1
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Wang C, Vidal B, Sural S, Loer C, Aguilar GR, Merritt DM, Toker IA, Vogt MC, Cros C, Hobert O. A neurotransmitter atlas of C. elegans males and hermaphrodites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.24.573258. [PMID: 38895397 PMCID: PMC11185579 DOI: 10.1101/2023.12.24.573258] [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
Mapping neurotransmitter identities to neurons is key to understanding information flow in a nervous system. It also provides valuable entry points for studying the development and plasticity of neuronal identity features. In the C. elegans nervous system, neurotransmitter identities have been largely assigned by expression pattern analysis of neurotransmitter pathway genes that encode neurotransmitter biosynthetic enzymes or transporters. However, many of these assignments have relied on multicopy reporter transgenes that may lack relevant cis-regulatory information and therefore may not provide an accurate picture of neurotransmitter usage. We analyzed the expression patterns of 16 CRISPR/Cas9-engineered knock-in reporter strains for all main types of neurotransmitters in C. elegans (glutamate, acetylcholine, GABA, serotonin, dopamine, tyramine, and octopamine) in both the hermaphrodite and the male. Our analysis reveals novel sites of expression of these neurotransmitter systems within both neurons and glia, as well as non-neural cells. The resulting expression atlas defines neurons that may be exclusively neuropeptidergic, substantially expands the repertoire of neurons capable of co-transmitting multiple neurotransmitters, and identifies novel neurons that uptake monoaminergic neurotransmitters. Furthermore, we also observed unusual co-expression patterns of monoaminergic synthesis pathway genes, suggesting the existence of novel monoaminergic transmitters. Our analysis results in what constitutes the most extensive whole-animal-wide map of neurotransmitter usage to date, paving the way for a better understanding of neuronal communication and neuronal identity specification in C. elegans.
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Affiliation(s)
- Chen Wang
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Berta Vidal
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Surojit Sural
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Curtis Loer
- Department of Biology, University of San Diego, San Diego, California, USA
| | - G. Robert Aguilar
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Daniel M. Merritt
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Itai Antoine Toker
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Merly C. Vogt
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Cyril Cros
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, USA
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2
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Kramer TS, Flavell SW. Building and integrating brain-wide maps of nervous system function in invertebrates. Curr Opin Neurobiol 2024; 86:102868. [PMID: 38569231 DOI: 10.1016/j.conb.2024.102868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/13/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
The selection and execution of context-appropriate behaviors is controlled by the integrated action of neural circuits throughout the brain. However, how activity is coordinated across brain regions, and how nervous system structure enables these functional interactions, remain open questions. Recent technical advances have made it feasible to build brain-wide maps of nervous system structure and function, such as brain activity maps, connectomes, and cell atlases. Here, we review recent progress in this area, focusing on C. elegans and D. melanogaster, as recent work has produced global maps of these nervous systems. We also describe neural circuit motifs elucidated in studies of specific networks, which highlight the complexities that must be captured to build accurate models of whole-brain function.
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Affiliation(s)
- Talya S Kramer
- Picower Institute for Learning and Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA; MIT Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven W Flavell
- Picower Institute for Learning and Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Cheng H, Chen D, Li X, Al-Sheikh U, Duan D, Fan Y, Zhu L, Zeng W, Hu Z, Tong X, Zhao G, Zhang Y, Zou W, Duan S, Kang L. Phasic/tonic glial GABA differentially transduce for olfactory adaptation and neuronal aging. Neuron 2024; 112:1473-1486.e6. [PMID: 38447577 DOI: 10.1016/j.neuron.2024.02.006] [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: 05/05/2023] [Revised: 11/11/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Phasic (fast) and tonic (sustained) inhibition of γ-aminobutyric acid (GABA) are fundamental for regulating day-to-day activities, neuronal excitability, and plasticity. However, the mechanisms and physiological functions of glial GABA transductions remain poorly understood. Here, we report that the AMsh glia in Caenorhabditis elegans exhibit both phasic and tonic GABAergic signaling, which distinctively regulate olfactory adaptation and neuronal aging. Through genetic screening, we find that GABA permeates through bestrophin-9/-13/-14 anion channels from AMsh glia, which primarily activate the metabolic GABAB receptor GBB-1 in the neighboring ASH sensory neurons. This tonic action of glial GABA regulates the age-associated changes of ASH neurons and olfactory responses via a conserved signaling pathway, inducing neuroprotection. In addition, the calcium-evoked, vesicular glial GABA release acts upon the ionotropic GABAA receptor LGC-38 in ASH neurons to regulate olfactory adaptation. These findings underscore the fundamental significance of glial GABA in maintaining healthy aging and neuronal stability.
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Affiliation(s)
- Hankui Cheng
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Du Chen
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Xiao Li
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Umar Al-Sheikh
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Duo Duan
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Yuedan Fan
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Linhui Zhu
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Wanxin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhitao Hu
- Department of Neuroscience, City University of Hong Kong, Kowloon, China
| | - Xiajing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guohua Zhao
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Yongming Zhang
- Department of Ophthalmology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
| | - Wenjuan Zou
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Shumin Duan
- MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China
| | - Lijun Kang
- Department of Neurology of the Fourth Affiliated Hospital and School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Yiwu 322000, China; MOE Frontier Science Center for Brain Science and Brain machine Integration, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310053, China.
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Jiang L, Yu Z, Zhao Y, Yin D. Obesogenic potentials of environmental artificial sweeteners with disturbances on both lipid metabolism and neural responses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170755. [PMID: 38340820 DOI: 10.1016/j.scitotenv.2024.170755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Artificial sweeteners (ASs) entered the environments after application and emissions. Recent studies showed that some ASs had obesogenic risks. However, it remained unclear whether such risks are common and how they provoke such effects. Presently, the effects of 8 widely used ASs on lipid accumulation were measured in Caenorhabditis elegans. Potential mechanisms were explored with feeding and locomotion behavior, lipid metabolism and neural regulation. Results showed that acesulfame (ACE), aspartame (ASP), saccharin sodium (SOD), sucralose (SUC) and cyclamate (CYC) stimulated lipid accumulation at μg/L levels, showing obesogenic potentials. Behavior investigation showed that ACE, ASP, SOD, SUC and CYC biased more feeding in the energy intake aspect against the locomotion in the energy consumption one. Neotame (NEO), saccharin (SAC) and alitame (ALT) reduced the lipid accumulation without significant obesogenic potentials in the present study. However, all 8 ASs commonly disturbed enzymes (e.g., acetyl-CoA carboxylase) in lipogenesis and those (e.g., carnitine palmitoyl transferase) in lipolysis. In addition, ASs disturbed PPARγ (via expressions of nhr-49), TGF-β/DAF-7 (daf-7) and SREBP (sbp-1) pathways. Moreover, they also interfered neurotransmitters including serotonin (5-HT), dopamine (DA) and acetylcholine (ACh), with influences in Gsα (e.g., via expressions of gsα-1, ser-7), glutamate (e.g., mgl-1), and cGMP-dependent signaling pathways (e.g., egl-4). In summary, environmental ASs commonly disturbed neural regulation connecting behavior and lipid metabolism, and 5 out of 8 showed clear obesogenic potentials. ENVIRONMENTAL IMPLICATION: Artificial sweeteners (ASs) are become emerging pollutants after wide application and continuous emission. Recent studies showed that some environmental ASs had obesogenic risks. The present study employed Caenorhabditis elegans to explore the influences of 8 commonly used ASs on lipid metabolisms and also the underlying mechanisms. Five out of 8 ASs stimulated lipid accumulation at μg/L levels, and they biased energy intake against energy consumption. The other three ASs reduced the lipid accumulation. ASs commonly disturbed lipogenesis and lipolysis via PPARγ, TGF-β and SREBP pathways, and also influenced neurotransmitters with Gsα, glutamate and cGMP-dependent signaling pathways.
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Affiliation(s)
- Linhong Jiang
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
| | - Zhenyang Yu
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China.
| | - Yanbin Zhao
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China; School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Daqiang Yin
- State Key Laboratory of Pollution Control and Resource Reuse, Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, PR China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, PR China
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5
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Britz S, Luccardini C, Markert SM, Merrill SA, Bessereau JL, Stigloher C. Array tomography of in vivo labeled synaptic receptors. Methods Cell Biol 2024; 187:139-174. [PMID: 38705623 DOI: 10.1016/bs.mcb.2024.02.029] [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: 05/07/2024]
Abstract
Array tomography (AT) allows one to localize sub-cellular components within the structural context of cells in 3D through the imaging of serial sections. Using this technique, the z-resolution can be improved physically by cutting ultra-thin sections. Nevertheless, conventional immunofluorescence staining of those sections is time consuming and requires relatively large amounts of costly antibody solutions. Moreover, epitopes are only readily accessible at the section's surface, leaving the volume of the serial sections unlabeled. Localization of receptors at neuronal synapses in 3D in their native cellular ultrastructural context is important for understanding signaling processes. Here, we present in vivo labeling of receptors via fluorophore-coupled tags in combination with super-resolution AT. We present two workflows where we label receptors at the plasma membrane: first, in vivo labeling via microinjection with a setup consisting of readily available components and self-manufactured microscope table equipment and second, live receptor labeling by using a cell-permeable tag. To take advantage of a near-to-native preservation of tissues for subsequent scanning electron microscopy (SEM), we also apply high-pressure freezing and freeze substitution. The advantages and disadvantages of our workflows are discussed.
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Affiliation(s)
- Sebastian Britz
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany.
| | - Camilla Luccardini
- Centre d'Imagerie Quantitative Lyon Est (CIQLE), SFR Santé Lyon-Est CNRS UAR3453-INSERM US7, Université Claude Bernard Lyon 1, Lyon, France
| | - Sebastian M Markert
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany
| | - Sean A Merrill
- Department of Biology, University of Utah, Salt Lake City, UT, United States
| | - Jean-Louis Bessereau
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5284, INSERM U-1314, MeLiS, Institut NeuroMyoGene, Lyon, France
| | - Christian Stigloher
- Imaging Core Facility, Theodor-Boveri-Institute, Biocenter of the Julius-Maximilians-Universität Würzburg (JMU), Würzburg, Germany.
