1
|
Heiman MG, Bülow HE. Dendrite morphogenesis in Caenorhabditis elegans. Genetics 2024; 227:iyae056. [PMID: 38785371 PMCID: PMC11151937 DOI: 10.1093/genetics/iyae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Since the days of Ramón y Cajal, the vast diversity of neuronal and particularly dendrite morphology has been used to catalog neurons into different classes. Dendrite morphology varies greatly and reflects the different functions performed by different types of neurons. Significant progress has been made in our understanding of how dendrites form and the molecular factors and forces that shape these often elaborately sculpted structures. Here, we review work in the nematode Caenorhabditis elegans that has shed light on the developmental mechanisms that mediate dendrite morphogenesis with a focus on studies investigating ciliated sensory neurons and the highly elaborated dendritic trees of somatosensory neurons. These studies, which combine time-lapse imaging, genetics, and biochemistry, reveal an intricate network of factors that function both intrinsically in dendrites and extrinsically from surrounding tissues. Therefore, dendrite morphogenesis is the result of multiple tissue interactions, which ultimately determine the shape of dendritic arbors.
Collapse
Affiliation(s)
- Maxwell G Heiman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| |
Collapse
|
2
|
Brown AL, Meiborg AB, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick CJ, Werner MS. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 2024; 227:iyae041. [PMID: 38513719 PMCID: PMC11075575 DOI: 10.1093/genetics/iyae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.
Collapse
Affiliation(s)
- Audrey L Brown
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adriaan B Meiborg
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, 72074 Tübingen, Germany
| | - Spencer Gordon
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael S Werner
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| |
Collapse
|
3
|
Pop M, Klemke AL, Seidler L, Wernet N, Steudel PL, Baust V, Wohlmann E, Fischer R. Caenorhabditis elegans neuropeptide NLP-27 enhances neurodegeneration and paralysis in an opioid-like manner during fungal infection. iScience 2024; 27:109484. [PMID: 38784855 PMCID: PMC11112505 DOI: 10.1016/j.isci.2024.109484] [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: 03/02/2023] [Revised: 10/26/2023] [Accepted: 03/08/2024] [Indexed: 05/25/2024] Open
Abstract
The nervous system of metazoans is involved in host-pathogen interactions to control immune activation. In Caenorhabditis elegans, this includes sleep induction, mediated by neuropeptide-like proteins (NLPs), which increases the chance of survival after wounding. Here we analyzed the role of NLP-27 in the infection of C. elegans with the nematode-trapping fungus Arthrobotrys flagrans. Early responses of C. elegans were the upregulation of nlp-27, the induction of paralysis (sleep), and neurodegeneration of the mechanosensing PVD (Posterior Ventral Process D) neurons. Deletion of nlp-27 reduced neurodegeneration during fungal attack. Induction of nlp-27 was independent of the MAP kinase PMK-1, and expression of nlp-27 in the hypodermis was sufficient to induce paralysis, although NLP-27 was also upregulated in head neurons. NLP-27 contains the pentapeptide YGGYG sequence known to bind the human μ- and κ-type opioid receptors suggesting NLP-27 or peptides thereof act on opioid receptors. The opioid receptor antagonist naloxone shortened the paralysis time like overexpression of NLP-27.
Collapse
Affiliation(s)
- Maria Pop
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Anna-Lena Klemke
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Lena Seidler
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Nicole Wernet
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Pietrina Loredana Steudel
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Vanessa Baust
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Elke Wohlmann
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| | - Reinhard Fischer
- Karlsruhe Institute of Technology (KIT) - South Campus, Institute for Applied Biosciences, Department of Microbiology, Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| |
Collapse
|
4
|
Ebert MS, Bargmann CI. Evolution remodels olfactory and mating-receptive behaviors in the transition from female to hermaphrodite reproduction. Curr Biol 2024; 34:969-979.e4. [PMID: 38340714 DOI: 10.1016/j.cub.2024.01.050] [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: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Male/hermaphrodite species have arisen multiple times from a male/female ancestral state in nematodes, providing a model to study behavioral adaptations to different reproductive strategies. Here, we examined the mating behaviors of male/female (gonochoristic) Caenorhabditis species in comparison with male/hermaphrodite (androdiecious) close relatives. We find that females from two species in the Elegans group chemotax to volatile odor from males, but hermaphrodites do not. Females, but not hermaphrodites, also display known mating-receptive behaviors such as sedation when male reproductive structures contact the vulva. Focusing on the male/female species C. nigoni, we show that female chemotaxis to males is limited to adult females approaching adult or near-adult males and relies upon the AWA neuron-specific transcription factor ODR-7, as does male chemotaxis to female odor as previously shown in C. elegans. However, female receptivity during mating contact is odr-7 independent. All C. nigoni female behaviors are suppressed by mating and all are absent in young hermaphrodites from the sister species C. briggsae. However, latent receptivity during mating contact can be uncovered in mutant or aged C. briggsae hermaphrodites that lack self-sperm. These results reveal two mechanistically distinct components of the shift from female to hermaphrodite behavior: the loss of female-specific odr-7-dependent chemotaxis and a sperm-dependent state of reduced receptivity to mating contact. Hermaphrodites from a second androdioecious species, C. tropicalis, recover all female behaviors upon aging, including chemotaxis to males. Regaining mating receptivity after sperm depletion could maximize hermaphrodite fitness across their lifespan.
Collapse
Affiliation(s)
- Margaret S Ebert
- The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | | |
Collapse
|
5
|
Brinzer RA, Winter AD, Page AP. The relationship between intraflagellar transport and upstream protein trafficking pathways and macrocyclic lactone resistance in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkae009. [PMID: 38227795 PMCID: PMC10917524 DOI: 10.1093/g3journal/jkae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/08/2024] [Indexed: 01/18/2024]
Abstract
Parasitic nematodes are globally important and place a heavy disease burden on infected humans, crops, and livestock, while commonly administered anthelmintics used for treatment are being rendered ineffective by increasing levels of resistance. It has recently been shown in the model nematode Caenorhabditis elegans that the sensory cilia of the amphid neurons play an important role in resistance toward macrocyclic lactones such as ivermectin (an avermectin) and moxidectin (a milbemycin) either through reduced uptake or intertissue signaling pathways. This study interrogated the extent to which ciliary defects relate to macrocyclic lactone resistance and dye-filling defects using a combination of forward genetics and targeted resistance screening approaches and confirmed the importance of intraflagellar transport in this process. This approach also identified the protein trafficking pathways used by the downstream effectors and the components of the ciliary basal body that are required for effector entry into these nonmotile structures. In total, 24 novel C. elegans anthelmintic survival-associated genes were identified in this study. When combined with previously known resistance genes, there are now 46 resistance-associated genes that are directly involved in amphid, cilia, and intraflagellar transport function.
