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Ow MC, Nishiguchi MA, Dar AR, Butcher RA, Hall SE. RNAi-dependent expression of sperm genes in ADL chemosensory neurons is required for olfactory responses in Caenorhabditis elegans. Front Mol Biosci 2024; 11:1396587. [PMID: 39055986 PMCID: PMC11269235 DOI: 10.3389/fmolb.2024.1396587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent differentially expressed genes. Surprisingly, 214 of the ADL DE genes are considered "germline-expressed", including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.
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Affiliation(s)
- Maria C. Ow
- Biology Department, Syracuse University, Syracuse, NY, United States
| | | | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Sarah E. Hall
- Biology Department, Syracuse University, Syracuse, NY, United States
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2
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Chaubey AH, Sojka SE, Onukwufor JO, Ezak MJ, Vandermeulen MD, Bowitch A, Vodičková A, Wojtovich AP, Ferkey DM. The Caenorhabditis elegans innexin INX-20 regulates nociceptive behavioral sensitivity. Genetics 2023; 223:iyad017. [PMID: 36753530 PMCID: PMC10319955 DOI: 10.1093/genetics/iyad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 09/03/2022] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Organisms rely on chemical cues in their environment to indicate the presence or absence of food, reproductive partners, predators, or other harmful stimuli. In the nematode Caenorhabditis elegans, the bilaterally symmetric pair of ASH sensory neurons serves as the primary nociceptors. ASH activation by aversive stimuli leads to backward locomotion and stimulus avoidance. We previously reported a role for guanylyl cyclases in dampening nociceptive sensitivity that requires an innexin-based gap junction network to pass cGMP between neurons. Here, we report that animals lacking function of the gap junction component INX-20 are hypersensitive in their behavioral response to both soluble and volatile chemical stimuli that signal through G protein-coupled receptor pathways in ASH. We find that expressing inx-20 in the ADL and AFD sensory neurons is sufficient to dampen ASH sensitivity, which is supported by new expression analysis of endogenous INX-20 tagged with mCherry via the CRISPR-Cas9 system. Although ADL does not form gap junctions directly with ASH, it does so via gap junctions with the interneuron RMG and the sensory neuron ASK. Ablating either ADL or RMG and ASK also resulted in nociceptive hypersensitivity, suggesting an important role for RMG/ASK downstream of ADL in the ASH modulatory circuit. This work adds to our growing understanding of the repertoire of ways by which ASH activity is regulated via its connectivity to other neurons and identifies a previously unknown role for ADL and RMG in the modulation of aversive behavior.
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Affiliation(s)
- Aditi H Chaubey
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Savannah E Sojka
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - John O Onukwufor
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Meredith J Ezak
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Matthew D Vandermeulen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Alexander Bowitch
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Anežka Vodičková
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Andrew P Wojtovich
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Anesthesiology and Perioperative Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Denise M Ferkey
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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3
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Liu Y, Zhou J, Zhang N, Wu X, Zhang Q, Zhang W, Li X, Tian Y. Two sensory neurons coordinate the systemic mitochondrial stress response via GPCR signaling in C. elegans. Dev Cell 2022; 57:2469-2482.e5. [DOI: 10.1016/j.devcel.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/11/2022] [Accepted: 10/04/2022] [Indexed: 11/03/2022]
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McDonagh A, Crew J, van der Linden AM. Dietary vitamin B12 regulates chemosensory receptor gene expression via the MEF2 transcription factor in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:6580222. [PMID: 35512190 PMCID: PMC9157118 DOI: 10.1093/g3journal/jkac107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/24/2022] [Indexed: 02/02/2023]
Abstract
Dynamic changes in chemoreceptor gene expression levels in sensory neurons are one strategy that an animal can use to modify their responses to dietary changes. However, the mechanisms underlying diet-dependent modulation of chemosensory gene expression are unclear. Here, we show that the expression of the srh-234 chemoreceptor gene localized in a single ADL sensory neuron type of Caenorhabditis elegans is downregulated when animals are fed a Comamonas aquatica bacterial diet, but not on an Escherichia coli diet. Remarkably, this diet-modulated effect on srh-234 expression is dependent on the micronutrient vitamin B12 endogenously produced by Comamonas aq. bacteria. Excess propionate and genetic perturbations in the canonical and shunt propionate breakdown pathways are able to override the repressive effects of vitamin B12 on srh-234 expression. The vitamin B12-mediated regulation of srh-234 expression levels in ADL requires the MEF-2 MADS domain transcription factor, providing a potential mechanism by which dietary vitamin B12 may transcriptionally tune individual chemoreceptor genes in a single sensory neuron type, which in turn may change animal responses to biologically relevant chemicals in their diet.
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Affiliation(s)
- Aja McDonagh
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Jeannette Crew
- Department of Biology, University of Nevada, Reno, NV 89557, USA
| | - Alexander M van der Linden
- Department of Biology, University of Nevada, Reno, NV 89557, USA,Corresponding author: Department of Biology, University of Nevada, Reno, NV 89557, USA.
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5
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Wu T, Duan F, Yang W, Liu H, Caballero A, Fernandes de Abreu DA, Dar AR, Alcedo J, Ch'ng Q, Butcher RA, Zhang Y. Pheromones Modulate Learning by Regulating the Balanced Signals of Two Insulin-like Peptides. Neuron 2019; 104:1095-1109.e5. [PMID: 31676170 PMCID: PMC7009321 DOI: 10.1016/j.neuron.2019.09.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/09/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Social environment modulates learning through unknown mechanisms. Here, we report that a pheromone mixture that signals overcrowding inhibits C. elegans from learning to avoid pathogenic bacteria. We find that learning depends on the balanced signaling of two insulin-like peptides (ILPs), INS-16 and INS-4, which act respectively in the pheromone-sensing neuron ADL and the bacteria-sensing neuron AWA. Pheromone exposure inhibits learning by disrupting this balance: it activates ADL and increases expression of ins-16, and this cellular effect reduces AWA activity and AWA-expressed ins-4. The activities of the sensory neurons are required for learning and the expression of the ILPs. Interestingly, pheromones also promote the ingestion of pathogenic bacteria while increasing resistance to the pathogen. Thus, the balance of the ILP signals integrates social information into the learning process as part of a coordinated adaptive response that allows consumption of harmful food during times of high population density.
