgen.1007559] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/22/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022] Open
Abstract
The biology and behavior of adults differ substantially from those of developing animals, and cell-specific information is critical for deciphering the biology of multicellular animals. Thus, adult tissue-specific transcriptomic data are critical for understanding molecular mechanisms that control their phenotypes. We used adult cell-specific isolation to identify the transcriptomes of C. elegans' four major tissues (or "tissue-ome"), identifying ubiquitously expressed and tissue-specific "enriched" genes. These data newly reveal the hypodermis' metabolic character, suggest potential worm-human tissue orthologies, and identify tissue-specific changes in the Insulin/IGF-1 signaling pathway. Tissue-specific alternative splicing analysis identified a large set of collagen isoforms. Finally, we developed a machine learning-based prediction tool for 76 sub-tissue cell types, which we used to predict cellular expression differences in IIS/FOXO signaling, stage-specific TGF-β activity, and basal vs. memory-induced CREB transcription. Together, these data provide a rich resource for understanding the biology governing multicellular adult animals.
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Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Victoria Yao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| | - April Williams
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alexi M. Runnels
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Shiyi Zhou
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| | - Coleen T. Murphy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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20
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Arey RN, Stein GM, Kaletsky R, Kauffman A, Murphy CT. Activation of G αq Signaling Enhances Memory Consolidation and Slows Cognitive Decline. Neuron 2018; 98:562-574.e5. [PMID: 29656871 DOI: 10.1016/j.neuron.2018.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/06/2017] [Accepted: 03/21/2018] [Indexed: 01/25/2023]
Abstract
Perhaps the most devastating decline with age is the loss of memory. Therefore, identifying mechanisms to restore memory function with age is critical. Using C. elegans associative learning and memory assays, we identified a gain-of-function Gαq signaling pathway mutant that forms a long-term (cAMP response element binding protein [CREB]-dependent) memory following one conditioned stimulus-unconditioned stimulus (CS-US) pairing, which usually requires seven CS-US pairings. Increased CREB activity in AIM interneurons reduces the threshold for memory consolidation through transcription of a set of previously identified "long-term memory" genes. Enhanced Gαq signaling in the AWC sensory neuron is both necessary and sufficient for improved memory and increased AIM CREB activity, and activation of Gαq specifically in aged animals rescues the ability to form memory. Activation of Gαq in AWC sensory neurons non-cell autonomously induces consolidation after one CS-US pairing, enabling both cognitive function maintenance with age and restoration of memory function in animals with impaired memory performance without decreased longevity.
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Affiliation(s)
- Rachel N Arey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Geneva M Stein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Amanda Kauffman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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21
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Son HG, Seo M, Ham S, Hwang W, Lee D, An SWA, Artan M, Seo K, Kaletsky R, Arey RN, Ryu Y, Ha CM, Kim YK, Murphy CT, Roh TY, Nam HG, Lee SJV. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun 2017; 8:14749. [PMID: 28276441 PMCID: PMC5347137 DOI: 10.1038/ncomms14749] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 01/30/2017] [Indexed: 12/14/2022] Open
Abstract
Long-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts. NMD components, including smg-2/UPF1, are required to achieve the longevity of several long-lived mutants, including daf-2 mutant worms. NMD in the nervous system of the animals is particularly important for RNA quality control to promote longevity. Furthermore, we find that downregulation of yars-2/tyrosyl-tRNA synthetase, an NMD target transcript, by daf-2 mutations contributes to longevity. We propose that NMD-mediated RNA surveillance is a crucial quality control process that contributes to longevity conferred by daf-2 mutations.