Collapse
Affiliation(s)
- Robert A Brinzer
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
| | - Alan D Winter
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
| | - Antony P Page
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Scotland G61 1QH, UK
| |
Collapse
|
6
|
Castelletto ML, Akimori D, Patel R, Schroeder NE, Hallem EA. Introduction to Strongyloides stercoralis Anatomy. J Nematol 2024; 56:20240019. [PMID: 38855080 PMCID: PMC11162604 DOI: 10.2478/jofnem-2024-0019] [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: 11/14/2023] [Indexed: 06/11/2024] Open
Abstract
Strongyloides stercoralis, commonly known as the human threadworm, is a skin-penetrating gastrointestinal parasitic nematode that infects hundreds of millions of people worldwide. Like other Strongyloides species, S. stercoralis is capable of cycling through a single free-living generation. Although S. stercoralis and the free-living nematode Caenorhabditis elegans are evolutionarily distant, the free-living adults of S. stercoralis are similar enough in size and morphology to C. elegans adults that techniques for generating transgenics and knockouts in C. elegans have been successfully adapted for use in S. stercoralis. High-quality genomic and transcriptomic data are also available for S. stercoralis. Thus, one can use a burgeoning array of functional genomic tools in S. stercoralis to probe questions about parasitic nematode development, physiology, and behavior. Knowledge gained from S. stercoralis will inform studies of other parasitic nematodes such as hookworms that are not yet amenable to genetic manipulation. This review describes the basic anatomy of S. stercoralis.
Collapse
Affiliation(s)
- Michelle L. Castelletto
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095
| | - Damia Akimori
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA, 90095
| | - Ruhi Patel
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095
| | - Nathan E. Schroeder
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Elissa A. Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095
| |
Collapse
|
7
|
Zhu J, Boivin JC, Pang S, Xu CS, Lu Z, Saalfeld S, Hess HF, Ohyama T. Comparative connectomics and escape behavior in larvae of closely related Drosophila species. Curr Biol 2023:S0960-9822(23)00675-9. [PMID: 37285846 DOI: 10.1016/j.cub.2023.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
Evolution has generated an enormous variety of morphological, physiological, and behavioral traits in animals. How do behaviors evolve in different directions in species equipped with similar neurons and molecular components? Here we adopted a comparative approach to investigate the similarities and differences of escape behaviors in response to noxious stimuli and their underlying neural circuits between closely related drosophilid species. Drosophilids show a wide range of escape behaviors in response to noxious cues, including escape crawling, stopping, head casting, and rolling. Here we find that D. santomea, compared with its close relative D. melanogaster, shows a higher probability of rolling in response to noxious stimulation. To assess whether this behavioral difference could be attributed to differences in neural circuitry, we generated focused ion beam-scanning electron microscope volumes of the ventral nerve cord of D. santomea to reconstruct the downstream partners of mdIV, a nociceptive sensory neuron in D. melanogaster. Along with partner interneurons of mdVI (including Basin-2, a multisensory integration neuron necessary for rolling) previously identified in D. melanogaster, we identified two additional partners of mdVI in D. santomea. Finally, we showed that joint activation of one of the partners (Basin-1) and a common partner (Basin-2) in D. melanogaster increased rolling probability, suggesting that the high rolling probability in D. santomea is mediated by the additional activation of Basin-1 by mdIV. These results provide a plausible mechanistic explanation for how closely related species exhibit quantitative differences in the likelihood of expressing the same behavior.
Collapse
Affiliation(s)
- Jiayi Zhu
- Department of Biology, McGill University, Docteur Penfield, Montreal, QC H3A 1B1, Canada; Integrated Program of Neuroscience, McGill University, Pine Avenue W., Montreal, QC H3A 1A1, Canada
| | - Jean-Christophe Boivin
- Department of Biology, McGill University, Docteur Penfield, Montreal, QC H3A 1B1, Canada; Integrated Program of Neuroscience, McGill University, Pine Avenue W., Montreal, QC H3A 1A1, Canada
| | - Song Pang
- Janelia Research Campus, Howard Hughes Medical Institute, Helix Drive, Ashburn, VA 20147, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Helix Drive, Ashburn, VA 20147, USA
| | - Zhiyuan Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Helix Drive, Ashburn, VA 20147, USA
| | - Stephan Saalfeld
- Janelia Research Campus, Howard Hughes Medical Institute, Helix Drive, Ashburn, VA 20147, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, Helix Drive, Ashburn, VA 20147, USA
| | - Tomoko Ohyama
- Department of Biology, McGill University, Docteur Penfield, Montreal, QC H3A 1B1, Canada; Alan Edwards Center for Research on Pain, McGill University, University Street, Montreal, QC H3A 2B4, Canada.
| |
Collapse
|
8
|
Kanzaki N, Ikeda Y, Shinya R. Onthodiplogaster japonica n. gen., n. sp. (Rhabditida: Diplogastridae) isolated from Onthophagus sp. (Coleoptera: Scarabaeidae) from Japan. Sci Rep 2023; 13:6470. [PMID: 37081071 PMCID: PMC10119125 DOI: 10.1038/s41598-023-33586-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
A diplogastrid nematode was isolated from a dung beetle, Onthophagus sp., collected from a rotten mushroom in Kyoto, Japan. The species is characterised by its cheilostomatal shape, separated into 12 narrow plates (rugae), deep stegostom, large ellipsoidal amphids, conical female tail and characteristic receptaculum seminis in the female. Based on its phylogenetic status and stomatal composition, the species is typologically similar to two other diplogastrid genera, Neodiplogaster and Mononchoides. The species can be distinguished from these two genera by the size and shape of the amphid (small pore in Neodiplogaster), female tail shape (long and filiform in Mononchoides) and presence of receptaculum seminis (absence in the two nominal genera), and is described as a monotypic member of a new genus, Onthodiplogaster japonica n. gen., n. sp. Observation of feeding behaviour suggested that O. japonica n. gen., n. sp. does not show clear stomatal dimorphism or polymorphism, which is found in its close relatives, but the species can feed on nematodes (predation), fungi and bacteria. This monomorphic omnivory possibly represents its habitat of dung and other rotten materials, where the environment is biologically divergent, and its condition changes rapidly.
Collapse
Affiliation(s)
- Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, 68 Nagaikyutaroh, Momoyama, Fushimi, Kyoto, 612-0855, Japan.
| | - Yuya Ikeda
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| | - Ryoji Shinya
- School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571, Japan
| |
Collapse
|
9
|
Lenuzzi M, Witte H, Riebesell M, Rödelsperger C, Hong RL, Sommer RJ. Influence of environmental temperature on mouth-form plasticity in Pristionchus pacificus acts through daf-11-dependent cGMP signaling. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:214-224. [PMID: 34379868 DOI: 10.1002/jez.b.23094] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/14/2021] [Accepted: 07/30/2021] [Indexed: 12/16/2022]
Abstract
Mouth-form plasticity in the nematode Pristionchus pacificus has become a powerful system to identify the genetic and molecular mechanisms associated with developmental (phenotypic) plasticity. In particular, the identification of developmental switch genes that can sense environmental stimuli and reprogram developmental processes has confirmed long-standing evolutionary theory. However, how these genes are involved in the direct sensing of the environment, or if the switch genes act downstream of another, primary environmental sensing mechanism, remains currently unknown. Here, we study the influence of environmental temperature on mouth-form plasticity. We find that environmental temperature does influence mouth-form plasticity in most of the 10 wild isolates of P. pacificus tested in this study. We used one of these strains, P. pacificus RSA635, for detailed molecular analysis. Using forward and reverse genetic technology including CRISPR/Cas9, we show that mutations in the guanylyl cyclase Ppa-daf-11, the Ppa-daf-25/AnkMy2, and the cyclic nucleotide-gated channel Ppa-tax-2 eliminate the response to elevated temperatures. Together, our study indicates that DAF-11, DAF-25, and TAX-2 have been co-opted for environmental sensing during mouth-form plasticity regulation in P. pacificus.