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6
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior. EMBO J 2024; 43:956-992. [PMID: 38360995 PMCID: PMC10943081 DOI: 10.1038/s44318-024-00049-w] [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: 09/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
While most glial cell types in the central nervous system (CNS) arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which envelop the brain neuropil and separate it from the circulatory system cavity. Transcriptome analysis shows that GLR glia combine astrocytic and endothelial characteristics, which are relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor also expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, the UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and promotes salt-induced paralysis, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neuronal differentiation, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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Affiliation(s)
- Nikolaos Stefanakis
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Jessica Jiang
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yupu Liang
- Research Bioinformatics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Alexion Pharmaceuticals, Boston, MA, 02135, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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7
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Correa E, Mialon M, Cizeron M, Bessereau JL, Pinan-Lucarre B, Kratsios P. UNC-30/PITX coordinates neurotransmitter identity with postsynaptic GABA receptor clustering. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580278. [PMID: 38405977 PMCID: PMC10888783 DOI: 10.1101/2024.02.14.580278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Terminal selectors are transcription factors that control neuronal identity by regulating the expression of key effector molecules, such as neurotransmitter (NT) biosynthesis proteins, ion channels and neuropeptides. Whether and how terminal selectors control neuronal connectivity is poorly understood. Here, we report that UNC-30 (PITX2/3), the terminal selector of GABA motor neuron identity in C. elegans , is required for NT receptor clustering, a hallmark of postsynaptic differentiation. Animals lacking unc-30 or madd-4B, the short isoform of the MN-secreted synapse organizer madd-4 ( Punctin/ADAMTSL ), display severe GABA receptor type A (GABA A R) clustering defects in postsynaptic muscle cells. Mechanistically, UNC-30 acts directly to induce and maintain transcription of madd-4B and GABA biosynthesis genes (e.g., unc-25/GAD , unc-47/VGAT ). Hence, UNC-30 controls GABA A R clustering on postsynaptic muscle cells and GABA biosynthesis in presynaptic cells, transcriptionally coordinating two critical processes for GABA neurotransmission. Further, we uncover multiple target genes and a dual role for UNC-30 both as an activator and repressor of gene transcription. Our findings on UNC-30 function may contribute to our molecular understanding of human conditions, such as Axenfeld-Rieger syndrome, caused by PITX2 and PITX3 gene mutations.
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Weishaupt AK, Lamann K, Tallarek E, Pezacki AT, Matier CD, Schwerdtle T, Aschner M, Chang CJ, Stürzenbaum SR, Bornhorst J. Dysfunction in atox-1 and ceruloplasmin alters labile Cu levels and consequently Cu homeostasis in C. elegans. Front Mol Biosci 2024; 11:1354627. [PMID: 38389896 PMCID: PMC10882093 DOI: 10.3389/fmolb.2024.1354627] [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: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Copper (Cu) is an essential trace element, however an excess is toxic due to its redox properties. Cu homeostasis therefore needs to be tightly regulated via cellular transporters, storage proteins and exporters. An imbalance in Cu homeostasis has been associated with neurodegenerative disorders such as Wilson's disease, but also Alzheimer's or Parkinson's disease. In our current study, we explored the utility of using Caenorhabditis elegans (C. elegans) as a model of Cu dyshomeostasis. The application of excess Cu dosing and the use of mutants lacking the intracellular Cu chaperone atox-1 and major Cu storage protein ceruloplasmin facilitated the assessment of Cu status, functional markers including total Cu levels, labile Cu levels, Cu distribution and the gene expression of homeostasis-related genes. Our data revealed a decrease in total Cu uptake but an increase in labile Cu levels due to genetic dysfunction, as well as altered gene expression levels of Cu homeostasis-associated genes. In addition, the data uncovered the role ceruloplasmin and atox-1 play in the worm's Cu homeostasis. This study provides insights into suitable functional Cu markers and Cu homeostasis in C. elegans, with a focus on labile Cu levels, a promising marker of Cu dysregulation during disease progression.
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Affiliation(s)
- Ann-Kathrin Weishaupt
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
| | | | | | - Aidan T Pezacki
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Carson D Matier
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Tanja Schwerdtle
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
- German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Christopher J Chang
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Stephen R Stürzenbaum
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Julia Bornhorst
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany
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9
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Moreira P, Papatheodorou P, Deng S, Gopal S, Handley A, Powell DR, Pocock R. Nuclear factor Y is a pervasive regulator of neuronal gene expression. Cell Rep 2023; 42:113582. [PMID: 38096055 DOI: 10.1016/j.celrep.2023.113582] [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: 02/12/2023] [Revised: 10/12/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
Nervous system function relies on the establishment of complex gene expression programs that provide neuron-type-specific and core pan-neuronal features. These complementary regulatory paradigms are controlled by terminal selector and parallel-acting transcription factors (TFs), respectively. Here, we identify the nuclear factor Y (NF-Y) TF as a pervasive direct and indirect regulator of both neuron-type-specific and pan-neuronal gene expression. Mapping global NF-Y targets reveals direct binding to the cis-regulatory regions of pan-neuronal genes and terminal selector TFs. We show that NFYA-1 controls pan-neuronal gene expression directly through binding to CCAAT boxes in target gene promoters and indirectly by regulating the expression of terminal selector TFs. Further, we find that NFYA-1 regulation of neuronal gene expression is important for neuronal activity and motor function. Thus, our research sheds light on how global neuronal gene expression programs are buffered through direct and indirect regulatory mechanisms.
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Affiliation(s)
- Pedro Moreira
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Paul Papatheodorou
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Shuer Deng
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Sandeep Gopal
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Ava Handley
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Melbourne, VIC 3800, Australia
| | - Roger Pocock
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia.
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10
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Stefanakis N, Jiang J, Liang Y, Shaham S. LET-381/FoxF and UNC-30/Pitx2 control the development of C. elegans mesodermal glia that regulate motor behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563501. [PMID: 37961181 PMCID: PMC10634723 DOI: 10.1101/2023.10.23.563501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
While most CNS glia arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which ensheath the brain neuropil and separate it from the circulatory-system cavity. Transcriptome analysis suggests GLR glia merge astrocytic and endothelial characteristics relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naïve cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and induces salt hypersensitivity, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neurons, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
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11
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Huang YC, Luo J, Huang W, Baker CM, Gomes MA, Meng B, Byrne AB, Flavell SW. A single neuron in C. elegans orchestrates multiple motor outputs through parallel modes of transmission. Curr Biol 2023; 33:4430-4445.e6. [PMID: 37769660 PMCID: PMC10860333 DOI: 10.1016/j.cub.2023.08.088] [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: 03/15/2023] [Revised: 07/24/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
Animals generate a wide range of highly coordinated motor outputs, which allows them to execute purposeful behaviors. Individual neurons in the circuits that generate behaviors have a remarkable capacity for flexibility as they exhibit multiple axonal projections, transmitter systems, and modes of neural activity. How these multi-functional properties of neurons enable the generation of adaptive behaviors remains unknown. Here, we show that the HSN neuron in C. elegans evokes multiple motor programs over different timescales to enable a suite of behavioral changes during egg laying. Using HSN activity perturbations and in vivo calcium imaging, we show that HSN acutely increases egg laying and locomotion while also biasing the animals toward low-speed dwelling behavior over minutes. The acute effects of HSN on egg laying and high-speed locomotion are mediated by separate sets of HSN transmitters and different HSN axonal compartments. The long-lasting effects on dwelling are mediated in part by HSN release of serotonin, which is taken up and re-released by NSM, another serotonergic neuron class that directly evokes dwelling. Our results show how the multi-functional properties of a single neuron allow it to induce a coordinated suite of behaviors and also reveal that neurons can borrow serotonin from one another to control behavior.
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Affiliation(s)
- Yung-Chi Huang
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jinyue Luo
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenjia Huang
- Department of Neurobiology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Casey M Baker
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew A Gomes
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bohan Meng
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandra B Byrne
- Department of Neurobiology, UMass Chan Medical School, Worcester, MA 01655, USA
| | - Steven W Flavell
- Picower Institute for Learning & Memory, Department of Brain & Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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12
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Koutsoumparis A, Busack I, Chen CK, Hayashi Y, Braeckman BP, Meierhofer D, Bringmann H. Reverse genetic screening during L1 arrest reveals a role of the diacylglycerol kinase 1 gene dgk-1 and sphingolipid metabolism genes in sleep regulation. Genetics 2023; 225:iyad124. [PMID: 37682641 DOI: 10.1093/genetics/iyad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/01/2023] [Indexed: 09/10/2023] Open
Abstract
Sleep is a fundamental state of behavioral quiescence and physiological restoration. Sleep is controlled by environmental conditions, indicating a complex regulation of sleep by multiple processes. Our knowledge of the genes and mechanisms that control sleep during various conditions is, however, still incomplete. In Caenorhabditis elegans, sleep is increased when development is arrested upon starvation. Here, we performed a reverse genetic sleep screen in arrested L1 larvae for genes that are associated with metabolism. We found over 100 genes that are associated with a reduced sleep phenotype. Enrichment analysis revealed sphingolipid metabolism as a key pathway that controls sleep. A strong sleep loss was caused by the loss of function of the diacylglycerol kinase 1 gene, dgk-1, a negative regulator of synaptic transmission. Rescue experiments indicated that dgk-1 is required for sleep in cholinergic and tyraminergic neurons. The Ring Interneuron S (RIS) neuron is crucial for sleep in C. elegans and activates to induce sleep. RIS activation transients were abolished in dgk-1 mutant animals. Calcium transients were partially rescued by a reduction-of-function mutation of unc-13, suggesting that dgk-1 might be required for RIS activation by limiting synaptic vesicle release. dgk-1 mutant animals had impaired L1 arrest survival and dampened expression of the protective heat shock factor gene hsp-12.6. These data suggest that dgk-1 impairment causes broad physiological deficits. Microcalorimetry and metabolomic analyses of larvae with impaired RIS showed that RIS is broadly required for energy conservation and metabolic control, including for the presence of sphingolipids. Our data support the notion that metabolism broadly influences sleep and that sleep is associated with profound metabolic changes. We thus provide novel insights into the interplay of lipids and sleep and provide a rich resource of mutants and metabolic pathways for future sleep studies.
