1
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Vogt MC, Hobert O. Starvation-induced changes in somatic insulin/IGF-1R signaling drive metabolic programming across generations. SCIENCE ADVANCES 2023; 9:eade1817. [PMID: 37027477 PMCID: PMC10081852 DOI: 10.1126/sciadv.ade1817] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/08/2023] [Indexed: 05/30/2023]
Abstract
Exposure to adverse nutritional and metabolic environments during critical periods of development can exert long-lasting effects on health outcomes of an individual and its descendants. Although such metabolic programming has been observed in multiple species and in response to distinct nutritional stressors, conclusive insights into signaling pathways and mechanisms responsible for initiating, mediating, and manifesting changes to metabolism and behavior across generations remain scarce. By using a starvation paradigm in Caenorhabditis elegans, we show that starvation-induced changes in dauer formation-16/forkhead box transcription factor class O (DAF-16/FoxO) activity, the main downstream target of insulin/insulin-like growth factor 1 (IGF-1) receptor signaling, are responsible for metabolic programming phenotypes. Tissue-specific depletion of DAF-16/FoxO during distinct developmental time points demonstrates that DAF-16/FoxO acts in somatic tissues, but not directly in the germline, to both initiate and manifest metabolic programming. In conclusion, our study deciphers multifaceted and critical roles of highly conserved insulin/IGF-1 receptor signaling in determining health outcomes and behavior across generations.
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Gallot A, Desouhant E, Lhuillier V, Lepetit D, El Filali A, Mouton L, Vieira-Heddi C, Amat I. The for gene as one of the drivers of foraging variations in a parasitic wasp. Mol Ecol 2022; 32:1760-1776. [PMID: 36571434 DOI: 10.1111/mec.16834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/08/2022] [Accepted: 12/22/2022] [Indexed: 12/27/2022]
Abstract
Foraging behaviours encompass strategies to locate resources and to exploit them. In many taxa, these behaviours are driven by a major gene called for, but the mechanisms of gene regulation vary between species. In the parasitoid wasp Venturia canescens, sexual and asexual populations coexist in sympatry but differ in life-history traits, physiology and behaviours, which could impact their foraging strategies. Here, we explored the molecular bases underpinning divergence in behaviours by testing two mutually nonexclusive hypotheses: first, the divergence in the for gene correlates with differences in foraging strategies, and second, the latter rely on a divergence in whole-genome expression. Using comparative genomics, we showed that the for gene was conserved across insects considering both sequence and gene model complexity. Polymorphism analysis did not support the occurrence of two allelic variants diverging across the two populations, yet the asexual population exhibited less polymorphism than the sexual population. Sexual and asexual transcriptomes split sharply, with 10.9% differentially expressed genes, but these were not enriched in behaviour-related genes. We showed that the for gene was more highly expressed in asexual female heads than in sexual heads and that those differences correlate with divergence in foraging behaviours in our experiment given that asexuals explored the environment more and exploited more host patches. Overall, these results suggested that fine tuning of for gene expression between populations may have led to distinct foraging behaviours. We hypothesized that reproductive polymorphism and coexistence in sympatry of sexual and asexual populations specialized to different ecological niches via divergent optima on phenotypic traits could imply adaptation through different expression patterns of the for gene and at many other loci throughout the genome.
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Affiliation(s)
- Aurore Gallot
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Emmanuel Desouhant
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Vincent Lhuillier
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - David Lepetit
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Adil El Filali
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Laurence Mouton
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Cristina Vieira-Heddi
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
| | - Isabelle Amat
- LBBE - Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon1, Villeurbanne, France
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3
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Wang X, Rosikiewicz W, Sedkov Y, Mondal B, Martinez T, Kallappagoudar S, Tvardovskiy A, Bajpai R, Xu B, Pruett-Miller SM, Schneider R, Herz HM. The MLL3/4 complexes and MiDAC co-regulate H4K20ac to control a specific gene expression program. Life Sci Alliance 2022; 5:e202201572. [PMID: 35820704 PMCID: PMC9275676 DOI: 10.26508/lsa.202201572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Abstract
The mitotic deacetylase complex MiDAC has recently been shown to play a vital physiological role in embryonic development and neurite outgrowth. However, how MiDAC functionally intersects with other chromatin-modifying regulators is poorly understood. Here, we describe a physical interaction between the histone H3K27 demethylase UTX, a complex-specific subunit of the enhancer-associated MLL3/4 complexes, and MiDAC. We demonstrate that UTX bridges the association of the MLL3/4 complexes and MiDAC by interacting with ELMSAN1, a scaffolding subunit of MiDAC. Our data suggest that MiDAC constitutes a negative genome-wide regulator of H4K20ac, an activity which is counteracted by the MLL3/4 complexes. MiDAC and the MLL3/4 complexes co-localize at many genomic regions, which are enriched for H4K20ac and the enhancer marks H3K4me1, H3K4me2, and H3K27ac. We find that MiDAC antagonizes the recruitment of UTX and MLL4 and negatively regulates H4K20ac, and to a lesser extent H3K4me2 and H3K27ac, resulting in transcriptional attenuation of associated genes. In summary, our findings provide a paradigm how the opposing roles of chromatin-modifying components, such as MiDAC and the MLL3/4 complexes, balance the transcriptional output of specific gene expression programs.
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Affiliation(s)
- Xiaokang Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yurii Sedkov
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baisakhi Mondal
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanner Martinez
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Satish Kallappagoudar
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Richa Bajpai
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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4
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Unno T, Takatsuka H, Ohnishi Y, Ito M, Kubota Y. A class I histone deacetylase HDA-2 is essential for embryonic development and size regulation of fertilized eggs in Caenorhabditis elegans. Genes Genomics 2021; 44:343-357. [PMID: 34843089 DOI: 10.1007/s13258-021-01195-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/21/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Caenorhabditis elegans encodes three class I histone deacetylases (HDACs), HDA-1, HDA-2, and HDA-3. Although HDA-1 is known to be involved in embryogenesis, the regulatory roles of HDA-2 and HDA-3 in embryonic development remain unexplored. OBJECTIVE To elucidate the functional roles of the three class I HDACs in C. elegans embryonic development. METHODS The roles of Class I HDACs, HDA-1, HDA-2, and HDA-3 in Caenorhabditis elegans during embryogenesis were investigated through the analysis of embryonic lethality via gene knockdown or deletion mutants. Additionally, the size of these knockdown and mutant eggs was observed using a differential interference contrast microscope. Finally, expression pattern and tissue-specific role of hda-2 and transcriptome of the hda-2 mutant were analyzed. RESULTS Here, we report that HDA-1 and HDA-2, but not HDA-3, play essential roles in Caenorhabditis elegans embryonic development. Our observations of the fertilized egg size variance demonstrated that HDA-2 is involved in regulating the size of fertilized eggs. Combined analysis of expression patterns and sheath cell-specific rescue experiments indicated that the transgenerational role of HDA-2 is involved in the viability of embryonic development and fertilized egg size regulation. Furthermore, transcriptome analysis of hda-2 mutant embryos implies that HDA-2 is involved in epigenetic regulation of embryonic biological processes by downregulating and upregulating the gene expression. CONCLUSION Our finding suggests that HDA-2 regulates the embryonic development in Caenorhabditis elegans by controling a specific subset of genes, and this function might be mediated by transgenerational epigenetic effect.