Collapse
Affiliation(s)
- Maša Lenuzzi
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
| | - Metta Riebesell
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ray L Hong
- Department of Biology, California State University, Northridge, California, USA
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
10
|
Lo WS, Roca M, Dardiry M, Mackie M, Eberhardt G, Witte H, Hong R, Sommer RJ, Lightfoot JW. Evolution and Diversity of TGF-β Pathways are Linked with Novel Developmental and Behavioral Traits. Mol Biol Evol 2022; 39:msac252. [PMID: 36469861 PMCID: PMC9733428 DOI: 10.1093/molbev/msac252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/19/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Transforming growth factor-β (TGF-β) signaling is essential for numerous biologic functions. It is a highly conserved pathway found in all metazoans including the nematode Caenorhabditis elegans, which has also been pivotal in identifying many components. Utilizing a comparative evolutionary approach, we explored TGF-β signaling in nine nematode species and revealed striking variability in TGF-β gene frequency across the lineage. Of the species analyzed, gene duplications in the DAF-7 pathway appear common with the greatest disparity observed in Pristionchus pacificus. Specifically, multiple paralogues of daf-3, daf-4 and daf-7 were detected. To investigate this additional diversity, we induced mutations in 22 TGF-β components and generated corresponding double, triple, and quadruple mutants revealing both conservation and diversification in function. Although the DBL-1 pathway regulating body morphology appears highly conserved, the DAF-7 pathway exhibits functional divergence, notably in some aspects of dauer formation. Furthermore, the formation of the phenotypically plastic mouth in P. pacificus is partially influenced through TGF-β with the strongest effect in Ppa-tag-68. This appears important for numerous processes in P. pacificus but has no known function in C. elegans. Finally, we observe behavioral differences in TGF-β mutants including in chemosensation and the establishment of the P. pacificus kin-recognition signal. Thus, TGF-β signaling in nematodes represents a stochastic genetic network capable of generating novel functions through the duplication and deletion of associated genes.
Collapse
Affiliation(s)
- Wen-Sui Lo
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology Tübingen, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Marianne Roca
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior—Caesar, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Mohannad Dardiry
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology Tübingen, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Marisa Mackie
- Department of Biology, California State University, Northridge, CA
| | - Gabi Eberhardt
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology Tübingen, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology Tübingen, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - Ray Hong
- Department of Biology, California State University, Northridge, CA
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Biology Tübingen, Max-Planck Ring 9, 72076 Tübingen, Germany
| | - James W Lightfoot
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior—Caesar, Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| |
Collapse
|
11
|
Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
|
12
|
Pomari E, Malerba G, Veschetti L, Franceschi A, Moron Dalla Tor L, Deiana M, Degani M, Mistretta M, Patuzzo C, Ragusa A, Mori A, Bisoffi Z, Buonfrate D. Identification of miRNAs of Strongyloides stercoralis L1 and iL3 larvae isolated from human stool. Sci Rep 2022; 12:9957. [PMID: 35705621 PMCID: PMC9200769 DOI: 10.1038/s41598-022-14185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
Strongyloidiasis is a neglected tropical disease caused by the soil-transmitted nematode by Strongyloides stercoralis, that affects approximately 600 million people worldwide. In immunosuppressed individuals disseminated strongyloidiasis can rapidly lead to fatal outcomes. There is no gold standard for diagnosing strongyloidiasis, and infections are frequently misdiagnosed. A better understanding of the molecular biology of this parasite can be useful for example for the discovery of potential new biomarkers. Interestingly, recent evidence showed the presence of small RNAs in Strongyloididae, but no data was provided for S. stercoralis. In this study, we present the first identification of miRNAs of both L1 and iL3 larval stages of S. stercoralis. For our purpose, the aims were: (i) to analyse the miRNome of L1 and iL3 S. stercoralis and to identify potential miRNAs of this nematode, (ii) to obtain the mRNAs profiles in these two larval stages and (iii) to predict potential miRNA target sites in mRNA sequences. Total RNA was isolated from L1 and iL3 collected from the stool of 5 infected individuals. For the miRNAs analysis, we used miRDeep2 software and a pipeline of bio-informatic tools to construct a catalog of a total of 385 sequences. Among these, 53% were common to S. ratti, 19% to S. papillosus, 1% to Caenorhabditis elegans and 44% were novel. Using a differential analysis between the larval stages, we observed 6 suggestive modulated miRNAs (STR-MIR-34A-3P, STR-MIR-8397-3P, STR-MIR-34B-3P and STR-MIR-34C-3P expressed more in iL3, and STR-MIR-7880H-5P and STR-MIR-7880M-5P expressed more in L1). Along with this analysis, we obtained also the mRNAs profiles in the same samples of larvae. Multiple testing found 81 statistically significant mRNAs of the total 1553 obtained (FDR < 0.05; 32 genes expressed more in L1 than iL3; 49 genes expressed more in L3 than iL1). Finally, we found 33 predicted mRNA targets of the modulated miRNAs, providing relevant data for a further validation to better understand the role of these small molecules in the larval stages and their valuein clinical diagnostics.
Collapse
Affiliation(s)
- Elena Pomari
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy.
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Laura Veschetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Alessandra Franceschi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | | | - Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Monica Degani
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Manuela Mistretta
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Andrea Ragusa
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| | - Zeno Bisoffi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy.,Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Dora Buonfrate
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, Verona, Italy
| |
Collapse
|
13
|
Maurya AK. Structural diversity in a stereotypic organelle - Sensory cilia of Caenorhabditis elegans. J Cell Physiol 2022; 237:2668-2672. [PMID: 35686462 DOI: 10.1002/jcp.30732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/07/2022]
Abstract
Sensory cilia, an ancient organelle, displays a high degree of conservation in its structure and functioning. Sensory cilia also fulfill a wide range of sensory functions, from sensing environmental signals (light, sound, chemicals, and mechanical forces) to interpreting intercellular developmental signals. One way they appear to fulfill these diverse and specialized roles is by adopting a variety of shapes and sizes. We are only beginning to document and appreciate this complexity. Here in this review, using the varied and specialized cilia found on Caenorhabditis elegans sensory neurons, I highlight some of the most obvious examples of this structural diversity and the underlying mechanisms if known. Such structural diversity appears to arise from the modulation of deeply conserved molecular pathways and also from cell- and species-specific mechanisms. Studying these ciliary specializations will thus provide for a comprehensive understanding of ciliary biology and might uncover understudied aspects of ciliary disease biology.
Collapse
Affiliation(s)
- Ashish K Maurya
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| |
Collapse
|
14
|
Eren GG, Roca M, Han Z, Lightfoot JW. Genomic integration of transgenes using UV irradiation in Pristionchus pacificus. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000576. [PMID: 35693893 PMCID: PMC9187223 DOI: 10.17912/micropub.biology.000576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
Transgenes are widely used throughout molecular biology for numerous applications. In Caenorhabditis elegans, stable transgenes are usually generated by microinjection into the germline establishing extrachromosomal arrays. Furthermore, numerous technologies exist to integrate transgenes into the C. elegans genome. In the nematode Pristionchus pacificus, transgenes are possible, however, their establishment is less efficient and dependent on the formation of complex arrays containing the transgene of interest and host carrier DNA. Additionally, genomic integration has only been reported via biolistic methods. Here we describe a simple technique using UV irradiation to facilitate the integration of transgenes into the P. pacificus genome.