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Affiliation(s)
- Heehwa G. Son
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Mihwa Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988, South Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Wooseon Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Dongyeop Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Seon Woo A. An
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Murat Artan
- Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Keunhee Seo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Rachel N. Arey
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Youngjae Ryu
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Chang Man Ha
- Research Division, Korea Brain Research Institute, Daegu 41068, South Korea
| | - Yoon Ki Kim
- Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul 02841, South Korea
- Division of Life Sciences, Korea University, Seoul 02841, South Korea
| | - Coleen T. Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science, Daegu 42988, South Korea
- Department of New Biology, DGIST, Daegu 42988, South Korea
| | - Seung-Jae V. Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
- Information Technology Convergence Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, South Korea
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22
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Kaletsky R, Lakhina V, Arey R, Williams A, Landis J, Ashraf J, Murphy CT. The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators. Nature 2015; 529:92-6. [PMID: 26675724 PMCID: PMC4708089 DOI: 10.1038/nature16483] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022]
Abstract
Insulin/IGF-1 signaling (IIS) is a critical regulator of an organism’s most important biological decisions, from growth, development, and metabolism to reproduction and longevity. It primarily does so through the activity of the DAF-16/FOXO transcription factor, whose global targets were identified in C. elegans using whole-worm transcriptional analyses more than a decade ago1. IIS and FOXO also regulate important neuronal and adult behavioral phenotypes, such as the maintenance of memory2 and axon regeneration3 with age, in both mammals4 and C. elegans, but the neuron-specific IIS/FOXO targets that regulate these functions are still unknown. By isolating adult C. elegans neurons for transcriptional profiling, we identified both the wild-type and IIS/FOXO adult neuronal transcriptomes for the first time. IIS/FOXO neuron-specific targets are distinct from canonical IIS/FOXO-regulated longevity and metabolism targets, and are required for IIS/daf-2 mutants’ extended memory. We also discovered that the activity of the forkhead transcription factor FKH-9 in neurons is required for daf-2’s ability to regenerate axons with age, and its activity in non-neuronal tissues is required for daf-2’s long lifespan. Together, neuron-specific and canonical IIS/FOXO-regulated targets enable the coordinated extension of neuronal activities, metabolism, and longevity under low insulin-signaling conditions.
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Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Vanisha Lakhina
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Rachel Arey
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - April Williams
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jessica Landis
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Jasmine Ashraf
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology &LSI Genomics, Princeton University, Princeton, New Jersey 08544, USA
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23
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Wang J, Kaletsky R, Silva M, Williams A, Haas LA, Androwski RJ, Landis JN, Patrick C, Rashid A, Santiago-Martinez D, Gravato-Nobre M, Hodgkin J, Hall DH, Murphy CT, Barr MM. Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis. Curr Biol 2015; 25:3232-8. [PMID: 26687621 DOI: 10.1016/j.cub.2015.10.057] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
Cilia and extracellular vesicles (EVs) are signaling organelles [1]. Cilia act as cellular sensory antennae, with defects resulting in human ciliopathies. Cilia both release and bind to EVs [1]. EVs are sub-micron-sized particles released by cells and function in both short- and long-range intercellular communication. In C. elegans and mammals, the autosomal dominant polycystic kidney disease (ADPKD) gene products polycystin-1 and polycystin-2 localize to both cilia and EVs, act in the same genetic pathway, and function in a sensory capacity, suggesting ancient conservation [2]. A fundamental understanding of EV biology and the relationship between the polycystins, cilia, and EVs is lacking. To define properties of a ciliated EV-releasing cell, we performed RNA-seq on 27 GFP-labeled EV-releasing neurons (EVNs) isolated from adult C. elegans. We identified 335 significantly overrepresented genes, of which 61 were validated by GFP reporters. The EVN transcriptional profile uncovered new pathways controlling EV biogenesis and polycystin signaling and also identified EV cargo, which included an antimicrobial peptide and ASIC channel. Tumor-necrosis-associated factor (TRAF) homologs trf-1 and trf-2 and the p38 mitogen-activated protein kinase (MAPK) pmk-1 acted in polycystin-signaling pathways controlling male mating behaviors. pmk-1 was also required for EV biogenesis, independent of the innate immunity MAPK signaling cascade. This first high-resolution transcriptome profile of a subtype of ciliated sensory neurons isolated from adult animals reveals the functional components of an EVN.
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Affiliation(s)
- Juan Wang
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Rachel Kaletsky
- Department of Molecular Biology and Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Malan Silva
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - April Williams
- Department of Molecular Biology and Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Leonard A Haas
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Rebecca J Androwski
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Jessica N Landis
- Department of Molecular Biology and Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Cory Patrick
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | - Alina Rashid
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA
| | | | | | - Jonathan Hodgkin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - David H Hall
- Center for C. elegans Anatomy, Albert Einstein College of Medicine, 1410 Pelham Parkway, Bronx, NY 10461, USA
| | - Coleen T Murphy
- Department of Molecular Biology and Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA
| | - Maureen M Barr
- Department of Genetics and Human Genetics Institute, Rutgers University, Piscataway, NJ 08854, USA.
