1
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Eliad B, Schneider N, Ben-Naim Zgayer O, Amichan Y, Glaser F, Erdmann EA, Rajendren S, Hundley HA, Lamm AT. ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection. Nucleic Acids Res 2024:gkae641. [PMID: 39036970 DOI: 10.1093/nar/gkae641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/05/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans, it is not, making them invaluable for RNA editing research. In C. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.
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Affiliation(s)
- Berta Eliad
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Noa Schneider
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Orna Ben-Naim Zgayer
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Yarden Amichan
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Fabian Glaser
- Technion Center for Structural Biology, Technion Human Health Initiative, Technion, Haifa 32000, Israel
| | - Emily A Erdmann
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Suba Rajendren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Heather A Hundley
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ayelet T Lamm
- Faculty of Biology, Technion- Israel Institute of Technology, Technion City, Haifa 3200003, Israel
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2
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Lu YM, Yan S, Ti SC, Zheng C. Editing of endogenous tubulins reveals varying effects of tubulin posttranslational modifications on axonal growth and regeneration. eLife 2024; 13:RP94583. [PMID: 38949652 PMCID: PMC11216746 DOI: 10.7554/elife.94583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
Tubulin posttranslational modifications (PTMs) modulate the dynamic properties of microtubules and their interactions with other proteins. However, the effects of tubulin PTMs were often revealed indirectly through the deletion of modifying enzymes or the overexpression of tubulin mutants. In this study, we directly edited the endogenous tubulin loci to install PTM-mimicking or -disabling mutations and studied their effects on microtubule stability, neurite outgrowth, axonal regeneration, cargo transport, and sensory functions in the touch receptor neurons of Caenorhabditis elegans. We found that the status of β-tubulin S172 phosphorylation and K252 acetylation strongly affected microtubule dynamics, neurite growth, and regeneration, whereas α-tubulin K40 acetylation had little influence. Polyglutamylation and detyrosination in the tubulin C-terminal tail had more subtle effects on microtubule stability likely by modulating the interaction with kinesin-13. Overall, our study systematically assessed and compared several tubulin PTMs for their impacts on neuronal differentiation and regeneration and established an in vivo platform to test the function of tubulin PTMs in neurons.
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Affiliation(s)
- Yu-Ming Lu
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SARHong KongChina
| | - Shan Yan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Shih-Chieh Ti
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong KongHong KongChina
| | - Chaogu Zheng
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong SARHong KongChina
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3
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Eliad B, Schneider N, Zgayer OBN, Amichan Y, Glaser F, Erdmann EA, Rajendren S, Hundley HA, Lamm AT. ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.14.540679. [PMID: 38895382 PMCID: PMC11185548 DOI: 10.1101/2023.05.14.540679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans , it is not, making them invaluable for RNA editing research. In C. elegans , ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans . In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.
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4
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Kimmich MJ, Sundaramurthy S, Geary MA, Lesanpezeshki L, Yingling CV, Vanapalli SA, Littlefield RS, Pruyne D. FHOD-1/profilin-mediated actin assembly protects sarcomeres against contraction-induced deformation in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582848. [PMID: 38559004 PMCID: PMC10979920 DOI: 10.1101/2024.02.29.582848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Formin HOmology Domain 2-containing (FHOD) proteins are a subfamily of actin-organizing formins important for striated muscle development in many animals. We showed previously that absence of the sole FHOD protein, FHOD-1, from C. elegans results in thin body-wall muscles with misshapen dense bodies that serve as sarcomere Z-lines. We demonstrate here that actin polymerization by FHOD-1 is required for its function in muscle development, and that FHOD-1 cooperates with profilin PFN-3 for dense body morphogenesis, and profilins PFN-2 and PFN-3 to promote body-wall muscle growth. We further demonstrate dense bodies in fhod-1 and pfn-3 mutants are less stable than in wild type animals, having a higher proportion of dynamic protein, and becoming distorted by prolonged muscle contraction. We also observe accumulation of actin depolymerization factor/cofilin homolog UNC-60B in body-wall muscle of these mutants. Such accumulations may indicate targeted disassembly of thin filaments dislodged from unstable dense bodies, and may account for the abnormally slow growth and reduced strength of body-wall muscle in fhod-1 mutants. Overall, these results show the importance of FHOD protein-mediated actin assembly to forming stable sarcomere Z-lines, and identify profilin as a new contributor to FHOD activity in striated muscle development.
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Affiliation(s)
- Michael J. Kimmich
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Sumana Sundaramurthy
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Meaghan A. Geary
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Leila Lesanpezeshki
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409
| | - Curtis V. Yingling
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Siva A. Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409
| | | | - David Pruyne
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
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5
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Wang C, Yang M, Liu D, Zheng C. Metabolic rescue of α-synuclein-induced neurodegeneration through propionate supplementation and intestine-neuron signaling in C. elegans. Cell Rep 2024; 43:113865. [PMID: 38412096 DOI: 10.1016/j.celrep.2024.113865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/29/2024] Open
Abstract
Microbial metabolites that can modulate neurodegeneration are promising therapeutic targets. Here, we found that the short-chain fatty acid propionate protects against α-synuclein-induced neuronal death and locomotion defects in a Caenorhabditis elegans model of Parkinson's disease (PD) through bidirectional regulation between the intestine and neurons. Both depletion of dietary vitamin B12, which induces propionate breakdown, and propionate supplementation suppress neurodegeneration and reverse PD-associated transcriptomic aberrations. Neuronal α-synuclein aggregation induces intestinal mitochondrial unfolded protein response (mitoUPR), which leads to reduced propionate levels that trigger transcriptional reprogramming in the intestine and cause defects in energy production. Weakened intestinal metabolism exacerbates neurodegeneration through interorgan signaling. Genetically enhancing propionate production or overexpressing metabolic regulators downstream of propionate in the intestine rescues neurodegeneration, which then relieves mitoUPR. Importantly, propionate supplementation suppresses neurodegeneration without reducing α-synuclein aggregation, demonstrating metabolic rescue of neuronal proteotoxicity downstream of protein aggregates. Our study highlights the involvement of small metabolites in the gut-brain interaction in neurodegenerative diseases.
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Affiliation(s)
- Chenyin Wang
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Meigui Yang
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dongyao Liu
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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6
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Liu J, Murray JI. Mechanisms of lineage specification in Caenorhabditis elegans. Genetics 2023; 225:iyad174. [PMID: 37847877 DOI: 10.1093/genetics/iyad174] [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: 08/26/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
The studies of cell fate and lineage specification are fundamental to our understanding of the development of multicellular organisms. Caenorhabditis elegans has been one of the premiere systems for studying cell fate specification mechanisms at single cell resolution, due to its transparent nature, the invariant cell lineage, and fixed number of somatic cells. We discuss the general themes and regulatory mechanisms that have emerged from these studies, with a focus on somatic lineages and cell fates. We next review the key factors and pathways that regulate the specification of discrete cells and lineages during embryogenesis and postembryonic development; we focus on transcription factors and include numerous lineage diagrams that depict the expression of key factors that specify embryonic founder cells and postembryonic blast cells, and the diverse somatic cell fates they generate. We end by discussing some future perspectives in cell and lineage specification.
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Affiliation(s)
- Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John Isaac Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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7
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Land R, Fetter R, Liang X, Tzeng CP, Taylor CA, Shen K. Endoplasmic Reticulum Exit Sites scale with somato-dendritic size in neurons. Mol Biol Cell 2023; 34:ar106. [PMID: 37556208 PMCID: PMC10559313 DOI: 10.1091/mbc.e23-03-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Nervous systems exhibit dramatic diversity in cell morphology and size. How neurons regulate their biosynthetic and secretory machinery to support such diversity is not well understood. Endoplasmic reticulum exit sites (ERESs) are essential for maintaining secretory flux, and are required for normal dendrite development, but how neurons of different size regulate secretory capacity remains unknown. In Caenorhabditis elegans, we find that the ERES number is strongly correlated with the size of a neuron's dendritic arbor. The elaborately branched sensory neuron, PVD, has especially high ERES numbers. Asymmetric cell division provides PVD with a large initial cell size critical for rapid establishment of PVD's high ERES number before neurite outgrowth, and these ERESs are maintained throughout development. Maintenance of ERES number requires the cell fate transcription factor MEC-3, C. elegans TOR (ceTOR/let-363), and nutrient availability, with mec-3 and ceTOR/let-363 mutant PVDs both displaying reductions in ERES number, soma size, and dendrite size. Notably, mec-3 mutant animals exhibit reduced expression of a ceTOR/let-363 reporter in PVD, and starvation reduces ERES number and somato-dendritic size in a manner genetically redundant with ceTOR/let-363 perturbation. Our data suggest that both asymmetric cell division and nutrient sensing pathways regulate secretory capacities to support elaborate dendritic arbors.