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Affiliation(s)
- Anastasios Koutsoumparis
- Chair of Cellular Circuits and Systems, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Am Tatzberg 47/49, Dresden, Saxony 01307, Germany
| | - Inka Busack
- Chair of Cellular Circuits and Systems, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Am Tatzberg 47/49, Dresden, Saxony 01307, Germany
| | - Chung-Kuan Chen
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Yu Hayashi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Bart P Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - David Meierhofer
- Mass Spectrometry Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Henrik Bringmann
- Chair of Cellular Circuits and Systems, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Am Tatzberg 47/49, Dresden, Saxony 01307, Germany
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13
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Chang AS, Wirak GS, Li D, Gabel CV, Connor CW. Measures of Information Content during Anesthesia and Emergence in the Caenorhabditis elegans Nervous System. Anesthesiology 2023; 139:49-62. [PMID: 37027802 PMCID: PMC10266588 DOI: 10.1097/aln.0000000000004579] [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] [Indexed: 04/09/2023]
Abstract
BACKGROUND Suppression of behavioral and physical responses defines the anesthetized state. This is accompanied, in humans, by characteristic changes in electroencephalogram patterns. However, these measures reveal little about the neuron or circuit-level physiologic action of anesthetics nor how information is trafficked between neurons. This study assessed whether entropy-based metrics can differentiate between the awake and anesthetized state in Caenorhabditis elegans and characterize emergence from anesthesia at the level of interneuronal communication. METHODS Volumetric fluorescence imaging measured neuronal activity across a large portion of the C. elegans nervous system at cellular resolution during distinct states of isoflurane anesthesia, as well as during emergence from the anesthetized state. Using a generalized model of interneuronal communication, new entropy metrics were empirically derived that can distinguish the awake and anesthetized states. RESULTS This study derived three new entropy-based metrics that distinguish between stable awake and anesthetized states (isoflurane, n = 10) while possessing plausible physiologic interpretations. State decoupling is elevated in the anesthetized state (0%: 48.8 ± 3.50%; 4%: 66.9 ± 6.08%; 8%: 65.1 ± 5.16%; 0% vs. 4%, P < 0.001; 0% vs. 8%, P < 0.001), while internal predictability (0%: 46.0 ± 2.94%; 4%: 27.7 ± 5.13%; 8%: 30.5 ± 4.56%; 0% vs. 4%, P < 0.001; 0% vs. 8%, P < 0.001), and system consistency (0%: 2.64 ± 1.27%; 4%: 0.97 ± 1.38%; 8%: 1.14 ± 0.47%; 0% vs. 4%, P = 0.006; 0% vs. 8%, P = 0.015) are suppressed. These new metrics also resolve to baseline during gradual emergence of C. elegans from moderate levels of anesthesia to the awake state (n = 8). The results of this study show that early emergence from isoflurane anesthesia in C. elegans is characterized by the rapid resolution of an elevation in high frequency activity (n = 8, P = 0.032). The entropy-based metrics mutual information and transfer entropy, however, did not differentiate well between the awake and anesthetized states. CONCLUSIONS Novel empirically derived entropy metrics better distinguish the awake and anesthetized states compared to extant metrics and reveal meaningful differences in information transfer characteristics between states. EDITOR’S PERSPECTIVE
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Affiliation(s)
- Andrew S Chang
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston University, Boston, Massachusetts
| | - Gregory S Wirak
- Department of Physiology and Biophysics, Boston University, Boston, Massachusetts
| | - Duan Li
- Center for Consciousness Science, Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christopher V Gabel
- Department of Physiology and Biophysics, Boston University, Boston, Massachusetts
| | - Christopher W Connor
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Biomedical Engineering, Physiology and Biophysics, Boston University, Boston, Massachusetts
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14
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Hao Y, Liu H, Zeng XT, Wang Y, Zeng WX, Qian KY, Li L, Chi MX, Gao S, Hu Z, Tong XJ. UNC-43/CaMKII-triggered anterograde signals recruit GABA ARs to mediate inhibitory synaptic transmission and plasticity at C. elegans NMJs. Nat Commun 2023; 14:1436. [PMID: 36918518 PMCID: PMC10015018 DOI: 10.1038/s41467-023-37137-0] [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: 07/17/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023] Open
Abstract
Disturbed inhibitory synaptic transmission has functional impacts on neurodevelopmental and psychiatric disorders. An essential mechanism for modulating inhibitory synaptic transmission is alteration of the postsynaptic abundance of GABAARs, which are stabilized by postsynaptic scaffold proteins and recruited by presynaptic signals. However, how GABAergic neurons trigger signals to transsynaptically recruit GABAARs remains elusive. Here, we show that UNC-43/CaMKII functions at GABAergic neurons to recruit GABAARs and modulate inhibitory synaptic transmission at C. elegans neuromuscular junctions. We demonstrate that UNC-43 promotes presynaptic MADD-4B/Punctin secretion and NRX-1α/Neurexin surface delivery. Together, MADD-4B and NRX-1α recruit postsynaptic NLG-1/Neuroligin and stabilize GABAARs. Further, the excitation of GABAergic neurons potentiates the recruitment of NLG-1-stabilized-GABAARs, which depends on UNC-43, MADD-4B, and NRX-1. These data all support that UNC-43 triggers MADD-4B and NRX-1α, which act as anterograde signals to recruit postsynaptic GABAARs. Thus, our findings elucidate a mechanism for pre- and postsynaptic communication and inhibitory synaptic transmission and plasticity.
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Affiliation(s)
- Yue Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Haowen Liu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xian-Ting Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ya Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wan-Xin Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Kang-Ying Qian
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Li
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ming-Xuan Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shangbang Gao
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhitao Hu
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research (CJCADR), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Xia-Jing Tong
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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15
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Reed HM, Han Z, Schroeder NE. GABA Immunoreactivity and Pharmacological Effects vary Among Stylet-Bearing Nematodes. J Nematol 2023; 55:20230049. [PMID: 38026555 PMCID: PMC10657207 DOI: 10.2478/jofnem-2023-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 12/01/2023] Open
Abstract
Plant-parasitic nematodes conduct a series of sophisticated behaviors to complete their life cycles. Among these, locomotion behaviors, including finding the host and migrating to the feeding site, directly affect the success of parasitism. Thus, disrupting locomotion behaviors has the potential to control these parasites. γ-Aminobutyric acid (GABA) is the prominent inhibitory neurotransmitter in nematodes. GABA-immunoreactive neurons are mostly found in motor neurons, where they regulate behaviors in the model nematode C. elegans. However, the GABA system in most stylet-bearing nematodes has received little attention. Using immunohistochemistry, we found variation in the pattern of GABA-immunoreactivity among two major plant-parasites and a fungal feeder. Some of these GABA-immunoreactive neurons lack clear homologs to C. elegans. Pharmaceutical assays showed that applying GABA, its agonist, and its antagonist, can disrupt the locomotion behaviors of these nematodes, although sensitivity to a given compound varied between species. Our data suggest that the GABA system is a potential target for the control of plant-parasitic nematodes.
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Affiliation(s)
- Hannah M. Reed
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL
| | - Ziduan Han
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Nathan E. Schroeder
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL
- Neuroscience Program, University of Illinois at Urbana-Champaign, IL
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16
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Lazaro-Pena MI, Cornwell AB, Diaz-Balzac CA, Das R, Macoretta N, Thakar J, Samuelson AV. Homeodomain-interacting protein kinase maintains neuronal homeostasis during normal Caenorhabditis elegans aging and systemically regulates longevity from serotonergic and GABAergic neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523661. [PMID: 36711523 PMCID: PMC9882034 DOI: 10.1101/2023.01.11.523661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network. We have discovered the Caenorhabditis elegans h omeodomain-interacting p rotein k inase (HPK-1) acts as a key transcriptional effector to preserve neuronal integrity, function, and proteostasis during aging. Loss of hpk-1 results in drastic dysregulation in expression of neuronal genes, including genes associated with neuronal aging. During normal aging hpk-1 expression increases throughout the nervous system more broadly than any other kinase. Within the aging nervous system, hpk-1 is co-expressed with key longevity transcription factors, including daf-16 (FOXO), hlh-30 (TFEB), skn-1 (Nrf2), and hif-1 , which suggests hpk-1 expression mitigates natural age-associated physiological decline. Consistently, pan-neuronal overexpression of hpk-1 extends longevity, preserves proteostasis both within and outside of the nervous system, and improves stress resistance. Neuronal HPK-1 improves proteostasis through kinase activity. HPK-1 functions cell non-autonomously within serotonergic and GABAergic neurons to improve proteostasis in distal tissues by specifically regulating distinct components of the proteostatic network. Increased serotonergic HPK-1 enhances the heat shock response and survival to acute stress. In contrast, GABAergic HPK-1 induces basal autophagy and extends longevity. Our work establishes hpk-1 as a key neuronal transcriptional regulator critical for preservation of neuronal function during aging. Further, these data provide novel insight as to how the nervous system partitions acute and chronic adaptive response pathways to delay aging by maintaining organismal homeostasis.
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17
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Wu J, Wang L, Ervin JF, Wang SHJ, Soderblom E, Ko D, Yan D. GABA signaling triggered by TMC-1/Tmc delays neuronal aging by inhibiting the PKC pathway in C. elegans. SCIENCE ADVANCES 2022; 8:eadc9236. [PMID: 36542715 PMCID: PMC9770988 DOI: 10.1126/sciadv.adc9236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Aging causes functional decline and degeneration of neurons and is a major risk factor of neurodegenerative diseases. To investigate the molecular mechanisms underlying neuronal aging, we developed a new pipeline for neuronal proteomic profiling in young and aged animals. While the overall translational machinery is down-regulated, certain proteins increase expressions upon aging. Among these aging-up-regulated proteins, the conserved channel protein TMC-1/Tmc has an anti-aging function in all neurons tested, and the neuroprotective function of TMC-1 occurs by regulating GABA signaling. Moreover, our results show that metabotropic GABA receptors and G protein GOA-1/Goα are required for the anti-neuronal aging functions of TMC-1 and GABA, and the activation of GABA receptors prevents neuronal aging by inhibiting the PLCβ-PKC pathway. Last, we show that the TMC-1-GABA-PKC signaling axis suppresses neuronal functional decline caused by a pathogenic form of human Tau protein. Together, our findings reveal the neuroprotective function of the TMC-1-GABA-PKC signaling axis in aging and disease conditions.
