1
|
Ghaddar A, Armingol E, Huynh C, Gevirtzman L, Lewis NE, Waterston R, O’Rourke EJ. Whole-body gene expression atlas of an adult metazoan. SCIENCE ADVANCES 2023; 9:eadg0506. [PMID: 37352352 PMCID: PMC10289653 DOI: 10.1126/sciadv.adg0506] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Gene activity defines cell identity, drives intercellular communication, and underlies the functioning of multicellular organisms. We present the single-cell resolution atlas of gene activity of a fertile adult metazoan: Caenorhabditis elegans. This compendium comprises 180 distinct cell types and 19,657 expressed genes. We predict 7541 transcription factor expression profile associations likely responsible for defining cellular identity. We predict thousands of intercellular interactions across the C. elegans body and the ligand-receptor pairs that mediate them, some of which we experimentally validate. We identify 172 genes that show consistent expression across cell types, are involved in basic and essential functions, and are conserved across phyla; therefore, we present them as experimentally validated housekeeping genes. We developed the WormSeq application to explore these data. In addition to the integrated gene-to-systems biology, we present genome-scale single-cell resolution testable hypotheses that we anticipate will advance our understanding of the molecular mechanisms, underlying the functioning of a multicellular organism and the perturbations that lead to its malfunction.
Collapse
Affiliation(s)
- Abbas Ghaddar
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
| | - Erick Armingol
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chau Huynh
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Louis Gevirtzman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert Waterston
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eyleen J. O’Rourke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, VA 22903, USA
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
- Robert M. Berne Cardiovascular Research Center, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
2
|
Huang QT, Sheng CW, Jones AK, Jiang J, Tang T, Han ZJ, Zhao CQ. Functional Characteristics of the Lepidopteran Ionotropic GABA Receptor 8916 Subunit Interacting with the LCCH3 or the RDL Subunit. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11582-11591. [PMID: 34555899 DOI: 10.1021/acs.jafc.1c00385] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The ionotropic γ-aminobutyric acid (iGABA) receptor is commonly considered as a fast inhibitory channel and is an important insecticide target. Since 1990, RDL, LCCH3, and GRD have been successively isolated and found to be potential subunits of the insect iGABA receptor. More recently, one orphan gene named 8916 was found and considered to be another potential iGABA receptor subunit according to its amino acid sequence. However, little information about 8916 has been reported. Here, the 8916 subunit from Chilo suppressalis was studied to determine whether it can form part of a functional iGABA receptor by co-expressing this subunit with CsRDL1 or CsLCCH3 in the Xenopus oocyte system. Cs8916 or CsLCCH3 did not form functional ion channels when expressed alone. However, Cs8916 was able to form heteromeric ion channels when expressed with either CsLCCH3 or CsRDL1. The recombinant heteromeric Cs8916/LCCH3 channel was a cation-selective channel, which was sensitive to GABA or β-alanine. The current of the Cs8916/LCCH3 channel was inhibited by dieldrin, endosulfan, fipronil, or ethiprole. In contrast, fluralaner, broflanilide, and avermectin showed little effect on the Cs8916/LCCH3 channel (IC50s > 10 000 nM). The Cs8916/RDL1 channel was sensitive to GABA, but was significantly different in EC50 and Imax for GABA to those of homomeric CsRDL1. Fluralaner, fipronil, or dieldrin showed antagonistic actions on Cs8916/RDL1. In conclusion, Cs8916 is a potential iGABA receptor subunit, which can interact with CsLCCH3 to generate a cation-selective channel that is sensitive to several insecticides. Also, as Cs8916/RDL1 has a higher EC50 than homomeric CsRDL1, Cs8916 may affect the physiological functions of CsRDL1 and therefore play a role in fine-tuning GABAergic signaling.