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Affiliation(s)
- Ruben Land
- Department of Biology, Stanford University, Stanford, CA 94305
- Neurosciences IDP, Stanford University, Stanford, CA 94305
| | - Richard Fetter
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Xing Liang
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Christopher P. Tzeng
- Department of Biology, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Caitlin A. Taylor
- Department of Biology, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
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8
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Zhu Y, Li W, Dong Y, Xia C, Fu R. C. elegans Hemidesmosomes Sense Collagen Damage to Trigger Innate Immune Response in the Epidermis. Cells 2023; 12:2223. [PMID: 37759445 PMCID: PMC10526450 DOI: 10.3390/cells12182223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The collagens are an enormous family of extracellular matrix proteins that play dominant roles in cell adhesion, migration and tissue remodeling under many physiological and pathological conditions. However, their function mechanisms in regulating innate immunity remain largely undiscovered. Here we use C. elegans epidermis as the model to address this question. The C. elegans epidermis is covered with a collagen-rich cuticle exoskeleton and can produce antimicrobial peptides (AMPs) against invading pathogens or physical injury. Through an RNAi screen against collagen-encoding genes, we found that except the previously reported six DPY collagens and the BLI-1 collagen, the majority of collagens tested appear unable to trigger epidermal immune defense when damaged. Further investigation suggests that the six DPY collagens form a specific substructure, which regulates the interaction between BLI-1 and the hemidesmosome receptor MUP-4. The separation of BLI-1 with MUP-4 caused by collagen damage leads to the detachment of the STAT transcription factor-like protein STA-2 from hemidesmosomes and the induction of AMPs. Our findings uncover the mechanism how collagens are organized into a damage sensor and how the epidermis senses collagen damage to mount an immune defense.
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Affiliation(s)
| | | | | | | | - Rong Fu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (Y.Z.)
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Bozzo M, Bellitto D, Amaroli A, Ferrando S, Schubert M, Candiani S. Retinoic Acid and POU Genes in Developing Amphioxus: A Focus on Neural Development. Cells 2023; 12:cells12040614. [PMID: 36831281 PMCID: PMC9953854 DOI: 10.3390/cells12040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
POU genes are a family of evolutionarily conserved transcription factors with key functions in cell type specification and neurogenesis. In vitro experiments have indicated that the expression of some POU genes is controlled by the intercellular signaling molecule retinoic acid (RA). In this work, we aimed to characterize the roles of RA signaling in the regulation of POU genes in vivo. To do so, we studied POU genes during the development of the cephalochordate amphioxus, an animal model crucial for understanding the evolutionary origins of vertebrates. The expression patterns of amphioxus POU genes were assessed at different developmental stages by chromogenic in situ hybridization and hybridization chain reaction. Expression was further assessed in embryos subjected to pharmacological manipulation of endogenous RA signaling activity. In addition to a detailed description of the effects of these treatments on amphioxus POU gene expression, our survey included the first description of Pou2 and Pou6 expression in amphioxus embryos. We found that Pit-1, Pou2, Pou3l, and Pou6 expression are not affected by alterations of endogenous RA signaling levels. In contrast, our experiments indicated that Brn1/2/4 and Pou4 expression are regulated by RA signaling in the endoderm and the nerve cord, respectively. The effects of the treatments on Pou4 expression in the nerve cord revealed that, in developing amphioxus, RA signaling plays a dual role by (1) providing anteroposterior patterning information to neural cells and (2) specifying neural cell types. This finding is coherent with a terminal selector function of Pou4 for GABAergic neurons in amphioxus and represents the first description of RA-induced changes in POU gene expression in vivo.
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Affiliation(s)
- Matteo Bozzo
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
| | - Deianira Bellitto
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Andrea Amaroli
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Sara Ferrando
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Simona Candiani
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
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10
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Affiliation(s)
- Sven Truckenbrodt
- Convergent Research, E11 Bio. 1600 Harbor Bay Parkway, Alameda, California94502, United States
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11
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Masoudi N, Schnabel R, Yemini E, Leyva-Díaz E, Hobert O. Cell-specific effects of the sole C. elegans Daughterless/E protein homolog, HLH-2, on nervous system development. Development 2023; 150:286219. [PMID: 36595352 PMCID: PMC10108603 DOI: 10.1242/dev.201366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 01/04/2023]
Abstract
Are there common mechanisms of neurogenesis used throughout an entire nervous system? We explored to what extent canonical proneural class I/II bHLH complexes are responsible for neurogenesis throughout the entire Caenorhabditis elegans nervous system. Distinct, lineage-specific proneural class II bHLH factors are generally thought to operate via interaction with a common, class I bHLH subunit, encoded by Daughterless in flies, the E proteins in vertebrates and HLH-2 in C. elegans. To eliminate function of all proneuronal class I/II bHLH complexes, we therefore genetically removed maternal and zygotic hlh-2 gene activity. We observed broad effects on neurogenesis, but still detected normal neurogenesis in many distinct neuron-producing lineages of the central and peripheral nervous system. Moreover, we found that hlh-2 selectively affects some aspects of neuron differentiation while leaving others unaffected. Although our studies confirm the function of proneuronal class I/II bHLH complexes in many different lineages throughout a nervous system, we conclude that their function is not universal, but rather restricted by lineage, cell type and components of differentiation programs affected.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA.,University of Massachusetts, Department of Neurobiology, Worcester, MA 1605-2324, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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Widespread employment of conserved C. elegans homeobox genes in neuronal identity specification. PLoS Genet 2022; 18:e1010372. [PMID: 36178933 PMCID: PMC9524666 DOI: 10.1371/journal.pgen.1010372] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
Homeobox genes are prominent regulators of neuronal identity, but the extent to which their function has been probed in animal nervous systems remains limited. In the nematode Caenorhabditis elegans, each individual neuron class is defined by the expression of unique combinations of homeobox genes, prompting the question of whether each neuron class indeed requires a homeobox gene for its proper identity specification. We present here progress in addressing this question by extending previous mutant analysis of homeobox gene family members and describing multiple examples of homeobox gene function in different parts of the C. elegans nervous system. To probe homeobox function, we make use of a number of reporter gene tools, including a novel multicolor reporter transgene, NeuroPAL, which permits simultaneous monitoring of the execution of multiple differentiation programs throughout the entire nervous system. Using these tools, we add to the previous characterization of homeobox gene function by identifying neuronal differentiation defects for 14 homeobox genes in 24 distinct neuron classes that are mostly unrelated by location, function and lineage history. 12 of these 24 neuron classes had no homeobox gene function ascribed to them before, while in the other 12 neuron classes, we extend the combinatorial code of transcription factors required for specifying terminal differentiation programs. Furthermore, we demonstrate that in a particular lineage, homeotic identity transformations occur upon loss of a homeobox gene and we show that these transformations are the result of changes in homeobox codes. Combining the present with past analyses, 113 of the 118 neuron classes of C. elegans are now known to require a homeobox gene for proper execution of terminal differentiation programs. Such broad deployment indicates that homeobox function in neuronal identity specification may be an ancestral feature of animal nervous systems.
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Identification, molecular characterization, and in silico structural analysis of larval salivary glands Netrin-A as a potent biomarker from Lucilia sericata (Diptera: Calliphoridae). Genetica 2022; 150:379-394. [PMID: 36136258 DOI: 10.1007/s10709-022-00164-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 07/29/2022] [Indexed: 11/04/2022]
Abstract
The greenbottle blowfly Lucilia sericata (L. sericata) is increasingly used in larval therapy of chronic wounds. Netrins as bifunctional proteins are in the superfamily of Laminins secreted from larval salivary glands. The Netrin protein has a significant instructive role in axon guidance, causing neuronal outgrowth, angiogenesis, and cell migration. It seems to be crucial in wound healing and acts as a potential biomarker in diagnosing some clinical diseases. This survey aimed to identify molecular features and analyze in silico structural configuration of Netrin-A in L. sericata larvae. The larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericata Netrin-A (LSN-A) was then identified using rapid amplification of circular DNA ends (RACE) and rapid amplification of genomic ends (RAGE). Parts of the Netrin-A gene, including the middle, 3'-, and 5'-ends, were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its estimated molecular weight was 78.6 kDa. Sequencing of this fragment and its BLAST analysis revealed laminin-based high (95%) similarity with the mRNA sequence of Lucilia cuprina Netrin-A. The 3-D structure of Netrin-A drawn by SWISS-MODEL exhibited its partial resemblance to the reference molecule Netrin-1 of Homo sapiens. This study supports the molecular and structural analyses of LSN-A protein, which could lead to wound treatment. Ultimately, it can be an effective candidate to ameliorate injury. Our next attempt is to produce LSN-A recombinant protein for use in biomedical sciences.
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Caenorhabditis elegans sine oculis/SIX-type homeobox genes act as homeotic switches to define neuronal subtype identities. Proc Natl Acad Sci U S A 2022; 119:e2206817119. [PMID: 36067313 PMCID: PMC9478639 DOI: 10.1073/pnas.2206817119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Anatomical and molecular studies have revealed that in many animal nervous systems, neuronal cell types can often be subclassified into highly related subtypes with only small phenotypic differences. We decipher here the regulatory logic of such cell type diversification processes. We show that identity features of neurons that are highly similar to one another are controlled by master regulatory transcription factors and that phenotypic differences between related cell types are controlled by downstream acting transcription factors that promote or antagonize the ability of master regulatory factors to control unique identity features. Our findings help explain how neuronal cell types diversify and suggest hypothetical scenarios for neuronal cell-type evolution. The classification of neurons into distinct types reveals hierarchical taxonomic relationships that reflect the extent of similarity between neuronal cell types. At the base of such taxonomies are neuronal cells that are very similar to one another but differ in a small number of reproducible and select features. How are very similar members of a neuron class that share many features instructed to diversify into distinct subclasses? We show here that the six very similar members of the Caenorhabditis elegans IL2 sensory neuron class, which are all specified by a homeobox terminal selector, unc-86/BRN3, differentiate into two subtly distinct subclasses, a dorsoventral subclass and a lateral subclass, by the toggle switch–like action of the sine oculis/SIX homeobox gene unc-39. unc-39 is expressed only in the lateral IL2 neurons, and loss of unc-39 leads to a homeotic transformation of the lateral into the dorsoventral class; conversely, ectopic unc-39 expression converts the dorsoventral subclass into the lateral subclass. Hence, a terminal selector homeobox gene controls both class- as well as subclass-specific features, while a subordinate homeobox gene determines the ability of the class-specific homeobox gene to activate subtype-specific target genes. We find a similar regulatory mechanism operating in a distinct class of six motor neurons. Our findings underscore the importance of homeobox genes in neuronal identity control and invite speculations about homeotic identity transformations as potential drivers of evolutionary novelty during cell-type evolution in the brain.