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Affiliation(s)
- Taihong Wu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Fengyun Duan
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Wenxing Yang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - He Liu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Antonio Caballero
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK
| | - Diana Andrea Fernandes de Abreu
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK
| | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Joy Alcedo
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - QueeLim Ch'ng
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK
| | - Rebecca A Butcher
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Yun Zhang
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity. PLoS Biol 2018; 16:e2004979. [PMID: 29672507 PMCID: PMC5908064 DOI: 10.1371/journal.pbio.2004979] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/12/2018] [Indexed: 11/19/2022] Open
Abstract
Proneural genes are among the most early-acting genes in nervous system development, instructing blast cells to commit to a neuronal fate. Drosophila Atonal and Achaete-Scute complex (AS-C) genes, as well as their vertebrate orthologs, are basic helix-loop-helix (bHLH) transcription factors with such proneural activity. We show here that a C. elegans AS-C homolog, hlh-4, functions in a fundamentally different manner. In the embryonic, larval, and adult nervous systems, hlh-4 is expressed exclusively in a single nociceptive neuron class, ADL, and its expression in ADL is maintained via transcriptional autoregulation throughout the life of the animal. However, in hlh-4 null mutants, the ADL neuron is generated and still appears neuronal in overall morphology and expression of panneuronal and pansensory features. Rather than acting as a proneural gene, we find that hlh-4 is required for the ADL neuron to function properly, to adopt its correct morphology, to express its unusually large repertoire of olfactory receptor-encoding genes, and to express other known features of terminal ADL identity, including neurotransmitter phenotype, neuropeptides, ion channels, and electrical synapse proteins. hlh-4 is sufficient to induce ADL identity features upon ectopic expression in other neuron types. The expression of ADL terminal identity features is directly controlled by HLH-4 via a phylogenetically conserved E-box motif, which, through bioinformatic analysis, we find to constitute a predictive feature of ADL-expressed terminal identity markers. The lineage that produces the ADL neuron was previously shown to require the conventional, transient proneural activity of another AS-C homolog, hlh-14, demonstrating sequential activities of distinct AS-C-type bHLH genes in neuronal specification. Taken together, we have defined here an unconventional function of an AS-C-type bHLH gene as a terminal selector of neuronal identity and we speculate that such function could be reflective of an ancestral function of an "ur-" bHLH gene.
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Vidal B, Aghayeva U, Sun H, Wang C, Glenwinkel L, Bayer EA, Hobert O. An atlas of Caenorhabditis elegans chemoreceptor expression. PLoS Biol 2018; 16:e2004218. [PMID: 29293491 PMCID: PMC5749674 DOI: 10.1371/journal.pbio.2004218] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/22/2017] [Indexed: 12/20/2022] Open
Abstract
One goal of modern day neuroscience is the establishment of molecular maps that assign unique features to individual neuron types. Such maps provide important starting points for neuron classification, for functional analysis, and for developmental studies aimed at defining the molecular mechanisms of neuron identity acquisition and neuron identity diversification. In this resource paper, we describe a nervous system-wide map of the potential expression sites of 244 members of the largest gene family in the C. elegans genome, rhodopsin-like (class A) G-protein-coupled receptor (GPCR) chemoreceptors, using classic gfp reporter gene technology. We cover representatives of all sequence families of chemoreceptor GPCRs, some of which were previously entirely uncharacterized. Most reporters are expressed in a very restricted number of cells, often just in single cells. We assign GPCR reporter expression to all but two of the 37 sensory neuron classes of the sex-shared, core nervous system. Some sensory neurons express a very small number of receptors, while others, particularly nociceptive neurons, coexpress several dozen GPCR reporter genes. GPCR reporters are also expressed in a wide range of inter- and motorneurons, as well as non-neuronal cells, suggesting that GPCRs may constitute receptors not just for environmental signals, but also for internal cues. We observe only one notable, frequent association of coexpression patterns, namely in one nociceptive amphid (ASH) and two nociceptive phasmid sensory neurons (PHA, PHB). We identified GPCRs with sexually dimorphic expression and several GPCR reporters that are expressed in a left/right asymmetric manner. We identified a substantial degree of GPCR expression plasticity; particularly in the context of the environmentally-induced dauer diapause stage when one third of all tested GPCRs alter the cellular specificity of their expression within and outside the nervous system. Intriguingly, in a number of cases, the dauer-specific alterations of GPCR reporter expression in specific neuron classes are maintained during postdauer life and in some case new patterns are induced post-dauer, demonstrating that GPCR gene expression may serve as traits of life history. Taken together, our resource provides an entry point for functional studies and also offers a host of molecular markers for studying molecular patterning and plasticity of the nervous system.