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Affiliation(s)
- Takuma Unno
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Hisashi Takatsuka
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yuto Ohnishi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.,Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yukihiko Kubota
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
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5
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Yan J, Chen Y, Zhu Y, Paquet-Durand F. Programmed Non-Apoptotic Cell Death in Hereditary Retinal Degeneration: Crosstalk between cGMP-Dependent Pathways and PARthanatos? Int J Mol Sci 2021; 22:10567. [PMID: 34638907 PMCID: PMC8508647 DOI: 10.3390/ijms221910567] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Programmed cell death (PCD) is a highly regulated process that results in the orderly destruction of a cell. Many different forms of PCD may be distinguished, including apoptosis, PARthanatos, and cGMP-dependent cell death. Misregulation of PCD mechanisms may be the underlying cause of neurodegenerative diseases of the retina, including hereditary retinal degeneration (RD). RD relates to a group of diseases that affect photoreceptors and that are triggered by gene mutations that are often well known nowadays. Nevertheless, the cellular mechanisms of PCD triggered by disease-causing mutations are still poorly understood, and RD is mostly still untreatable. While investigations into the neurodegenerative mechanisms of RD have focused on apoptosis in the past two decades, recent evidence suggests a predominance of non-apoptotic processes as causative mechanisms. Research into these mechanisms carries the hope that the knowledge created can eventually be used to design targeted treatments to prevent photoreceptor loss. Hence, in this review, we summarize studies on PCD in RD, including on apoptosis, PARthanatos, and cGMP-dependent cell death. Then, we focus on a possible interplay between these mechanisms, covering cGMP-signaling targets, overactivation of poly(ADP-ribose)polymerase (PARP), energy depletion, Ca2+-permeable channels, and Ca2+-dependent proteases. Finally, an outlook is given into how specific features of cGMP-signaling and PARthanatos may be targeted by therapeutic interventions.
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Affiliation(s)
| | | | | | - François Paquet-Durand
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (J.Y.); (Y.C.); (Y.Z.)
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6
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Ow MC, Hall SE. piRNAs and endo-siRNAs: Small molecules with large roles in the nervous system. Neurochem Int 2021; 148:105086. [PMID: 34082061 DOI: 10.1016/j.neuint.2021.105086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/23/2021] [Accepted: 05/26/2021] [Indexed: 01/02/2023]
Abstract
Since their discovery, small non-coding RNAs have emerged as powerhouses in the regulation of numerous cellular processes. In addition to guarding the integrity of the reproductive system, small non-coding RNAs play critical roles in the maintenance of the soma. Accumulating evidence indicates that small non-coding RNAs perform vital functions in the animal nervous system such as restricting the activity of deleterious transposable elements, regulating nerve regeneration, and mediating learning and memory. In this review, we provide an overview of the current understanding of the contribution of two major classes of small non-coding RNAs, piRNAs and endo-siRNAs, to the nervous system development and function, and present highlights on how the dysregulation of small non-coding RNA pathways can assist in understanding the neuropathology of human neurological disorders.
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Affiliation(s)
- Maria C Ow
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
| | - Sarah E Hall
- Biology Department, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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7
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Ravi B, Zhao J, Chaudhry I, Signorelli R, Bartole M, Kopchock RJ, Guijarro C, Kaplan JM, Kang L, Collins KM. Presynaptic Gαo (GOA-1) signals to depress command neuron excitability and allow stretch-dependent modulation of egg laying in Caenorhabditis elegans. Genetics 2021; 218:6284136. [PMID: 34037773 DOI: 10.1093/genetics/iyab080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022] Open
Abstract
Egg laying in the nematode worm Caenorhabditis elegans is a two-state behavior modulated by internal and external sensory input. We have previously shown that homeostatic feedback of embryo accumulation in the uterus regulates bursting activity of the serotonergic HSN command neurons that sustains the egg-laying active state. How sensory feedback of egg release signals to terminate the egg-laying active state is less understood. We find that Gαo, a conserved Pertussis Toxin-sensitive G protein, signals within HSN to inhibit egg-laying circuit activity and prevent entry into the active state. Gαo signaling hyperpolarizes HSN, reducing HSN Ca2+ activity and input onto the postsynaptic vulval muscles. Loss of inhibitory Gαo signaling uncouples presynaptic HSN activity from a postsynaptic, stretch-dependent homeostat, causing precocious entry into the egg-laying active state when only a few eggs are present in the uterus. Feedback of vulval opening and egg release activates the uv1 neuroendocrine cells which release NLP-7 neuropeptides which signal to inhibit egg laying through Gαo-independent mechanisms in the HSNs and Gαo-dependent mechanisms in cells other than the HSNs. Thus, neuropeptide and inhibitory Gαo signaling maintains a bi-stable state of electrical excitability that dynamically controls circuit activity in response to both external and internal sensory input to drive a two-state behavior output.
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Affiliation(s)
- Bhavya Ravi
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | - Jian Zhao
- Department of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA 02114
| | - I Chaudhry
- Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | | | - Mattingly Bartole
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
| | | | | | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA USA 02114
| | - Lijun Kang
- Department of Neuroscience, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Kevin M Collins
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL USA 33136.,Department of Biology, University of Miami, Coral Gables, FL USA 33146
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8
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Abstract
Memories encoded in the parent's brain should not be able to transfer to the progeny. This assumption, which is compatible with the tenets of modern neuroscience and genetics, is challenged by new insights regarding inheritance of transgenerational epigenetic responses. Here we reflect on new discoveries regarding "molecular memories" in light of older and scandalous work on "Memory transfer" spearheaded by James V. McConnell and Georges Ungar. While the history of this field is filled with controversies, mechanisms for transmission of information across generations are being elucidated in different organisms. Most strikingly, it is now clear that in Caenorhabditis elegans nematodes, somatic responses can control gene activity in descendants via heritable small RNA molecules, and that this type of inheritance is tightly regulated by dedicated machinery. In this perspective we will focus mostly on studies conducted using C. elegans, and examine recent work on the connection between small RNAs in the nervous system and germline. We will discuss the evidence for the inheritance of brain-orchestrated behavior, and its possible significance.