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15
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Ono S, Lewis M, Ono K. Mutual dependence between tropomodulin and tropomyosin in the regulation of sarcomeric actin assembly in Caenorhabditis elegans striated muscle. Eur J Cell Biol 2022; 101:151215. [PMID: 35306452 PMCID: PMC9081161 DOI: 10.1016/j.ejcb.2022.151215] [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: 12/07/2021] [Revised: 02/24/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Tropomodulin and tropomyosin are important components of sarcomeric thin filaments in striated muscles. Tropomyosin decorates the side of actin filaments and enhances tropomodulin capping at the pointed ends of the filaments. Their functional relationship has been extensively characterized in vitro, but in vivo and cellular studies in mammals are often complicated by the presence of functionally redundant isoforms. Here, we used the nematode Caenorhabditis elegans, which has a relatively simple composition of tropomodulin and tropomyosin genes, and demonstrated that tropomodulin (unc-94) and tropomyosin (lev-11) are mutually dependent on each other in their sarcomere localization and regulation of sarcomeric actin assembly. Mutation of tropomodulin caused sarcomere disorganization with formation of actin aggregates. However, the actin aggregation was suppressed when tropomyosin was depleted in the tropomodulin mutant. Tropomyosin was mislocalized to the actin aggregates in the tropomodulin mutants, while sarcomere localization of tropomodulin was lost when tropomyosin was depleted. These results indicate that tropomodulin and tropomyosin are interdependent in the regulation of organized sarcomeric assembly of actin filaments in vivo.
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Affiliation(s)
- Shoichiro Ono
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA.
| | - Mario Lewis
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Kanako Ono
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, USA; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
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16
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Lynch TR, Xue M, Czerniak CW, Lee C, Kimble J. Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal. Development 2022; 149:274985. [PMID: 35394007 PMCID: PMC9058496 DOI: 10.1242/dev.200332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/16/2022] [Indexed: 11/20/2022]
Abstract
A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. Reporter constructs, cell culture assays and computational modeling have made major contributions to answering this question, but analysis of elements in their natural context is an important complement. Here, we mutate Notch-dependent LAG-1 binding sites (LBSs) in the endogenous Caenorhabditis elegans sygl-1 gene, which encodes a key stem cell regulator, and analyze the consequences on sygl-1 expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of one LBS in a three-element cluster approximately halved both expression and stem cell pool size, whereas mutation of two LBSs essentially abolished them. Heterozygous LBS mutant clusters provided intermediate values. Our results lead to two major conclusions. First, both LBS number and configuration impact cluster activity: LBSs act additively in trans and synergistically in cis. Second, the SYGL-1 gradient promotes self-renewal above its functional threshold and triggers differentiation below the threshold. Our approach of coupling CRISPR/Cas9 LBS mutations with effects on both molecular and biological readouts establishes a powerful model for in vivo analyses of DNA cis-regulatory elements. Summary: Notch-dependent DNA cis-regulatory elements work together in their developmental context in C. elegans to shape a transcriptional gradient, control stem cell pool size, and govern differentiation onset.
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Affiliation(s)
- Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
| | - Mingyu Xue
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Cazza W. Czerniak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Joint Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
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17
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Jimeno-Martín A, Sousa E, Brocal-Ruiz R, Daroqui N, Maicas M, Flames N. Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity. Genome Res 2022; 32:459-473. [PMID: 35074859 PMCID: PMC8896470 DOI: 10.1101/gr.275623.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 01/19/2022] [Indexed: 11/24/2022]
Abstract
To systematically investigate the complexity of neuron specification regulatory networks, we performed an RNA interference (RNAi) screen against all 875 transcription factors (TFs) encoded in Caenorhabditis elegans genome and searched for defects in nine different neuron types of the monoaminergic (MA) superclass and two cholinergic motoneurons. We identified 91 TF candidates to be required for correct generation of these neuron types, of which 28 were confirmed by mutant analysis. We found that correct reporter expression in each individual neuron type requires at least nine different TFs. Individual neuron types do not usually share TFs involved in their specification but share a common pattern of TFs belonging to the five most common TF families: homeodomain (HD), basic helix loop helix (bHLH), zinc finger (ZF), basic leucine zipper domain (bZIP), and nuclear hormone receptors (NHR). HD TF members are overrepresented, supporting a key role for this family in the establishment of neuronal identities. These five TF families are also prevalent when considering mutant alleles with previously reported neuronal phenotypes in C. elegans, Drosophila, and mouse. In addition, we studied terminal differentiation complexity focusing on the dopaminergic terminal regulatory program. We found two HD TFs (UNC-62 and VAB-3) that work together with known dopaminergic terminal selectors (AST-1, CEH-43, CEH-20). Combined TF binding sites for these five TFs constitute a cis-regulatory signature enriched in the regulatory regions of dopaminergic effector genes. Our results provide new insights on neuron-type regulatory programs in C. elegans that could help better understand neuron specification and evolution of neuron types.
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Affiliation(s)
- Angela Jimeno-Martín
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Rebeca Brocal-Ruiz
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Noemi Daroqui
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, 46010, Spain
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18
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Loer CM. Antibody Staining for Nematodes with Heat-induced Antigen Retrieval (HIAR). Methods Mol Biol 2022; 2468:133-140. [PMID: 35320564 DOI: 10.1007/978-1-0716-2181-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immunocytochemistry remains a valuable and necessary tool for biologists working with nematodes, even those nematode model organisms with advanced molecular genetic tools and transgenics. Because of the highly idiosyncratic nature of successful immunostaining procedures, innovations can still be found for this long-established technique. Heat-induced antigen retrieval (HIAR) is well known from other systems, but seems not to have been applied to antibody staining in nematodes. For some antigens, adding HIAR to an established antibody staining protocol for nematodes can reveal strong and reliable staining that without HIAR is poor or completely absent.
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Affiliation(s)
- Curtis M Loer
- Fletcher Jones Professor of Biology, Department of Biology, University of San Diego, San Diego, CA, USA.
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19
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Ozment E, Tamvacakis AN, Zhou J, Rosiles-Loeza PY, Escobar-Hernandez EE, Fernandez-Valverde SL, Nakanishi N. Cnidarian hair cell development illuminates an ancient role for the class IV POU transcription factor in defining mechanoreceptor identity. eLife 2021; 10:74336. [PMID: 34939935 PMCID: PMC8846589 DOI: 10.7554/elife.74336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Although specialized mechanosensory cells are found across animal phylogeny, early evolutionary histories of mechanoreceptor development remain enigmatic. Cnidaria (e.g. sea anemones and jellyfishes) is the sister group to well-studied Bilateria (e.g. flies and vertebrates), and has two mechanosensory cell types – a lineage-specific sensory effector known as the cnidocyte, and a classical mechanosensory neuron referred to as the hair cell. While developmental genetics of cnidocytes is increasingly understood, genes essential for cnidarian hair cell development are unknown. Here, we show that the class IV POU homeodomain transcription factor (POU-IV) – an indispensable regulator of mechanosensory cell differentiation in Bilateria and cnidocyte differentiation in Cnidaria – controls hair cell development in the sea anemone cnidarian Nematostella vectensis. N. vectensis POU-IV is postmitotically expressed in tentacular hair cells, and is necessary for development of the apical mechanosensory apparatus, but not of neurites, in hair cells. Moreover, it binds to deeply conserved DNA recognition elements, and turns on a unique set of effector genes – including the transmembrane receptor-encoding gene polycystin 1 – specifically in hair cells. Our results suggest that POU-IV directs differentiation of cnidarian hair cells and cnidocytes via distinct gene regulatory mechanisms, and support an evolutionarily ancient role for POU-IV in defining the mature state of mechanosensory neurons.
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Affiliation(s)
- Ethan Ozment
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Arianna N Tamvacakis
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Jianhong Zhou
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
| | - Pablo Yamild Rosiles-Loeza
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | | | - Selene L Fernandez-Valverde
- Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Mexico
| | - Nagayasu Nakanishi
- Department of Biological Sciences, University of Arkansas, Fayetteville, United States
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20
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Palumbos SD, Skelton R, McWhirter R, Mitchell A, Swann I, Heifner S, Von Stetina S, Miller DM. cAMP controls a trafficking mechanism that maintains the neuron specificity and subcellular placement of electrical synapses. Dev Cell 2021; 56:3235-3249.e4. [PMID: 34741804 DOI: 10.1016/j.devcel.2021.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/30/2021] [Accepted: 10/08/2021] [Indexed: 11/28/2022]
Abstract
Electrical synapses are established between specific neurons and within distinct subcellular compartments, but the mechanisms that direct gap junction assembly in the nervous system are largely unknown. Here, we show that a developmental program tunes cAMP signaling to direct the neuron-specific assembly and placement of electrical synapses in the C. elegans motor circuit. We use live-cell imaging to visualize electrical synapses in vivo and an optogenetic assay to confirm that they are functional. In ventral A class (VA) motor neurons, the UNC-4 transcription factor blocks expression of cAMP antagonists that promote gap junction miswiring. In unc-4 mutants, VA electrical synapses are established with an alternative synaptic partner and are repositioned from the VA axon to soma. cAMP counters these effects by driving gap junction trafficking into the VA axon for electrical synapse assembly. Thus, our experiments establish that cAMP regulates gap junction trafficking for the biogenesis of functional electrical synapses.