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Affiliation(s)
- Jieyu Wu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - John F. Ervin
- Bryan Brain Bank and Biorepository, Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shih-Hsiu J. Wang
- Department of Pathology & Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Erik Soderblom
- Proteomics and Metabolomics Shared Resource and Duke Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC 27710, USA
| | - Dennis Ko
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Dong Yan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
- Department of Neurobiology, Regeneration Next, and Duke Institute for Brain Sciences, Duke University Medical Center, Durham, NC 27710, USA
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18
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Santiago E, Shelar A, Christie N, Lewis-Hayre M, Koelle M. Using NeuroPAL Multicolor Fluorescence Labeling to Identify Neurons in C. elegans. Curr Protoc 2022; 2:e610. [PMID: 36521003 PMCID: PMC10257892 DOI: 10.1002/cpz1.610] [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: 12/23/2022]
Abstract
NeuroPAL (Neuronal Polychromatic Atlas of Landmarks) is a recently developed transgene that labels each of the 118 classes of neurons in C. elegans with various combinations of four fluorescent proteins. This neuron-type-specific labeling helps identify neurons that could otherwise be confused with neighboring neurons. Neuron identification enables researchers to combine new data that they generate on a C. elegans neuron with existing datasets on that same neuron, such as its synaptic connections, neurotransmitters, and transcriptome. An impediment to using NeuroPAL, however, is overcoming the steep learning curve for interpreting three-dimensional (3D) fluorescence images of crowded neural ganglia within which different neurons may be similarly colored, some neurons are only very faintly labeled, and the positions of some neurons are variable. Here, we provide protocols that allow researchers to learn to accurately identify neurons within 3D images of NeuroPAL-labeled animals. We provide 3D reference images that illustrate NeuroPAL labeling of each body region, and additional 3D images as training exercises to learn to accurately carry out C. elegans neuron identifications. We also provide tools to annotate images in 3D, and suggest that such 3D annotated images should be the standard for documenting C. elegans neuron identifications for publication. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Using Imaris software to view and annotate images of NeuroPAL-labeled animals in 3D Alternate Protocol: Using FIJI/ImageJ software to view and annotate images of NeuroPAL-labeled animals in 3D Basic Protocol 2: Identifying tail neurons-an introduction to identifying neurons Basic Protocol 3: Identifying midbody neurons Basic Protocol 4: Identifying anterior head neurons Basic Protocol 5: Identifying posterior head neurons Basic Protocol 6: Identifying ventral head and retrovesicular ganglion neurons.
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Affiliation(s)
- E.R. Santiago
- Department of Molecular, Cellular, and Developmental Biology, Yale University
- These authors contributed equally to this work
| | - A. Shelar
- Department of Molecular Biophysics and Biochemistry, Yale University
- These authors contributed equally to this work
| | - N.T.M. Christie
- Department of Molecular Biophysics and Biochemistry, Yale University
| | - M.R. Lewis-Hayre
- Department of Molecular, Cellular, and Developmental Biology, Yale University
| | - M.R. Koelle
- Department of Molecular Biophysics and Biochemistry, Yale University
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19
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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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20
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Chai CM, Torkashvand M, Seyedolmohadesin M, Park H, Venkatachalam V, Sternberg PW. Interneuron control of C. elegans developmental decision-making. Curr Biol 2022; 32:2316-2324.e4. [PMID: 35447086 DOI: 10.1016/j.cub.2022.03.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 01/18/2023]
Abstract
Natural environments are highly dynamic, and this complexity challenges animals to accurately integrate external cues to shape their responses. Adaptive developmental plasticity enables organisms to remodel their physiology, morphology, and behavior to better suit the predicted future environment and ultimately enhance their ecological success.1 Understanding how an animal generates a neural representation of current and forecasted environmental conditions and converts these circuit computations into a predictive adaptive physiological response may provide fundamental insights into the molecular and cellular basis of decision-making over developmentally relevant timescales. Although it is known that sensory cues usually trigger the developmental switch and that downstream inter-tissue signaling pathways enact the alternative developmental phenotype, the integrative neural mechanisms that transduce external inputs into effector pathways are less clear.2,3 In adverse environments, Caenorhabditis elegans larvae can enter a stress-resistant diapause state with arrested metabolism and reproductive physiology.4 Amphid sensory neurons feed into both rapid chemotactic and short-term foraging mode decisions, mediated by amphid and pre-motor interneurons, as well as the long-term diapause entry decision. Here, we identify amphid interneurons that integrate pheromone cues and propagate this information via a neuropeptidergic pathway to influence larval developmental fate, bypassing the pre-motor system. AIA interneuron-derived FLP-2 neuropeptide signaling promotes reproductive growth, and AIA activity is suppressed by pheromones. FLP-2 signaling is inhibited by upstream glutamatergic transmission via the metabotropic receptor MGL-1 and mediated by the broadly expressed neuropeptide G-protein-coupled receptor NPR-30. Thus, metabotropic signaling allows the reuse of parts of a sensory system for a decision with a distinct timescale.
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Affiliation(s)
- Cynthia M Chai
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA.
| | - Mahdi Torkashvand
- Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA
| | | | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA
| | - Vivek Venkatachalam
- Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115, USA.
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Blvd, Pasadena, CA 91125, USA.
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21
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Xia Y, Qadota H, Wang ZH, Liu P, Liu X, Ye KX, Matheny CJ, Berglund K, Yu SP, Drake D, Bennett DA, Wang XC, Yankner BA, Benian GM, Ye K. Neuronal C/EBPβ/AEP pathway shortens life span via selective GABAnergic neuronal degeneration by FOXO repression. SCIENCE ADVANCES 2022; 8:eabj8658. [PMID: 35353567 PMCID: PMC8967231 DOI: 10.1126/sciadv.abj8658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/07/2022] [Indexed: 05/05/2023]
Abstract
The age-related cognitive decline of normal aging is exacerbated in neurodegenerative diseases including Alzheimer's disease (AD). However, it remains unclear whether age-related cognitive regulators in AD pathologies contribute to life span. Here, we show that C/EBPβ, an Aβ and inflammatory cytokine-activated transcription factor that promotes AD pathologies via activating asparagine endopeptidase (AEP), mediates longevity in a gene dose-dependent manner in neuronal C/EBPβ transgenic mice. C/EBPβ selectively triggers inhibitory GABAnergic neuronal degeneration by repressing FOXOs and up-regulating AEP, leading to aberrant neural excitation and cognitive dysfunction. Overexpression of CEBP-2 or LGMN-1 (AEP) in Caenorhabditis elegans neurons but not muscle stimulates neural excitation and shortens life span. CEBP-2 or LGMN-1 reduces daf-2 mutant-elongated life span and diminishes daf-16-induced longevity. C/EBPβ and AEP are lower in humans with extended longevity and inversely correlated with REST/FOXO1. These findings demonstrate a conserved mechanism of aging that couples pathological cognitive decline to life span by the neuronal C/EBPβ/AEP pathway.
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Affiliation(s)
- Yiyuan Xia
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Hiroshi Qadota
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Zhi-Hao Wang
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Pai Liu
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Neuroscience program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Xia Liu
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Karen X. Ye
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Courtney J. Matheny
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ken Berglund
- Department of Neurosurgery, Emory University, Atlanta, GA 30322, USA
| | - Shan Ping Yu
- Department of Anesthesiology, Emory University, Atlanta, GA 30322, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Xiao-Chuan Wang
- Department of Pathophysiology, Key Laboratory of Ministry of Education of Neurological Diseases, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, Jiangsu 226001, China
| | | | - Guy M. Benian
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Keqiang Ye
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, China
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22
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Rapti G. Open Frontiers in Neural Cell Type Investigations; Lessons From Caenorhabditis elegans and Beyond, Toward a Multimodal Integration. Front Neurosci 2022; 15:787753. [PMID: 35321480 PMCID: PMC8934944 DOI: 10.3389/fnins.2021.787753] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Nervous system cells, the building blocks of circuits, have been studied with ever-progressing resolution, yet neural circuits appear still resistant to schemes of reductionist classification. Due to their sheer numbers, complexity and diversity, their systematic study requires concrete classifications that can serve reduced dimensionality, reproducibility, and information integration. Conventional hierarchical schemes transformed through the history of neuroscience by prioritizing criteria of morphology, (electro)physiological activity, molecular content, and circuit function, influenced by prevailing methodologies of the time. Since the molecular biology revolution and the recent advents in transcriptomics, molecular profiling gains ground toward the classification of neurons and glial cell types. Yet, transcriptomics entails technical challenges and more importantly uncovers unforeseen spatiotemporal heterogeneity, in complex and simpler nervous systems. Cells change states dynamically in space and time, in response to stimuli or throughout their developmental trajectory. Mapping cell type and state heterogeneity uncovers uncharted terrains in neurons and especially in glial cell biology, that remains understudied in many aspects. Examining neurons and glial cells from the perspectives of molecular neuroscience, physiology, development and evolution highlights the advantage of multifaceted classification schemes. Among the amalgam of models contributing to neuroscience research, Caenorhabditis elegans combines nervous system anatomy, lineage, connectivity and molecular content, all mapped at single-cell resolution, and can provide valuable insights for the workflow and challenges of the multimodal integration of cell type features. This review reflects on concepts and practices of neuron and glial cells classification and how research, in C. elegans and beyond, guides nervous system experimentation through integrated multidimensional schemes. It highlights underlying principles, emerging themes, and open frontiers in the study of nervous system development, regulatory logic and evolution. It proposes unified platforms to allow integrated annotation of large-scale datasets, gene-function studies, published or unpublished findings and community feedback. Neuroscience is moving fast toward interdisciplinary, high-throughput approaches for combined mapping of the morphology, physiology, connectivity, molecular function, and the integration of information in multifaceted schemes. A closer look in mapped neural circuits and understudied terrains offers insights for the best implementation of these approaches.