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Affiliation(s)
- Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom; Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom; Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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9
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Ferkey DM, Sengupta P, L’Etoile ND. Chemosensory signal transduction in Caenorhabditis elegans. Genetics 2021; 217:iyab004. [PMID: 33693646 PMCID: PMC8045692 DOI: 10.1093/genetics/iyab004] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/16/2022] Open
Abstract
Chemosensory neurons translate perception of external chemical cues, including odorants, tastants, and pheromones, into information that drives attraction or avoidance motor programs. In the laboratory, robust behavioral assays, coupled with powerful genetic, molecular and optical tools, have made Caenorhabditis elegans an ideal experimental system in which to dissect the contributions of individual genes and neurons to ethologically relevant chemosensory behaviors. Here, we review current knowledge of the neurons, signal transduction molecules and regulatory mechanisms that underlie the response of C. elegans to chemicals, including pheromones. The majority of identified molecules and pathways share remarkable homology with sensory mechanisms in other organisms. With the development of new tools and technologies, we anticipate that continued study of chemosensory signal transduction and processing in C. elegans will yield additional new insights into the mechanisms by which this animal is able to detect and discriminate among thousands of chemical cues with a limited sensory neuron repertoire.
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Affiliation(s)
- Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Noelle D L’Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143, USA
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10
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Turnbull RE, Fairall L, Saleh A, Kelsall E, Morris KL, Ragan TJ, Savva CG, Chandru A, Millard CJ, Makarova OV, Smith CJ, Roseman AM, Fry AM, Cowley SM, Schwabe JWR. The MiDAC histone deacetylase complex is essential for embryonic development and has a unique multivalent structure. Nat Commun 2020; 11:3252. [PMID: 32591534 PMCID: PMC7319964 DOI: 10.1038/s41467-020-17078-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/05/2020] [Indexed: 12/31/2022] Open
Abstract
MiDAC is one of seven distinct, large multi-protein complexes that recruit class I histone deacetylases to the genome to regulate gene expression. Despite implications of involvement in cell cycle regulation and in several cancers, surprisingly little is known about the function or structure of MiDAC. Here we show that MiDAC is important for chromosome alignment during mitosis in cancer cell lines. Mice lacking the MiDAC proteins, DNTTIP1 or MIDEAS, die with identical phenotypes during late embryogenesis due to perturbations in gene expression that result in heart malformation and haematopoietic failure. This suggests that MiDAC has an essential and unique function that cannot be compensated by other HDAC complexes. Consistent with this, the cryoEM structure of MiDAC reveals a unique and distinctive mode of assembly. Four copies of HDAC1 are positioned at the periphery with outward-facing active sites suggesting that the complex may target multiple nucleosomes implying a processive deacetylase function.
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Affiliation(s)
- Robert E Turnbull
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Louise Fairall
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Almutasem Saleh
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Emma Kelsall
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- AstraZeneca, Milstein Building, Granta Park, Cambridge, CB21 6GH, UK
| | - Kyle L Morris
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- MRC London Institute of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - T J Ragan
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Christos G Savva
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Aditya Chandru
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Christopher J Millard
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Olga V Makarova
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Alan M Roseman
- Division of Molecular and Cellular Function, University of Manchester, Manchester, M13 9PL, UK
| | - Andrew M Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Shaun M Cowley
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - John W R Schwabe
- Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, LE1 7RH, UK.
- Department of Molecular and Cell Biology, University of Leicester, Leicester, LE1 7RH, UK.
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11
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Mondal B, Jin H, Kallappagoudar S, Sedkov Y, Martinez T, Sentmanat MF, Poet GJ, Li C, Fan Y, Pruett-Miller SM, Herz HM. The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression program to control neurite outgrowth. eLife 2020; 9:57519. [PMID: 32297854 PMCID: PMC7192582 DOI: 10.7554/elife.57519] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
The mitotic deacetylase complex (MiDAC) is a recently identified histone deacetylase (HDAC) complex. While other HDAC complexes have been implicated in neurogenesis, the physiological role of MiDAC remains unknown. Here, we show that MiDAC constitutes an important regulator of neural differentiation. We demonstrate that MiDAC functions as a modulator of a neurodevelopmental gene expression program and binds to important regulators of neurite outgrowth. MiDAC upregulates gene expression of pro-neural genes such as those encoding the secreted ligands SLIT3 and NETRIN1 (NTN1) by a mechanism suggestive of H4K20ac removal on promoters and enhancers. Conversely, MiDAC inhibits gene expression by reducing H3K27ac on promoter-proximal and -distal elements of negative regulators of neurogenesis. Furthermore, loss of MiDAC results in neurite outgrowth defects that can be rescued by supplementation with SLIT3 and/or NTN1. These findings indicate a crucial role for MiDAC in regulating the ligands of the SLIT3 and NTN1 signaling axes to ensure the proper integrity of neurite development.
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Affiliation(s)
- Baisakhi Mondal
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hongjian Jin
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Satish Kallappagoudar
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yurii Sedkov
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tanner Martinez
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Monica F Sentmanat
- Genome Engineering & iPS Center, Department of Genetics, Washington University, St. Louis, United States
| | - Greg J Poet
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Hans-Martin Herz
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, United States
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12
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Abstract
In this issue, Moore et al. and Posner et al., provide evidence for how the activity of the nervous system in C. elegans results in gene expression changes in the germline to pass on parental experiences and learned behavior to their progeny.
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Affiliation(s)
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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13
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Power M, Das S, Schütze K, Marigo V, Ekström P, Paquet-Durand F. Cellular mechanisms of hereditary photoreceptor degeneration - Focus on cGMP. Prog Retin Eye Res 2019; 74:100772. [PMID: 31374251 DOI: 10.1016/j.preteyeres.2019.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/25/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Abstract
The cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood, a problem that is exacerbated by the enormous genetic heterogeneity of this disease group. However, the last decade has yielded a wealth of new knowledge on degenerative pathways and their diversity. Notably, a central role of cGMP-signalling has surfaced for photoreceptor cell death triggered by a subset of disease-causing mutations. In this review, we examine key aspects relevant for photoreceptor degeneration of hereditary origin. The topics covered include energy metabolism, epigenetics, protein quality control, as well as cGMP- and Ca2+-signalling, and how the related molecular and metabolic processes may trigger photoreceptor demise. We compare and integrate evidence on different cell death mechanisms that have been associated with photoreceptor degeneration, including apoptosis, necrosis, necroptosis, and PARthanatos. A special focus is then put on the mechanisms of cGMP-dependent cell death and how exceedingly high photoreceptor cGMP levels may cause activation of Ca2+-dependent calpain-type proteases, histone deacetylases and poly-ADP-ribose polymerase. An evaluation of the available literature reveals that a large group of patients suffering from hereditary photoreceptor degeneration carry mutations that are likely to trigger cGMP-dependent cell death, making this pathway a prime target for future therapy development. Finally, an outlook is given into technological and methodological developments that will with time likely contribute to a comprehensive overview over the entire metabolic complexity of photoreceptor cell death. Building on such developments, new imaging technology and novel biomarkers may be used to develop clinical test strategies, that fully consider the genetic heterogeneity of hereditary retinal degenerations, in order to facilitate clinical testing of novel treatment approaches.
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Affiliation(s)
- Michael Power
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Centre for Integrative Neurosciences (CIN), University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | - Soumyaparna Das
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany; Graduate Training Centre of Neuroscience (GTC), University of Tübingen, Germany
| | | | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Per Ekström
- Ophthalmology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Sweden
| | - François Paquet-Durand
- Cell Death Mechanism Group, Institute for Ophthalmic Research, University of Tübingen, Germany.