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Affiliation(s)
- Berta Vidal
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Ulkar Aghayeva
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Haosheng Sun
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Chen Wang
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Lori Glenwinkel
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Emily A. Bayer
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
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8
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Alqadah A, Hsieh YW, Xiong R, Chuang CF. Stochastic left-right neuronal asymmetry in Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0407. [PMID: 27821536 DOI: 10.1098/rstb.2015.0407] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 12/28/2022] Open
Abstract
Left-right asymmetry in the nervous system is observed across species. Defects in left-right cerebral asymmetry are linked to several neurological diseases, but the molecular mechanisms underlying brain asymmetry in vertebrates are still not very well understood. The Caenorhabditis elegans left and right amphid wing 'C' (AWC) olfactory neurons communicate through intercellular calcium signalling in a transient embryonic gap junction neural network to specify two asymmetric subtypes, AWCOFF (default) and AWCON (induced), in a stochastic manner. Here, we highlight the molecular mechanisms that establish and maintain stochastic AWC asymmetry. As the components of the AWC asymmetry pathway are highly conserved, insights from the model organism C. elegans may provide a window onto how brain asymmetry develops in humans.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
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Affiliation(s)
- Amel Alqadah
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Yi-Wen Hsieh
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Rui Xiong
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
| | - Chiou-Fen Chuang
- Department of Biological Sciences, University of Illinois at Chicago, IL 60607, USA
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9
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Cell-Autonomous and Non-Cell-Autonomous Regulation of a Feeding State-Dependent Chemoreceptor Gene via MEF-2 and bHLH Transcription Factors. PLoS Genet 2016; 12:e1006237. [PMID: 27487365 PMCID: PMC4972359 DOI: 10.1371/journal.pgen.1006237] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Food and feeding-state dependent changes in chemoreceptor gene expression may allow Caenorhabditis elegans to modify their chemosensory behavior, but the mechanisms essential for these expression changes remain poorly characterized. We had previously shown that expression of a feeding state-dependent chemoreceptor gene, srh-234, in the ADL sensory neuron of C. elegans is regulated via the MEF-2 transcription factor. Here, we show that MEF-2 acts together with basic helix-loop-helix (bHLH) transcription factors to regulate srh-234 expression as a function of feeding state. We identify a cis-regulatory MEF2 binding site that is necessary and sufficient for the starvation-induced down regulation of srh-234 expression, while an E-box site known to bind bHLH factors is required to drive srh-234 expression in ADL. We show that HLH-2 (E/Daughterless), HLH-3 and HLH-4 (Achaete-scute homologs) act in ADL neurons to regulate srh-234 expression. We further demonstrate that the expression levels of srh-234 in ADL neurons are regulated remotely by MXL-3 (Max-like 3 homolog) and HLH-30 (TFEB ortholog) acting in the intestine, which is dependent on insulin signaling functioning specifically in ADL neurons. We also show that this intestine-to-neuron feeding-state regulation of srh-234 involves a subset of insulin-like peptides. These results combined suggest that chemoreceptor gene expression is regulated by both cell-autonomous and non-cell-autonomous transcriptional mechanisms mediated by MEF2 and bHLH factors, which may allow animals to fine-tune their chemosensory responses in response to changes in their feeding state. Plasticity in chemoreceptor gene expression may be a simple strategy by which an animal can modulate its chemosensory responses in changing external and internal state conditions. However, the transcriptional mechanisms required for these chemoreceptor gene expression changes are poorly understood. Here, we describe the identification of a transcriptional module(s) consisting of MEF-2 and basic helix-loop-helix (bHLH) transcription factors and their cognate binding sites in Caenorhabditis elegans that act together in ADL sensory neurons to properly regulate expression of a feeding-state dependent chemoreceptor gene. We also showed that chemoreceptor gene expression in ADL neurons are regulated remotely by bHLH factors acting in the intestine through an insulin-mediated signaling pathway, implying a sensory neuron-gut interaction for modulating chemoreceptor gene expression as a function of feeding state. This work describes transcriptional mechanisms mediated by MEF-2 and bHLH factors by which the expression of individual chemoreceptor genes in C. elegans are changed in response to changes in feeding state conditions.
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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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11
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Yu Y, Zhi L, Guan X, Wang D, Wang D. FLP-4 neuropeptide and its receptor in a neuronal circuit regulate preference choice through functions of ASH-2 trithorax complex in Caenorhabditis elegans. Sci Rep 2016; 6:21485. [PMID: 26887501 PMCID: PMC4757837 DOI: 10.1038/srep21485] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/25/2016] [Indexed: 01/19/2023] Open
Abstract
Preference choice on food is an important response strategy for animals living in the environment. Using assay system of preference choice on bacterial foods, OP50 and PA14, we identified the involvement of ADL sensory neurons in the control of preference choice in Caenorhabditis elegans. Both genetically silencing and ChR2-mediated activation of ADL sensory neurons significantly affected preference choice. ADL regulated preference choice by inhibiting function of G protein-coupled receptor (GPCR)/SRH-220. ADL sensory neurons might regulate preference choice through peptidergic signals of FLP-4 and NLP-10, and function of FLP-4 or NLP-10 in regulating preference choice was regulated by SRH-220. FLP-4 released from ADL sensory neurons further regulated preference choice through its receptor of NPR-4 in AIB interneurons. In AIB interneurons, NPR-4 was involved in the control of preference choice by activating the functions of ASH-2 trithorax complex consisting of SET-2, ASH-2, and WDR-5, implying the crucial role of molecular machinery of trimethylation of histone H3K4 in the preference choice control. The identified novel neuronal circuit and the underlying molecular mechanisms will strengthen our understanding neuronal basis of preference choice in animals.
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Affiliation(s)
- Yonglin Yu
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Lingtong Zhi
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Xiangmin Guan
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Daoyong Wang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
| | - Dayong Wang
- Key Laboratory of Developmental Genes and Human Disease in Ministry of Education, Medical School, Southeast University, Nanjing 210009, China
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12
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Gruner M, van der Linden AM. Plasticity of chemoreceptor gene expression: Sensory and circuit inputs modulate state-dependent chemoreceptors. WORM 2015; 4:e1023497. [PMID: 26430563 PMCID: PMC4588537 DOI: 10.1080/21624054.2015.1023497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 10/25/2022]
Abstract
Animals dramatically modify their chemosensory behaviors when starved, which could allow them to alter and optimize their food-search strategies. Dynamic changes in the gene expression of chemoreceptors may be a general mechanism underlying food and state-dependent changes in chemosensory behaviors. In our recent study,(1) we identified chemoreceptors in the ADL sensory neuron type of C. elegans that are modulated by feeding state and food availability. Here, we highllight our recent findings by which sensory inputs into ADL, neuronal outputs from ADL, and circuit inputs from the RMG interneuron, which is electrically connected to ADL, are required to regulate an ADL-expressed chemoreceptor. This sensory and circuit-mediated regulation of chemoreceptor gene expression is dependent on cell-autonomous pathways acting in ADL, e.g. KIN-29, DAF-2, OCR-2 and calcium signaling, and circuit inputs from RMG mediated by NPR-1. Based on these findings, we propose an intriguing but speculative feedback modulatory circuit mechanism by which sensory perception of food and internal state signals may be coupled to regulate ADL-expressed chemoreceptors, which may allow animals to precisely regulate and fine-tune their chemosensory neuron responses as a function of feeding state.
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Affiliation(s)
- Matthew Gruner
- Department of Biology; University of Nevada ; Reno, NV USA
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The C. elegans HGF/plasminogen-like protein SVH-1 has protease-dependent and -independent functions. Cell Rep 2014; 9:1628-1634. [PMID: 25464847 DOI: 10.1016/j.celrep.2014.10.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/14/2014] [Accepted: 10/22/2014] [Indexed: 01/01/2023] Open
Abstract
Hepatocyte growth factor (HGF) and fibrinolytic serine protease plasminogen may have evolved from a common ancestor in vertebrates. This has been hard to ascertain, as no ancestral form has been identified in other lineages. In Caenorhabditis elegans, an HGF/plasminogen-like protein SVH-1 regulates axon regeneration via the HGF receptor homolog SVH-2. In this study, we report that both the svh-1 and svh-2 genes are conserved in many invertebrates. We also show that SVH-1 has an additional function, independent of SVH-2, which controls larval growth. SVH-1 protease activity is essential for larval growth, but not for axon regeneration. Deletion of svh-1 causes abnormal accumulation of FBL-1 protein, an extracellular matrix (ECM) component fibulin, around the pharynx, and this growth defect is partially suppressed by FBL-1 depletion. These results suggest that SVH-1 acts as both a growth factor and a protease, and they also provide insights into the evolution of HGF/plasminogen in animals.