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Affiliation(s)
- Sierra D Palumbos
- Neuroscience Program, Vanderbilt University, Nashville, TN 37212, USA
| | - Rachel Skelton
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Amanda Mitchell
- Vanderbilt Summer Science Academy, Vanderbilt University, Nashville, TN 37212, USA
| | - Isaiah Swann
- Vanderbilt Summer Science Academy, Vanderbilt University, Nashville, TN 37212, USA
| | | | - Stephen Von Stetina
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - David M Miller
- Neuroscience Program, Vanderbilt University, Nashville, TN 37212, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37212, USA.
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21
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Sousa E, Flames N. Transcriptional regulation of neuronal identity. Eur J Neurosci 2021; 55:645-660. [PMID: 34862697 PMCID: PMC9306894 DOI: 10.1111/ejn.15551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/29/2022]
Abstract
Neuronal diversity is an intrinsic feature of the nervous system. Transcription factors (TFs) are key regulators in the establishment of different neuronal identities; how are the actions of different TFs coordinated to orchestrate this diversity? Are there common features shared among the different neuron types of an organism or even among different animal groups? In this review, we provide a brief overview on common traits emerging on the transcriptional regulation of neuron type diversification with a special focus on the comparison between mouse and Caenorhabditis elegans model systems. In the first part, we describe general concepts on neuronal identity and transcriptional regulation of gene expression. In the second part of the review, TFs are classified in different categories according to their key roles at specific steps along the protracted process of neuronal specification and differentiation. The same TF categories can be identified both in mammals and nematodes. Importantly, TFs are very pleiotropic: Depending on the neuron type or the time in development, the same TF can fulfil functions belonging to different categories. Finally, we describe the key role of transcriptional repression at all steps controlling neuronal diversity and propose that acquisition of neuronal identities could be considered a metastable process.
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Affiliation(s)
- Erick Sousa
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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22
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Mao S, Fan X, Hu J. Correlation for tree-shaped datasets and its Bayesian estimation. Comput Stat Data Anal 2021. [DOI: 10.1016/j.csda.2021.107307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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23
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O'Hagan R, Topalidou I. Fixation and Immunostaining of Endogenous Proteins or Post-translational Modificationsin Caenorhabditis elegans. Bio Protoc 2021; 11:e4172. [PMID: 34722819 DOI: 10.21769/bioprotoc.4172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 11/02/2022] Open
Abstract
Although the advent of genetically-encoded fluorescent markers, such as the green fluorescent protein (GFP; Chalfie et al., 1994 ), has enabled convenient visualization of gene expression in vivo, this method is generally not effective for detecting post-translational modifications because they are not translated from DNA sequences. Genetically-encoded, fluorescently-tagged transgene products can also be misleading for observing expression patterns because transgenes may lack endogenous regulatory DNA elements needed for precise regulation of expression that could result in over or under expression. Fluorescently-tagged proteins created by CRISPR genome editing are less prone to defective expression patterns because the loci retain endogenous DNA elements that regulate their transcription (Nance and Frøkjær-Jensen, 2019). However, even CRISPR alleles encoding heritable fluorescently-tagged protein markers can result in defects in function or localization of the gene product if the fluorescent tag obstructs or otherwise interferes with important protein interaction domains or affects the protein structure. Indirect immunofluorescence is a method for detecting endogenous gene expression or post-translational modifications without the need for transgenesis or genome editing. Here, we present a reliable protocol in which C. elegans nematodes are fixed, preserved, and permeabilized for staining with a primary antibody to bind proteins or post-translational modifications, which are then labeled with a secondary antibody conjugated to a fluorescent dye. Use of this method may be limited by the availability of (or ability to generate) a primary antibody that binds the epitope of interest in fixed animals. Thousands of animals are simultaneously subjected to a series of chemical treatments and washes in a single centrifuge tube, allowing large numbers of identically-treated stained animals to be examined. We have successfully used this protocol (O' Hagan et al., 2011 and 2017; Power et al., 2020 ) to preserve and detect post-translational modifications of tubulin in C. elegans ciliated sensory neurons and to detect non-modified endogenous protein (Topalidou and Chalfie, 2011).
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Affiliation(s)
- Robert O'Hagan
- Biology Department, Montclair State University, Montclair, USA
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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24
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Imaging of Actin Cytoskeleton in the Nematode Caenorhabditis elegans. Methods Mol Biol 2021. [PMID: 34542852 DOI: 10.1007/978-1-0716-1661-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The nematode Caenorhabditis elegans is one of the major model organisms in cell and developmental biology. This organism is easy to culture in laboratories and suitable for microscopic investigation of the cytoskeleton. Because the worms are small and transparent, the actin cytoskeleton in many tissues and cells can be observed with appropriate visualization techniques without sectioning or dissection. This chapter describes the introduction to representative methods for imaging the actin cytoskeleton in C. elegans and a protocol for staining worms with fluorescent phalloidin.
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25
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Tekieli T, Yemini E, Nejatbakhsh A, Wang C, Varol E, Fernandez RW, Masoudi N, Paninski L, Hobert O. Visualizing the organization and differentiation of the male-specific nervous system of C. elegans. Development 2021; 148:dev199687. [PMID: 34415309 PMCID: PMC8489020 DOI: 10.1242/dev.199687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023]
Abstract
Sex differences in the brain are prevalent throughout the animal kingdom and particularly well appreciated in the nematode Caenorhabditis elegans, where male animals contain a little-studied set of 93 male-specific neurons. To make these neurons amenable for future study, we describe here how a multicolor reporter transgene, NeuroPAL, is capable of visualizing the distinct identities of all male-specific neurons. We used NeuroPAL to visualize and characterize a number of features of the male-specific nervous system. We provide several proofs of concept for using NeuroPAL to identify the sites of expression of gfp-tagged reporter genes and for cellular fate analysis by analyzing the effect of removal of several developmental patterning genes on neuronal identity acquisition. We use NeuroPAL and its intrinsic cohort of more than 40 distinct differentiation markers to show that, even though male-specific neurons are generated throughout all four larval stages, they execute their terminal differentiation program in a coordinated manner in the fourth larval stage. This coordinated wave of differentiation, which we call 'just-in-time' differentiation, couples neuronal maturation programs with the appearance of sexual organs.
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Affiliation(s)
- Tessa Tekieli
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Amin Nejatbakhsh
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Chen Wang
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Erdem Varol
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Robert W. Fernandez
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Liam Paninski
- Departments of Statistics and Neuroscience, Grossman Center for the Statistics of Mind, Center for Theoretical Neuroscience, Zuckerman Institute, Columbia University, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
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A 4D single-cell protein atlas of transcription factors delineates spatiotemporal patterning during embryogenesis. Nat Methods 2021; 18:893-902. [PMID: 34312566 DOI: 10.1038/s41592-021-01216-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/17/2021] [Indexed: 12/27/2022]
Abstract
Complex biological processes such as embryogenesis require precise coordination of cell differentiation programs across both space and time. Using protein-fusion fluorescent reporters and four-dimensional live imaging, we present a protein expression atlas of transcription factors (TFs) mapped onto developmental cell lineages during Caenorhabditis elegans embryogenesis, at single-cell resolution. This atlas reveals a spatiotemporal combinatorial code of TF expression, and a cascade of lineage-specific, tissue-specific and time-specific TFs that specify developmental states. The atlas uncovers regulators of embryogenesis, including an unexpected role of a skin specifier in neurogenesis and the critical function of an uncharacterized TF in convergent muscle differentiation. At the systems level, the atlas provides an opportunity to model cell state-fate relationships, revealing a lineage-dependent state diversity within functionally related cells and a winding trajectory of developmental state progression. Collectively, this single-cell protein atlas represents a valuable resource for elucidating metazoan embryogenesis at the molecular and systems levels.
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27
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Lee J, Magescas J, Fetter RD, Feldman JL, Shen K. Inherited apicobasal polarity defines the key features of axon-dendrite polarity in a sensory neuron. Curr Biol 2021; 31:3768-3783.e3. [PMID: 34270949 DOI: 10.1016/j.cub.2021.06.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/05/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022]
Abstract
Neurons are highly polarized cells with morphologically and functionally distinct dendritic and axonal processes. The molecular mechanisms that establish axon-dendrite polarity in vivo are poorly understood. Here, we describe the initial polarization of posterior deirid (PDE), a ciliated mechanosensory neuron, during development in vivo through 4D live imaging with endogenously tagged proteins. PDE inherits and maintains apicobasal polarity from its epithelial precursor. Its apical domain is directly transformed into the ciliated dendritic tip through apical constriction, which is followed by axonal outgrowth from the opposite basal side of the cell. The apical Par complex and junctional proteins persistently localize at the developing dendritic domain throughout this transition. Consistent with their instructive role in axon-dendrite polarization, conditional depletion of the Par complex and junctional proteins results in robust defects in dendrite and axon formation. During apical constriction, a microtubule-organizing center (MTOC) containing the microtubule nucleator γ-tubulin ring complex (γ-TuRC) forms along the apical junction between PDE and its sister cell in a manner dependent on the Par complex and junctional proteins. This junctional MTOC patterns neuronal microtubule polarity and facilitate the dynein-dependent recruitment of the basal body for ciliogenesis. When non-ciliated neurons are genetically manipulated to obtain ciliated neuronal fate, inherited apicobasal polarity is required for generating ciliated dendritic tips. We propose that inherited apicobasal polarity, together with apical cell-cell interactions drive the morphological and cytoskeletal polarity in early neuronal differentiation.