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14
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Posner R, Toker IA, Antonova O, Star E, Anava S, Azmon E, Hendricks M, Bracha S, Gingold H, Rechavi O. Neuronal Small RNAs Control Behavior Transgenerationally. Cell 2019; 177:1814-1826.e15. [PMID: 31178120 PMCID: PMC6579485 DOI: 10.1016/j.cell.2019.04.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/18/2019] [Accepted: 04/13/2019] [Indexed: 12/21/2022]
Abstract
It is unknown whether the activity of the nervous system can be inherited. In Caenorhabditis elegans nematodes, parental responses can transmit heritable small RNAs that regulate gene expression transgenerationally. In this study, we show that a neuronal process can impact the next generations. Neurons-specific synthesis of RDE-4-dependent small RNAs regulates germline amplified endogenous small interfering RNAs (siRNAs) and germline gene expression for multiple generations. Further, the production of small RNAs in neurons controls the chemotaxis behavior of the progeny for at least three generations via the germline Argonaute HRDE-1. Among the targets of these small RNAs, we identified the conserved gene saeg-2, which is transgenerationally downregulated in the germline. Silencing of saeg-2 following neuronal small RNA biogenesis is required for chemotaxis under stress. Thus, we propose a small-RNA-based mechanism for communication of neuronal processes transgenerationally. C. elegans neuronal small RNAs are characterized by RNA sequencing RDE-4-dependent neuronal endogenous small RNAs communicate with the germline Germline HRDE-1 mediates transgenerational regulation by neuronal small RNAs Neuronal small RNAs regulate germline genes to control behavior transgenerationally
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Affiliation(s)
- Rachel Posner
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itai Antoine Toker
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Olga Antonova
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ekaterina Star
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Eran Azmon
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michael Hendricks
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Shahar Bracha
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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15
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Olson A, Koelle M. The protein kinase G orthologs, EGL-4 and PKG-2, mediate serotonin-induced paralysis of C. elegans. MICROPUBLICATION BIOLOGY 2019; 2019. [PMID: 32550449 PMCID: PMC7252333 DOI: 10.17912/micropub.biology.000115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Andrew Olson
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, SHM CE30, New Haven, CT 06520-8024
| | - Michael Koelle
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, SHM CE30, New Haven, CT 06520-8024
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16
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Parca L, Beck M, Bork P, Ori A. Quantifying compartment-associated variations of protein abundance in proteomics data. Mol Syst Biol 2018; 14:e8131. [PMID: 29967062 PMCID: PMC6056770 DOI: 10.15252/msb.20178131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022] Open
Abstract
Quantitative mass spectrometry enables to monitor the abundance of thousands of proteins across biological conditions. Currently, most data analysis approaches rely on the assumption that the majority of the observed proteins remain unchanged across compared samples. Thus, gross morphological differences between cell states, deriving from, e.g., differences in size or number of organelles, are often not taken into account. Here, we analyzed multiple published datasets and frequently observed that proteins associated with a particular cellular compartment collectively increase or decrease in their abundance between conditions tested. We show that such effects, arising from underlying morphological differences, can skew the outcome of differential expression analysis. We propose a method to detect and normalize morphological effects underlying proteomics data. We demonstrate the applicability of our method to different datasets and biological questions including the analysis of sub-cellular proteomes in the context of Caenorhabditis elegans aging. Our method provides a complementary perspective to classical differential expression analysis and enables to uncouple overall abundance changes from stoichiometric variations within defined group of proteins.
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Affiliation(s)
- Luca Parca
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
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17
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Trifunović D, Arango-Gonzalez B, Comitato A, Barth M, Del Amo EM, Kulkarni M, Sahaboglu A, Hauck SM, Urtti A, Arsenijevic Y, Ueffing M, Marigo V, Paquet-Durand F. HDAC inhibition in the cpfl1 mouse protects degenerating cone photoreceptors in vivo. Hum Mol Genet 2018; 25:4462-4472. [PMID: 28172811 DOI: 10.1093/hmg/ddw275] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 12/21/2022] Open
Abstract
Cone photoreceptor cell death as it occurs in certain hereditary retinal diseases is devastating, with the affected patients suffering from a loss of accurate and colour vision. Regrettably, these hereditary cone diseases are still untreatable to date. Thus, the identification of substances able to block or restrain cone cell death is of primary importance. We studied the neuroprotective effects of a histone deacetylase inhibitor, Trichostatin A (TSA), in a mouse model of inherited, primary cone degeneration (cpfl1). We show that HDAC inhibition protects cpfl1 cones in vitro, in retinal explant cultures. More importantly, in vivo, a single intravitreal TSA injection significantly increased cone survival for up to 16 days post-injection. In addition, the abnormal, incomplete cone migration pattern in the cpfl1 retina was significantly improved by HDAC inhibition. These findings suggest a crucial role for HDAC activity in primary cone degeneration and highlight a new avenue for future therapy developments for cone dystrophies and retinal diseases associated with impaired cone migration.