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Gruner M, Nelson D, Winbush A, Hintz R, Ryu L, Chung SH, Kim K, Gabel CV, van der Linden AM. Feeding state, insulin and NPR-1 modulate chemoreceptor gene expression via integration of sensory and circuit inputs. PLoS Genet 2014; 10:e1004707. [PMID: 25357003 PMCID: PMC4214617 DOI: 10.1371/journal.pgen.1004707] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 08/26/2014] [Indexed: 12/24/2022] Open
Abstract
Feeding state and food availability can dramatically alter an animals' sensory response to chemicals in its environment. Dynamic changes in the expression of chemoreceptor genes may underlie some of these food and state-dependent changes in chemosensory behavior, but the mechanisms underlying these expression changes are unknown. Here, we identified a KIN-29 (SIK)-dependent chemoreceptor, srh-234, in C. elegans whose expression in the ADL sensory neuron type is regulated by integration of sensory and internal feeding state signals. We show that in addition to KIN-29, signaling is mediated by the DAF-2 insulin-like receptor, OCR-2 TRPV channel, and NPR-1 neuropeptide receptor. Cell-specific rescue experiments suggest that DAF-2 and OCR-2 act in ADL, while NPR-1 acts in the RMG interneurons. NPR-1-mediated regulation of srh-234 is dependent on gap-junctions, implying that circuit inputs regulate the expression of chemoreceptor genes in sensory neurons. Using physical and genetic manipulation of ADL neurons, we show that sensory inputs from food presence and ADL neural output regulate srh-234 expression. While KIN-29 and DAF-2 act primarily via the MEF-2 (MEF2) and DAF-16 (FOXO) transcription factors to regulate srh-234 expression in ADL neurons, OCR-2 and NPR-1 likely act via a calcium-dependent but MEF-2- and DAF-16-independent pathway. Together, our results suggest that sensory- and circuit-mediated regulation of chemoreceptor genes via multiple pathways may allow animals to precisely regulate and fine-tune their chemosensory responses as a function of internal and external conditions. Animals dramatically modify their chemosensory behaviors to attractive and noxious chemical stimuli when starved. This could allow them to alter and optimize their food-search strategies to increase their survival and reproduction. Changes in the gene expression of chemoreceptors specialized in detecting environmental stimuli is observed in fish, insects and nematodes, and may be a general mechanism underlying the changes in chemosensory behaviors observed in starved animals. To elucidate this mechanism, we have developed an in vivo reporter assay in C. elegans for monitoring the expression of a candidate chemoreceptor gene in a single sensory neuron type, called ADL, as a function of feeding state. Using this reporter assay, we show that sensory inputs into ADL and neural outputs from ADL, as well as inputs from the RMG interneuron, which is electrically connected to ADL, are required to fine-tune expression of chemoreceptor genes in ADL. Sensory and circuit-mediated regulation of chemoreceptor gene expression is dependent on multiple pathways, including the neuropeptide receptor, NPR-1, and the DAF-2 insulin-like receptor. Our results reveal mechanisms underlying chemoreceptor gene expression, and provide insight into how expression changes in chemoreceptor genes may contribute to changes in chemosensory behavior as a function of feeding state.
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Affiliation(s)
- Matthew Gruner
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Dru Nelson
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Ari Winbush
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Rebecca Hintz
- Department of Agriculture, Nutrition and Veterinary Sciences, University of Nevada, Reno, Nevada, United States of America
| | - Leesun Ryu
- Department of Brain Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Samuel H. Chung
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Boston University Photonics Center, Boston, Massachusetts, United States of America
| | - Kyuhyung Kim
- Department of Brain Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Chrisopher V. Gabel
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Boston University Photonics Center, Boston, Massachusetts, United States of America
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15
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Tehseen M, Liao C, Dacres H, Dumancic M, Trowell S, Anderson A. Oligomerisation of C. elegans olfactory receptors, ODR-10 and STR-112, in yeast. PLoS One 2014; 9:e108680. [PMID: 25254556 PMCID: PMC4177895 DOI: 10.1371/journal.pone.0108680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 09/02/2014] [Indexed: 01/08/2023] Open
Abstract
It is widely accepted that vertebrate G-Protein Coupled Receptors (GPCRs) associate with each other as homo- or hetero-dimers or higher-order oligomers. The C. elegans genome encodes hundreds of olfactory GPCRs, which may be expressed in fewer than a dozen chemosensory neurons, suggesting an opportunity for oligomerisation. Here we show, using three independent lines of evidence: co-immunoprecipitation, bioluminescence resonance energy transfer and a yeast two-hybrid assay that nematode olfactory receptors (ORs) oligomerise when heterologously expressed in yeast. Specifically, the nematode receptor ODR-10 is able to homo-oligomerise and can also form heteromers with the related nematode receptor STR-112. ODR-10 also oligomerised with the rat I7 OR but did not oligomerise with the human somatostatin receptor 5, a neuropeptide receptor. In this study, the question of functional relevance was not addressed and remains to be investigated.