Collapse
Affiliation(s)
- Güniz Göze Eren
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany
| | - Marianne Roca
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany
| | - Ziduan Han
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tuebingen, Germany
| | - James W Lightfoot
- Max Planck Research Group Genetics of Behavior, Max Planck Institute for Neurobiology of Behavior – caesar, Bonn, Germany.
,
Correspondence to: James W Lightfoot (
)
| |
Collapse
|
15
|
Bryant AS, Ruiz F, Lee JH, Hallem EA. The neural basis of heat seeking in a human-infective parasitic worm. Curr Biol 2022; 32:2206-2221.e6. [PMID: 35483361 PMCID: PMC9158753 DOI: 10.1016/j.cub.2022.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/21/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023]
Abstract
Soil-transmitted parasitic nematodes infect over one billion people and cause devastating morbidity worldwide. Many of these parasites have infective larvae that locate hosts using thermal cues. Here, we identify the thermosensory neurons of the human threadworm Strongyloides stercoralis and show that they display unique functional adaptations that enable the precise encoding of temperatures up to human body temperature. We demonstrate that experience-dependent thermal plasticity regulates the dynamic range of these neurons while preserving their ability to encode host-relevant temperatures. We describe a novel behavior in which infective larvae spontaneously reverse attraction to heat sources at sub-body temperatures and show that this behavior is mediated by rapid adaptation of the thermosensory neurons. Finally, we identify thermoreceptors that confer parasite-specific sensitivity to body heat. Our results pinpoint the parasite-specific neural adaptations that enable parasitic nematodes to target humans and provide the foundation for drug development to prevent human infection.
Collapse
Affiliation(s)
- Astra S Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Felicitas Ruiz
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joon Ha Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
16
|
Quach KT, Chalasani SH. Flexible reprogramming of Pristionchus pacificus motivation for attacking Caenorhabditis elegans in predator-prey competition. Curr Biol 2022; 32:1675-1688.e7. [PMID: 35259340 PMCID: PMC9050875 DOI: 10.1016/j.cub.2022.02.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/18/2021] [Accepted: 02/09/2022] [Indexed: 12/16/2022]
Abstract
Animals with diverse diets must adapt their food priorities to a wide variety of environmental conditions. This diet optimization problem is especially complex for predators that compete with prey for food. Although predator-prey competition is widespread and ecologically critical, it remains difficult to disentangle predatory and competitive motivations for attacking competing prey. Here, we dissect the foraging decisions of the omnivorous nematode Pristionchus pacificus to reveal that its seemingly failed predatory attempts against Caenorhabditis elegans are actually motivated acts of efficacious territorial aggression. While P. pacificus easily kills and eats larval C. elegans with a single bite, adult C. elegans typically survives and escapes bites. However, non-fatal biting can provide competitive benefits by reducing access of adult C. elegans and its progeny to bacterial food that P. pacificus also eats. We show that the costs and benefits of both predatory and territorial outcomes influence how P. pacificus decides which food goal, prey or bacteria, should guide its motivation for biting. These predatory and territorial motivations impose different sets of rules for adjusting willingness to bite in response to changes in bacterial abundance. In addition to biting, predatory and territorial motivations also influence which search tactic P. pacificus uses to increase encounters with C. elegans. When treated with an octopamine receptor antagonist, P. pacificus switches from territorial to predatory motivation for both biting and search. Overall, we demonstrate that P. pacificus assesses alternate outcomes of attacking C. elegans and flexibly reprograms its foraging strategy to prioritize either prey or bacterial food.
Collapse
Affiliation(s)
- Kathleen T. Quach
- Neurosciences Graduate Program, University of California San Diego, Gilman Drive, La Jolla, CA 92037, USA.,Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sreekanth H. Chalasani
- Neurosciences Graduate Program, University of California San Diego, Gilman Drive, La Jolla, CA 92037, USA.,Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, North Torrey Pines Road, La Jolla, CA 92037, USA.,Lead Contact,Correspondence: , Twitter: @shreklab
| |
Collapse
|
17
|
Synergistic interaction of gut microbiota enhances the growth of nematode through neuroendocrine signaling. Curr Biol 2022; 32:2037-2050.e4. [PMID: 35397201 DOI: 10.1016/j.cub.2022.03.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/23/2022] [Accepted: 03/18/2022] [Indexed: 01/21/2023]
Abstract
Animals are associated with a diverse bacterial community that impacts host physiology. It is well known that nutrients and enzymes synthesized by bacteria largely expand host metabolic capacity. Bacteria also impact a wide range of animal physiology that solely depends on host genetics through direct interaction. However, studying the synergistic effects of the bacterial community remains challenging due to its complexity. The omnivorous nematode Pristionchus pacificus has limited digestive efficiency on bacteria. Therefore, we established a bacterial collection that represents the natural gut microbiota that are resistant to digestion. Using this collection, we show that the bacterium Lysinibacillus xylanilyticus by itself provides limited nutritional value, but in combination with Escherichia coli, it significantly promotes life-history traits of P. pacificus by regulating the neuroendocrine peptide in sensory neurons. This gut-to-brain communication depends on undigested L. xylanilyticus providing Pristionchus nematodes a specific fitness advantage to compete with nematodes that rupture bacteria efficiently. Using RNA-seq and CRISPR-induced mutants, we show that 1-h exposure to L. xylanilyticus is sufficient to stimulate the expression of daf-7-type TGF-β signaling ligands, which induce a global transcriptome change. In addition, several effects of L. xylanilyticus depend on TGF-β signaling, including olfaction, body size regulation, and a switch of energy allocation from lipid storage to reproduction. Our results reveal the beneficial effects of a gut bacterium to modify life-history traits and maximize nematode survival in natural habitats.
Collapse
|
18
|
Lev I, Zimmer M. Predator–prey interactions: Strategic biting. Curr Biol 2022; 32:R367-R370. [DOI: 10.1016/j.cub.2022.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
19
|
Harry CJ, Messar SM, Ragsdale EJ. Comparative reconstruction of the predatory feeding structures of the polyphenic nematode Pristionchus pacificus. Evol Dev 2022; 24:16-36. [PMID: 35239990 PMCID: PMC9286642 DOI: 10.1111/ede.12397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/06/2022] [Accepted: 02/01/2022] [Indexed: 12/25/2022]
Abstract
Pristionchus pacificus is a nematode model for the developmental genetics of morphological polyphenism, especially at the level of individual cells. Morphological polyphenism in this species includes an evolutionary novelty, moveable teeth, which have enabled predatory feeding in this species and others in its family (Diplogastridae). From transmission electron micrographs of serial thin sections through an adult hermaphrodite of P. pacificus, we three‐dimensionally reconstructed all epithelial and myoepithelial cells and syncytia, corresponding to 74 nuclei, of its face, mouth, and pharynx. We found that the epithelia that produce the predatory morphology of P. pacificus are identical to Caenorhabditis elegans in the number of cell classes and nuclei. However, differences in cell form, spatial relationships, and nucleus position correlate with gross morphological differences from C. elegans and outgroups. Moreover, we identified fine‐structural features, especially in the anteriormost pharyngeal muscles, that underlie the conspicuous, left‐right asymmetry that characterizes the P. pacificus feeding apparatus. Our reconstruction provides an anatomical map for studying the genetics of polyphenism, feeding behavior, and the development of novel form in a satellite model to C. elegans. All cells making the dimorphic, novel form of an animal with cell constancy were identified. Although the number of cells is fully conserved, divergence in form and connectivity—including fixed asymmetries—sheds light on the origins of this trait.