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23
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Zheng C, Lee HMT, Pham K. Nervous system-wide analysis of Hox regulation of terminal neuronal fate specification in Caenorhabditis elegans. PLoS Genet 2022; 18:e1010092. [PMID: 35226663 PMCID: PMC8912897 DOI: 10.1371/journal.pgen.1010092] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/10/2022] [Accepted: 02/12/2022] [Indexed: 12/01/2022] Open
Abstract
Hox genes encode evolutionarily conserved transcription factors that specify regional identities along the anterior-posterior (A-P) axis. Although some Hox genes are known to regulate the differentiation of certain neurons, to what extent Hox genes are involved in the terminal specification of the entire nervous system is unclear. Here, we systematically mapped the expression of all six Hox genes in C. elegans nervous system and found Hox expression in 97 (32%) of the 302 neurons in adult hermaphrodites. Our results are generally consistent with previous high-throughput expression mapping and single-cell transcriptomic studies. Detailed analysis of the fate markers for these neurons revealed that Hox genes regulate the differentiation of 29 (25%) of the 118 classes of C. elegans neurons. Hox genes not only regulate the specification of terminal neuronal fates through multiple mechanisms but also control subtype diversification along the A-P axis. The widespread involvement of Hox genes in neuronal differentiation indicates their roles in establishing complex nervous systems. The nervous system contains an extraordinary array of neuron types. How this neuronal diversity arises during development and what genes regulate the differentiation of each neuron type are among the major questions of neurobiology. Hox genes are a set of transcription factors highly conserved in the animal kingdom and are involved in setting up the body plan in the embryos. Hox genes are known to regulate the differentiation of some neurons, but their contribution to the overall development of a nervous system is unclear. In this study, we analyzed the activity of the Hox genes in the differentiation of the 302 neurons of the C. elegans nervous system in its entirety. We found that the six Hox genes are expressed in 32% of all neurons and five Hox genes regulate the differentiation of 25% of all neuron types through multiple mechanisms and act at various stages of cellular development. Thus, our results suggest that a small number of Hox genes could control the development of a significant portion of the nervous system. Given the conserved functions of Hox genes across species, we suspect that the increasing number of Hox genes may have allowed increased complexity in the nervous system in animal evolution.
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Affiliation(s)
- Chaogu Zheng
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
- * E-mail:
| | - Ho Ming Terence Lee
- School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Kenneth Pham
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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24
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Xu H, Wang X, Zhang X, Cheng J, Zhang J, Chen M, Wu T. A Deep Learning Analysis Reveals Nitrogen-Doped Graphene Quantum Dots Damage Neurons of Nematode Caenorhabditis elegans. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:3314. [PMID: 34947663 PMCID: PMC8703693 DOI: 10.3390/nano11123314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 12/03/2021] [Indexed: 11/16/2022]
Abstract
Along with the rapidly increasing applications of nitrogen-doped graphene quantum dots (N-GQDs) in the field of biomedicine, the exposure of N-GQDs undoubtedly pose a risk to the health of human beings, especially in the nervous system. In view of the lack of data from in vivo studies, this study used the nematode Caenorhabditis elegans (C. elegans), which has become a valuable animal model in nanotoxicological studies due to its multiple advantages, to undertake a bio-safety assessment of N-GQDs in the nervous system with the assistance of a deep learning model. The findings suggested that accumulated N-GQDs in the nematodes' bodies damaged their normal behavior in a dose- and time-dependent manner, and the impairments of the nervous system were obviously severe when the exposure dosages were above 100 μg/mL. When assessing the morphological changes of neurons caused by N-GQDs, a quantitative image-based analysis based on a deep neural network algorithm (YOLACT) was used because traditional image-based analysis is labor-intensive and limited to qualitative evaluation. The quantitative results indicated that N-GQDs damaged dopaminergic and glutamatergic neurons, which are involved in the neurotoxic effects of N-GQDs in the nematode C. elegans. This study not only suggests a fast and economic C. elegans model to undertake the risk assessment of nanomaterials in the nervous system, but also provides a valuable deep learning approach to quantitatively track subtle morphological changes of neurons at an unbiased level in a nanotoxicological study using C. elegans.
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Affiliation(s)
- Hongsheng Xu
- College of Energy and Electrical Engineering, Hohai University, Nanjing 210098, China;
| | - Xinyu Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
| | - Xiaomeng Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
| | - Jin Cheng
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
| | - Jixiang Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
| | - Min Chen
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
| | - Tianshu Wu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China; (X.W.); (X.Z.); (J.C.); (J.Z.); (M.C.)
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25
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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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26
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Bozzo M, Costa S, Obino V, Bachetti T, Marcenaro E, Pestarino M, Schubert M, Candiani S. Functional Conservation and Genetic Divergence of Chordate Glycinergic Neurotransmission: Insights from Amphioxus Glycine Transporters. Cells 2021; 10:cells10123392. [PMID: 34943900 PMCID: PMC8699752 DOI: 10.3390/cells10123392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/24/2022] Open
Abstract
Glycine is an important neurotransmitter in vertebrates, performing both excitatory and inhibitory actions. Synaptic levels of glycine are tightly controlled by the action of two glycine transporters, GlyT1 and GlyT2, located on the surface of glial cells and neurons, respectively. Only limited information is available on glycinergic neurotransmission in invertebrates, and the evolution of glycinergic neurotransmission is poorly understood. Here, by combining phylogenetic and gene expression analyses, we characterized the glycine transporter complement of amphioxus, an important invertebrate model for studying the evolution of chordates. We show that amphioxus possess three glycine transporter genes. Two of these (GlyT2.1 and GlyT2.2) are closely related to GlyT2 of vertebrates, whereas the third (GlyT) is a member of an ancestral clade of deuterostome glycine transporters. GlyT2.2 expression is predominantly non-neural, whereas GlyT and GlyT2.1 are widely expressed in the amphioxus nervous system and are differentially expressed, respectively, in neurons and glia. Vertebrate glycinergic neurons express GlyT2 and glia GlyT1, suggesting that the evolution of the chordate glycinergic system was accompanied by a paralog-specific inversion of gene expression. Despite this genetic divergence between amphioxus and vertebrates, we found strong evidence for conservation in the role glycinergic neurotransmission plays during larval swimming, the implication being that the neural networks controlling the rhythmic movement of chordate bodies may be homologous.
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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; (S.C.); (T.B.); (M.P.)
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
| | - Simone Costa
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Valentina Obino
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Tiziana Bachetti
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - Emanuela Marcenaro
- Dipartimento di Medicina Sperimentale (DIMES), Università degli Studi di Genova, 16132 Genoa, Italy; (V.O.); (E.M.)
| | - Mario Pestarino
- Dipartimento di Scienze della Terra, dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy; (S.C.); (T.B.); (M.P.)
| | - 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; (S.C.); (T.B.); (M.P.)
- Correspondence: (M.B.); (S.C.); Tel.: +39-010-335-8043 (M.B.); +39-010-335-8051 (S.C.)
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27
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Suthakaran N, Wiggins J, Giles A, Opperman KJ, Grill B, Dawson-Scully K. O-GlcNAc transferase OGT-1 and the ubiquitin ligase EEL-1 modulate seizure susceptibility in C. elegans. PLoS One 2021; 16:e0260072. [PMID: 34797853 PMCID: PMC8604358 DOI: 10.1371/journal.pone.0260072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Neurodevelopmental disorders such as epilepsy and autism have been linked to an imbalance of excitation and inhibition (E/I) in the central nervous system. The simplicity and tractability of C. elegans allows our electroconvulsive seizure (ES) assay to be used as a behavioral readout of the locomotor circuit and neuronal function. C. elegans possess conserved nervous system features such as gamma-aminobutyric acid (GABA) and GABA receptors in inhibitory neurotransmission, and acetylcholine (Ach) and acetylcholine receptors in excitatory neurotransmission. Our previously published data has shown that decreasing inhibition in the motor circuit, via GABAergic manipulation, will extend the time of locomotor recovery following electroshock. Similarly, mutations in a HECT E3 ubiquitin ligase called EEL-1 leads to impaired GABAergic transmission, E/I imbalance and altered sensitivity to electroshock. Mutations in the human ortholog of EEL-1, called HUWE1, are associated with both syndromic and non-syndromic intellectual disability. Both EEL-1 and its previously established binding protein, OGT-1, are expressed in GABAergic motor neurons, localize to GABAergic presynaptic terminals, and function in parallel to regulate GABA neuron function. In this study, we tested behavioral responses to electroshock in wildtype, ogt-1, eel-1 and ogt-1; eel-1 double mutants. Both ogt-1 and eel-1 null mutants have decreased inhibitory GABAergic neuron function and increased electroshock sensitivity. Consistent with EEL-1 and OGT-1 functioning in parallel pathways, ogt-1; eel-1 double mutants showed enhanced electroshock susceptibility. Expression of OGT-1 in the C. elegans nervous system rescued enhanced electroshock defects in ogt-1; eel-1 double mutants. Application of a GABA agonist, Baclofen, decreased electroshock susceptibility in all animals. Our C. elegans electroconvulsive seizure assay was the first to model a human X-linked Intellectual Disability (XLID) associated with epilepsy and suggests a potential novel role for the OGT-1/EEL-1 complex in seizure susceptibility.
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Affiliation(s)
- Nirthieca Suthakaran
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Jonathan Wiggins
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Andrew Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Karla J. Opperman
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ken Dawson-Scully
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
- * E-mail:
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28
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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; 148:271902. [PMID: 34415309 DOI: 10.1242/dev.199687] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [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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29
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Pham K, Masoudi N, Leyva-Díaz E, Hobert O. A nervous system-specific subnuclear organelle in Caenorhabditis elegans. Genetics 2021; 217:1-17. [PMID: 33683371 DOI: 10.1093/genetics/iyaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/12/2020] [Indexed: 12/26/2022] Open
Abstract
We describe here phase-separated subnuclear organelles in the nematode Caenorhabditis elegans, which we term NUN (NUclear Nervous system-specific) bodies. Unlike other previously described subnuclear organelles, NUN bodies are highly cell type specific. In fully mature animals, 4-10 NUN bodies are observed exclusively in the nucleus of neuronal, glial and neuron-like cells, but not in other somatic cell types. Based on co-localization and genetic loss of function studies, NUN bodies are not related to other previously described subnuclear organelles, such as nucleoli, splicing speckles, paraspeckles, Polycomb bodies, promyelocytic leukemia bodies, gems, stress-induced nuclear bodies, or clastosomes. NUN bodies form immediately after cell cycle exit, before other signs of overt neuronal differentiation and are unaffected by the genetic elimination of transcription factors that control many other aspects of neuronal identity. In one unusual neuron class, the canal-associated neurons, NUN bodies remodel during larval development, and this remodeling depends on the Prd-type homeobox gene ceh-10. In conclusion, we have characterized here a novel subnuclear organelle whose cell type specificity poses the intriguing question of what biochemical process in the nucleus makes all nervous system-associated cells different from cells outside the nervous system.