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Affiliation(s)
- Joo Lee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jérémy Magescas
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Richard D Fetter
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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28
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Puri D, Ponniah K, Biswas K, Basu A, Dey S, Lundquist EA, Ghosh-Roy A. Wnt signaling establishes the microtubule polarity in neurons through regulation of Kinesin-13. J Cell Biol 2021; 220:212396. [PMID: 34137792 DOI: 10.1083/jcb.202005080] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Neuronal polarization is facilitated by the formation of axons with parallel arrays of plus-end-out and dendrites with the nonuniform orientation of microtubules. In C. elegans, the posterior lateral microtubule (PLM) neuron is bipolar with its two processes growing along the anterior-posterior axis under the guidance of Wnt signaling. Here we found that loss of the Kinesin-13 family microtubule-depolymerizing enzyme KLP-7 led to the ectopic extension of axon-like processes from the PLM cell body. Live imaging of the microtubules and axonal transport revealed mixed polarity of the microtubules in the short posterior process, which is dependent on both KLP-7 and the minus-end binding protein PTRN-1. KLP-7 is positively regulated in the posterior process by planar cell polarity components of Wnt involving rho-1/rock to induce mixed polarity of microtubules, whereas it is negatively regulated in the anterior process by the unc-73/ced-10 cascade to establish a uniform microtubule polarity. Our work elucidates how evolutionarily conserved Wnt signaling establishes the microtubule polarity in neurons through Kinesin-13.
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Affiliation(s)
- Dharmendra Puri
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Keerthana Ponniah
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Kasturi Biswas
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Atrayee Basu
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Swagata Dey
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
| | - Erik A Lundquist
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | - Anindya Ghosh-Roy
- Department of Cellular and Molecular Neuroscience, National Brain Research Centre, Manesar, Gurgaon, Haryana, India
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29
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Masoudi N, Yemini E, Schnabel R, Hobert O. Piecemeal regulation of convergent neuronal lineages by bHLH transcription factors in Caenorhabditis elegans. Development 2021; 148:dev199224. [PMID: 34100067 PMCID: PMC8217713 DOI: 10.1242/dev.199224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/29/2021] [Indexed: 11/20/2022]
Abstract
Cells of the same type can be generated by distinct cellular lineages that originate in different parts of the developing embryo ('lineage convergence'). Several Caenorhabditis elegans neuron classes composed of left/right or radially symmetric class members display such lineage convergence. We show here that the C. elegans Atonal homolog lin-32 is differentially expressed in neuronal lineages that give rise to left/right or radially symmetric class members. Loss of lin-32 results in the selective loss of the expression of pan-neuronal markers and terminal selector-type transcription factors that confer neuron class-specific features. Another basic helix-loop-helix (bHLH) gene, the Achaete-Scute homolog hlh-14, is expressed in a mirror image pattern relative to lin-32 and is required to induce neuronal identity and terminal selector expression on the contralateral side of the animal. These findings demonstrate that distinct lineage histories converge via different bHLH factors at the level of induction of terminal selector identity determinants, which thus serve as integrators of distinct lineage histories. We also describe neuron-to-neuron identity transformations in lin-32 mutants, which we propose to also be the result of misregulation of terminal selector gene expression.
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Affiliation(s)
- Neda Masoudi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
| | - Ralf Schnabel
- Institute of Genetics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027, USA
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30
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Kumar S, Olson AC, Koelle MR. The neural G protein Gαo tagged with GFP at an internal loop is functional in C. elegans. G3-GENES GENOMES GENETICS 2021; 11:6277897. [PMID: 34003969 PMCID: PMC8496287 DOI: 10.1093/g3journal/jkab167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/01/2021] [Indexed: 11/23/2022]
Abstract
Gαo is the alpha subunit of the major heterotrimeric G protein in neurons and mediates signaling by every known neurotransmitter, yet the signaling mechanisms activated by Gαo remain to be fully elucidated. Genetic analysis in Caenorhabditis elegans has shown that Gαo signaling inhibits neuronal activity and neurotransmitter release, but studies of the molecular mechanisms underlying these effects have been limited by lack of tools to complement genetic studies with other experimental approaches. Here, we demonstrate that inserting the green fluorescent protein (GFP) into an internal loop of the Gαo protein results in a tagged protein that is functional in vivo and that facilitates cell biological and biochemical studies of Gαo. Transgenic expression of Gαo-GFP rescues the defects caused by loss of endogenous Gαo in assays of egg laying and locomotion behaviors. Defects in body morphology caused by loss of Gαo are also rescued by Gαo-GFP. The Gαo-GFP protein is localized to the plasma membrane of neurons, mimicking localization of endogenous Gαo. Using GFP as an epitope tag, Gαo-GFP can be immunoprecipitated from C. elegans lysates to purify Gαo protein complexes. The Gαo-GFP transgene reported in this study enables studies involving in vivo localization and biochemical purification of Gαo to compliment the already well-developed genetic analysis of Gαo signaling.
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Affiliation(s)
- Santosh Kumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA
| | - Andrew C Olson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA
| | - Michael R Koelle
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520 USA
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31
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Tournière O, Dolan D, Richards GS, Sunagar K, Columbus-Shenkar YY, Moran Y, Rentzsch F. NvPOU4/Brain3 Functions as a Terminal Selector Gene in the Nervous System of the Cnidarian Nematostella vectensis. Cell Rep 2021; 30:4473-4489.e5. [PMID: 32234481 DOI: 10.1016/j.celrep.2020.03.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/08/2020] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
Terminal selectors are transcription factors that control the morphological, physiological, and molecular features that characterize distinct cell types. Here, we show that, in the sea anemone Nematostella vectensis, NvPOU4 is expressed in post-mitotic cells that give rise to a diverse set of neural cell types, including cnidocytes and NvElav1-expressing neurons. Morphological analyses of NvPOU4 mutants crossed to transgenic reporter lines show that the loss of NvPOU4 does not affect the initial specification of neural cells. Transcriptomes derived from the mutants and from different neural cell populations reveal that NvPOU4 is required for the execution of the terminal differentiation program of these neural cells. These findings suggest that POU4 genes have ancient functions as terminal selectors for morphologically and functionally disparate types of neurons and they provide experimental support for the relevance of terminal selectors for understanding the evolution of cell types.
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Affiliation(s)
- Océane Tournière
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
| | - David Dolan
- Computational Biology Unit, Department for Informatics, University of Bergen, 5006 Bergen, Norway
| | - Gemma Sian Richards
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway
| | - Kartik Sunagar
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel; Evolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, Bangalore 560012, India
| | - Yaara Y Columbus-Shenkar
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behaviour, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway; Department for Biological Sciences, University of Bergen, 5006 Bergen, Norway.
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32
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Yingling CV, Pruyne D. FHOD formin and SRF promote post-embryonic striated muscle growth through separate pathways in C. elegans. Exp Cell Res 2021; 398:112388. [PMID: 33221314 PMCID: PMC7750259 DOI: 10.1016/j.yexcr.2020.112388] [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: 09/21/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/28/2022]
Abstract
Previous work with cultured cells has shown transcription of muscle genes by serum response factor (SRF) can be stimulated by actin polymerization driven by proteins of the formin family. However, it is not clear if endogenous formins similarly promote SRF-dependent transcription during muscle development in vivo. We tested whether formin activity promotes SRF-dependent transcription in striated muscle in the simple animal model, Caenorhabditis elegans. Our lab has shown FHOD-1 is the only formin that directly promotes sarcomere formation in the worm's striated muscle. We show here FHOD-1 and SRF homolog UNC-120 both support muscle growth and also muscle myosin II heavy chain A expression. However, while a hypomorphic unc-120 allele blunts expression of a set of striated muscle genes, these genes are largely upregulated or unchanged by absence of FHOD-1. Instead, pharmacological inhibition of the proteasome restores myosin protein levels in worms lacking FHOD-1, suggesting elevated proteolysis accounts for their myosin deficit. Interestingly, proteasome inhibition does not restore normal muscle growth to fhod-1(Δ) mutants, suggesting formin contributes to muscle growth by some alternative mechanism. Overall, we find SRF does not depend on formin to promote muscle gene transcription in a simple in vivo system.
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Affiliation(s)
- Curtis V Yingling
- Department of Cell and Developmental Biology, 107 Weiskotten Hall, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA.
| | - David Pruyne
- Department of Cell and Developmental Biology, 107 Weiskotten Hall, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA.