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Affiliation(s)
- Muhammad Tehseen
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Chunyan Liao
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
| | - Helen Dacres
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
| | - Mira Dumancic
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
| | - Stephen Trowell
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
| | - Alisha Anderson
- CSIRO Food Futures National Research Flagship & CSIRO Ecosystem Sciences, Australia, Canberra, ACT, Australia
- * E-mail:
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Diverse cell type-specific mechanisms localize G protein-coupled receptors to Caenorhabditis elegans sensory cilia. Genetics 2014; 197:667-84. [PMID: 24646679 DOI: 10.1534/genetics.114.161349] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The localization of signaling molecules such as G protein-coupled receptors (GPCRs) to primary cilia is essential for correct signal transduction. Detailed studies over the past decade have begun to elucidate the diverse sequences and trafficking mechanisms that sort and transport GPCRs to the ciliary compartment. However, a systematic analysis of the pathways required for ciliary targeting of multiple GPCRs in different cell types in vivo has not been reported. Here we describe the sequences and proteins required to localize GPCRs to the cilia of the AWB and ASK sensory neuron types in Caenorhabditis elegans. We find that GPCRs expressed in AWB or ASK utilize conserved and novel sequences for ciliary localization, and that the requirement for a ciliary targeting sequence in a given GPCR is different in different neuron types. Consistent with the presence of multiple ciliary targeting sequences, we identify diverse proteins required for ciliary localization of individual GPCRs in AWB and ASK. In particular, we show that the TUB-1 Tubby protein is required for ciliary localization of a subset of GPCRs, implying that defects in GPCR localization may be causal to the metabolic phenotypes of tub-1 mutants. Together, our results describe a remarkable complexity of mechanisms that act in a protein- and cell-specific manner to localize GPCRs to cilia, and suggest that this diversity allows for precise regulation of GPCR-mediated signaling as a function of external and internal context.
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17
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The olfactory signal transduction for attractive odorants in Caenorhabditis elegans. Biotechnol Adv 2014; 32:290-5. [DOI: 10.1016/j.biotechadv.2013.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/14/2013] [Accepted: 10/28/2013] [Indexed: 11/20/2022]
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Sanders J, Nagy S, Fetterman G, Wright C, Treinin M, Biron D. The Caenorhabditis elegans interneuron ALA is (also) a high-threshold mechanosensor. BMC Neurosci 2013; 14:156. [PMID: 24341457 PMCID: PMC3878553 DOI: 10.1186/1471-2202-14-156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 12/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To survive dynamic environments, it is essential for all animals to appropriately modulate their behavior in response to various stimulus intensities. For instance, the nematode Caenorhabditis elegans suppresses the rate of egg-laying in response to intense mechanical stimuli, in a manner dependent on the mechanosensory neurons FLP and PVD. We have found that the unilaterally placed single interneuron ALA acted as a high-threshold mechanosensor, and that it was required for this protective behavioral response. RESULTS ALA was required for the inhibition of egg-laying in response to a strong (picking-like) mechanical stimulus, characteristic of routine handling of the animals. Moreover, ALA did not respond physiologically to less intense touch stimuli, but exhibited distinct physiological responses to anterior and posterior picking-like touch, suggesting that it could distinguish between spatially separated stimuli. These responses required neither neurotransmitter nor neuropeptide release from potential upstream neurons. In contrast, the long, bilaterally symmetric processes of ALA itself were required for producing its physiological responses; when they were severed, responses to stimuli administered between the cut and the cell body were unaffected, while responses to stimuli administered posterior to the cut were abolished. CONCLUSION C. elegans neurons are typically classified into three major groups: sensory neurons with specialized sensory dendrites, interneurons, and motoneurons with neuromuscular junctions. Our findings suggest that ALA can autonomously sense intense touch and is thus a dual-function neuron, i.e., an interneuron as well as a novel high-threshold mechanosensor.
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Affiliation(s)
| | | | | | | | | | - David Biron
- The Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
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19
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Abstract
Transforming Growth Factor-β (TGF-β) superfamily ligands regulate many aspects of cell identity, function, and survival in multicellular animals. Genes encoding five TGF-β family members are present in the genome of C. elegans. Two of the ligands, DBL-1 and DAF-7, signal through a canonical receptor-Smad signaling pathway; while a third ligand, UNC-129, interacts with a noncanonical signaling pathway. No function has yet been associated with the remaining two ligands. Here we summarize these signaling pathways and their biological functions.
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Affiliation(s)
- Tina L Gumienny
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center College of Medicine, College Station, TX 77843, USA
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20
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Cunningham KA, Hua Z, Srinivasan S, Liu J, Lee BH, Edwards RH, Ashrafi K. AMP-activated kinase links serotonergic signaling to glutamate release for regulation of feeding behavior in C. elegans. Cell Metab 2012; 16:113-21. [PMID: 22768843 PMCID: PMC3413480 DOI: 10.1016/j.cmet.2012.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 03/08/2012] [Accepted: 05/29/2012] [Indexed: 01/01/2023]
Abstract
Serotonergic regulation of feeding behavior has been studied intensively, both for an understanding of the basic neurocircuitry of energy balance in various organisms and as a therapeutic target for human obesity. However, its underlying molecular mechanisms remain poorly understood. Here, we show that neural serotonin signaling in C. elegans modulates feeding behavior through inhibition of AMP-activated kinase (AMPK) in interneurons expressing the C. elegans counterpart of human SIM1, a transcription factor associated with obesity. In turn, glutamatergic signaling links these interneurons to pharyngeal neurons implicated in feeding behavior. We show that AMPK-mediated regulation of glutamatergic release is conserved in rat hippocampal neurons. These findings reveal cellular and molecular mediators of serotonergic signaling.
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Affiliation(s)
- Katherine A. Cunningham
- Department of Physiology and Cardiovascular Research Institute and the UCSF Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Zhaolin Hua
- Departments of Physiology and Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Supriya Srinivasan
- Department of Chemical Physiology and Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, USA
| | - Jason Liu
- Department of Physiology and Cardiovascular Research Institute and the UCSF Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Brian H. Lee
- Department of Physiology and Cardiovascular Research Institute and the UCSF Diabetes Center, University of California, San Francisco, San Francisco, California, USA
| | - Robert H. Edwards
- Departments of Physiology and Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Kaveh Ashrafi
- Department of Physiology and Cardiovascular Research Institute and the UCSF Diabetes Center, University of California, San Francisco, San Francisco, California, USA
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21
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Nagarathnam B, Kalaimathy S, Balakrishnan V, Sowdhamini R. Cross-Genome Clustering of Human and C. elegans G-Protein Coupled Receptors. Evol Bioinform Online 2012; 8:229-59. [PMID: 22807621 PMCID: PMC3396462 DOI: 10.4137/ebo.s9405] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are one of the largest groups of membrane proteins and are popular drug targets. The work reported here attempts to perform cross-genome phylogeny on GPCRs from two widely different taxa, human versus C. elegans genomes and to address the issues on evolutionary plasticity, to identify functionally related genes, orthologous relationship, and ligand binding properties through effective bioinformatic approaches. Through RPS blast around 1106 nematode GPCRs were given chance to associate with previously established 8 types of human GPCR profiles at varying E-value thresholds and resulted 32 clusters were illustrating co-clustering and class-specific retainsionship. In the significant thresholds, 81% of the C. elegans GPCRs were associated with 32 clusters and 27 C. elegans GPCRs (2%) inferred for orthology. 177 hypothetical proteins were observed in cluster association and could be reliably associated with one of 32 clusters. Several nematode-specific GPCR clades were observed suggesting lineage-specific functional recruitment in response to environment.