Collapse
Affiliation(s)
- Clayton J Harry
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Sonia M Messar
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Erik J Ragsdale
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| |
Collapse
|
20
|
Lo WS, Sommer RJ. Vitamin B 12 and predatory behavior in nematodes. VITAMINS AND HORMONES 2022; 119:471-489. [PMID: 35337632 DOI: 10.1016/bs.vh.2022.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The round worms or nematodes are the largest phylum of animals with an estimated species number of more than one million. Nematodes have invaded all ecosystems and are known from all continents including Antarctica. Parasitic species infest plants, animals and humans often with high host-specificity. Free-living species are known from marine, fresh water and soil systems, the latter of which contain many culturable species. This includes Caenorhabditis elegans, a species that was developed as one of the most prominent model systems in modern biology since the 1960ies. Pristionchus pacificus is a second nematode model organism that can easily be cultured in the laboratory. This species shows a number of complex traits including omnivorous feeding and the capability of predation on other nematodes. Predation depends on the formation of teeth-like denticles in the mouth of P. pacificus, structures unknown from C. elegans and most other nematodes. Here, we review the current knowledge about the role of vitamin B12 for the predatory behavior in P. pacificus and correlate its role with that on the physiology and development in C. elegans.
Collapse
Affiliation(s)
- Wen-Sui Lo
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Biology Tübingen, Tübingen, Germany.
| |
Collapse
|
21
|
Chai CM, Chen W, Wong WR, Park H, Cohen SM, Wan X, Sternberg PW. A conserved behavioral role for a nematode interneuron neuropeptide receptor. Genetics 2022; 220:iyab198. [PMID: 34741504 PMCID: PMC8733633 DOI: 10.1093/genetics/iyab198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 01/14/2023] Open
Abstract
Neuropeptides are evolutionarily conserved modulators of many aspects of animal behavior and physiology, and expand the repertoire of processes that can be controlled by a limited number of neurons. Deciphering the neuropeptidergic codes that govern distinct processes requires systematic functional analyses of neuropeptides and their cognate receptors. Even in well-studied model organisms like Caenorhabditis elegans, however, such efforts have been precluded by a lack of mutant reagents. Here, we generated and screened 21 C. elegans neuropeptide G-protein coupled receptor mutants with no pre-existing reagents for the touch-evoked escape response, and implicated six receptors expressed in diverse neuron classes representing multiple circuit levels in this behavior. We further characterized the mutant with the most severe phenotype, frpr-14, which was defective in multiple behavioral paradigms. We leveraged this range of phenotypes to reveal that FRPR-14 modulation of different precommand interneuron classes, AVH and AIB, can drive distinct behavioral subsets, demonstrating cellular context-dependent roles for FRPR-14 signaling. We then show that Caenorhabditis briggsae CBR-FRPR-14 modulates an AVH-like interneuron pair to regulate the same behaviors as C. elegans but to a smaller extent. Our results also suggest that differences in touch-evoked escape circuit architecture between closely related species results from changes in neuropeptide receptor expression pattern, as opposed to ligand-receptor pairing. This study provides insights into the principles utilized by a compact, multiplexed nervous system to generate intraspecific behavioral complexity and interspecific variation.
Collapse
Affiliation(s)
- Cynthia M Chai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wen Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Wan-Rong Wong
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heenam Park
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Sarah M Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xuan Wan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| |
Collapse
|
22
|
Heckman EL, Doe CQ. Presynaptic contact and activity opposingly regulate postsynaptic dendrite outgrowth. eLife 2022; 11:82093. [PMID: 36448675 PMCID: PMC9728994 DOI: 10.7554/elife.82093] [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: 07/27/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The organization of neural circuits determines nervous system function. Variability can arise during neural circuit development (e.g. neurite morphology, axon/dendrite position). To ensure robust nervous system function, mechanisms must exist to accommodate variation in neurite positioning during circuit formation. Previously, we developed a model system in the Drosophila ventral nerve cord to conditionally induce positional variability of a proprioceptive sensory axon terminal, and used this model to show that when we altered the presynaptic position of the sensory neuron, its major postsynaptic interneuron partner modified its dendritic arbor to match the presynaptic contact, resulting in functional synaptic input (Sales et al., 2019). Here, we investigate the cellular mechanisms by which the interneuron dendrites detect and match variation in presynaptic partner location and input strength. We manipulate the presynaptic sensory neuron by (a) ablation; (b) silencing or activation; or (c) altering its location in the neuropil. From these experiments we conclude that there are two opposing mechanisms used to establish functional connectivity in the face of presynaptic variability: presynaptic contact stimulates dendrite outgrowth locally, whereas presynaptic activity inhibits postsynaptic dendrite outgrowth globally. These mechanisms are only active during an early larval critical period for structural plasticity. Collectively, our data provide new insights into dendrite development, identifying mechanisms that allow dendrites to flexibly respond to developmental variability in presynaptic location and input strength.
Collapse
Affiliation(s)
- Emily L Heckman
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of OregonEugeneUnited States
| |
Collapse
|
23
|
Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler W, Shroff H, Colón-Ramos DA. Differential adhesion regulates neurite placement via a retrograde zippering mechanism. eLife 2021; 10:71171. [PMID: 34783657 PMCID: PMC8843091 DOI: 10.7554/elife.71171] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.
Collapse
Affiliation(s)
- Titas Sengupta
- Yale University School of Medicine, New Haven, United States
| | - Noelle L Koonce
- Yale University School of Medicine, New Haven, United States
| | | | - Mark W Moyle
- Yale University School of Medicine, New Haven, United States
| | | | - Sarah E Emerson
- Yale University School of Medicine, New Haven, United States
| | - Xiaofei Han
- National Institutes of Health, Bethesda, United States
| | - Lin Shao
- Yale University School of Medicine, New Haven, United States
| | - Yicong Wu
- National Institutes of Health, Bethesda, United States
| | - Anthony Santella
- Developmental Biology Program, Molecular Cytology Core, Sloan-Kettering Institute, New York, United States
| | - Li Fan
- Helen and Robert Appel Alzheimer's Disease Institute, Weill Cornell Medicine, New York, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - William Mohler
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Hari Shroff
- National Institutes of Health, Bethesda, United States
| | | |
Collapse
|
24
|
Schroeder NE. Introduction to Pristionchus pacificus anatomy. J Nematol 2021; 53:e2021-91. [PMID: 34761228 PMCID: PMC8574906 DOI: 10.21307/jofnem-2021-091] [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: 09/22/2021] [Indexed: 12/02/2022] Open
Abstract
Pristionchus pacificus has emerged as an important nematode species used to understand the evolution of development and behavior. While P. pacificus (Diplogasteridae) is only distantly related to Caenorhabditis elegans (Rhabditidae), both use an identical reproductive strategy, are easily reared on bacteria in Petri dishes and complete their life cycles within a few days. Over the past 25 years, several detailed light and electron microscopy studies have elucidated the anatomy of P. pacificus and have demonstrated clear homology to many cells in C. elegans. Despite this similarity, sufficient anatomical differences between C. elegans and P. pacificus have allowed the latter to be used in comparative evo-devo studies. For example, the stoma of P. pacificus contains a large dorsal tooth used during predation on other nematodes when supplementing its primarily bacterial diet. This review discusses the main anatomical features of P. pacificus with emphasis on comparison to C. elegans.