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Affiliation(s)
- Dragana Trifunović
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | | | - Antonella Comitato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Melanie Barth
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Eva M Del Amo
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Manoj Kulkarni
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Ayse Sahaboglu
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Neuherberg, Germany
| | - Arto Urtti
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland.,Centre for Drug Research, Division of Pharmaceutical Bioscience, University of Helsinki, Helsinki, Finland
| | - Yvan Arsenijevic
- Unit of Gene Therapy & Stem Cell Biology, Hôpital Ophtalmique Jules Gonin, University of Lausanne, Lausanne, Switzerland
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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18
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Sims JR, Ow MC, Nishiguchi MA, Kim K, Sengupta P, Hall SE. Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways. eLife 2016; 5. [PMID: 27351255 PMCID: PMC4924998 DOI: 10.7554/elife.11642] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 05/09/2016] [Indexed: 02/01/2023] Open
Abstract
Environmental stress during early development can impact adult phenotypes via programmed changes in gene expression. C. elegans larvae respond to environmental stress by entering the stress-resistant dauer diapause pathway and resume development once conditions improve (postdauers). Here we show that the osm-9 TRPV channel gene is a target of developmental programming and is down-regulated specifically in the ADL chemosensory neurons of postdauer adults, resulting in a corresponding altered olfactory behavior that is mediated by ADL in an OSM-9-dependent manner. We identify a cis-acting motif bound by the DAF-3 SMAD and ZFP-1 (AF10) proteins that is necessary for the differential regulation of osm-9, and demonstrate that both chromatin remodeling and endo-siRNA pathways are major contributors to the transcriptional silencing of the osm-9 locus. This work describes an elegant mechanism by which developmental experience influences adult phenotypes by establishing and maintaining transcriptional changes via RNAi and chromatin remodeling pathways. DOI:http://dx.doi.org/10.7554/eLife.11642.001 Increasing evidence suggests that experiencing stressful environments early on in life can have profound effects on the health and behavior of adults. For example, stressful conditions in the womb have been linked to adult depression and metabolic disorders. These effects are thought to be the result of changes in the way that genes in specific tissues are regulated in the individuals that have experienced the stress. However, it is not clear how a particular stress can cause long-term changes in gene activity in specific tissues. A microscopic worm called Caenorhabditis elegans is often used as a simple animal model to study how animals develop and behave. Previous studies have shown that adult worms that experienced stress early in life show differences in behavior and gene activity compared to genetically identical worms that did not experience the stress. Here, Sims, Ow et al. asked what signals are required for these changes to happen. The experiments show that a gene called osm-9 – which plays a role in the nervous system – is less active in sensory nerve cells in worms that experienced stress early on in life. This loss of activity resulted in the worms being unable to respond to a particular odor. Two proteins called DAF-3 and ZFP-1 are able to bind to a section of DNA in the osm-9 gene to decrease its activity in response to stress. These proteins are similar to human proteins that are important for development and are associated with some types of leukemia. Further experiments show that small molecules of ribonucleic acid in the “RNA interference” pathway also help to decrease the activity of osm-9 after stress. Together, Sims, Ow et al.’s findings suggest that environmental conditions in early life regulate the osm-9 gene through the coordinated effort of DAF-3, ZFP-1 and the RNA interference pathway. The next steps are to investigate how these molecules are able to target osm-9 and to identify other proteins that regulate gene activity in response to stress in early life. DOI:http://dx.doi.org/10.7554/eLife.11642.002
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Affiliation(s)
- Jennie R Sims
- Department of Biology, Syracuse University, Syracuse, United States
| | - Maria C Ow
- Department of Biology, Syracuse University, Syracuse, United States
| | | | - Kyuhyung Kim
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Piali Sengupta
- National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Sarah E Hall
- Department of Biology, Syracuse University, Syracuse, United States
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19
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Dopamine regulates body size in Caenorhabditis elegans. Dev Biol 2016; 412:128-138. [DOI: 10.1016/j.ydbio.2016.02.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/08/2016] [Accepted: 02/23/2016] [Indexed: 12/31/2022]
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20
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The Importance of cGMP Signaling in Sensory Cilia for Body Size Regulation in Caenorhabditis elegans. Genetics 2015; 201:1497-510. [PMID: 26434723 DOI: 10.1534/genetics.115.177543] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 10/01/2015] [Indexed: 01/24/2023] Open
Abstract
The body size of Caenorhabditis elegans is thought to be controlled by sensory inputs because many mutants with sensory cilium structure defects exhibit small body size. The EGL-4 cGMP-dependent protein kinase acts in sensory neurons to reduce body size when animals fail to perceive sensory signals. In addition to body size control, EGL-4 regulates various other behavioral and developmental pathways, including those involved in the regulation of egg laying and chemotaxis behavior. Here we have identified gcy-12, which encodes a receptor-type guanylyl cyclase, as a gene involved in the sensory regulation of body size. Analyses with GFP fusion constructs showed that gcy-12 is expressed in several sensory neurons and localizes to sensory cilia. Genetic analyses indicated that GCY-12 acts upstream of EGL-4 in body size control but does not affect other EGL-4 functions. Our studies indicate that the function of the GCY-12 guanylyl cyclase is to provide cGMP to the EGL-4 cGMP-dependent kinase only for limited tasks including body size regulation. We also found that the PDE-2 cyclic nucleotide phosphodiesterase negatively regulates EGL-4 in controlling body size. Thus, the cGMP level is precisely controlled by GCY-12 and PDE-2 to determine body size through EGL-4, and the defects in the sensory cilium structure may disturb the balanced control of the cGMP level. The large number of guanylyl cyclases encoded in the C. elegans genome suggests that EGL-4 exerts pleiotropic effects by partnering with different guanylyl cyclases for different downstream functions.
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21
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Itoh T, Fairall L, Muskett FW, Milano CP, Watson PJ, Arnaudo N, Saleh A, Millard CJ, El-Mezgueldi M, Martino F, Schwabe JWR. Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting. Nucleic Acids Res 2015; 43:2033-44. [PMID: 25653165 PMCID: PMC4344507 DOI: 10.1093/nar/gkv068] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex.
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Affiliation(s)
- Toshimasa Itoh
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Frederick W Muskett
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Charles P Milano
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Peter J Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Nadia Arnaudo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Almutasem Saleh
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Christopher J Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Mohammed El-Mezgueldi
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
| | - Fabrizio Martino
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - John W R Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Lancaster Road, Leicester LE1 9HN, UK
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22
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Koiwai K, Kubota T, Watanabe N, Hori K, Koiwai O, Masai H. Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites. Genes Cells 2015; 20:242-54. [PMID: 25619743 DOI: 10.1111/gtc.12216] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/04/2014] [Indexed: 12/26/2022]
Abstract
TdIF1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through in vitro selection assays (SELEX), we recently showed that TdIF1 recognizes both AT-tract and a specific DNA sequence motif, 5'-TGCATG-3', and can up-regulate the expression of RAB20 through the latter motif. However, whether TdIF1 binds to these sequences in the cells has not been clear and its other target genes remain to be identified. Here, we determined in vivo TdIF1-binding sequences (TdIF1-invivoBMs) on the human chromosomes through ChIP-seq analyses. The result showed a 160-base pair cassette containing 'AT-tract~palindrome (inverted repeat)~AT-tract' as a likely target sequence of TdIF1. Interestingly, the core sequence of the palindrome in the TdIF1-invivoBMs shares significant similarity to the above 5'-TGCATG-3' motif determined by SELEX in vitro. Furthermore, spacer sequences between AT-tract and the palindrome contain many potential transcription factor binding sites. In luciferase assays, TdIF1 can up-regulate transcription activity of the promoters containing the TdIF1-invivoBM, and this effect is mainly through the palindrome. Clusters of this motif were found in the potential target genes. Gene ontology analysis and RT-qPCR showed the enrichment of some candidate targets of TdIF1 among the genes involved in the regulation of ossification. Potential modes of transcription activation by TdIF1 are discussed.
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Affiliation(s)
- Kotaro Koiwai
- Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
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23
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Arango-Gonzalez B, Trifunović D, Sahaboglu A, Kranz K, Michalakis S, Farinelli P, Koch S, Koch F, Cottet S, Janssen-Bienhold U, Dedek K, Biel M, Zrenner E, Euler T, Ekström P, Ueffing M, Paquet-Durand F. Identification of a common non-apoptotic cell death mechanism in hereditary retinal degeneration. PLoS One 2014; 9:e112142. [PMID: 25392995 PMCID: PMC4230983 DOI: 10.1371/journal.pone.0112142] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 10/13/2014] [Indexed: 01/10/2023] Open
Abstract
Cell death in neurodegenerative diseases is often thought to be governed by apoptosis; however, an increasing body of evidence suggests the involvement of alternative cell death mechanisms in neuronal degeneration. We studied retinal neurodegeneration using 10 different animal models, covering all major groups of hereditary human blindness (rd1, rd2, rd10, Cngb1 KO, Rho KO, S334ter, P23H, Cnga3 KO, cpfl1, Rpe65 KO), by investigating metabolic processes relevant for different forms of cell death. We show that apoptosis plays only a minor role in the inherited forms of retinal neurodegeneration studied, where instead, a non-apoptotic degenerative mechanism common to all mutants is of major importance. Hallmark features of this pathway are activation of histone deacetylase, poly-ADP-ribose-polymerase, and calpain, as well as accumulation of cyclic guanosine monophosphate and poly-ADP-ribose. Our work thus demonstrates the prevalence of alternative cell death mechanisms in inherited retinal degeneration and provides a rational basis for the design of mutation-independent treatments.