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Affiliation(s)
- Balasubramanian Nagarathnam
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
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22
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Burghoorn J, Piasecki BP, Crona F, Phirke P, Jeppsson KE, Swoboda P. The in vivo dissection of direct RFX-target gene promoters in C. elegans reveals a novel cis-regulatory element, the C-box. Dev Biol 2012; 368:415-26. [PMID: 22683808 DOI: 10.1016/j.ydbio.2012.05.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 04/23/2012] [Accepted: 05/25/2012] [Indexed: 11/26/2022]
Abstract
At the core of the primary transcriptional network regulating ciliary gene expression in Caenorhabditis elegans sensory neurons is the RFX/DAF-19 transcription factor, which binds and thereby positively regulates 13-15 bp X-box promoter motifs found in the cis-regulatory regions of many ciliary genes. However, the variable expression of direct RFX-target genes in various sets of ciliated sensory neurons (CSNs) occurs through as of yet uncharacterized mechanisms. In this study the cis-regulatory regions of 41 direct RFX-target genes are compared using in vivo genetic analyses and computational comparisons of orthologous nematode sequences. We find that neither the proximity to the translational start site nor the exact sequence composition of the X-box promoter motif of the respective ciliary gene can explain the variation in expression patterns observed among different direct RFX-target genes. Instead, a novel enhancer element appears to co-regulate ciliary genes in a DAF-19 dependent manner. This cytosine- and thymidine-rich sequence, the C-box, was found in the cis-regulatory regions in close proximity to the respective X-box motif for 84% of the most broadly expressed direct RFX-target genes sampled in this study. Molecular characterization confirmed that these 8-11 bp C-box sequences act as strong enhancer elements for direct RFX-target genes. An artificial promoter containing only an X-box promoter motif and two of the C-box enhancer elements was able to drive strong expression of a GFP reporter construct in many C. elegans CSNs. These data provide a much-improved understanding of how direct RFX-target genes are differentially regulated in C. elegans and will provide a molecular model for uncovering the transcriptional network mediating ciliary gene expression in animals.
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Affiliation(s)
- Jan Burghoorn
- Karolinska Institute, Center for Biosciences at NOVUM, Department of Biosciences and Nutrition, Hälsovägen 7, S-141 83 Huddinge, Sweden
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23
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The growth factor SVH-1 regulates axon regeneration in C. elegans via the JNK MAPK cascade. Nat Neurosci 2012; 15:551-7. [DOI: 10.1038/nn.3052] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 01/19/2012] [Indexed: 11/09/2022]
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Lesch BJ, Bargmann CI. The homeodomain protein hmbx-1 maintains asymmetric gene expression in adult C. elegans olfactory neurons. Genes Dev 2010; 24:1802-15. [PMID: 20713521 DOI: 10.1101/gad.1932610] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Differentiated neurons balance the need to maintain a stable identity with their flexible responses to dynamic environmental inputs. Here we characterize these opposing influences on gene expression in Caenorhabditis elegans olfactory neurons. Using transcriptional reporters that are expressed differentially in two olfactory neurons, AWC(ON) and AWC(OFF), we identify mutations that affect the long-term maintenance of appropriate chemoreceptor expression. A newly identified gene from this screen, the conserved transcription factor hmbx-1, stabilizes AWC gene expression in adult animals through dosage-sensitive interactions with its transcriptional targets. The late action of hmbx-1 complements the early role of the transcriptional repressor gene nsy-7: Both repress expression of multiple AWC(OFF) genes in AWC(ON) neurons, but they act at different developmental stages. Environmental signals are superimposed onto this stable cell identity through at least two different transcriptional pathways that regulate individual chemoreceptor genes: a cGMP pathway regulated by sensory activity, and a daf-7 (TGF-beta)/daf-3 (SMAD repressor) pathway regulated by specific components of the density-dependent C. elegans dauer pheromone.
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Affiliation(s)
- Bluma J Lesch
- Howard Hughes Medical Institute, Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, NY 10065, USA
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25
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Nokes EB, Van Der Linden AM, Winslow C, Mukhopadhyay S, Ma K, Sengupta P. Cis-regulatory mechanisms of gene expression in an olfactory neuron type in Caenorhabditis elegans. Dev Dyn 2010; 238:3080-92. [PMID: 19924784 DOI: 10.1002/dvdy.22147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The generation of cellular diversity is dependent on the precise spatiotemporal regulation of gene expression by both cis- and trans-acting mechanisms. The developmental principles regulating expression of specific gene subsets in individual cell types are not fully understood. Here we define the cis-regulatory mechanisms driving expression of cell-selective and broadly expressed genes in vivo in the AWB olfactory neuron subtype in C. elegans. We identify an element that is necessary to drive expression of neuron-selective chemoreceptor genes in the AWB neurons, and show that this element functions in a context-dependent manner. We find that the expression of broadly expressed sensory neuronal genes in the AWB neurons is regulated by diverse cis- and trans-regulatory mechanisms that act partly in parallel to the pathways governing expression of AWB-selective genes. We further demonstrate that cis-acting mechanisms driving gene expression in the AWB neurons appear to have diverged in related nematode species. Our results provide insights into the cis-regulatory logic driving cell-specific gene expression, and suggest that variations in this logic contribute to the generation of functional diversity.