Collapse
Affiliation(s)
- Nathan E Schroeder
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| |
Collapse
|
25
|
Clemens J, Schöneich S, Kostarakos K, Hennig RM, Hedwig B. A small, computationally flexible network produces the phenotypic diversity of song recognition in crickets. eLife 2021; 10:e61475. [PMID: 34761750 PMCID: PMC8635984 DOI: 10.7554/elife.61475] [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: 07/27/2020] [Accepted: 11/03/2021] [Indexed: 01/31/2023] Open
Abstract
How neural networks evolved to generate the diversity of species-specific communication signals is unknown. For receivers of the signals, one hypothesis is that novel recognition phenotypes arise from parameter variation in computationally flexible feature detection networks. We test this hypothesis in crickets, where males generate and females recognize the mating songs with a species-specific pulse pattern, by investigating whether the song recognition network in the cricket brain has the computational flexibility to recognize different temporal features. Using electrophysiological recordings from the network that recognizes crucial properties of the pulse pattern on the short timescale in the cricket Gryllus bimaculatus, we built a computational model that reproduces the neuronal and behavioral tuning of that species. An analysis of the model's parameter space reveals that the network can provide all recognition phenotypes for pulse duration and pause known in crickets and even other insects. Phenotypic diversity in the model is consistent with known preference types in crickets and other insects, and arises from computations that likely evolved to increase energy efficiency and robustness of pattern recognition. The model's parameter to phenotype mapping is degenerate - different network parameters can create similar changes in the phenotype - which likely supports evolutionary plasticity. Our study suggests that computationally flexible networks underlie the diverse pattern recognition phenotypes, and we reveal network properties that constrain and support behavioral diversity.
Collapse
Affiliation(s)
- Jan Clemens
- European Neuroscience Institute Göttingen – A Joint Initiative of the University Medical Center Göttingen and the Max-Planck SocietyGöttingenGermany
- BCCN GöttingenGöttingenGermany
| | - Stefan Schöneich
- University of Cambridge, Department of ZoologyCambridgeUnited Kingdom
- Friedrich-Schiller-University Jena, Institute for Zoology and Evolutionary ResearchJenaGermany
| | - Konstantinos Kostarakos
- University of Cambridge, Department of ZoologyCambridgeUnited Kingdom
- Institute of Biology, University of GrazUniversitätsplatzAustria
| | - R Matthias Hennig
- Humboldt-Universität zu Berlin, Department of BiologyPhilippstrasseGermany
| | - Berthold Hedwig
- University of Cambridge, Department of ZoologyCambridgeUnited Kingdom
| |
Collapse
|
26
|
Britz S, Markert SM, Witvliet D, Steyer AM, Tröger S, Mulcahy B, Kollmannsberger P, Schwab Y, Zhen M, Stigloher C. Structural Analysis of the Caenorhabditis elegans Dauer Larval Anterior Sensilla by Focused Ion Beam-Scanning Electron Microscopy. Front Neuroanat 2021; 15:732520. [PMID: 34819841 PMCID: PMC8607169 DOI: 10.3389/fnana.2021.732520] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
At the end of the first larval stage, the nematode Caenorhabditis elegans developing in harsh environmental conditions is able to choose an alternative developmental path called the dauer diapause. Dauer larvae exhibit different physiology and behaviors from non-dauer larvae. Using focused ion beam-scanning electron microscopy (FIB-SEM), we volumetrically reconstructed the anterior sensory apparatus of C. elegans dauer larvae with unprecedented precision. We provide a detailed description of some neurons, focusing on structural details that were unknown or unresolved by previously published studies. They include the following: (1) dauer-specific branches of the IL2 sensory neurons project into the periphery of anterior sensilla and motor or putative sensory neurons at the sub-lateral cords; (2) ciliated endings of URX sensory neurons are supported by both ILso and AMso socket cells near the amphid openings; (3) variability in amphid sensory dendrites among dauers; and (4) somatic RIP interneurons maintain their projection into the pharyngeal nervous system. Our results support the notion that dauer larvae structurally expand their sensory system to facilitate searching for more favorable environments.
Collapse
Affiliation(s)
- Sebastian Britz
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Sebastian Matthias Markert
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Daniel Witvliet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Anna Maria Steyer
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Sarah Tröger
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, Julius-Maximilians-University, Würzburg, Germany
| | - Yannick Schwab
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, Physiology and Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Christian Stigloher
- Imaging Core Facility of the Biocenter, Theodor-Boveri-Institute, Julius-Maximilians-University, Würzburg, Germany
| |
Collapse
|
27
|
Oteiza P, Baldwin MW. Evolution of sensory systems. Curr Opin Neurobiol 2021; 71:52-59. [PMID: 34600187 DOI: 10.1016/j.conb.2021.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/26/2021] [Indexed: 01/14/2023]
Abstract
Sensory systems evolve and enable organisms to perceive their sensory Umwelt, the unique set of cues relevant for their survival. The multiple components that comprise sensory systems - the receptors, cells, organs, and dedicated high-order circuits - can vary greatly across species. Sensory receptor gene families can expand and contract across lineages, resulting in enormous sensory diversity. Comparative studies of sensory receptor function have uncovered the molecular basis of receptor properties and identified novel sensory receptor classes and noncanonical sensory strategies. Phylogenetically informed comparisons of sensory systems across multiple species can pinpoint when sensory changes evolve and highlight the role of contingency in sensory system evolution.
Collapse
Affiliation(s)
- Pablo Oteiza
- Flow Sensing Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany.
| |
Collapse
|
28
|
Carstensen HR, Villalon RM, Banerjee N, Hallem EA, Hong RL. Steroid hormone pathways coordinate developmental diapause and olfactory remodeling in Pristionchus pacificus. Genetics 2021; 218:6272519. [PMID: 33963848 DOI: 10.1093/genetics/iyab071] [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: 04/24/2020] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
Developmental and behavioral plasticity allow animals to prioritize alternative genetic programs during fluctuating environments. Behavioral remodeling may be acute in animals that interact with host organisms, since reproductive adults and the developmentally arrested larvae often have different ethological needs for chemical stimuli. To understand the genes that coordinate the development and host-seeking behavior, we used the entomophilic nematode Pristionchus pacificus to characterize dauer-constitutive mutants (Daf-c) that inappropriately enter developmental diapause to become dauer larvae. We found two Daf-c loci with dauer-constitutive and cuticle exsheathment phenotypes that can be rescued by the feeding of Δ7-dafachronic acid, and that are dependent on the conserved canonical steroid hormone receptor Ppa-DAF-12. Specifically at one locus, deletions in the sole hydroxysteroid dehydrogenase (HSD) in P. pacificus resulted in Daf-c phenotypes. Ppa-hsd-2 is expressed in the canal-associated neurons (CANs) and excretory cells whose homologous cells in Caenorhabditis elegans are not known to be involved in the dauer decision. While in wildtype only dauer larvae are attracted to host odors, hsd-2 mutant adults show enhanced attraction to the host beetle pheromone, along with ectopic activation of a marker for putative olfactory neurons, Ppa-odr-3. Surprisingly, this enhanced odor attraction acts independently of the Δ7-DA/DAF-12 module, suggesting that Ppa-HSD-2 may be responsible for several steroid hormone products involved in coordinating the dauer decision and host-seeking behavior in P. pacificus.