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Affiliation(s)
| | - Dragana Trifunović
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Ayse Sahaboglu
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Katharina Kranz
- Department of Neurobiology, University of Oldenburg, Oldenburg, Germany
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Pietro Farinelli
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
- Division of Ophthalmology, Department of Clinical Sciences, University of Lund, Lund, Sweden
| | - Susanne Koch
- Center for Integrated Protein Science Munich and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Fred Koch
- Center for Integrated Protein Science Munich and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Sandra Cottet
- Institute for Research in Ophthalmology, Sion, Switzerland
| | | | - Karin Dedek
- Department of Neurobiology, University of Oldenburg, Oldenburg, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich and Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Eberhart Zrenner
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
- Centre for Integrative Neuroscience, University of Tuebingen, Tuebingen, Germany
| | - Thomas Euler
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
- Centre for Integrative Neuroscience, University of Tuebingen, Tuebingen, Germany
| | - Per Ekström
- Division of Ophthalmology, Department of Clinical Sciences, University of Lund, Lund, Sweden
| | - Marius Ueffing
- Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
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24
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Juang BT, Gu C, Starnes L, Palladino F, Goga A, Kennedy S, L'Etoile ND. Endogenous nuclear RNAi mediates behavioral adaptation to odor. Cell 2013; 154:1010-1022. [PMID: 23993094 DOI: 10.1016/j.cell.2013.08.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 07/16/2013] [Accepted: 08/01/2013] [Indexed: 10/26/2022]
Abstract
Most eukaryotic cells express small regulatory RNAs. The purpose of one class, the somatic endogenous siRNAs (endo-siRNAs), remains unclear. Here, we show that the endo-siRNA pathway promotes odor adaptation in C. elegans AWC olfactory neurons. In adaptation, the nuclear Argonaute NRDE-3, which acts in AWC, is loaded with siRNAs targeting odr-1, a gene whose downregulation is required for adaptation. Concomitant with increased odr-1 siRNA in AWC, we observe increased binding of the HP1 homolog HPL-2 at the odr-1 locus in AWC and reduced odr-1 mRNA in adapted animals. Phosphorylation of HPL-2, an in vitro substrate of the EGL-4 kinase that promotes adaption, is necessary and sufficient for behavioral adaptation. Thus, environmental stimulation amplifies an endo-siRNA negative feedback loop to dynamically repress cognate gene expression and shape behavior. This class of siRNA may act broadly as a rheostat allowing prolonged stimulation to dampen gene expression and promote cellular memory formation. PAPERFLICK:
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Affiliation(s)
- Bi-Tzen Juang
- Departments of Cell & Tissue Biology and Medicine, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0512, USA
| | - Chen Gu
- Departments of Cell & Tissue Biology and Medicine, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0512, USA; Amunix, Inc., 500 Ellis Street, Mountain View, CA 94043, USA
| | - Linda Starnes
- Departments of Cell & Tissue Biology and Medicine, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0512, USA; Chromatin Structure and Function Group, NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3B, Room 4.3.07, 2200 Copenhagen N, Denmark
| | - Francesca Palladino
- École Normale Supérieure de Lyon, CNRS, Molecular Biology of the Cell Laboratory/ UMR5239, Université Claude Bernard Lyon, 69007 Lyon, France
| | - Andrei Goga
- Departments of Cell & Tissue Biology and Medicine, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0512, USA
| | - Scott Kennedy
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Noelle D L'Etoile
- Departments of Cell & Tissue Biology and Medicine, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143-0512, USA.
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Kubota T, Koiwai O, Hori K, Watanabe N, Koiwai K. TdIF1 recognizes a specific DNA sequence through its Helix-Turn-Helix and AT-hook motifs to regulate gene transcription. PLoS One 2013; 8:e66710. [PMID: 23874396 PMCID: PMC3707907 DOI: 10.1371/journal.pone.0066710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 05/09/2013] [Indexed: 12/27/2022] Open
Abstract
TdIF1 was originally identified as a protein that directly binds to DNA polymerase TdT. TdIF1 is also thought to function in transcription regulation, because it binds directly to the transcriptional factor TReP-132, and to histone deacetylases HDAC1 and HDAC2. Here we show that TdIF1 recognizes a specific DNA sequence and regulates gene transcription. By constructing TdIF1 mutants, we identify amino acid residues essential for its interaction with DNA. An in vitro DNA selection assay, SELEX, reveals that TdIF1 preferentially binds to the sequence 5′-GNTGCATG-3′ following an AT-tract, through its Helix-Turn-Helix and AT-hook motifs. We show that four repeats of this recognition sequence allow TdIF1 to regulate gene transcription in a plasmid-based luciferase reporter assay. We demonstrate that TdIF1 associates with the RAB20 promoter, and RAB20 gene transcription is reduced in TdIF1-knocked-down cells, suggesting that TdIF1 stimulates RAB20 gene transcription.
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Affiliation(s)
- Takashi Kubota
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Osamu Koiwai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | | | - Kotaro Koiwai
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, Aichi, Japan
- * E-mail:
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26
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Millard C, Watson P, Celardo I, Gordiyenko Y, Cowley S, Robinson C, Fairall L, Schwabe J. Class I HDACs share a common mechanism of regulation by inositol phosphates. Mol Cell 2013; 51:57-67. [PMID: 23791785 PMCID: PMC3710971 DOI: 10.1016/j.molcel.2013.05.020] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/23/2013] [Accepted: 05/16/2013] [Indexed: 01/06/2023]
Abstract
Class I histone deacetylases (HDAC1, HDAC2, and HDAC3) are recruited by cognate corepressor proteins into specific transcriptional repression complexes that target HDAC activity to chromatin resulting in chromatin condensation and transcriptional silencing. We previously reported the structure of HDAC3 in complex with the SMRT corepressor. This structure revealed the presence of inositol-tetraphosphate [Ins(1,4,5,6)P4] at the interface of the two proteins. It was previously unclear whether the role of Ins(1,4,5,6)P4 is to act as a structural cofactor or a regulator of HDAC3 activity. Here we report the structure of HDAC1 in complex with MTA1 from the NuRD complex. The ELM2-SANT domains from MTA1 wrap completely around HDAC1 occupying both sides of the active site such that the adjacent BAH domain is ideally positioned to recruit nucleosomes to the active site of the enzyme. Functional assays of both the HDAC1 and HDAC3 complexes reveal that Ins(1,4,5,6)P4 is a bona fide conserved regulator of class I HDAC complexes.