Collapse
Affiliation(s)
- Qiu Tang Huang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Cheng Wang Sheng
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Andrew K Jones
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, U.K
| | - Jie Jiang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Tao Tang
- Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, P. R. China
| | - Zhao Jun Han
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Chun Qing Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, P. R. China
| |
Collapse
|
3
|
Henry C, Cens T, Charnet P, Cohen-Solal C, Collet C, van-Dijk J, Guiramand J, de Jésus-Ferreira MC, Menard C, Mokrane N, Roussel J, Thibault JB, Vignes M, Rousset M. Heterogeneous expression of GABA receptor-like subunits LCCH3 and GRD reveals functional diversity of GABA receptors in the honeybee Apis mellifera. Br J Pharmacol 2020; 177:3924-3940. [PMID: 32436264 DOI: 10.1111/bph.15135] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 04/24/2020] [Accepted: 05/09/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND AND PURPOSE Despite a growing awareness, annual losses of honeybee colonies worldwide continue to reach threatening levels for food safety and global biodiversity. Among the biotic and abiotic stresses probably responsible for these losses, pesticides, including those targeting ionotropic GABA receptors, are one of the major drivers. Most insect genomes include the ionotropic GABA receptor subunit gene, Rdl, and two GABA-like receptor subunit genes, Lcch3 and Grd. Most studies have focused on Rdl which forms homomeric GABA-gated chloride channels, and a complete analysis of all possible molecular combinations of GABA receptors is still lacking. EXPERIMENTAL APPROACH We cloned the Rdl, Grd, and Lcch3 genes of Apis mellifera and systematically characterized the resulting GABA receptors expressed in Xenopus oocytes, using electrophysiological assays, fluorescence microscopy and co-immunoprecipitation techniques. KEY RESULTS The cloned subunits interacted with each other, forming GABA-gated heteromeric channels with particular properties. Strikingly, these heteromers were always more sensitive than AmRDL homomer to all the pharmacological agents tested. In particular, when expressed together, Grd and Lcch3 form a non-selective cationic channel that opens at low concentrations of GABA and with sensitivity to insecticides similar to that of homomeric Rdl channels. CONCLUSION AND IMPLICATIONS For off-target species like the honeybee, chronic sublethal exposure to insecticides constitutes a major threat. At these concentration ranges, homomeric RDL receptors may not be the most pertinent target to study and other ionotropic GABA receptor subtypes should be considered in order to understand more fully the molecular mechanisms of sublethal toxicity to insecticides.
Collapse
Affiliation(s)
| | - Thierry Cens
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | - Pierre Charnet
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | | | - Claude Collet
- UR 406 Abeilles et Environnement, INRAE, Avignon Cedex 9, France
| | | | | | | | - Claudine Menard
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | - Nawfel Mokrane
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | - Julien Roussel
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | | | - Michel Vignes
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| | - Matthieu Rousset
- IBMM UMR5247, University of Montpellier, CNRS, Montpellier, France
| |
Collapse
|
4
|
An N-myristoylated globin with a redox-sensing function that regulates the defecation cycle in Caenorhabditis elegans. PLoS One 2012; 7:e48768. [PMID: 23251335 PMCID: PMC3520999 DOI: 10.1371/journal.pone.0048768] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/04/2012] [Indexed: 01/17/2023] Open
Abstract
Globins occur in all kingdoms of life where they fulfill a wide variety of functions. In the past they used to be primarily characterized as oxygen transport/storage proteins, but since the discovery of new members of the globin family like neuroglobin and cytoglobin, more diverse and complex functions have been assigned to this heterogeneous family. Here we propose a function for a membrane-bound globin of C. elegans, GLB-26. This globin was predicted to be myristoylated at its N-terminus, a post-translational modification only recently described in the globin family. In vivo, this globin is found in the membrane of the head mesodermal cell and in the tail stomato-intestinal and anal depressor muscle cells. Since GLB-26 is almost directly oxidized when exposed to oxygen, we postulate a possible function as electron transfer protein. Phenotypical studies show that GLB-26 takes part in regulating the length of the defecation cycle in C. elegans under oxidative stress conditions.
Collapse
|
5
|
Cristina D, Cary M, Lunceford A, Clarke C, Kenyon C. A regulated response to impaired respiration slows behavioral rates and increases lifespan in Caenorhabditis elegans. PLoS Genet 2009; 5:e1000450. [PMID: 19360127 PMCID: PMC2660839 DOI: 10.1371/journal.pgen.1000450] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Accepted: 03/11/2009] [Indexed: 11/18/2022] Open
Abstract
When mitochondrial respiration or ubiquinone production is inhibited in Caenorhabditis elegans, behavioral rates are slowed and lifespan is extended. Here, we show that these perturbations increase the expression of cell-protective and metabolic genes and the abundance of mitochondrial DNA. This response is similar to the response triggered by inhibiting respiration in yeast and mammalian cells, termed the “retrograde response”. As in yeast, genes switched on in C. elegans mitochondrial mutants extend lifespan, suggesting an underlying evolutionary conservation of mechanism. Inhibition of fstr-1, a potential signaling gene that is up-regulated in clk-1 (ubiquinone-defective) mutants, and its close homolog fstr-2 prevents the expression of many retrograde-response genes and accelerates clk-1 behavioral and aging rates. Thus, clk-1 mutants live in “slow motion” because of a fstr-1/2–dependent pathway that responds to ubiquinone. Loss of fstr-1/2 does not suppress the phenotypes of all long-lived mitochondrial mutants. Thus, although different mitochondrial perturbations activate similar transcriptional and physiological responses, they do so in different ways. Mitochondrial respiration generates energy in the form of adenosine triphospate (ATP), a molecule that powers many cellular processes. When respiration is inhibited in C. elegans, rates of behavior and growth are slowed and, interestingly, lifespan is extended. In this study, we investigated the mechanism of this response. We find that inhibiting respiration increases the expression of genes predicted to protect and metabolically remodel the animal. This pattern of gene expression is reminiscent of the expression profile of long-lived respiration-defective yeast, suggesting ancient evolutionary conservation. Mutations in clk-1, which inhibit the synthesis of the respiratory-chain factor ubiquinone, produce gene expression, longevity, and behavioral phenotypes similar to those produced by inhibiting components of the respiratory chain. We find that knocking down the activities of two similar genes—fsrt-1 and fstr-2—accelerates the behaviors and aging rates of clk-1 mutants and inhibits the clk-1(−) transcriptional response. Thus, fstr-1/2, which encode potential signaling proteins, appear to be part of a mechanism that actively slows rates of growth, behavior, and aging in response to altered ubiquinone synthesis. Unexpectedly, fsrt-1/2 are not required for the longevity and behavioral phenotypes produced by inhibiting the gene isp-1, which encodes a different component of the respiratory chain. Our findings suggest that different types of mitochondrial perturbations activate distinct pathways that converge on similar downstream processes to slow behavioral rates and extend lifespan.