Collapse
Affiliation(s)
- Heather R Carstensen
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
| | - Reinard M Villalon
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
| | - Navonil Banerjee
- Department of Microbiology, Immunology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology & Molecular Genetics and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ray L Hong
- Department of Biology, California State University, Northridge, Northridge, CA 91330-8303, USA
| |
Collapse
|
29
|
Bryant AS, Hallem EA. The Wild Worm Codon Adapter: a web tool for automated codon adaptation of transgenes for expression in non-Caenorhabditis nematodes. G3 (BETHESDA, MD.) 2021; 11:6259089. [PMID: 33914084 PMCID: PMC8496300 DOI: 10.1093/g3journal/jkab146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 01/22/2023]
Abstract
Advances in genomics techniques are expanding the range of nematode species that are amenable to transgenesis. Due to divergent codon usage biases across species, codon optimization is often a critical step for the successful expression of exogenous transgenes in nematodes. Platforms for generating DNA sequences codon-optimized for the free-living model nematode Caenorhabditis elegans are broadly available. However, until now such tools did not exist for non-Caenorhabditis nematodes. We therefore developed the Wild Worm Codon Adapter, a tool for rapid transgene codon optimization for expression in non-Caenorhabditis nematodes. The app includes built-in optimization for parasitic nematodes in the Strongyloides, Nippostrongylus, and Brugia genera as well as the predatory nematode Pristionchus pacificus. The app also supports custom optimization for any species using user-provided optimization rules. In addition, the app supports automated insertion of synthetic or native introns, as well as the analysis of codon bias in transgene and native sequences. Here, we describe this web-based tool and demonstrate how it may be used to analyze genome-wide codon bias in Strongyloides species.
Collapse
Affiliation(s)
- Astra S Bryant
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elissa A Hallem
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Corresponding author: University of California, Los Angeles, MIMG, 237 BSRB, 615 Charles E. Young Dr. S., Los Angeles, CA 90095, USA.
| |
Collapse
|
30
|
Ishita Y, Chihara T, Okumura M. Different combinations of serotonin receptors regulate predatory and bacterial feeding behaviors in the nematode Pristionchus pacificus. G3-GENES GENOMES GENETICS 2021; 11:6104620. [PMID: 33598706 PMCID: PMC8022940 DOI: 10.1093/g3journal/jkab011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/28/2020] [Indexed: 11/23/2022]
Abstract
Feeding behavior is one of the most fundamental behaviors in animals, and regulation of this behavior is critical for proper food intake. The nematode Pristionchus pacificus exhibits dimorphism in feeding behavior, bacterial feeding and predatory feeding on other nematodes, and the latter behavior is assumed to be an evolutionarily novel behavior. Both types of feeding behavior are modulated by serotonin; however, the downstream mechanism that modulates these behaviors is still to be clarified. Here, we focused on serotonin receptors and examined their expression patterns in P. pacificus. We also generated knockout mutants of the serotonin receptors using the CRISPR/Cas9 system and examined feeding behaviors. We found that Ppa-ser-5 mutants and the Ppa-ser-1; Ppa-ser-7 double mutant decreased predation. Detailed observation of the pharyngeal movement revealed that the Ppa-ser-1; Ppa-ser-7 double mutant reduces tooth movement, which is required for efficient predatory feeding. Conversely, Ppa-ser-7 and Ppa-mod-1 mutants decreased bacterial feeding. This study revealed that specific combinations of serotonin receptors are essential for the modulation of these distinct feeding behaviors, providing insight into the evolution of neural pathways to regulate novel feeding behavior.
Collapse
Affiliation(s)
- Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.,Department of Biological Science, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Athanasouli M, Witte H, Weiler C, Loschko T, Eberhardt G, Sommer RJ, Rödelsperger C. Comparative genomics and community curation further improve gene annotations in the nematode Pristionchus pacificus. BMC Genomics 2020; 21:708. [PMID: 33045985 PMCID: PMC7552371 DOI: 10.1186/s12864-020-07100-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
Background Nematode model organisms such as Caenorhabditis elegans and Pristionchus pacificus are powerful systems for studying the evolution of gene function at a mechanistic level. However, the identification of P. pacificus orthologs of candidate genes known from C. elegans is complicated by the discrepancy in the quality of gene annotations, a common problem in nematode and invertebrate genomics. Results Here, we combine comparative genomic screens for suspicious gene models with community-based curation to further improve the quality of gene annotations in P. pacificus. We extend previous curations of one-to-one orthologs to larger gene families and also orphan genes. Cross-species comparisons of protein lengths, screens for atypical domain combinations and species-specific orphan genes resulted in 4311 candidate genes that were subject to community-based curation. Corrections for 2946 gene models were implemented in a new version of the P. pacificus gene annotations. The new set of gene annotations contains 28,896 genes and has a single copy ortholog completeness level of 97.6%. Conclusions Our work demonstrates the effectiveness of comparative genomic screens to identify suspicious gene models and the scalability of community-based approaches to improve the quality of thousands of gene models. Similar community-based approaches can help to improve the quality of gene annotations in other invertebrate species, including parasitic nematodes.
Collapse
Affiliation(s)
- Marina Athanasouli
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Hanh Witte
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Weiler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Gabi Eberhardt
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck-Ring 9, 72076, Tübingen, Germany.
| |
Collapse
|
33
|
Quach KT, Chalasani SH. Intraguild predation between Pristionchus pacificus and Caenorhabditis elegans: a complex interaction with the potential for aggressive behaviour. J Neurogenet 2020; 34:404-419. [PMID: 33054476 PMCID: PMC7836027 DOI: 10.1080/01677063.2020.1833004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/20/2020] [Indexed: 12/20/2022]
Abstract
The related nematodes Pristionchus pacificus and Caenorhabditis elegans both eat bacteria for nutrition and are therefore competitors when they exploit the same bacterial resource. In addition to competing with each other, P. pacificus is a predator of C. elegans larval prey. These two relationships together form intraguild predation, which is the killing and sometimes eating of potential competitors. In killing C. elegans, the intraguild predator P. pacificus may achieve dual benefits of immediate nutrition and reduced competition for bacteria. Recent studies of P. pacificus have characterized many aspects of its predatory biting behaviour as well as underlying molecular and genetic mechanisms. However, little has been explored regarding the potentially competitive aspect of P. pacificus biting C. elegans. Moreover, aggression may also be implicated if P. pacificus intentionally bites C. elegans with the goal of reducing competition for bacteria. The aim of this review is to broadly outline how aggression, predation, and intraguild predation relate to each other, as well as how these concepts may be applied to future studies of P. pacificus in its interactions with C. elegans.