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Affiliation(s)
- Christopher J. Millard
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Peter J. Watson
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Ivana Celardo
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Yuliya Gordiyenko
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Shaun M. Cowley
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - Carol V. Robinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Louise Fairall
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
| | - John W.R. Schwabe
- Henry Wellcome Laboratories of Structural Biology, Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK
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Krzyzanowski MC, Brueggemann C, Ezak MJ, Wood JF, Michaels KL, Jackson CA, Juang BT, Collins KD, Yu MC, L'Etoile ND, Ferkey DM. The C. elegans cGMP-dependent protein kinase EGL-4 regulates nociceptive behavioral sensitivity. PLoS Genet 2013; 9:e1003619. [PMID: 23874221 PMCID: PMC3708839 DOI: 10.1371/journal.pgen.1003619] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 05/23/2013] [Indexed: 11/25/2022] Open
Abstract
Signaling levels within sensory neurons must be tightly regulated to allow cells to integrate information from multiple signaling inputs and to respond to new stimuli. Herein we report a new role for the cGMP-dependent protein kinase EGL-4 in the negative regulation of G protein-coupled nociceptive chemosensory signaling. C. elegans lacking EGL-4 function are hypersensitive in their behavioral response to low concentrations of the bitter tastant quinine and exhibit an elevated calcium flux in the ASH sensory neurons in response to quinine. We provide the first direct evidence for cGMP/PKG function in ASH and propose that ODR-1, GCY-27, GCY-33 and GCY-34 act in a non-cell-autonomous manner to provide cGMP for EGL-4 function in ASH. Our data suggest that activated EGL-4 dampens quinine sensitivity via phosphorylation and activation of the regulator of G protein signaling (RGS) proteins RGS-2 and RGS-3, which in turn downregulate Gα signaling and behavioral sensitivity.
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Affiliation(s)
- Michelle C. Krzyzanowski
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Chantal Brueggemann
- Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America
| | - Meredith J. Ezak
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Jordan F. Wood
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Kerry L. Michaels
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Christopher A. Jackson
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Bi-Tzen Juang
- Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America
| | - Kimberly D. Collins
- Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America
| | - Michael C. Yu
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Noelle D. L'Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America
| | - Denise M. Ferkey
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
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28
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Ziolo MT, Biesiadecki BJ. Moving into a new neighborhood: NOS goes nuclear. J Mol Cell Cardiol 2013; 62:214-6. [PMID: 23800603 DOI: 10.1016/j.yjmcc.2013.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 06/10/2013] [Accepted: 06/14/2013] [Indexed: 01/21/2023]
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Kim GW, Lin JE, Waldman SA. GUCY2C: at the intersection of obesity and cancer. Trends Endocrinol Metab 2013; 24:165-73. [PMID: 23375388 PMCID: PMC3617062 DOI: 10.1016/j.tem.2013.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 12/26/2012] [Accepted: 01/02/2013] [Indexed: 12/13/2022]
Abstract
Guanylyl cyclase C (GUCY2C) has canonical centrality in defense of key intestinal homeostatic mechanisms, encompassing fluid and electrolyte balance, epithelial dynamics, antitumorigenesis, and intestinal barrier function. Recent discoveries expand the homeostatic role of GUCY2C to reveal a novel gut-brain endocrine axis regulating appetite, anchored by hypothalamic GUCY2C which is responsive to intestine-derived uroguanylin. Thus, GUCY2C may represent a new target for anti-obesity pharmacotherapy. Moreover, the coincident regulation of energy balance and tumor suppression by a single hormone receptor system suggests that the GUCY2C axis might contribute to the established relationship between obesity and colorectal cancer. This confluence suggests that hormone supplementation to reconstitute GUCY2C signaling may be an elegant strategy to reverse both pathophysiologic processes.
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Affiliation(s)
- Gilbert W Kim
- Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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30
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Gaglia MM, Jeong DE, Ryu EA, Lee D, Kenyon C, Lee SJ. Genes that act downstream of sensory neurons to influence longevity, dauer formation, and pathogen responses in Caenorhabditis elegans. PLoS Genet 2012; 8:e1003133. [PMID: 23284299 PMCID: PMC3527274 DOI: 10.1371/journal.pgen.1003133] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 10/15/2012] [Indexed: 12/11/2022] Open
Abstract
The sensory systems of multicellular organisms are designed to provide information about the environment and thus elicit appropriate changes in physiology and behavior. In the nematode Caenorhabditis elegans, sensory neurons affect the decision to arrest during development in a diapause state, the dauer larva, and modulate the lifespan of the animals in adulthood. However, the mechanisms underlying these effects are incompletely understood. Using whole-genome microarray analysis, we identified transcripts whose levels are altered by mutations in the intraflagellar transport protein daf-10, which result in impaired development and function of many sensory neurons in C. elegans. In agreement with existing genetic data, the expression of genes regulated by the transcription factor DAF-16/FOXO was affected by daf-10 mutations. In addition, we found altered expression of transcriptional targets of the DAF-12/nuclear hormone receptor in the daf-10 mutants and showed that this pathway influences specifically the dauer formation phenotype of these animals. Unexpectedly, pathogen-responsive genes were repressed in daf-10 mutant animals, and these sensory mutants exhibited altered susceptibility to and behavioral avoidance of bacterial pathogens. Moreover, we found that a solute transporter gene mct-1/2, which was induced by daf-10 mutations, was necessary and sufficient for longevity. Thus, sensory input seems to influence an extensive transcriptional network that modulates basic biological processes in C. elegans. This situation is reminiscent of the complex regulation of physiology by the mammalian hypothalamus, which also receives innervations from sensory systems, most notably the visual and olfactory systems. The senses provide animals with information about their environment, which affects not only their behavior but also their internal state and physiological outputs. How this information is processed is still unclear. In this study, we used mutant C. elegans roundworms that had defective sensory neurons to investigate how changes in sensation alter the expression of genes and regulate physiology, specifically the worms' choice to hibernate during growth and their longevity as fully-grown adults. We showed that defects in sensory neurons change the pattern of gene expression and regulate these outputs through known hormonal pathways, including insulin/IGF-1 and steroid pathways. We also identified a new regulator of longevity, MCT-1, that is predicted to transport small metabolites and hormones in the body. Unexpectedly, we found that sensory impairment altered yet another physiological output, the response to infectious agents. It prevented the worms from avoiding infectious bacteria and reduced the expression of potentially protective factors, but also increased the worms' resistance to infection, suggesting a complex network of responses to environmental stimuli. Understanding how sensory information is relayed in this relatively simple organism may inform our understanding of sensory processing in higher organisms like mammals.