Collapse
Affiliation(s)
- David Cristina
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | | | | | | | | |
Collapse
|
6
|
Etchberger JF, Lorch A, Sleumer MC, Zapf R, Jones SJ, Marra MA, Holt RA, Moerman DG, Hobert O. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron. Genes Dev 2007; 21:1653-74. [PMID: 17606643 PMCID: PMC1899474 DOI: 10.1101/gad.1560107] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Taste receptor cells constitute a highly specialized cell type that perceives and conveys specific sensory information to the brain. The detailed molecular composition of these cells and the mechanisms that program their fate are, in general, poorly understood. We have generated serial analysis of gene expression (SAGE) libraries from two distinct populations of single, isolated sensory neuron classes, the gustatory neuron class ASE and the thermosensory neuron class AFD, from the nematode Caenorhabditis elegans. By comparing these two libraries, we have identified >1000 genes that define the ASE gustatory neuron class on a molecular level. This set of genes contains determinants of the differentiated state of the ASE neuron, such as a surprisingly complex repertoire of transcription factors (TFs), ion channels, neurotransmitters, and receptors, as well as seven-transmembrane receptor (7TMR)-type putative gustatory receptor genes. Through the in vivo dissection of the cis-regulatory regions of several ASE-expressed genes, we identified a small cis-regulatory motif, the "ASE motif," that is required for the expression of many ASE-expressed genes. We demonstrate that the ASE motif is a binding site for the C2H2 zinc finger TF CHE-1, which is essential for the correct differentiation of the ASE gustatory neuron. Taken together, our results provide a unique view of the molecular landscape of a single neuron type and reveal an important aspect of the regulatory logic for gustatory neuron specification in C. elegans.
Collapse
Affiliation(s)
- John F. Etchberger
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032, USA
| | - Adam Lorch
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Monica C. Sleumer
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Richard Zapf
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Steven J. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Robert A. Holt
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Donald G. Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Oliver Hobert
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, New York 10032, USA
- Corresponding author.E-MAIL ; FAX (212) 342-1810
| |
Collapse
|
7
|
Vermeirssen V, Barrasa MI, Hidalgo CA, Babon JAB, Sequerra R, Doucette-Stamm L, Barabási AL, Walhout AJ. Transcription factor modularity in a gene-centered C. elegans core neuronal protein-DNA interaction network. Genome Res 2007; 17:1061-71. [PMID: 17513831 PMCID: PMC1899117 DOI: 10.1101/gr.6148107] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription regulatory networks play a pivotal role in the development, function, and pathology of metazoan organisms. Such networks are comprised of protein-DNA interactions between transcription factors (TFs) and their target genes. An important question pertains to how the architecture of such networks relates to network functionality. Here, we show that a Caenorhabditis elegans core neuronal protein-DNA interaction network is organized into two TF modules. These modules contain TFs that bind to a relatively small number of target genes and are more systems specific than the TF hubs that connect the modules. Each module relates to different functional aspects of the network. One module contains TFs involved in reproduction and target genes that are expressed in neurons as well as in other tissues. The second module is enriched for paired homeodomain TFs and connects to target genes that are often exclusively neuronal. We find that paired homeodomain TFs are specifically expressed in C. elegans and mouse neurons, indicating that the neuronal function of paired homeodomains is evolutionarily conserved. Taken together, we show that a core neuronal C. elegans protein-DNA interaction network possesses TF modules that relate to different functional aspects of the complete network.
Collapse
Affiliation(s)
- Vanessa Vermeirssen
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - M. Inmaculada Barrasa
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - César A. Hidalgo
- Center for Complex Network Research, Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jenny Aurielle B. Babon
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | | | | | - Albert-László Barabási
- Center for Complex Network Research, Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Albertha J.M. Walhout
- Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
- Corresponding author.E-mail ; fax (508) 856-5460
| |
Collapse
|