Collapse
Affiliation(s)
- Kathleen T. Quach
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Sreekanth H. Chalasani
- Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| |
Collapse
|
34
|
Barrière A, Bertrand V. Neuronal specification in C. elegans: combining lineage inheritance with intercellular signaling. J Neurogenet 2020; 34:273-281. [PMID: 32603241 DOI: 10.1080/01677063.2020.1781850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nervous system is composed of a high diversity of neuronal types. How this diversity is generated during development is a key question in neurobiology. Addressing this question is one of the reasons that led Sydney Brenner to develop the nematode C. elegans as a model organism. While there was initially a debate on whether the neuronal specification follows a 'European' model (determined by ancestry) or an 'American' model (determined by intercellular communication), several decades of research have established that the truth lies somewhere in between. Neurons are specified by the combination of transcription factors inherited from the ancestor cells and signaling between neighboring cells (especially Wnt and Notch signaling). This converges to the activation in newly generated postmitotic neurons of a specific set of terminal selector transcription factors that initiate and maintain the differentiation of the neuron. In this review, we also discuss the evolution of these specification mechanisms in other nematodes and beyond.
Collapse
Affiliation(s)
- Antoine Barrière
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Center for Living Systems, Marseille, France
| |
Collapse
|
35
|
Zhao Z, McBride CS. Evolution of olfactory circuits in insects. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2020; 206:353-367. [PMID: 31984441 PMCID: PMC7192870 DOI: 10.1007/s00359-020-01399-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 12/12/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023]
Abstract
Recent years have seen an explosion of interest in the evolution of neural circuits. Comparison of animals from different families, orders, and phyla reveals fascinating variation in brain morphology, circuit structure, and neural cell types. However, it can be difficult to connect the complex changes that occur across long evolutionary distances to behavior. Luckily, these changes accumulate through processes that should also be observable in recent time, making more tractable comparisons of closely related species relevant and complementary. Here, we review several decades of research on the evolution of insect olfactory circuits across short evolutionary time scales. We describe two well-studied systems, Drosophila sechellia flies and Heliothis moths, in detailed case studies. We then move through key types of circuit evolution, cataloging examples from other insects and looking for general patterns. The literature is dominated by changes in sensory neuron number and tuning at the periphery-often enhancing neural response to odorants with new ecological or social relevance. However, changes in the way olfactory information is processed by central circuits is clearly important in a few cases, and we suspect the development of genetic tools in non-model species will reveal a broad role for central circuit evolution. Moving forward, such tools should also be used to rigorously test causal links between brain evolution and behavior.
Collapse
Affiliation(s)
- Zhilei Zhao
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
| | - Carolyn S McBride
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA.
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, 08544, USA.
| |
Collapse
|
36
|
Dong C, Weadick CJ, Truffault V, Sommer RJ. Convergent evolution of small molecule pheromones in Pristionchus nematodes. eLife 2020; 9:55687. [PMID: 32338597 PMCID: PMC7224695 DOI: 10.7554/elife.55687] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/24/2020] [Indexed: 01/05/2023] Open
Abstract
The small molecules that mediate chemical communication between nematodes-so-called 'nematode-derived-modular-metabolites' (NDMMs)-are of major interest because of their ability to regulate development, behavior, and life-history. Pristionchus pacificus nematodes produce an impressive diversity of structurally complex NDMMs, some of which act as primer pheromones that are capable of triggering irreversible developmental switches. Many of these NDMMs have only ever been found in P. pacificus but no attempts have been made to study their evolution by profiling closely related species. This study brings a comparative perspective to the biochemical study of NDMMs through the systematic MS/MS- and NMR-based analysis of exo-metabolomes from over 30 Pristionchus species. We identified 36 novel compounds and found evidence for the convergent evolution of complex NDMMs in separate branches of the Pristionchus phylogeny. Our results demonstrate that biochemical innovation is a recurrent process in Pristionchus nematodes, a pattern that is probably typical across the animal kingdom.
Collapse
Affiliation(s)
- Chuanfu Dong
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Cameron J Weadick
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| |
Collapse
|
37
|
Mechanism of murderous mushrooms paves path for parasitic helminth halt. Proc Natl Acad Sci U S A 2020; 117:6974-6975. [PMID: 32152107 DOI: 10.1073/pnas.2002662117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
38
|
Akduman N, Lightfoot JW, Röseler W, Witte H, Lo WS, Rödelsperger C, Sommer RJ. Bacterial vitamin B 12 production enhances nematode predatory behavior. ISME JOURNAL 2020; 14:1494-1507. [PMID: 32152389 PMCID: PMC7242318 DOI: 10.1038/s41396-020-0626-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/26/2020] [Indexed: 02/07/2023]
Abstract
Although the microbiota is known to affect host development, metabolism, and immunity, its impact on host behavior is only beginning to be understood. In order to better characterize behavior modulation by host-associated microorganisms, we investigated how bacteria modulate complex behaviors in the nematode model organism Pristionchus pacificus. This nematode is a predator that feeds on the larvae of other nematodes, including Caenorhabditis elegans. By growing P. pacificus on different bacteria and testing their ability to kill C. elegans, we reveal large differences in killing efficiencies, with a Novosphingobium species showing the strongest enhancement. This enhanced killing was not accompanied by an increase in feeding, which is a phenomenon known as surplus killing, whereby predators kill more prey than necessary for sustenance. Our RNA-seq data demonstrate widespread metabolic rewiring upon exposure to Novosphingobium, which facilitated screening of bacterial mutants with altered transcriptional responses. We identified bacterial production of vitamin B12 as an important cause of such enhanced predatory behavior. Although vitamin B12 is an essential cofactor for detoxification and metabolite biosynthesis, shown previously to accelerate development in C. elegans, supplementation with this enzyme cofactor amplified surplus killing in P. pacificus, whereas mutants in vitamin B12-dependent pathways reduced surplus killing. By demonstrating that production of vitamin B12 by host-associated microbiota can affect complex host behaviors, we reveal new connections between animal diet, microbiota, and nervous system.
Collapse
Affiliation(s)
- Nermin Akduman
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - James W Lightfoot
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - Waltraud Röseler
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - Hanh Witte
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - Wen-Sui Lo
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - Christian Rödelsperger
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Max Planck Ring 9, 72076, Tübingen, Germany.
| |
Collapse
|
39
|
Cebul ER, McLachlan IG, Heiman MG. Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1. Development 2020; 147:dev.180448. [PMID: 31988188 DOI: 10.1242/dev.180448] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022]
Abstract
Dendrites develop elaborate morphologies in concert with surrounding glia, but the molecules that coordinate dendrite and glial morphogenesis are mostly unknown. C. elegans offers a powerful model for identifying such factors. Previous work in this system examined dendrites and glia that develop within epithelia, similar to mammalian sense organs. Here, we focus on the neurons BAG and URX, which are not part of an epithelium but instead form membranous attachments to a single glial cell at the nose, reminiscent of dendrite-glia contacts in the mammalian brain. We show that these dendrites develop by retrograde extension, in which the nascent dendrite endings anchor to the presumptive nose and then extend by stretching during embryo elongation. Using forward genetic screens, we find that dendrite development requires the adhesion protein SAX-7/L1CAM and the cytoplasmic protein GRDN-1/CCDC88C to anchor dendrite endings at the nose. SAX-7 acts in neurons and glia, while GRDN-1 acts in glia to non-autonomously promote dendrite extension. Thus, this work shows how glial factors can help to shape dendrites, and identifies a novel molecular mechanism for dendrite growth by retrograde extension.
Collapse
Affiliation(s)
- Elizabeth R Cebul
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Ian G McLachlan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| |
Collapse
|