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Lakhina V, Arey RN, Kaletsky R, Kauffman A, Stein G, Keyes W, Xu D, Murphy CT. Genome-wide functional analysis of CREB/long-term memory-dependent transcription reveals distinct basal and memory gene expression programs. Neuron 2015; 85:330-45. [PMID: 25611510 DOI: 10.1016/j.neuron.2014.12.029] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2014] [Indexed: 12/30/2022]
Abstract
Induced CREB activity is a hallmark of long-term memory, but the full repertoire of CREB transcriptional targets required specifically for memory is not known in any system. To obtain a more complete picture of the mechanisms involved in memory, we combined memory training with genome-wide transcriptional analysis of C. elegans CREB mutants. This approach identified 757 significant CREB/memory-induced targets and confirmed the involvement of known memory genes from other organisms, but also suggested new mechanisms and novel components that may be conserved through mammals. CREB mediates distinct basal and memory transcriptional programs at least partially through spatial restriction of CREB activity: basal targets are regulated primarily in nonneuronal tissues, while memory targets are enriched for neuronal expression, emanating from CREB activity in AIM neurons. This suite of novel memory-associated genes will provide a platform for the discovery of orthologous mammalian long-term memory components.
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Affiliation(s)
- Vanisha Lakhina
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rachel N Arey
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Rachel Kaletsky
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Amanda Kauffman
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Geneva Stein
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - William Keyes
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Daniel Xu
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Coleen T Murphy
- Department of Molecular Biology & LSI Genomics, Princeton University, Princeton, NJ 08544, USA.
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Kauffman A, Parsons L, Stein G, Wills A, Kaletsky R, Murphy C. C. elegans positive butanone learning, short-term, and long-term associative memory assays. J Vis Exp 2011:2490. [PMID: 21445035 PMCID: PMC3197297 DOI: 10.3791/2490] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The memory of experiences and learned information is critical for organisms to make choices that aid their survival. C. elegans navigates its environment through neuron-specific detection of food and chemical odors, and can associate nutritive states with chemical odors, temperature, and the pathogenicity of a food source. Here, we describe assays of C. elegans associative learning and short- and long-term associative memory. We modified an aversive olfactory learning paradigm to instead produce a positive response; the assay involves starving ~400 worms, then feeding the worms in the presence of the AWC neuron-sensed volatile chemoattractant butanone at a concentration that elicits a low chemotactic index (similar to Toroyama et al.). A standard population chemotaxis assay1 tests the worms' attraction to the odorant immediately or minutes to hours after conditioning. After conditioning, wild-type animals' chemotaxis to butanone increases ~0.6 Chemotaxis Index units, its "Learning Index". Associative learning is dependent on the presence of both food and butanone during training. Pairing food and butanone for a single conditioning period ("massed training") produces short-term associative memory that lasts ~2 hours. Multiple conditioning periods with rest periods between ("spaced training") yields long-term associative memory (<40 hours), and is dependent on the cAMP Response Element Binding protein (CREB), a transcription factor required for long-term memory across species. Our protocol also includes image analysis methods for quick and accurate determination of chemotaxis indices. High-contrast images of animals on chemotaxis assay plates are captured and analyzed by worm counting software in MatLab. The software corrects for uneven background using a morphological tophat transformation. Otsu's method is then used to determine a threshold to separate worms from the background. Very small particles are removed automatically and larger non-worm regions (plate edges or agar punches) are removed by manual selection. The software then estimates the size of single worm by ignoring regions that are above a specified maximum size and taking the median size of the remaining regions. The number of worms is then estimated by dividing the total area identified as occupied by worms by the estimated size of a single worm. We have found that learning and short- and long-term memory can be distinguished, and that these processes share similar key molecules with higher organisms. Our assays can quickly test novel candidate genes or molecules that affect learning and short- or long-term memory in C. elegans that are relevant across species.
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Affiliation(s)
- Amanda Kauffman
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, USA
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Abstract
Aging is characterized by general physiological decline over time. A hallmark of human senescence is the onset of various age-related afflictions including neurodegeneration, cardiovascular disease and cancer. Although environmental and stochastic factors undoubtedly contribute to the increased incidence of disease with age, recent studies suggest that intrinsic genetic determinants govern both life span and overall health. Current aging research aims at achieving the 'longevity dividend', in which life span extension in humans is accomplished with a concomitant increase in the quality of life (Olshansky et al., 2007). Significant progress has been made using model organisms, especially the nematode worm Caenorhabditis elegans, to delineate the genetic and biochemical pathways involved in aging to identify strategies for therapeutic intervention in humans. In this review, we discuss how C. elegans has contributed to our understanding of insulin signaling and aging.