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Affiliation(s)
- Kenneth Pham
- 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
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical 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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Nomura K, Yoshizumi S, Ozoe F, Ozoe Y. Molecular cloning and pharmacology of Min-UNC-49B, a GABA receptor from the southern root-knot nematode Meloidogyne incognita. PEST MANAGEMENT SCIENCE 2021; 77:3763-3776. [PMID: 32954620 DOI: 10.1002/ps.6096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/11/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Root-knot nematodes are plant-parasitic nematodes that cause immense damage to a broad range of cultivated crops by forming root galls, resulting in yield losses in crops. To facilitate the development of faster-acting selective nematicides, we cloned three cDNAs encoding UNC-49B proteins from the southern root-knot nematode Meloidogyne incognita and examined their functional and pharmacological properties by two-electrode voltage clamp electrophysiology using a Xenopus oocyte expression system. RESULTS The three cloned cDNAs encoded Min-UNC-49B, Min-UNC-49B-L and Min-UNC-49B-XL; the last two proteins have longer N-terminal regions than the first protein. When expressed in Xenopus oocytes, these proteins responded to γ-aminobutyric acid (GABA) to activate currents with high-micromolar or low-millimolar half-maximal effective concentration (EC50 ) values, indicating the formation of functional homo-pentameric GABA receptors. Fipronil and picrotoxinin inhibited GABA-induced currents with high-nanomolar and low-micromolar half-maximal inhibitory concentration (IC50 ) values, respectively, in oocytes expressing Min-UNC-49B. The G2'A and T6'M mutations in the second transmembrane domain of Min-UNC-49B enhanced and reduced the sensitivity of Min-UNC-49B to these two antagonists, respectively. Samaderine B and SF-14 inhibited GABA responses in oocytes expressing Min-UNC-49B with low-micromolar and high-nanomolar IC50 values, respectively. Ivermectin, α-terpineol, thymol and methyl eugenol exerted dual effects on Min-UNC-49B by potentiating currents induced by low concentrations of GABA and inhibiting currents induced by high concentrations of GABA. CONCLUSION We have shown that structurally diverse compounds act at Min-UNC-49B GABA receptors. Our results may serve as a starting point to decipher the molecular function of native GABA receptors of plant-parasitic nematodes, which could aid in the structure-based design of novel nematicides. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Kazuki Nomura
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
| | - Satoru Yoshizumi
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
| | - Fumiyo Ozoe
- Interdisciplinary Institute for Science Research, Organization for Research and Academic Information, Shimane University, Matsue, Shimane, Japan
| | - Yoshihisa Ozoe
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane, Japan
- Interdisciplinary Institute for Science Research, Organization for Research and Academic Information, Shimane University, Matsue, Shimane, Japan
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31
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Rapti G. A perspective on C. elegans neurodevelopment: from early visionaries to a booming neuroscience research. J Neurogenet 2021; 34:259-272. [PMID: 33446023 DOI: 10.1080/01677063.2020.1837799] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The formation of the nervous system and its striking complexity is a remarkable feat of development. C. elegans served as a unique model to dissect the molecular events in neurodevelopment, from its early visionaries to the current booming neuroscience community. Soon after being introduced as a model, C. elegans was mapped at the level of genes, cells, and synapses, providing the first metazoan with a complete cell lineage, sequenced genome, and connectome. Here, I summarize mechanisms underlying C. elegans neurodevelopment, from the generation and diversification of neural components to their navigation and connectivity. I point out recent noteworthy findings in the fields of glia biology, sex dimorphism and plasticity in neurodevelopment, highlighting how current research connects back to the pioneering studies by Brenner, Sulston and colleagues. Multifaceted investigations in model organisms, connecting genes to cell function and behavior, expand our mechanistic understanding of neurodevelopment while allowing us to formulate emerging questions for future discoveries.
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Affiliation(s)
- Georgia Rapti
- European Molecular Biology Laboratory, Unit of Developmental Biology, Heidelberg, Germany
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32
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Taylor SR, Santpere G, Weinreb A, Barrett A, Reilly MB, Xu C, Varol E, Oikonomou P, Glenwinkel L, McWhirter R, Poff A, Basavaraju M, Rafi I, Yemini E, Cook SJ, Abrams A, Vidal B, Cros C, Tavazoie S, Sestan N, Hammarlund M, Hobert O, Miller DM. Molecular topography of an entire nervous system. Cell 2021; 184:4329-4347.e23. [PMID: 34237253 DOI: 10.1016/j.cell.2021.06.023] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/09/2021] [Accepted: 06/14/2021] [Indexed: 02/08/2023]
Abstract
We have produced gene expression profiles of all 302 neurons of the C. elegans nervous system that match the single-cell resolution of its anatomy and wiring diagram. Our results suggest that individual neuron classes can be solely identified by combinatorial expression of specific gene families. For example, each neuron class expresses distinct codes of ∼23 neuropeptide genes and ∼36 neuropeptide receptors, delineating a complex and expansive "wireless" signaling network. To demonstrate the utility of this comprehensive gene expression catalog, we used computational approaches to (1) identify cis-regulatory elements for neuron-specific gene expression and (2) reveal adhesion proteins with potential roles in process placement and synaptic specificity. Our expression data are available at https://cengen.org and can be interrogated at the web application CengenApp. We expect that this neuron-specific directory of gene expression will spur investigations of underlying mechanisms that define anatomy, connectivity, and function throughout the C. elegans nervous system.
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Affiliation(s)
- Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Alexis Weinreb
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Alec Barrett
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Chuan Xu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Erdem Varol
- Department of Statistics, Columbia University, New York, NY, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Lori Glenwinkel
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Rebecca McWhirter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abigail Poff
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Manasa Basavaraju
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Steven J Cook
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Alexander Abrams
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Berta Vidal
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Cyril Cros
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, USA; Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, NY, USA; Howard Hughes Medical Institute, Columbia University, New York, NY, USA.
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Program in Neuroscience, Vanderbilt University School of Medicine, Nashville, TN, USA.
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33
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Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM, Hobert O. In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system. eLife 2021; 10:e64906. [PMID: 34165430 PMCID: PMC8225391 DOI: 10.7554/elife.64906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The generation of the enormous diversity of neuronal cell types in a differentiating nervous system entails the activation of neuron type-specific gene batteries. To examine the regulatory logic that controls the expression of neuron type-specific gene batteries, we interrogate single cell expression profiles of all 118 neuron classes of the Caenorhabditis elegans nervous system for the presence of DNA binding motifs of 136 neuronally expressed C. elegans transcription factors. Using a phylogenetic footprinting pipeline, we identify cis-regulatory motif enrichments among neuron class-specific gene batteries and we identify cognate transcription factors for 117 of the 118 neuron classes. In addition to predicting novel regulators of neuronal identities, our nervous system-wide analysis at single cell resolution supports the hypothesis that many transcription factors directly co-regulate the cohort of effector genes that define a neuron type, thereby corroborating the concept of so-called terminal selectors of neuronal identity. Our analysis provides a blueprint for how individual components of an entire nervous system are genetically specified.
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Affiliation(s)
- Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | | | - Laura Pereira
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Manasa Basavaraju
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Roger Pocock
- Biotech Research and Innovation Centre, University of CopenhagenCopenhagenDenmark
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash UniversityMelbourneAustralia
| | - Nenad Sestan
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Marc Hammarlund
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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34
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Emmons SW, Yemini E, Zimmer M. Methods for analyzing neuronal structure and activity in Caenorhabditis elegans. Genetics 2021; 218:6303616. [PMID: 34151952 DOI: 10.1093/genetics/iyab072] [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: 02/04/2021] [Accepted: 04/20/2021] [Indexed: 11/12/2022] Open
Abstract
The model research animal Caenorhabditis elegans has unique properties making it particularly advantageous for studies of the nervous system. The nervous system is composed of a stereotyped complement of neurons connected in a consistent manner. Here, we describe methods for studying nervous system structure and function. The transparency of the animal makes it possible to visualize and identify neurons in living animals with fluorescent probes. These methods have been recently enhanced for the efficient use of neuron-specific reporter genes. Because of its simple structure, for a number of years, C. elegans has been at the forefront of connectomic studies defining synaptic connectivity by electron microscopy. This field is burgeoning with new, more powerful techniques, and recommended up-to-date methods are here described that encourage the possibility of new work in C. elegans. Fluorescent probes for single synapses and synaptic connections have allowed verification of the EM reconstructions and for experimental approaches to synapse formation. Advances in microscopy and in fluorescent reporters sensitive to Ca2+ levels have opened the way to observing activity within single neurons across the entire nervous system.
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Affiliation(s)
- Scott W Emmons
- Department of Genetics and Dominick Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 1041, USA
| | - Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Manuel Zimmer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna 1090, Austria and.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna 1030, Austria
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35
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Rawsthorne H, Calahorro F, Holden-Dye L, O’ Connor V, Dillon J. Investigating autism associated genes in C. elegans reveals candidates with a role in social behaviour. PLoS One 2021; 16:e0243121. [PMID: 34043629 PMCID: PMC8158995 DOI: 10.1371/journal.pone.0243121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/29/2021] [Indexed: 11/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterised by a triad of behavioural impairments and includes disruption in social behaviour. ASD has a clear genetic underpinning and hundreds of genes are implicated in its aetiology. However, how single penetrant genes disrupt activity of neural circuits which lead to affected behaviours is only beginning to be understood and less is known about how low penetrant genes interact to disrupt emergent behaviours. Investigations are well served by experimental approaches that allow tractable investigation of the underpinning genetic basis of circuits that control behaviours that operate in the biological domains that are neuro-atypical in autism. The model organism C. elegans provides an experimental platform to investigate the effect of genetic mutations on behavioural outputs including those that impact social biology. Here we use progeny-derived social cues that modulate C. elegans food leaving to assay genetic determinants of social behaviour. We used the SAFRI Gene database to identify C. elegans orthologues of human ASD associated genes. We identified a number of mutants that displayed selective deficits in response to progeny. The genetic determinants of this complex social behaviour highlight the important contribution of synaptopathy and implicates genes within cell signalling, epigenetics and phospholipid metabolism functional domains. The approach overlaps with a growing number of studies that investigate potential molecular determinants of autism in C. elegans. However, our use of a complex, sensory integrative, emergent behaviour provides routes to enrich new or underexplored biology with the identification of novel candidate genes with a definable role in social behaviour.