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Affiliation(s)
- Marta M Gaglia
- Neuroscience Graduate Program and Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
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31
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Hesabi B, Danziger RS, Kotlo KU. Heterogeneous nuclear ribonucleoprotein A1 is a novel cellular target of atrial natriuretic peptide signaling in renal epithelial cells. Cell Signal 2012; 24:1100-8. [PMID: 22285803 PMCID: PMC3288234 DOI: 10.1016/j.cellsig.2012.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/20/2011] [Accepted: 01/10/2012] [Indexed: 10/14/2022]
Abstract
Two classes of guanylyl cyclases (GC) form intracellular cGMP. One is a receptor for atrial natriuretic peptide (ANP) and the other for nitric oxide (NO). The ANP receptor guanylyl cyclase (GC-A) is a membrane-bound, single subunit protein. Nitric oxide activated or soluble guanylyl cyclases (NOGC) are heme-containing heterodimers. These have been shown to be important in cGMP mediated regulation of arterial vascular resistance and renal sodium transport. Recent studies have shown that cGMP produced by both GCs is compartmentalized in the heart and vascular smooth muscle cells. To date, however, how intracellular cGMP generated by ANP and NO is compartmentalized and how it triggers specific downstream targets in kidney cells has not been investigated. Our studies show that intracellular cGMP formed by NO is targeted to cytosolic and cytoskeletal compartments whereas cGMP formed by ANP is restricted to nuclear and membrane compartments. We used two dimensional difference in gel electrophoresis and MALDI-TOF/TOF to identify distinct sub-cellular targets that are specific to ANP and NO signaling in HK-2 cells. A nucleocytoplasmic shuttling protein, heterogeneous nuclear ribonucleo protein A1 (hnRNP A1) is preferentially phosphorylated by ANP/cGMP/cGK signaling. ANP stimulation of HK-2 cells leads to increased cGK activity in the nucleus and translocation of cGK and hnRNP A1 to the nucleus. Phosphodiestaerase-5 (PDE-5 inhibitor) sildenafil augmented ANP-mediated effects on hnRNPA1 phosphorylation, translocation to nucleus and nuclear cGK activity. Our results suggest that cGMP generated by ANP and SNAP is differentially compartmentalized, localized but not global changes in cGMP, perhaps at different sub-cellular fractions of the cell, may more closely correlate with their effects by preferential phosphorylation of cellular targets.
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Affiliation(s)
- Bahar Hesabi
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
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32
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Kroetz SM, Srinivasan J, Yaghoobian J, Sternberg PW, Hong RL. The cGMP signaling pathway affects feeding behavior in the necromenic nematode Pristionchus pacificus. PLoS One 2012; 7:e34464. [PMID: 22563372 PMCID: PMC3338501 DOI: 10.1371/journal.pone.0034464] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
Background The genetic tractability and the species-specific association with beetles make the nematode Pristionchus pacificus an exciting emerging model organism for comparative studies in development and behavior. P. pacificus differs from Caenorhabditis elegans (a bacterial feeder) by its buccal teeth and the lack of pharyngeal grinders, but almost nothing is known about which genes coordinate P. pacificus feeding behaviors, such as pharyngeal pumping rate, locomotion, and fat storage. Methodology/Principal Findings We analyzed P. pacificus pharyngeal pumping rate and locomotion behavior on and off food, as well as on different species of bacteria (Escherichia coli, Bacillus subtilis, and Caulobacter crescentus). We found that the cGMP-dependent protein kinase G (PKG) Ppa-EGL-4 in P. pacificus plays an important role in regulating the pumping rate, mouth form dimorphism, the duration of forward locomotion, and the amount of fat stored in intestine. In addition, Ppa-EGL-4 interacts with Ppa-OBI-1, a recently identified protein involved in chemosensation, to influence feeding and locomotion behavior. We also found that C. crescentus NA1000 increased pharyngeal pumping as well as fat storage in P. pacificus. Conclusions The PKG EGL-4 has conserved functions in regulating feeding behavior in both C. elegans and P. pacificus nematodes. The Ppa-EGL-4 also has been co-opted during evolution to regulate P. pacificus mouth form dimorphism that indirectly affect pharyngeal pumping rate. Specifically, the lack of Ppa-EGL-4 function increases pharyngeal pumping, time spent in forward locomotion, and fat storage, in part as a result of higher food intake. Ppa-OBI-1 functions upstream or parallel to Ppa-EGL-4. The beetle-associated omnivorous P. pacificus respond differently to changes in food state and food quality compared to the exclusively bacteriovorous C. elegans.
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Affiliation(s)
- Silvina M. Kroetz
- Department of Biology, California State University Northridge, Northridge, California, United States of America
| | - Jagan Srinivasan
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Jonathan Yaghoobian
- Department of Biology, California State University Northridge, Northridge, California, United States of America
| | - Paul W. Sternberg
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Ray L. Hong
- Department of Biology, California State University Northridge, Northridge, California, United States of America
- * E-mail:
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33
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Miller CL, Cai Y, Oikawa M, Thomas T, Dostmann WR, Zaccolo M, Fujiwara K, Yan C. Cyclic nucleotide phosphodiesterase 1A: a key regulator of cardiac fibroblast activation and extracellular matrix remodeling in the heart. Basic Res Cardiol 2011; 106:1023-39. [PMID: 22012077 DOI: 10.1007/s00395-011-0228-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 10/07/2011] [Accepted: 10/10/2011] [Indexed: 11/26/2022]
Abstract
Cardiac fibroblasts become activated and differentiate to smooth muscle-like myofibroblasts in response to hypertension and myocardial infarction (MI), resulting in extracellular matrix (ECM) remodeling, scar formation and impaired cardiac function. cAMP and cGMP-dependent signaling have been implicated in cardiac fibroblast activation and ECM synthesis. Dysregulation of cyclic nucleotide phosphodiesterase (PDE) activity/expression is also associated with various diseases and several PDE inhibitors are currently available or in development for treating these pathological conditions. The objective of this study is to define and characterize the specific PDE isoform that is altered during cardiac fibroblast activation and functionally important for regulating myofibroblast activation and ECM synthesis. We have found that Ca(2+)/calmodulin-stimulated PDE1A isoform is specifically induced in activated cardiac myofibroblasts stimulated by Ang II and TGF-β in vitro as well as in vivo within fibrotic regions of mouse, rat, and human diseased hearts. Inhibition of PDE1A function via PDE1-selective inhibitor or PDE1A shRNA significantly reduced Ang II or TGF-β-induced myofibroblast activation, ECM synthesis, and pro-fibrotic gene expression in rat cardiac fibroblasts. Moreover, the PDE1 inhibitor attenuated isoproterenol-induced interstitial fibrosis in mice. Mechanistic studies revealed that PDE1A modulates unique pools of cAMP and cGMP, predominantly in perinuclear and nuclear regions of cardiac fibroblasts. Further, both cAMP-Epac-Rap1 and cGMP-PKG signaling was involved in PDE1A-mediated regulation of collagen synthesis. These results suggest that induction of PDE1A plays a critical role in cardiac fibroblast activation and cardiac fibrosis, and targeting PDE1A may lead to regression of the adverse cardiac remodeling associated with various cardiac diseases.
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Affiliation(s)
- Clint L Miller
- Department of Pharmacology and Physiology, Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Box CVRI, Rochester, NY 14642, USA
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