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Affiliation(s)
- Rachel Kaletsky
- Department of Molecular Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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Wang Y, Freedman Z, Lu-Irving P, Kaletsky R, Barkay T. An initial characterization of the mercury resistance (mer) system of the thermophilic bacterium Thermus thermophilus HB27. FEMS Microbiol Ecol 2009; 67:118-29. [PMID: 19120462 DOI: 10.1111/j.1574-6941.2008.00603.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The evolutionary origin of the broadly distributed mer system, which plays an important role in mercury detoxification and biogeochemistry, is presently unknown. The phylum Deinococcus/Thermus was found to be one of the deepest-branching bacterial lineage to have a homolog of merA, which specifies reduction of ionic to elemental mercury, and the mercuric reductase (MerA) of Thermus thermophilus HB27 was found to be basal to all bacterial MerA when this protein's phylogeny was constructed. A merA mutant of HB27 was fourfolds more sensitive to mercury toxicity than the wild type (wt), and lost detectable MerA-specific activities. The merA gene in HB27 was transcribed on a polycistronic message downstream from ORF encoding for homologs of O-acetyl-l-homoserine/O-acetyl-serine (OAH/OAS) sulfhydrylase and MerR, the mer operon transcription regulator, from a promoter located 69 nucleotides upstream of the sulfhydrylase translation start codon. The transcription of the putative mer operon in HB27 was induced 66.8+/-15.8-fold by exposure to 1 muM HgCl2. The optimal temperature for MerA-specific activity corresponded to this strain's optimal growth temperature, 70 degrees C. Thus, T. thermophilus is the earliest mercury-resistant bacterium identified to date, a finding consistent with the hypothesis that the mer system originated among thermophilic microorganisms from geothermal environments.
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Affiliation(s)
- Yanping Wang
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Agosto LM, Yu JJ, Dai J, Kaletsky R, Monie D, O'Doherty U. HIV-1 integrates into resting CD4+ T cells even at low inoculums as demonstrated with an improved assay for HIV-1 integration. Virology 2007; 368:60-72. [PMID: 17631931 PMCID: PMC2140271 DOI: 10.1016/j.virol.2007.06.001] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 04/28/2007] [Accepted: 06/01/2007] [Indexed: 12/16/2022]
Abstract
Human Immunodeficiency Virus Type 1 (HIV-1) establishes a latent reservoir early in infection that is resistant to the host immune response and treatment with highly active antiretroviral therapy (HAART). The best understood of these reservoirs forms in resting CD4(+) T cells. While it remains unclear how reservoirs form, a popular model holds that the virus can only integrate in activated CD4(+) T cells. Contrary to this model, our previous results suggest that HIV-1 can integrate directly into the genomes of resting CD4(+) T cells. However, a limitation of our previous studies was that they were conducted at high viral inoculum and these conditions may lead to cellular activation or saturation of restriction factors. In the present study, we tested if our previous findings were an artifact of high inoculum. To do this, we enhanced the sensitivity of our integration assay by incorporating a repetitive sampling technique that allowed us to capture rare integration events that occur near an Alu repeat. The new technique represents a significant advance as it enabled us to measure integration accurately down to 1 provirus/well in 15,000 genomes--a 40-fold enhancement over our prior assay. Using this assay, we demonstrate that HIV can integrate into resting CD4(+) T cells in vitro even at low viral inoculum. These findings suggest there is no threshold number of virions required for HIV to integrate into resting CD4(+) T cells.
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Affiliation(s)
- Luis M. Agosto
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104-3905
| | - Jianqing J. Yu
- Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, PA 19104-3905
| | - Jihong Dai
- Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, PA 19104-3905
| | - Rachel Kaletsky
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104-3905
| | - Daphne Monie
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205-2196
| | - Una O'Doherty
- Department of Pathology and Laboratory Medicine, Division of Transfusion Medicine, University of Pennsylvania, Philadelphia, PA 19104-3905
- Corresponding author: Una O'Doherty, Phone: 215-573-7273,
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Kaletsky R. Handling flammable liquids. Occup Health Saf 1998; 67:62-5. [PMID: 9465427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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