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Affiliation(s)
- Helena Rawsthorne
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Fernando Calahorro
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Lindy Holden-Dye
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - Vincent O’ Connor
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
| | - James Dillon
- School of Biological Sciences, Highfield Campus, University of Southampton, Southampton, United Kingdom
- * E-mail:
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36
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Zhang W, Li W, Li J, Chang X, Niu S, Wu T, Kong L, Zhang T, Tang M, Xue Y. Neurobehavior and neuron damage following prolonged exposure of silver nanoparticles with/without polyvinylpyrrolidone coating in Caenorhabditis elegans. J Appl Toxicol 2021; 41:2055-2067. [PMID: 33993517 DOI: 10.1002/jat.4197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/15/2021] [Accepted: 05/01/2021] [Indexed: 12/18/2022]
Abstract
Silver nanoparticles (AgNPs) have become widespread in the environment with increasing industrial applications. But the studies about their potential health risks are far from enough, especially in neurotoxic effects. This study aimed to investigate the neurotoxic effects of longer-term exposure (prolonged exposure for 48 h and chronic exposure for 6 days) of 20nm AgNPs with/without polyvinylpyrrolidone (PVP) coating at low concentrations (0.01-10 mg·L-1 ) to Caenorhabditis elegans. The results suggested that exposure to AgNPs induced damage to nematode survival, with the longest and relative average life span reduced. Exposure to AgNPs caused neurotoxicity on locomotion behaviors (head thrashes, body bends, pharyngeal pumping frequency, and defecation interval) and sensory perception behaviors (chemotaxis assay and thermotaxis assay), as well as impaired dopaminergic, GABAergic, and cholinergic neurons, except for glutamatergic, based on the alters fluorescence intensity, in a dose- and time-dependent manner. Further investigations suggested that the low-dose AgNPs (0.01-0.1 mg·L-1 ) exposure raises receptors of GABAergic and dopamine in C. elegans at the genetic level, whereas opposite results were observed at higher doses (1-10 mg·L-1 ), which implied that AgNPs could cause neurotoxicity by impairing neurotransmitter delivery. The PVP-AgNPs could cause a higher fatality rate and neurotoxicity at the same dose. Notably, AgNPs did not cause any deleterious effect on nematodes at the lowest dose of 0.01 mg·L-1 . In general, these results suggested that AgNPs possess the neurotoxic potential in C. elegans and provided useful information to understand the neurotoxicity of AgNPs, which would offer an inspiring perspective on the safe application.
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Affiliation(s)
- Wenli Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Wenhua Li
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Jiangyan Li
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiaoru Chang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shuyan Niu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Tianshu Wu
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Lu Kong
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Ting Zhang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Meng Tang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Yuying Xue
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
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37
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Otarigho B, Aballay A. Immunity-longevity tradeoff neurally controlled by GABAergic transcription factor PITX1/UNC-30. Cell Rep 2021; 35:109187. [PMID: 34038721 PMCID: PMC8227953 DOI: 10.1016/j.celrep.2021.109187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/01/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
A body of evidence indicates that metazoan immune and aging pathways are largely interconnected, but the mechanisms involved in their homeostatic control remain unclear. In this study, we find that the PITX (paired-like homeodomain) transcription factor UNC-30 controls the tradeoff between immunity and longevity from the nervous system in Caenorhabditis elegans. PITX/UNC-30 functional loss enhances immunity in a GATA/ELT-2- and p38 MAPK/PMK-1-dependent manner and reduced longevity by activating MXD/MDL-1 and the C2H2-type zinc finger transcription factor PQM-1. The immune inhibitory and longevity stimulatory functions of PITX/UNC-30 require the sensory neuron ASG and a signaling pathway controlled by NPR-1, which is a G protein-coupled receptor related to mammalian neuropeptide Y receptors. Our findings uncover a suppressive role of GABAergic signaling in the neural control of a biological tradeoff where energy is allocated toward immunity at the expense of longevity.
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Affiliation(s)
- Benson Otarigho
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Alejandro Aballay
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR 97239, USA.
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38
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George VK, Puppo F, Silva GA. Computing Temporal Sequences Associated With Dynamic Patterns on the C. elegans Connectome. Front Syst Neurosci 2021; 15:564124. [PMID: 33767613 PMCID: PMC7985353 DOI: 10.3389/fnsys.2021.564124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/04/2021] [Indexed: 12/03/2022] Open
Abstract
Understanding how the structural connectivity and spatial geometry of a network constrains the dynamics it is able to support is an active and open area of research. We simulated the plausible dynamics resulting from the known C. elegans connectome using a recent model and theoretical analysis that computes the dynamics of neurobiological networks by focusing on how local interactions among connected neurons give rise to the global dynamics in an emergent way. We studied the dynamics which resulted from stimulating a chemosensory neuron (ASEL) in a known feeding circuit, both in isolation and embedded in the full connectome. We show that contralateral motorneuron activations in ventral (VB) and dorsal (DB) classes of motorneurons emerged from the simulations, which are qualitatively similar to rhythmic motorneuron firing pattern associated with locomotion of the worm. One interpretation of these results is that there is an inherent—and we propose—purposeful structural wiring to the C. elegans connectome that has evolved to serve specific behavioral functions. To study network signaling pathways responsible for the dynamics we developed an analytic framework that constructs Temporal Sequences (TSeq), time-ordered walks of signals on graphs. We found that only 5% of TSeq are preserved between the isolated feeding network relative to its embedded counterpart. The remaining 95% of signaling pathways computed in the isolated network are not present in the embedded network. This suggests a cautionary note for computational studies of isolated neurobiological circuits and networks.
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Affiliation(s)
- Vivek Kurien George
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Center for Engineered Natural Intelligence, University of California, San Diego, San Diego, CA, United States
| | - Francesca Puppo
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Center for Engineered Natural Intelligence, University of California, San Diego, San Diego, CA, United States.,BioCircuits Institute, University of California, San Diego, San Diego, CA, United States
| | - Gabriel A Silva
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States.,Center for Engineered Natural Intelligence, University of California, San Diego, San Diego, CA, United States.,BioCircuits Institute, University of California, San Diego, San Diego, CA, United States.,Department of Neurosciences, University of California, San Diego, San Diego, CA, United States
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39
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Chaudhary S, Lee SA, Li Y, Patel DS, Lu H. Graphical-model framework for automated annotation of cell identities in dense cellular images. eLife 2021; 10:e60321. [PMID: 33625357 PMCID: PMC8032398 DOI: 10.7554/elife.60321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/23/2021] [Indexed: 12/11/2022] Open
Abstract
Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here, we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in Caenorhabditis elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.
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Affiliation(s)
- Shivesh Chaudhary
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Sol Ah Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Yueyi Li
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Hang Lu
- School of Chemical & Biomolecular Engineering, Georgia Institute of TechnologyAtlantaUnited States
- Petit Institute for Bioengineering and Bioscience, Georgia Institute of TechnologyAtlantaUnited States
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40
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Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O. NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell 2021; 184:272-288.e11. [PMID: 33378642 PMCID: PMC10494711 DOI: 10.1016/j.cell.2020.12.012] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 06/30/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Comprehensively resolving neuronal identities in whole-brain images is a major challenge. We achieve this in C. elegans by engineering a multicolor transgene called NeuroPAL (a neuronal polychromatic atlas of landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that resolves all neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. We showcase three applications that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding for these stimuli.
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Affiliation(s)
- Eviatar Yemini
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA.
| | - Albert Lin
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, 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
| | - 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
| | - Ruoxi Sun
- 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
| | - Gonzalo E Mena
- Department of Statistics and Data Science Initiative, Harvard University, Cambridge, MA 02138, USA
| | - Aravinthan D T Samuel
- Department of Physics, Center for Brain Science, Harvard University, Cambridge, MA 02138, 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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41
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Abstract
Large amounts of effort have been invested in trying to understand how a single genome is able to specify the identity of hundreds of cell types. Inspired by some aspects of Caenorhabditis elegans biology, we implemented an in silico evolutionary strategy to produce gene regulatory networks (GRNs) that drive cell-specific gene expression patterns, mimicking the process of terminal cell differentiation. Dynamics of the gene regulatory networks are governed by a thermodynamic model of gene expression, which uses DNA sequences and transcription factor degenerate position weight matrixes as input. In a version of the model, we included chromatin accessibility. Experimentally, it has been determined that cell-specific and broadly expressed genes are regulated differently. In our in silico evolved GRNs, broadly expressed genes are regulated very redundantly and the architecture of their cis-regulatory modules is different, in accordance to what has been found in C. elegans and also in other systems. Finally, we found differences in topological positions in GRNs between these two classes of genes, which help to explain why broadly expressed genes are so resilient to mutations. Overall, our results offer an explanatory hypothesis on why broadly expressed genes are regulated so redundantly compared to cell-specific genes, which can be extrapolated to phenomena such as ChIP-seq HOT regions.
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Affiliation(s)
- Carlos Mora-Martinez
- Evo-devo Helsinki community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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42
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Zhang H, Wang H, Shen X, Jia X, Yu S, Qiu X, Wang Y, Du J, Yan J, He J. The landscape of regulatory genes in brain-wide neuronal phenotypes of a vertebrate brain. eLife 2021; 10:68224. [PMID: 34895465 PMCID: PMC8769648 DOI: 10.7554/elife.68224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/05/2021] [Indexed: 11/18/2022] Open
Abstract
Multidimensional landscapes of regulatory genes in neuronal phenotypes at whole-brain levels in the vertebrate remain elusive. We generated single-cell transcriptomes of ~67,000 region- and neurotransmitter/neuromodulator-identifiable cells from larval zebrafish brains. Hierarchical clustering based on effector gene profiles ('terminal features') distinguished major brain cell types. Sister clusters at hierarchical termini displayed similar terminal features. It was further verified by a population-level statistical method. Intriguingly, glutamatergic/GABAergic sister clusters mostly expressed distinct transcription factor (TF) profiles ('convergent pattern'), whereas neuromodulator-type sister clusters predominantly expressed the same TF profiles ('matched pattern'). Interestingly, glutamatergic/GABAergic clusters with similar TF profiles could also display different terminal features ('divergent pattern'). It led us to identify a library of RNA-binding proteins that differentially marked divergent pair clusters, suggesting the post-transcriptional regulation of neuron diversification. Thus, our findings reveal multidimensional landscapes of transcriptional and post-transcriptional regulators in whole-brain neuronal phenotypes in the zebrafish brain.