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33
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Kalichamy SS, Alcantara AV, Kim BS, Park J, Yoon KH, Lee JI. Muscle and epidermal contributions of the structural protein β-spectrin promote hypergravity-induced motor neuron axon defects in C. elegans. Sci Rep 2020; 10:21214. [PMID: 33273580 PMCID: PMC7713079 DOI: 10.1038/s41598-020-78414-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/23/2020] [Indexed: 11/09/2022] Open
Abstract
Biology is adapted to Earth's gravity force, and the long-term effects of varying gravity on the development of animals is unclear. Previously, we reported that high gravity, called hypergravity, increases defects in the development of motor neuron axons in the nematode Caenorhabditis elegans. Here, we show that a mutation in the unc-70 gene that encodes the cytoskeletal β-spectrin protein suppresses hypergravity-induced axon defects. UNC-70 expression is required in both muscle and epidermis to promote the axon defects in high gravity. We reveal that the location of axon defects is correlated to the size of the muscle cell that the axon traverses. We also show that mutations that compromise key proteins of hemidesmosomal structures suppress hypergravity-induced axon defects. These hemidesmosomal structures play a crucial role in coupling mechanical force between the muscle, epidermis and the external cuticle. We speculate a model in which the rigid organization of muscle, epidermal and cuticular layers under high gravity pressure compresses the narrow axon migration pathways in the extracellular matrix hindering proper axon pathfinding of motor neurons.
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Affiliation(s)
- Saraswathi S Kalichamy
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Alfredo V Alcantara
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Ban-Seok Kim
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Junsoo Park
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea
| | - Kyoung-Hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, 26426, South Korea.
| | - Jin I Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus 304, 1 Yonseidae-gil, Wonju, Gangwon-do, 26493, South Korea.
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Sundaramurthy S, Votra S, Laszlo A, Davies T, Pruyne D. FHOD-1 is the only formin in Caenorhabditis elegans that promotes striated muscle growth and Z-line organization in a cell autonomous manner. Cytoskeleton (Hoboken) 2020; 77:422-441. [PMID: 33103378 DOI: 10.1002/cm.21639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 11/06/2022]
Abstract
The striated body wall muscles of Caenorhabditis elegans are a simple model for sarcomere assembly. Previously, we observed deletion mutants for two formin genes, fhod-1 and cyk-1, develop thin muscles with abnormal dense bodies (the sarcomere Z-line analogs). However, this work left in question whether these formins work in a muscle cell autonomous manner, particularly since cyk-1(∆) deletion has pleiotropic effects on development. Using a fast acting temperature-sensitive cyk-1(ts) mutant, we show here that neither postembryonic loss nor acute loss of CYK-1 during embryonic sarcomerogenesis cause lasting muscle defects. Furthermore, mosaic expression of CYK-1 in cyk-1(∆) mutants is unable to rescue muscle defects in a cell autonomous manner, suggesting muscle phenotypes caused by cyk-1(∆) are likely indirect. Conversely, mosaic expression of FHOD-1 in fhod-1(Δ) mutants promotes muscle cell growth and proper dense body organization in a muscle cell autonomous manner. As we observe no effect of loss of any other formin on muscle development, we conclude FHOD-1 is the only worm formin that directly promotes striated muscle development, and the effects on formin loss in C. elegans are surprisingly modest compared to other systems.
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Affiliation(s)
- Sumana Sundaramurthy
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - SarahBeth Votra
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Arianna Laszlo
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Tim Davies
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA.,Department of Biosciences, Durham University, Durham, UK
| | - David Pruyne
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA
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35
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Abstract
The regulation of gliogenesis is a fundamental process for nervous system development, as the appropriate glial number and identity is required for a functional nervous system. To investigate the molecular mechanisms involved in gliogenesis, we used C. elegans as a model and identified the function of the proneural gene lin-32/Atoh1 in gliogenesis. We found that lin-32 functions during embryonic development to negatively regulate the number of AMsh glia. The ectopic AMsh cells at least partially arise from cells originally fated to become CEPsh glia, suggesting that lin-32 is involved in the specification of specific glial subtypes. Moreover, we show that lin-32 acts in parallel with cnd-1/ NeuroD1 and ngn-1/ Neurog1 in negatively regulating an AMsh glia fate. Furthermore, expression of murine Atoh1 fully rescues lin-32 mutant phenotypes, suggesting lin-32/Atoh1 may have a conserved role in glial specification.
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36
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Coppa A, Guha S, Fourcade S, Parameswaran J, Ruiz M, Moser AB, Schlüter A, Murphy MP, Lizcano JM, Miranda-Vizuete A, Dalfó E, Pujol A. The peroxisomal fatty acid transporter ABCD1/PMP-4 is required in the C. elegans hypodermis for axonal maintenance: A worm model for adrenoleukodystrophy. Free Radic Biol Med 2020; 152:797-809. [PMID: 32017990 PMCID: PMC7611262 DOI: 10.1016/j.freeradbiomed.2020.01.177] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Adrenoleukodystrophy is a neurometabolic disorder caused by a defective peroxisomal ABCD1 transporter of very long-chain fatty acids (VLCFAs). Its pathogenesis is incompletely understood. Here we characterize a nematode model of X-ALD with loss of the pmp-4 gene, the worm orthologue of ABCD1. These mutants recapitulate the hallmarks of X-ALD: i) VLCFAs accumulation and impaired mitochondrial redox homeostasis and ii) axonal damage coupled to locomotor dysfunction. Furthermore, we identify a novel role for PMP-4 in modulating lipid droplet dynamics. Importantly, we show that the mitochondria targeted antioxidant MitoQ normalizes lipid droplets size, and prevents axonal degeneration and locomotor disability, highlighting its therapeutic potential. Moreover, PMP-4 acting solely in the hypodermis rescues axonal and locomotion abnormalities, suggesting a myelin-like role for the hypodermis in providing essential peroxisomal functions for the nematode nervous system.
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Affiliation(s)
- Andrea Coppa
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | - Sanjib Guha
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Janani Parameswaran
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | - Ann B Moser
- Peroxisomal Diseases Laboratory, Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain
| | | | - Jose Miguel Lizcano
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain
| | - Antonio Miranda-Vizuete
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío /CSIC/ Universidad de Sevilla, E-41013, Sevilla, Spain
| | - Esther Dalfó
- Departament de Bioquímica i Biologia Molecular, Institut de Neurociències, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra (Barcelona), Spain; Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), 08500, Vic, Spain.
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Spain; CIBERER U759, Center for Biomedical Research on Rare Diseases, Spain; ICREA (Institució Catalana de Recerca i Estudis Avançats), Barcelona, Spain.
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Yu CC(J, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES. Expansion microscopy of C. elegans. eLife 2020; 9:e46249. [PMID: 32356725 PMCID: PMC7195193 DOI: 10.7554/elife.46249] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
We recently developed expansion microscopy (ExM), which achieves nanoscale-precise imaging of specimens at ~70 nm resolution (with ~4.5x linear expansion) by isotropic swelling of chemically processed, hydrogel-embedded tissue. ExM of C. elegans is challenged by its cuticle, which is stiff and impermeable to antibodies. Here we present a strategy, expansion of C. elegans (ExCel), to expand fixed, intact C. elegans. ExCel enables simultaneous readout of fluorescent proteins, RNA, DNA location, and anatomical structures at resolutions of ~65-75 nm (3.3-3.8x linear expansion). We also developed epitope-preserving ExCel, which enables imaging of endogenous proteins stained by antibodies, and iterative ExCel, which enables imaging of fluorescent proteins after 20x linear expansion. We demonstrate the utility of the ExCel toolbox for mapping synaptic proteins, for identifying previously unreported proteins at cell junctions, and for gene expression analysis in multiple individual neurons of the same animal.
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Affiliation(s)
- Chih-Chieh (Jay) Yu
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nicholas C Barry
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Asmamaw T Wassie
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Anubhav Sinha
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia UniversityNew YorkUnited States
| | - Shoh Asano
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chi Zhang
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Fei Chen
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia UniversityNew YorkUnited States
| | - Miriam B Goodman
- Department of Molecular and Cellular Physiology, Stanford UniversityStanfordUnited States
| | - Gal Haspel
- Federated Department of Biological Sciences, New Jersey Institute of Technology and Rutgers University-NewarkNewarkUnited States
- The Brain Research Institute, New Jersey Institute of TechnologyNewarkUnited States
| | - Edward S Boyden
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridgeUnited States
- Media Lab, Massachusetts Institute of TechnologyCambridgeUnited States
- McGovern Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Koch Institute, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Brain and Cognitive Sciences, Massachusetts Institute of TechnologyCambridgeUnited States
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38
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Leyva-Díaz E, Masoudi N, Serrano-Saiz E, Glenwinkel L, Hobert O. Brn3/POU-IV-type POU homeobox genes-Paradigmatic regulators of neuronal identity across phylogeny. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 9:e374. [PMID: 32012462 DOI: 10.1002/wdev.374] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/18/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
One approach to understand the construction of complex systems is to investigate whether there are simple design principles that are commonly used in building such a system. In the context of nervous system development, one may ask whether the generation of its highly diverse sets of constituents, that is, distinct neuronal cell types, relies on genetic mechanisms that share specific common features. Specifically, are there common patterns in the function of regulatory genes across different neuron types and are those regulatory mechanisms not only used in different parts of one nervous system, but are they conserved across animal phylogeny? We address these questions here by focusing on one specific, highly conserved and well-studied regulatory factor, the POU homeodomain transcription factor UNC-86. Work over the last 30 years has revealed a common and paradigmatic theme of unc-86 function throughout most of the neuron types in which Caenorhabditis elegans unc-86 is expressed. Apart from its role in preventing lineage reiterations during development, UNC-86 operates in combination with distinct partner proteins to initiate and maintain terminal differentiation programs, by coregulating a vast array of functionally distinct identity determinants of specific neuron types. Mouse orthologs of unc-86, the Brn3 genes, have been shown to fulfill a similar function in initiating and maintaining neuronal identity in specific parts of the mouse brain and similar functions appear to be carried out by the sole Drosophila ortholog, Acj6. The terminal selector function of UNC-86 in many different neuron types provides a paradigm for neuronal identity regulation across phylogeny. This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Invertebrate Organogenesis > Worms Nervous System Development > Vertebrates: Regional Development.