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Affiliation(s)
- Eva B Nokes
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02454, USA
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26
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A TRPV channel modulates C. elegans neurosecretion, larval starvation survival, and adult lifespan. PLoS Genet 2008; 4:e1000213. [PMID: 18846209 PMCID: PMC2556084 DOI: 10.1371/journal.pgen.1000213] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 09/03/2008] [Indexed: 12/22/2022] Open
Abstract
For most organisms, food is only intermittently available; therefore, molecular mechanisms that couple sensation of nutrient availability to growth and development are critical for survival. These mechanisms, however, remain poorly defined. In the absence of nutrients, newly hatched first larval (L1) stage Caenorhabditis elegans halt development and survive in this state for several weeks. We isolated mutations in unc-31, encoding a calcium-activated regulator of neural dense-core vesicle release, which conferred enhanced starvation survival. This extended survival was reminiscent of that seen in daf-2 insulin-signaling deficient mutants and was ultimately dependent on daf-16, which encodes a FOXO transcription factor whose activity is inhibited by insulin signaling. While insulin signaling modulates metabolism, adult lifespan, and dauer formation, insulin-independent mechanisms that also regulate these processes did not promote starvation survival, indicating that regulation of starvation survival is a distinct program. Cell-specific rescue experiments identified a small subset of primary sensory neurons where unc-31 reconstitution modulated starvation survival, suggesting that these neurons mediate perception of food availability. We found that OCR-2, a transient receptor potential vanilloid (TRPV) channel that localizes to the cilia of this subset of neurons, regulates peptide-hormone secretion and L1 starvation survival. Moreover, inactivation of ocr-2 caused a significant extension in adult lifespan. These findings indicate that TRPV channels, which mediate sensation of diverse noxious, thermal, osmotic, and mechanical stimuli, couple nutrient availability to larval starvation survival and adult lifespan through modulation of neural dense-core vesicle secretion. Starvation is a common physiological condition encountered by most organisms in their natural environments. However, the molecular mechanisms that allow organisms to accurately sense nutrient availability and match their energetic demands accordingly are not well understood. To elucidate these mechanisms, we isolated mutants in C. elegans that survive about 50% longer than wild-type animals when starved. For one such mutant, we found that the extended survival was due to mutation in the unc-31 gene, which functions in the nervous system to mediate release of neuroendocrine signaling molecules including insulin. Although this gene is broadly expressed in the nervous system, we found that its activity is required in a small subset of sensory neurons to regulate starvation survival. These neurons have ciliated endings that function in detection of environmental cues. Disruption of these cilia, or inactivation of a TRPV channel localized to these cilia, mimicked the perception of nutrient deprivation leading to extended starvation survival, which is dependent on an insulin-regulated transcription factor. Disruption of this channel also extended adult lifespan. Taken together, our findings reveal that TRPV channels couple nutritional cues to neuroendocrine secretion, which in turn determines adult lifespan and larval starvation survival.
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27
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Thomas JH, Robertson HM. The Caenorhabditis chemoreceptor gene families. BMC Biol 2008; 6:42. [PMID: 18837995 PMCID: PMC2576165 DOI: 10.1186/1741-7007-6-42] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Accepted: 10/06/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. RESULTS Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. CONCLUSION Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.
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Affiliation(s)
- James H Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois, Urbana-Champaign, IL, USA
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Doyon JB, Liu DR. Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination. Nucleic Acids Res 2007; 35:5851-60. [PMID: 17720707 PMCID: PMC2034452 DOI: 10.1093/nar/gkm634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Understanding the regulatory logic of a eukaryotic promoter requires the elucidation of the regulatory elements within that promoter. Current experimental or computational methods to discover regulatory motifs within a promoter can be labor intensive and may miss redundant, unprecedented or weakly activating elements. We have developed an unbiased combinatorial approach to rapidly identify new upstream activating sequences (UASs) in a promoter. This approach couples nonhomologous random recombination with an in vivo screen to efficiently identify UASs and does not rely on preconceived hypotheses about promoter regulation or on similarity to known activating sequences. We validated this method using the unfolded protein response (UPR) in yeast and were able to identify both known and potentially novel UASs involved in the UPR. One of the new UASs discovered using this approach implicates Crz1 as a possible activator of Hac1, a transcription factor involved in the UPR. This method has several advantages over existing methods for UAS discovery including its speed, potential generality, sensitivity and lack of false positives and negatives.
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Affiliation(s)
| | - David R. Liu
- *To whom correspondence should be addressed. Tel:+ 1 617 496 1067; Fax:+ 1 617 496 5688
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29
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Mah AK, Armstrong KR, Chew DS, Chu JS, Tu DK, Johnsen RC, Chen N, Chamberlin HM, Baillie DL. Transcriptional regulation of AQP-8, a Caenorhabditis elegans aquaporin exclusively expressed in the excretory system, by the POU homeobox transcription factor CEH-6. J Biol Chem 2007; 282:28074-86. [PMID: 17660295 DOI: 10.1074/jbc.m703305200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Due to the ever changing environmental conditions in soil, regulation of osmotic homeostasis in the soil-dwelling nematode Caenorhabditis elegans is critical. AQP-8 is a C. elegans aquaporin that is expressed in the excretory cell, a renal equivalent tissue, where the protein participates in maintaining water balance. To better understand the regulation of AQP-8, we undertook a promoter analysis to identify the aqp-8 cis-regulatory elements. Using progressive 5' deletions of upstream sequence, we have mapped an essential regulatory region to roughly 300 bp upstream of the translational start site of aqp-8. Analysis of this region revealed a sequence corresponding to a known DNA functional element (octamer motif), which interacts with POU homeobox transcription factors. Phylogenetic footprinting showed that this site is perfectly conserved in four nematode species. The octamer site's function was further confirmed by deletion analyses, mutagenesis, functional studies, and electrophoretic mobility shift assays. Of the three POU homeobox proteins encoded in the C. elegans genome, CEH-6 is the only member that is expressed in the excretory cell. We show that expression of AQP-8 is regulated by CEH-6 by performing RNA interference experiments. CEH-6's mammalian ortholog, Brn1, is expressed both in the kidney and the central nervous system and binds to the same octamer consensus binding site to drive gene expression. These parallels in transcriptional control between Brn1 and CEH-6 suggest that C. elegans may well be an appropriate model for determining gene-regulatory networks in the developing vertebrate kidney.
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Affiliation(s)
- Allan K Mah
- Department Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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30
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Abstract
Odour perception is initiated by specific interactions between odorants and a large repertoire of receptors in olfactory neurons. During the past few years, considerable progress has been made in tracing olfactory perception from the odorant receptor protein to the activity of olfactory neurons to higher processing centres and, ultimately, to behaviour. The most complete picture is emerging for the simplest olfactory system studied--that of the fruitfly Drosophila melanogaster. Comparison of rodent, insect and nematode olfaction reveals surprising differences and unexpected similarities among chemosensory systems.