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Affiliation(s)
- Hui Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xiaoyu Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xinling Jia
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Shuguang Yu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Xiaoying Qiu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Yufan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,University of Chinese Academy of SciencesBeijingChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
| | - Jiulin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina,School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina,School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Jie He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of SciencesShanghaiChina,Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
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43
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You J, Pan F, Wang S, Wang Y, Hu Y. FMRFamide-Like Peptide 22 Influences the Head Movement, Host Finding, and Infection of Heterodera glycines. FRONTIERS IN PLANT SCIENCE 2021; 12:673354. [PMID: 34239524 PMCID: PMC8258376 DOI: 10.3389/fpls.2021.673354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/17/2021] [Indexed: 05/13/2023]
Abstract
The FMRFamide-like peptides (FLPs) represent the largest family of nematode neuropeptides and are involved in multiple parasitic activities. The immunoreactivity to FMRFamide within the nervous system of Heterodera glycines, the most economically damaging parasite of soybean [Glycine max L. (Merr)], has been reported in previous research. However, the family of genes encoding FLPs of H. glycines were not identified and functionally characterized. In this study, an FLP encoding gene Hg-flp-22 was cloned from H. glycines, and its functional characterization was uncovered by using in vitro RNA interference and application of synthetic peptides. Bioinformatics analysis showed that flp-22 is widely expressed in multiple nematode species, where they encode the highly conserved KWMRFamide motifs. Quantitative real-time (qRT)-PCR results revealed that Hg-flp-22 was highly expressed in the infective second-stage juveniles (J2s) and adult males. Silencing of Hg-flp-22 resulted in the reduced movement of J2s to the host root and reduced penetration ability, as well as a reduction in their subsequent number of females. Behavior and infection assays demonstrated that application of synthetic peptides Hg-FLP-22b (TPQGKWMRFa) and Hg-FLP-22c (KMAIEGGKWVRFa) significantly increased the head movement frequency and host invasion abilities in H. glycines but not in Meloidogyne incognita. In addition, the number of H. glycines females on the host roots was found to be significantly higher in Hg-FLP-22b treated nematodes than the ddH2O-treated control J2s. These results presented in this study elucidated that Hg-flp-22 plays a role in regulating locomotion and infection of H. glycines. This suggests the potential of FLP signaling as putative control targets for H. glycines in soybean production.
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Affiliation(s)
- Jia You
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Institute of Pratacultural Science, Heilongjiang Academy of Agricultural Science, Harbin, China
| | - Fengjuan Pan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Shuo Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Yu Wang
- College of Agricultural Resource and Environment, Heilongjiang University, Harbin, China
| | - Yanfeng Hu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- *Correspondence: Yanfeng Hu,
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44
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Konstantinides N, Desplan C. Neuronal differentiation strategies: insights from single-cell sequencing and machine learning. Development 2020; 147:dev193631. [PMID: 33293292 PMCID: PMC7746664 DOI: 10.1242/dev.193631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Neuronal replacement therapies rely on the in vitro differentiation of specific cell types from embryonic or induced pluripotent stem cells, or on the direct reprogramming of differentiated adult cells via the expression of transcription factors or signaling molecules. The factors used to induce differentiation or reprogramming are often identified by informed guesses based on differential gene expression or known roles for these factors during development. Moreover, differentiation protocols usually result in partly differentiated cells or the production of a mix of cell types. In this Hypothesis article, we suggest that, to overcome these inefficiencies and improve neuronal differentiation protocols, we need to take into account the developmental history of the desired cell types. Specifically, we present a strategy that uses single-cell sequencing techniques combined with machine learning as a principled method to select a sequence of programming factors that are important not only in adult neurons but also during differentiation.
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Affiliation(s)
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA
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45
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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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46
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Fenyves BG, Szilágyi GS, Vassy Z, Sőti C, Csermely P. Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network. PLoS Comput Biol 2020; 16:e1007974. [PMID: 33347479 PMCID: PMC7785220 DOI: 10.1371/journal.pcbi.1007974] [Citation(s) in RCA: 6] [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: 05/19/2020] [Revised: 01/05/2021] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network of Caenorhabditis elegans is a well-reconstructed directed network, but the signs of its connections are yet to be elucidated. Here, we present the gene expression-based sign prediction of the ionotropic chemical synapse connectome of C. elegans (3,638 connections and 20,589 synapses total), incorporating available presynaptic neurotransmitter and postsynaptic receptor gene expression data for three major neurotransmitter systems. We made predictions for more than two-thirds of these chemical synapses and observed an excitatory-inhibitory (E:I) ratio close to 4:1 which was found similar to that observed in many real-world networks. Our open source tool (http://EleganSign.linkgroup.hu) is simple but efficient in predicting polarities by integrating neuronal connectome and gene expression data.
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Affiliation(s)
- Bánk G. Fenyves
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
- Department of Emergency Medicine, Semmelweis University, Budapest, Hungary
| | - Gábor S. Szilágyi
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Vassy
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Csaba Sőti
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Peter Csermely
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
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47
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Yang L, Wang F, Strähle U. The Genetic Programs Specifying Kolmer-Agduhr Interneurons. Front Neurosci 2020; 14:577879. [PMID: 33162880 PMCID: PMC7581942 DOI: 10.3389/fnins.2020.577879] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 01/21/2023] Open
Abstract
Kolmer-Agduhr (KA) cells are a subgroup of interneurons positioned adjacent to the neurocoele with cilia on the apical surface protruding into the central canal of the spinal cord. Although KA cells were identified almost a century ago, their development and functions are only beginning to be unfolded. Recent studies have revealed the characteristics of KA cells in greater detail, including their spatial distribution, the timing of their differentiation, and their specification via extrinsic signaling and a unique combination of transcription factors in zebrafish and mouse. Cell lineage-tracing experiments have demonstrated that two subsets of KA cells, named KA' and KA" cells, differentiate from motoneuronal progenitors and floor-plate precursors, respectively, in both zebrafish and mouse. Although KA' and KA" cells originate from different progenitors/precursors, they each share a common set of transcription factors. Intriguingly, the combination of transcription factors that promote the acquisition of KA' cell characteristics differs from those that promote a KA" cell identity. In addition, KA' and KA" cells exhibit separable neuronal targets and differential responses to bending of the spinal cord. In this review, we summarize what is currently known about the genetic programs defining the identities of KA' and KA" cell identities. We then discuss how these two subgroups of KA cells are genetically specified.
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Affiliation(s)
- Lixin Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feifei Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Uwe Strähle
- Institute of Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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48
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The Conserved ASCL1/MASH-1 Ortholog HLH-3 Specifies Sex-Specific Ventral Cord Motor Neuron Fate in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2020; 10:4201-4213. [PMID: 32973001 PMCID: PMC7642948 DOI: 10.1534/g3.120.401458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Neural specification is regulated by one or many transcription factors that control expression of effector genes that mediate function and determine neuronal type. Here we identify a novel role for one conserved proneural factor, the bHLH protein HLH-3, implicated in the specification of sex-specific ventral cord motor neurons in C. elegans. Proneural genes act in early stages of neurogenesis in early progenitors, but here, we demonstrate a later role for hlh-3. First, we document that differentiation of the ventral cord type C motor neuron class (VC) within their neuron class, is dynamic in time and space. Expression of VC class-specific and subclass-specific identity genes is distinct through development and is dependent on the VC position along the A-P axis and their proximity to the vulva. Our characterization of the expression of VC class and VC subclass-specific differentiation markers in the absence of hlh-3 function reveals that VC fate specification, differentiation, and morphology requires hlh-3 function. Finally, we conclude that hlh-3 cell-autonomously specifies VC cell fate.
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49
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Cook SJ, Crouse CM, Yemini E, Hall DH, Emmons SW, Hobert O. The connectome of the Caenorhabditis elegans pharynx. J Comp Neurol 2020; 528:2767-2784. [PMID: 32352566 PMCID: PMC7601127 DOI: 10.1002/cne.24932] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/06/2020] [Accepted: 04/17/2020] [Indexed: 12/31/2022]
Abstract
Detailed anatomical maps of individual organs and entire animals have served as invaluable entry points for ensuing dissection of their evolution, development, and function. The pharynx of the nematode Caenorhabditis elegans is a simple neuromuscular organ with a self-contained, autonomously acting nervous system, composed of 20 neurons that fall into 14 anatomically distinct types. Using serial electron micrograph (EM) reconstruction, we re-evaluate here the connectome of the pharyngeal nervous system, providing a novel and more detailed view of its structure and predicted function. Contrasting the previous classification of pharyngeal neurons into distinct inter- and motor neuron classes, we provide evidence that most pharyngeal neurons are also likely sensory neurons and most, if not all, pharyngeal neurons also classify as motor neurons. Together with the extensive cross-connectivity among pharyngeal neurons, which is more widespread than previously realized, the sensory-motor characteristics of most neurons define a shallow network architecture of the pharyngeal connectome. Network analysis reveals that the patterns of neuronal connections are organized into putative computational modules that reflect the known functional domains of the pharynx. Compared with the somatic nervous system, pharyngeal neurons both physically associate with a larger fraction of their neighbors and create synapses with a greater proportion of their neighbors. We speculate that the overall architecture of the pharyngeal nervous system may be reminiscent of the architecture of ancestral, primitive nervous systems.
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Affiliation(s)
- Steven J. Cook
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
| | - Charles M. Crouse
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
| | - David H. Hall
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Scott W. Emmons
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY 10027
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50
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Abstract
Caenorhabditis elegans' behavioral states, like those of other animals, are shaped by its immediate environment, its past experiences, and by internal factors. We here review the literature on C. elegans behavioral states and their regulation. We discuss dwelling and roaming, local and global search, mate finding, sleep, and the interaction between internal metabolic states and behavior.
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Affiliation(s)
- Steven W Flavell
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - David M Raizen
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Young-Jai You
- Division of Biological Science, Graduate School of Science, Nagoya University, 464-8602, Japan
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