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Affiliation(s)
- Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | | | - Lori Glenwinkel
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York
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Suresh A, Wightman B. The daf-2 insulin receptor functions in C. elegans embryo elongation. MICROPUBLICATION BIOLOGY 2020; 2020:10.17912/micropub.biology.000117. [PMID: 32550500 PMCID: PMC7252343 DOI: 10.17912/micropub.biology.000117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Annu Suresh
- Biology Department, Muhlenberg College, 2400 Chew St., Allentown, PA 18104 USA
| | - Bruce Wightman
- Biology Department, Muhlenberg College, 2400 Chew St., Allentown, PA 18104 USA,
Correspondence to: Bruce Wightman ()
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40
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Haupt KA, Law KT, Enright AL, Kanzler CR, Shin H, Wickens M, Kimble J. A PUF Hub Drives Self-Renewal in Caenorhabditis elegans Germline Stem Cells. Genetics 2020; 214:147-161. [PMID: 31740451 PMCID: PMC6944405 DOI: 10.1534/genetics.119.302772] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/05/2019] [Indexed: 01/12/2023] Open
Abstract
Stem cell regulation relies on extrinsic signaling from a niche plus intrinsic factors that respond and drive self-renewal within stem cells. A priori, loss of niche signaling and loss of the intrinsic self-renewal factors might be expected to have equivalent stem cell defects. Yet this simple prediction has not been borne out for most stem cells, including Caenorhabditis elegans germline stem cells (GSCs). The central regulators of C. elegans GSCs include extrinsically acting GLP-1/Notch signaling from the niche; intrinsically acting RNA-binding proteins in the PUF family, termed FBF-1 and FBF-2 (collectively FBF); and intrinsically acting PUF partner proteins that are direct Notch targets. Abrogation of either GLP-1/Notch signaling or its targets yields an earlier and more severe GSC defect than loss of FBF-1 and FBF-2, suggesting that additional intrinsic regulators must exist. Here, we report that those missing regulators are two additional PUF proteins, PUF-3 and PUF-11 Remarkably, an fbf-1fbf-2 ; puf-3puf-11 quadruple null mutant has a GSC defect virtually identical to that of a glp-1/Notch null mutant. PUF-3 and PUF-11 both affect GSC maintenance, both are expressed in GSCs, and epistasis experiments place them at the same position as FBF within the network. Therefore, action of PUF-3 and PUF-11 explains the milder GSC defect in fbf-1fbf-2 mutants. We conclude that a "PUF hub," comprising four PUF proteins and two PUF partners, constitutes the intrinsic self-renewal node of the C. elegans GSC RNA regulatory network. Discovery of this hub underscores the significance of PUF RNA-binding proteins as key regulators of stem cell maintenance.
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Affiliation(s)
- Kimberly A Haupt
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Kimberley T Law
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Amy L Enright
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Charlotte R Kanzler
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
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41
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Abstract
The nematode C. elegans is a useful model organism for studying neuronal development and function due to its extremely simple, well-defined nervous system, translucence, short life cycle, and abundance of genetic tools (WormBase. http://wormbase.org , 2018; WormBook. The C. elegans Research Community. http://www.wormbook.org , 2018). Due to the relative ease of genetic transformation, the majority of studies in C. elegans use transgenes (e.g., green fluorescent proteins) to assess the expression and distribution of specific proteins. In addition, large-scale in situ hybridization studies have described the distribution of mRNAs for thousands of genes throughout development. However, there may be qualitative and quantitative differences between expression of transgenic markers and the endogenous protein. Specific antibodies can be difficult to generate, but once generated antibodies can be used to study protein function and changes in expression and localization during development. Thus, genetic tools and immunohistochemistry are complementary techniques for studying cellular and developmental processes in C. elegans. Protocols for immunostaining in C. elegans are similar to those in other organisms; however, some features of these nematodes provide unique challenges. These include difficulties with antibody generation and access to the nervous system through the cuticle. This chapter describes a basic immunostaining technique that works in C. elegans for a variety of neural antigens in all stages of development to use in conjunction with the many tools available in this simple animal.
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RIMB-1/RIM-Binding Protein and UNC-10/RIM Redundantly Regulate Presynaptic Localization of the Voltage-Gated Calcium Channel in Caenorhabditis elegans. J Neurosci 2019; 39:8617-8631. [PMID: 31530643 DOI: 10.1523/jneurosci.0506-19.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 11/21/2022] Open
Abstract
Presynaptic active zones (AZs) contain many molecules essential for neurotransmitter release and are assembled in a highly organized manner. A network of adaptor proteins known as cytomatrix at the AZ (CAZ) is important for shaping the structural characteristics of AZ. Rab3-interacting molecule (RIM)-binding protein (RBP) family are binding partners of the CAZ protein RIM and also bind the voltage-gated calcium channels (VGCCs) in mice and flies. Here, we investigated the physiological roles of RIMB-1, the homolog of RBPs in the nematode Caenorhabditis elegans RIMB-1 is expressed broadly in neurons and predominantly localized at presynaptic sites. Loss-of-function animals of rimb-1 displayed slight defects in motility and response to pharmacological inhibition of synaptic transmission, suggesting a modest involvement of rimb-1 in synapse function. We analyzed genetic interactions of rimb-1 by testing candidate genes and by an unbiased forward genetic screen for rimb-1 enhancer. Both analyses identified the RIM homolog UNC-10 that acts together with RIMB-1 to regulate presynaptic localization of the P/Q-type VGCC UNC-2/Cav2. We also find that the precise localization of RIMB-1 to presynaptic sites requires presynaptic UNC-2/Cav2. RIMB-1 has multiple FN3 and SH3 domains. Our transgenic rescue analysis with RIMB-1 deletion constructs revealed a functional requirement of a C-terminal SH3 in regulating UNC-2/Cav2 localization. Together, these findings suggest a redundant role of RIMB-1/RBP and UNC-10/RIM to regulate the abundance of UNC-2/Cav2 at the presynaptic AZ in C. elegans, depending on the bidirectional interplay between CAZ adaptor and channel proteins.SIGNIFICANCE STATEMENT Presynaptic active zones (AZs) are highly organized structures for synaptic transmission with characteristic networks of adaptor proteins called cytomatrix at the AZ (CAZ). In this study, we characterized a CAZ protein RIMB-1, named for RIM-binding protein (RBP), in the nematode Caenorhabditis elegans Through systematic analyses of genetic interactions and an unbiased genetic enhancer screen of rimb-1, we revealed a redundant role of two CAZ proteins RIMB-1/RBP and UNC-10/RIM in regulating presynaptic localization of UNC-2/Cav2, a voltage-gated calcium channel (VGCC) critical for proper neurotransmitter release. Additionally, the precise localization of RIMB-1/RBP requires presynaptic UNC-2/Cav2. These findings provide new mechanistic insight about how the interplay among multiple CAZ adaptor proteins and VGCC contributes to the organization of presynaptic AZ.
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Loer C, Witte H, Sommer R, Hobert O. An antibody staining protocol variation for nematodes that adds heat-induced antigen retrieval (HIAR). MICROPUBLICATION BIOLOGY 2019; 2019. [PMID: 32550428 PMCID: PMC7252300 DOI: 10.17912/micropub.biology.000135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Curtis Loer
- Department of Biology, University of San Diego, CA, USA.,Department of Biological Sciences, HHMI, Columbia University, NY, USA [CL, while visiting scholar on sabbatical]
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ralf Sommer
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Hobert
- Department of Biological Sciences, HHMI, Columbia University, NY, USA [CL, while visiting scholar on sabbatical]
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Lee J, Taylor CA, Barnes KM, Shen A, Stewart EV, Chen A, Xiang YK, Bao Z, Shen K. A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes. eLife 2019; 8:e46703. [PMID: 31386623 PMCID: PMC6684318 DOI: 10.7554/elife.46703] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
Cellular differentiation requires both activation of target cell transcriptional programs and repression of non-target cell programs. The Myt1 family of zinc finger transcription factors contributes to fibroblast to neuron reprogramming in vitro. Here, we show that ztf-11 (Zinc-finger Transcription Factor-11), the sole Caenorhabditis elegans Myt1 homolog, is required for neurogenesis in multiple neuronal lineages from previously differentiated epithelial cells, including a neuron generated by a developmental epithelial-to-neuronal transdifferentiation event. ztf-11 is exclusively expressed in all neuronal precursors with remarkable specificity at single-cell resolution. Loss of ztf-11 leads to upregulation of non-neuronal genes and reduced neurogenesis. Ectopic expression of ztf-11 in epidermal lineages is sufficient to produce additional neurons. ZTF-11 functions together with the MuvB corepressor complex to suppress the activation of non-neuronal genes in neurons. These results dovetail with the ability of Myt1l (Myt1-like) to drive neuronal transdifferentiation in vitro in vertebrate systems. Together, we identified an evolutionarily conserved mechanism to specify neuronal cell fate by repressing non-neuronal genes.