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Affiliation(s)
- Cornelia I Bargmann
- Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
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31
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van der Linden AM, Nolan KM, Sengupta P. KIN-29 SIK regulates chemoreceptor gene expression via an MEF2 transcription factor and a class II HDAC. EMBO J 2006; 26:358-70. [PMID: 17170704 PMCID: PMC1783467 DOI: 10.1038/sj.emboj.7601479] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 11/07/2006] [Indexed: 11/09/2022] Open
Abstract
The expression of individual chemoreceptor (CR) genes in Caenorhabditis elegans is regulated by multiple environmental and developmental cues, possibly enabling C. elegans to modulate its sensory responses. We had previously shown that KIN-29, a member of the salt-inducible kinase family, acts in a subset of chemosensory neurons to regulate the expression of CR genes, body size and entry into the alternate dauer developmental stage. Here, we show that KIN-29 regulates these processes by phosphorylating the HDA-4 class II histone deacetylase (HDAC) and inhibiting the gene repression functions of HDA-4 and an MEF-2 MADS domain transcription factor. MEF-2 binds directly to the CR gene regulatory sequences, and is required only to repress but not activate CR gene expression. A calcineurin phosphatase antagonizes the KIN-29/MEF-2-regulated pathway to modulate levels of CR gene expression. Our results identify KIN-29 as a new regulator of MEF2/HDAC functions in the nervous system, reveal cell-specific mechanisms of action of this pathway in vivo and demonstrate remarkable complexity in the regulation of CR gene expression in C. elegans.
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Affiliation(s)
- Alexander M van der Linden
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Katherine M Nolan
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
| | - Piali Sengupta
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, MA, USA
- Department of Biology and National Center for Behavioral Genomics, Brandeis University, South St., Waltham, MA 02454, USA. Tel.: +1 781 736 2686; Fax: +1 781 736 3107; E-mail:
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32
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McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, Goszczynski B, Tian H, Krich ND, Khattra J, Holt RA, Baillie DL, Kohara Y, Marra MA, Jones SJM, Moerman DG, Robertson AG. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Dev Biol 2006; 302:627-45. [PMID: 17113066 DOI: 10.1016/j.ydbio.2006.10.024] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/08/2006] [Accepted: 10/14/2006] [Indexed: 12/18/2022]
Abstract
A SAGE library was prepared from hand-dissected intestines from adult Caenorhabditis elegans, allowing the identification of >4000 intestinally-expressed genes; this gene inventory provides fundamental information for understanding intestine function, structure and development. Intestinally-expressed genes fall into two broad classes: widely-expressed "housekeeping" genes and genes that are either intestine-specific or significantly intestine-enriched. Within this latter class of genes, we identified a subset of highly-expressed highly-validated genes that are expressed either exclusively or primarily in the intestine. Over half of the encoded proteins are candidates for secretion into the intestinal lumen to hydrolyze the bacterial food (e.g. lysozymes, amoebapores, lipases and especially proteases). The promoters of this subset of intestine-specific/intestine-enriched genes were analyzed computationally, using both a word-counting method (RSAT oligo-analysis) and a method based on Gibbs sampling (MotifSampler). Both methods returned the same over-represented site, namely an extended GATA-related sequence of the general form AHTGATAARR, which agrees with experimentally determined cis-acting control sequences found in intestine genes over the past 20 years. All promoters in the subset contain such a site, compared to <5% for control promoters; moreover, our analysis suggests that the majority (perhaps all) of genes expressed exclusively or primarily in the worm intestine are likely to contain such a site in their promoters. There are three zinc-finger GATA-type factors that are candidates to bind this extended GATA site in the differentiating C. elegans intestine: ELT-2, ELT-4 and ELT-7. All evidence points to ELT-2 being the most important of the three. We show that worms in which both the elt-4 and the elt-7 genes have been deleted from the genome are essentially wildtype, demonstrating that ELT-2 provides all essential GATA-factor functions in the intestine. The SAGE analysis also identifies more than a hundred other transcription factors in the adult intestine but few show an RNAi-induced loss-of-function phenotype and none (other than ELT-2) show a phenotype primarily in the intestine. We thus propose a simple model in which the ELT-2 GATA factor directly participates in the transcription of all intestine-specific/intestine-enriched genes, from the early embryo through to the dying adult. Other intestinal transcription factors would thus modulate the action of ELT-2, depending on the worm's nutritional and physiological needs.
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Affiliation(s)
- James D McGhee
- Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T2N 4N1.
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33
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Wang Y, Levy DE. C. elegans STAT cooperates with DAF-7/TGF-beta signaling to repress dauer formation. Curr Biol 2006; 16:89-94. [PMID: 16401427 DOI: 10.1016/j.cub.2005.11.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Revised: 11/15/2005] [Accepted: 11/16/2005] [Indexed: 10/25/2022]
Abstract
The DAF-7/TGF-beta pathway in C. elegans interprets environmental signals relayed through amphid neurons and actively inhibits dauer formation during reproductive developmental growth . In metazoans, the STAT pathway interprets external stimuli through regulated tyrosine phosphorylation, nuclear translocation, and gene expression , but its importance for developmental commitment, particularly in conjunction with TGF-beta, remains largely unknown. Here, we report that the nematode STAT ortholog STA-1 accumulated in the nuclei of five head neuron pairs, three of which are amphid neurons involved in dauer formation . Moreover, sta-1 mutants showed a synthetic dauer phenotype with selected TGF-beta mutations. sta-1 deficiency was complemented by reconstitution with wild-type protein, but not with a tyrosine mutant. Canonical TGF-beta signaling involves the DAF-7/TGF-beta ligand activating the DAF-1/DAF-4 receptor pair to regulate the DAF-8/DAF-14 Smads . Interestingly, STA-1 functioned in the absence of DAF-7, DAF-4, and DAF-14, but it required DAF-1 and DAF-8. Additionally, STA-1 expression was induced by TGF-beta in a DAF-3-dependent manner, demonstrating a homeostatic negative feedback loop. These results highlight a role for activated STAT proteins in repression of dauer formation. They also raise the possibility of an unexpected function for DAF-1 and DAF-8 that is independent of their normal upstream activator, DAF-7.
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Affiliation(s)
- Yaming Wang
- Department of Pathology, Department of Microbiology, NYU Cancer Institute, New York University School of Medicine, 550 1st Avenue, New York, New York 10016, USA
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