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Affiliation(s)
- Joo Lee
- Department of BiochemistryStanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Caitlin A Taylor
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Ao Shen
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | | | - Allison Chen
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Yang K Xiang
- Department of PharmacologyUniversity of California, DavisDavisUnited States
| | - Zhirong Bao
- Developmental Biology ProgramSloan-Kettering InstituteNew YorkUnited States
| | - Kang Shen
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
- Department of BiologyStanford UniversityStanfordUnited States
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Zheng C, Jin FQ, Trippe BL, Wu J, Chalfie M. Inhibition of cell fate repressors secures the differentiation of the touch receptor neurons of Caenorhabditis elegans. Development 2018; 145:dev.168096. [PMID: 30291162 DOI: 10.1242/dev.168096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/24/2018] [Indexed: 12/14/2022]
Abstract
Terminal differentiation generates the specialized features and functions that allow postmitotic cells to acquire their distinguishing characteristics. This process is thought to be controlled by transcription factors called 'terminal selectors' that directly activate a set of downstream effector genes. In Caenorhabditis elegans, the differentiation of both the mechanosensory touch receptor neurons (TRNs) and the multidendritic nociceptor FLP neurons uses the terminal selectors UNC-86 and MEC-3. The FLP neurons fail to activate TRN genes, however, because a complex of two transcriptional repressors (EGL-44/EGL-46) prevents their expression. Here, we show that the ZEB family transcriptional factor ZAG-1 promotes TRN differentiation not by activating TRN genes but by preventing the expression of EGL-44/EGL-46. As EGL-44/EGL-46 also inhibits the production of ZAG-1, these proteins form a bistable, negative-feedback loop that regulates the choice between the two neuronal fates.
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Affiliation(s)
- Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Felix Qiaochu Jin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Brian Loeber Trippe
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ji Wu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Martin Chalfie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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46
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Serrano-Saiz E, Leyva-Díaz E, De La Cruz E, Hobert O. BRN3-type POU Homeobox Genes Maintain the Identity of Mature Postmitotic Neurons in Nematodes and Mice. Curr Biol 2018; 28:2813-2823.e2. [PMID: 30146154 DOI: 10.1016/j.cub.2018.06.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 06/08/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022]
Abstract
Many distinct regulatory factors have been shown to be required for the proper initiation of neuron-type-specific differentiation programs, but much less is known about the regulatory programs that maintain the differentiated state in the adult [1-3]. One possibility is that regulatory factors that initiate a terminal differentiation program during development are continuously required to maintain the differentiated state. Here, we test this hypothesis by investigating the function of two orthologous POU homeobox genes in nematodes and mice. The C. elegans POU homeobox gene unc-86 is a terminal selector that is required during development to initiate the terminal differentiation program of several distinct neuron classes [4-13]. Through post-developmental removal of unc-86 activity, we show here that unc-86 is also continuously required throughout the life of many neuron classes to maintain neuron-class-specific identity features. Similarly, the mouse unc-86 ortholog Brn3a/POU4F1 has been shown to control the initiation of the terminal differentiation program of distinct neuron types across the mouse brain, such as the medial habenular neurons [14-20]. By conditionally removing Brn3a in the adult mouse central nervous system, we show that, like its invertebrate ortholog unc-86, Brn3a is also required for the maintenance of terminal identity features of medial habenular neurons. In addition, Brn3a is required for the survival of these neurons, indicating that identity maintenance and survival are genetically linked. We conclude that the continuous expression of transcription factors is essential for the active maintenance of the differentiated state of a neuron across phylogeny.
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Affiliation(s)
- Esther Serrano-Saiz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Estanislao De La Cruz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
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Yuan S, Sharma AK, Richart A, Lee J, Kim BE. CHCA-1 is a copper-regulated CTR1 homolog required for normal development, copper accumulation, and copper-sensing behavior in Caenorhabditis elegans. J Biol Chem 2018; 293:10911-10925. [PMID: 29784876 DOI: 10.1074/jbc.ra118.003503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 01/11/2023] Open
Abstract
Copper plays key roles in catalytic and regulatory biochemical reactions essential for normal growth, development, and health. Dietary copper deficiencies or mutations in copper homeostasis genes can lead to abnormal musculoskeletal development, cognitive disorders, and poor growth. In yeast and mammals, copper is acquired through the activities of the CTR1 family of high-affinity copper transporters. However, the mechanisms of systemic responses to dietary or tissue-specific copper deficiency remain unclear. Here, taking advantage of the animal model Caenorhabditis elegans for studying whole-body copper homeostasis, we investigated the role of a C. elegans CTR1 homolog, CHCA-1, in copper acquisition and in worm growth, development, and behavior. Using sequence homology searches, we identified 10 potential orthologs to mammalian CTR1 Among these genes, we found that chca-1, which is transcriptionally up-regulated in the intestine and hypodermis of C. elegans during copper deficiency, is required for normal growth, reproduction, and maintenance of systemic copper balance under copper deprivation. The intestinal copper transporter CUA-1 normally traffics to endosomes to sequester excess copper, and we found here that loss of chca-1 caused CUA-1 to mislocalize to the basolateral membrane under copper overload conditions. Moreover, animals lacking chca-1 exhibited significantly reduced copper avoidance behavior in response to toxic copper conditions compared with WT worms. These results establish that CHCA-1-mediated copper acquisition in C. elegans is crucial for normal growth, development, and copper-sensing behavior.
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Affiliation(s)
- Sai Yuan
- From the Department of Animal and Avian Sciences and
| | | | | | - Jaekwon Lee
- the Redox Biology Center, Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Byung-Eun Kim
- From the Department of Animal and Avian Sciences and .,Biological Sciences Graduate Program, University of Maryland, College Park, Maryland 20742 and
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48
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Barnes DE, Watabe E, Ono K, Kwak E, Kuroyanagi H, Ono S. Tropomyosin isoforms differentially affect muscle contractility in the head and body regions of the nematode Caenorhabditis elegans. Mol Biol Cell 2018; 29:1075-1088. [PMID: 29496965 PMCID: PMC5921574 DOI: 10.1091/mbc.e17-03-0152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 11/11/2022] Open
Abstract
Tropomyosin, one of the major actin filament-binding proteins, regulates actin-myosin interaction and actin-filament stability. Multicellular organisms express a number of tropomyosin isoforms, but understanding of isoform-specific tropomyosin functions is incomplete. The nematode Caenorhabditis elegans has a single tropomyosin gene, lev-11, which has been reported to express four isoforms by using two separate promoters and alternative splicing. Here, we report a fifth tropomyosin isoform, LEV-11O, which is produced by alternative splicing that includes a newly identified seventh exon, exon 7a. By visualizing specific splicing events in vivo, we find that exon 7a is predominantly selected in a subset of the body wall muscles in the head, while exon 7b, which is the alternative to exon 7a, is utilized in the rest of the body. Point mutations in exon 7a and exon 7b cause resistance to levamisole--induced muscle contraction specifically in the head and the main body, respectively. Overexpression of LEV-11O, but not LEV-11A, in the main body results in weak levamisole resistance. These results demonstrate that specific tropomyosin isoforms are expressed in the head and body regions of the muscles and contribute differentially to the regulation of muscle contractility.
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Affiliation(s)
- Dawn E. Barnes
- Department of Pathology, Department of Cell Biology, and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | - Eichi Watabe
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kanako Ono
- Department of Pathology, Department of Cell Biology, and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | - Euiyoung Kwak
- Department of Pathology, Department of Cell Biology, and Winship Cancer Institute, Emory University, Atlanta, GA 30322
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Shoichiro Ono
- Department of Pathology, Department of Cell Biology, and Winship Cancer Institute, Emory University, Atlanta, GA 30322
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Lloret-Fernández C, Maicas M, Mora-Martínez C, Artacho A, Jimeno-Martín Á, Chirivella L, Weinberg P, Flames N. A transcription factor collective defines the HSN serotonergic neuron regulatory landscape. eLife 2018; 7:32785. [PMID: 29553368 PMCID: PMC5916565 DOI: 10.7554/elife.32785] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/16/2018] [Indexed: 01/02/2023] Open
Abstract
Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis-regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in Caenorhabditis elegans. Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers. Among C. elegans neurons, the HSN transcriptome most closely resembles that of mouse serotonergic neurons. Mouse orthologs of the HSN TF collective also regulate serotonergic differentiation and can functionally substitute for their worm counterparts which suggests deep homology. Our results identify rules governing the regulatory landscape of a critically important neuronal type in two species separated by over 700 million years.
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Affiliation(s)
- Carla Lloret-Fernández
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Miren Maicas
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Carlos Mora-Martínez
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Alejandro Artacho
- Departamento de Genómica y Salud, Centro Superior de Investigación en Salud Pública, FISABIO, Valencia, Spain
| | - Ángela Jimeno-Martín
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Laura Chirivella
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
| | - Peter Weinberg
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University Medical Center, New York, United States
| | - Nuria Flames
- Developmental Neurobiology Unit, Instituto de Biomedicina de Valencia IBV-CSIC, Valencia, Spain
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50
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Inter-organ signalling by HRG-7 promotes systemic haem homeostasis. Nat Cell Biol 2017; 19:799-807. [PMID: 28581477 PMCID: PMC5594749 DOI: 10.1038/ncb3539] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 04/27/2017] [Indexed: 12/17/2022]
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